PaperBLAST
PaperBLAST Hits for tr|Q9HX55|Q9HX55_PSEAE Probable ATP-dependent helicase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3961 PE=4 SV=1 (838 a.a., MISLPIDAVV...)
Show query sequence
>tr|Q9HX55|Q9HX55_PSEAE Probable ATP-dependent helicase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3961 PE=4 SV=1
MISLPIDAVVPALRQALGAQHQAVLEAPPGAGKTTRVPLALLDEPWLAGQRILMLEPRRL
AARAAAERLAAELGEKVGETVGYRIRLESRVGPKTRIEVVTEGILARRLQDDPALDGVGL
VIFDEFHERSLDADLALALTLNGRELLRDEPPLKVLVMSATLEGERLAALLGEAPVVRSE
GRMFPVDIRWGRPAQPGEFIEPRVQQAVLQALAEESGSVLVFLPGQAEIRRVHEGLREAL
GGRPEVLLCPLHGELDLAAQRAAIEPASRGTRKVVLATNIAETSLTIDGVRVVIDAGLAR
VPRFDPGSGMTRLETQRISRASATQRAGRAGRLEPGVCYRLWSESQHEQLPAYGTAEILQ
ADLAGLALQLARWGVAPEELAWLDAPPAAAYAQARELLGRLGALNASGALSAHGQAMAEL
PTHPRIAHLLLRGQALGLGELACDVAALLGERDIQRGGGADLHSRLALLAGEARTGASRG
AVQRARQLARQFRGYLRGAASEAVVDPGHPRWLGCLLAFAYPDRIARQRRAGGGDYRLAN
GRAAQFGEPDSLMKQPWLVIADLGSRQGQREERIYLAAELDPRLFDTVLAEQVSQRDELQ
WDEREGVLRAERQRRVGELVLSSEALPGLDEAARSQALLGLVRRKGLELLPWTPELRQWQ
ARIGLLRRLDLEDKGESEWPDVSDAALLERLEEWLPAYLGKVTRLAHFANLDLASILAGL
LPWPLPQRLDEWAPKTLEVPSGSRIRLDYSETPPILAVRLQELFGLGDTPRIAQGRLAVK
LHLLSPAHRPVQVTQDLANFWRSTYAEVRKDLKGRYPKHYWPDDPLVAEATARAKPRK
Running BLASTp...
Found 286 similar proteins in the literature:
Q9HX55 Probable ATP-dependent helicase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3961 probable ATP-dependent helicase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...4198 Q9I208 953 Q9I5E3 2035 Q9I4P6 3117 Q9HX54 4199 Q9I212 954 Q9I5F5 2036 Q9I4P7 3118 Q9HX55 4200 Q9I213 955 Q9I5G5 2037 Q9I4P8 3119 Q9HX56 4201 Q9I214 956 Q9I5G7 2038 Q9I4P9 3120 Q9HX57 4202 Q9I215 957 Q9I5G8 2039 Q9I4Q0 3121 Q9HX58 4203 Q9I216 958 Q9I5J6 2040 Q9I4Q1...”
- Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences
Hausmann, RNA biology 2020 - “...by horizontal gene transfer [ 20 ]. In the P. aeruginosa PAO1 genome, the gene PA3961 encodes a predicted DExH-box helicase annotated as hrpB [ 21 ]. P. aeruginosa PAO1 HrpB ( Pa HrpB) has 47% amino acid sequence identity with E. coli HrpB ( Ec...”
- “...Figure 1. P. aeruginosa HrpB domain organization . (A) Linear representation of P. aeruginosa HrpB (PA3961), with the RecA1 and RecA2 domains in grey (light and dark grey, respectively), the winged-helix (WH) domain in orange, the helical bundle (HB) domain in brown, the oligonucleotide/oligosaccharide-binding (OB) domain...”
- Influence of O polysaccharides on biofilm development and outer membrane vesicle biogenesis in Pseudomonas aeruginosa PAO1
Murphy, Journal of bacteriology 2014 - “...PA4995 PA5036 PA3327 PA1572 PA2025 PA2978 PA1413 PA4937 PA3961 PA0623 PA2424 PA4226 PA0186 PA0172 PA2402 PA0622 PA1573 PA5253 PA1628 PA1031 PA4225 PA2787 ftsK...”
- Genomic islands of Pseudomonas aeruginosa
Battle, FEMS microbiology letters 2009 - “...PAGI-7 is not found within a tRNA gene, but instead is integrated within PAO1 ORF PA3961, which is predicted to encode HprB, a probable ATP-dependent helicase is also not a previously identified RGP. Although the island interrupts PA3961, no portion of this ORF is deleted or...”
PA14_12630 putative ATP-dependent helicase from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 91% coverage
- Pseudomonas aeruginosa Genomic Structure and Diversity
Klockgether, Frontiers in microbiology 2011 - “...1071133 G C PA14_12430 3 ladS Homolog to lost adherence sensor LadS 1082958 A G PA14_12630 syn. Putative ATP-dependent helicase 1356548 G C PA14_15920 R G yhjE Major facilitator transporter 1441164 T C PA14_16820 syn. Putative efflux transmembrane protein 1468998 C T PA14_17130 syn. dxr 1-deoxy-d-xylulose...”
XAC0293 ATP-dependent RNA helicase from Xanthomonas axonopodis pv. citri str. 306
50% identity, 100% coverage
- The ATP-dependent RNA helicase HrpB plays an important role in motility and biofilm formation in Xanthomonas citri subsp. citri
Granato, BMC microbiology 2016 - “...extensively studied. In this study, we characterize the ATP-dependent RNA helicase encoded by the hrpB (XAC0293) gene using deletion and genetic complementation assays. We provide insights into the function of the hrpB gene in Xanthomonas citri subsp. citri by investigating the roles of hrpB in biofilm...”
- “...X. citri ) for mutants that were associated with effects on biofilm and identified hrpB (XAC0293), which encodes a probable DEAH-box RNA helicase. The function of RNA helicases in the Gram negative bacteria X. citri has not been explored. X. citri causes citrus canker, one of...”
- Type IV Secretion System Is Not Involved in Infection Process in Citrus
Jacob, International journal of microbiology 2014 - “...XAC ID Gene Gene ID Product (NCBI Annotation) Primers (Forward) Primers (Reverse) Amplicon (bp) System XAC0293 hrpB 1154364 ATP-dependent RNA helicase GCCGTATCCCGTTGACCTT ACCGCCCCTTCATCTCTTTT 81 T3SS XAC0393 hpaF 1154464 HpaF protein GGCGAGCGTTTTGACAA CCGGAGATCCTGGCAGTTT 57 T3SS XAC0394 hrpF 1154465 HrpF protein GCCGCGACGCAGTTG CGGTGATCGAGTTGTTCAA 62 T3SS XAC0396 hpaB 1154467...”
BMI_I135 ATP-dependent helicase HrpB from Brucella microti CCM 4915
48% identity, 100% coverage
- Brucella microti: the genome sequence of an emerging pathogen
Audic, BMC genomics 2009 - “...BMI_I2199 orthologs in other brucella are smaller, hydrolase Genes impaired in almost all other Brucella BMI_I135 + BR0132 fs + fs fs fs fs fs fs + BMI_I135 ortholog is pseudogene BR0132, ATP- dependent helicase HrpB BMI_I947 + BR0949 * * * + * * *...”
- “...impaired in almost all Brucella , with some exceptions. For instance, the ATP-dependent helicase HtrB (BMI_I135), pseudogene BR0132 in B. suis 1330, presents a frameshift in all Brucella except B. ovis (BOV_0127) and is intact in O. anthropi . This is also the case for BMI_I947...”
BOV_0127 ATP-dependent helicase HrpB from Brucella ovis ATCC 25840
48% identity, 100% coverage
- Brucella microti: the genome sequence of an emerging pathogen
Audic, BMC genomics 2009 - “...pseudogene BR0132 in B. suis 1330, presents a frameshift in all Brucella except B. ovis (BOV_0127) and is intact in O. anthropi . This is also the case for BMI_I947 corresponding to pseudogene BR0949 in B. suis 1330. This gene exhibits an internal STOP codon in...”
XCV0300 ATP-dependent helicase HrpB from Xanthomonas campestris pv. vesicatoria str. 85-10
50% identity, 96% coverage
XCC0275 ATP-dependent RNA helicase from Xanthomonas campestris pv. campestris str. ATCC 33913
49% identity, 100% coverage
RL0059 putative ATP-dependent helicase protein from Rhizobium leguminosarum bv. viciae 3841
48% identity, 100% coverage
DR_0420 ATP-dependent helicase from Deinococcus radiodurans R1
52% identity, 100% coverage
XF1229 ATP-dependent helicase from Xylella fastidiosa 9a5c
46% identity, 99% coverage
PXO_03270 ATP-dependent RNA helicase from Xanthomonas oryzae pv. oryzae PXO99A
XOO4533 ATP-dependent RNA helicase from Xanthomonas oryzae pv. oryzae KACC10331
49% identity, 99% coverage
- Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics
Zhang, The Plant cell 2021 - “...six of which ( talC9d , xopF1 , avrBs2 , dnaE , PXO_03021 , and PXO_03270 ) interacted weakly with most blocks in rice QR-gene groups 2 and 3. The remaining three genes ( talC3a , avrXa27 , and glmU ) each interacted with 14 rice...”
- “...( PXO_00908 ), ATP-dependent RNA helicase DbpA ( PXO_00394 ), and ATP-dependent RNA helicase ( PXO_03270 ), involved in energy metabolism. The SV Xoo races are differentiated strongly from the WV/MV races at the three loci, suggesting the adaptation of Geng and Xian types races to...”
- The ATP-dependent RNA helicase HrpB plays an important role in motility and biofilm formation in Xanthomonas citri subsp. citri
Granato, BMC microbiology 2016 - “...K-12 str. DH10B; Xf1229, Xylella fastidiosa 9a5c; Xcc0275, Xanthomonas campestris pv. campestris str. ATCC 33913; Xoo4533, Xanthomonas oryzae pv. oryzae KACC 10331; Xac0293, Xanthomonas citri subsp. citri ; and Xcv0300, Xanthomonas campestris pv. vesicatoria str. 8510 Table 1 Protein alignments of Xanthomonas citri subsp. citri in...”
- A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes
Seo, BMC microbiology 2008 - “...3.1E-06 0.313 + XOCORF2466 hpa2 0.099664 -0.064 XOO0090 hrpB5 0.345847 0.076 XOCORF2451 hrcS 0.000253 0.003 XOO4533 hrpB 0.222464 0.063 + XOCORF2289 hrpB 0.063541 0.073 0 XOO0087 hrpB2 0.411161 0.057 XOCORF2457 hrpB2 0.119757 0.013 0 XOO0075 hpaB 0.444516 0.041 XOCORF2447 hpaB 0.029266 0.194 XOO0066 hrpF 0.792649 -0.019...”
EC958_RS00830 ATP-dependent helicase HrpB from Escherichia coli O25b:H4-ST131
47% identity, 100% coverage
YadO / b0148 RNA-dependent NTPase HrpB from Escherichia coli K-12 substr. MG1655 (see 4 papers)
P37024 nucleoside-triphosphate phosphatase (EC 3.6.1.15) from Escherichia coli (see paper)
hrpB / MB|P37024 ATP-dependent RNA helicase hrpB from Escherichia coli K12 (see paper)
NP_414690 RNA-dependent NTPase HrpB from Escherichia coli str. K-12 substr. MG1655
47% identity, 100% coverage
plu0882 ATP-dependent helicase HrpB from Photorhabdus luminescens subsp. laumondii TTO1
45% identity, 99% coverage
- Bacterial toxin effector-membrane targeting: outside in, then back again
Geissler, Frontiers in cellular and infection microbiology 2012 - “...IpgD T3SS SopB-like MLD, ubiquitination? Bordetella spp. BteA T3SS N-terminal 130aa, LRT Photorhabdus luminescens Plu4750, Plu0882 T3SS BteA-like LRT Plu1341, Plu1344, Plu3217, Plu3324 T1SS BteA-like LRT Photorhabdus asymbiotica RTX toxin T1SS BteA-like LRT Vibrio splendidus RTX toxin T1SS BteA-like LRT Multiple phytopathogens AvrB, AvrRpm1, XopE1, XopE2,...”
6hegA / P37024 Crystal structure of escherichia coli deah/rha helicase hrpb (see paper)
47% identity, 98% coverage
- Ligands: adenosine-5'-diphosphate; tetrafluoroaluminate ion (6hegA)
PSHAa2216 ATP-dependent helicase from Pseudoalteromonas haloplanktis TAC125
39% identity, 100% coverage
ZMO0565 ATP-dependent helicase HrpB from Zymomonas mobilis subsp. mobilis ZM4
40% identity, 99% coverage
ZZ6_0702 ATP-dependent helicase HrpB from Zymomonas mobilis subsp. mobilis ATCC 29191
40% identity, 99% coverage
Krad_1244 ATP-dependent helicase HrpB from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
44% identity, 100% coverage
PPA0155 ATP-dependent helicase from Propionibacterium acnes KPA171202
38% identity, 99% coverage
- CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes
Brüggemann, PloS one 2012 - “...). The island is inserted into the P. acnes core genome, and disrupts a gene (PPA0155 in strain KPA) encoding an ATP-dependent helicase. We blasted this island also against all partially sequenced P. acnes genomes and found it in 13 strains (HL078PA1, HL045PA1, HL007PA1, SK182, HL083PA1,...”
- “...The cluster is inserted into the backbone genome, within a gene encoding a ATP-dependent helicase (PPA0155 in KPA, upper genome). (PDF) Click here for additional data file. Figure S2 Location of protospacers in the parA gene of the TAD locus. One gene within the TAD locus...”
CDC28_SCHPO / Q10752 Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein cdc28; Pre-mRNA-processing protein 8; EC 3.6.4.13 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
cdc28 / RF|NP_595686.2 ATP-dependent RNA helicase Cdc28 from Schizosaccharomyces pombe (see paper)
SPBC19C2.01 ATP-dependent RNA helicase Cdc28 (PMID 8862522) from Schizosaccharomyces pombe
38% identity, 43% coverage
- function: Involved in pre-mRNA splicing. Is required together with ATP and at least one other factor, for the first cleavage-ligation reaction. Functions as a molecular motor in the activation of the precatalytic spliceosome for the first transesterification reaction of pre-mRNA splicing by hydrolyzing ATP to cause the activation of the spliceosome without the occurrence of splicing (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Cells show pre-mRNA splicing defects. Cdc28-P8 temperature-sensitive mutant causes cell-cycle arrest in G2 and exhibits a splicing defect that leads to accumulation of unspliced precursors at the restrictive temperature. Temperature-sensitive pre- mRNA splicing mutant Prp8-1 exhibits a cell-cycle phenotype identical to cdc28-p8. Prp8-1 mutant produces elongated cells, accumulates U6 snRNA precursor and has defects in an early step of TFIID pre-mRNA splicing at the nonpermissive temperature. - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex
Weigt, Epigenetics & chromatin 2021 - “...Brr2 U5 snRNP complex subunit Brr2 SPAC644.12 Cdc5 Cell division control protein, splicing factor Cdc5 SPBC19C2.01 Cdc28 ATP-dependent RNA helicase Prp8 SPBC16A3.18 Cip1 RNA-binding protein Cip1 SPBC215.12 Cwf10 U5 snRNP GTPase subunit Cwf10 SPCP1E11.07c Cwf18 Complexed with Cdc5 protein Cwf18 SPAC3A12.11c Cwf2 RNA-binding protein Cwf2 SPBC211.02c...”
DEAH6_ARATH / F4IJV4 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH6; DEAH RNA helicase homolog PRP2; Protein MATERNAL EFFECT EMBRYO ARREST 29; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_181077 helicase domain-containing protein from Arabidopsis thaliana
AT2G35340 MEE29 (maternal effect embryo arrest 29); ATP binding / ATP-dependent RNA helicase/ ATP-dependent helicase/ helicase/ nucleic acid binding from Arabidopsis thaliana
37% identity, 43% coverage
- function: May be involved in pre-mRNA splicing.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Embryo defective. Arrested at one-cell zygotic stage. - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_649788 NP_566469 NP_010304 DDB0233740 RHA DHX9 NP_001348 NP_476641 NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...stop codons was observed for several genes, including CHR34 ( AT2G21450 ) , MEE29 ( AT2G35340 ) , and FASCIATED STEM4 (FAS4 , AT1G33390 ) ( fig.3 ). The consistent identification of frameshift mutations is mis leading for the homolog of PIGMENT DEFECTIVE (AT5G08610 ) and...”
- HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight
Zupanska, International journal of molecular sciences 2019 - “...Auxin efflux carrier family protein X 1.0 BP developmental process GO:0032502 anatomical structure morphogenesis GO:0009653 AT2G35340 MEE29 helicase domain-containing protein X 3.2 AT3G63290 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase X 3.1 AT5G65930 ZWI kinesin-like calmodulin-binding protein (ZWICHEL) X 3.0 AT4G02460 PMS1 DNA mismatch repair protein, putative X...”
- A spatial dissection of the Arabidopsis floral transcriptome by MPSS
Peiffer, BMC plant biology 2008 - “...for the promoter:GUS fusions, staining was prevalent throughout all floral organs (Figure 4l ). Similarly, At2g35340 was assayed and the result confirmed MPSS predictions of null expression within the inflorescence tissues, (Figure 4m ) despite previous microarray characterizations within floral tissues [ 20 ]. Figure 4...”
- “...stamen/petal-enriched promoter: GUS . (K) At1g07930. MPSS- ap3 expression enriched relative to other mutants. (L) At2g35340. MPSS-predicted absence of floral expression. (M) At1g26270. MPSS-predicted ubiquitous floral expression. (N) At1g68200. MPSS- ap1 sole expression. (O) At2g43100. MPSS- ap3 expression enriched relative to other mutants. (P) At3g15160. MPSS...”
- Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis
Herr, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...99 3010 MOG4 Ce 100 99 PRP1 CDC28 Hs 6 Sp 100 PRP1 At2g35340 6 Sc 99 41 96 98 PRP22 Hs 71 ESP3 100 74 100 100 100 PRP22 Dm 99 At4g16680 99 99 100 100 PRP43...”
- “...x x 4 B M Se R L St F G At1g32490 At2g35340 At4g16680 ESP1 ESP4 x x x x 5 At1g27590 At1g27595 Actin ESP1 rRNA D AtCstF64 RRM ESP1 hinge PC4/sub1/res1 hinge...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...RRM, 1 Prp2 atPrp2-1a At1g32490 1 9 >1-2c DEAD, 1; Helicase_C, 1; HA2, 1 atPrp2-1b At2g35340 2 >1-2c DEAD, 1; Helicase_C, 1; HA2, 1 atPrp2-2 At4g16680 4 DEAD, 1; Helicase_C, 1; HA2, 1 Prp5 atPrp5-1a At3g09620 3 DEAD, 1; Helicase_C, 1 atPrp5-1b At1g20920 1 11 DEAD,...”
ESP3_ARATH / Q8VY00 Pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1; DEAH RNA helicase homolog PRP2; Protein EMBRYO DEFECTIVE 2733; Protein ENHANCED SILENCING PHENOTYPE 3; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_174527 RNA helicase family protein from Arabidopsis thaliana
AT1G32490 ESP3 (ENHANCED SILENCING PHENOTYPE 3); ATP binding / ATP-dependent RNA helicase/ ATP-dependent helicase/ helicase/ nucleic acid binding from Arabidopsis thaliana
36% identity, 43% coverage
- function: Involved in pre-mRNA splicing.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Embryo defective (PubMed:15266054). Reduced stature, early flowering and altered leaf morphology (PubMed:17008405). - Arabidopsis GSM1 is involved in ABI4-regulated ABA signaling under high-glucose condition in early seedling growth.
Zheng, Plant science : an international journal of experimental plant biology 2019 (PubMed)- GeneRIF: GSM1 plays an important role in the ABI4-regulated Glc-ABA signaling cascade during Arabidopsis early seedling growth. [GSM1]
- A temperature-sensitive allele of a putative mRNA splicing helicase down-regulates many cell wall genes and causes radial swelling in Arabidopsis thaliana.
Howles, Plant molecular biology 2016 (PubMed)- GeneRIF: These data showed that ESP3 is a helicase involved in mRNA splicing.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287 DDB0233454 SKI2W SKIV2L NP_008860 NP_524465 NP_190280 NP_012485 Cyclophilins...”
- Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations
Manggabarani, DNA research : an international journal for rapid publication of reports on genes and genomes 2022 - “...genes. 54 Glyma.01G040900 encodes a putative DExH box RNA helicase, the homolog of Arabidopsis ESP3 (AT1G32490). ESP3 has been investigated to play a role in controlling cell wall-related proteins, such as peroxidases and xyloglucan endotransglucosylases. 55 Glyma.15G008000 encoding the homolog of Arabidopsis epidermal patterning factor-Like 8,...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...Material online), differences in were still evident between genes, with the homologs of ESP3 ( AT1G32490 ) , EIF4A1 ( AT3G13920), EIF4A2 ( AT1G54270), AT1G51380, AT1G72730 ( VASL ), CHR12 (AT3G06010), CHR11 (AT3G06400), ABA OVERLY SENSITIVE 6 ( ABO6 ; AT5G04895), and others being under strong...”
- Arabidopsis GSM1 is involved in ABI4-regulated ABA signaling under high-glucose condition in early seedling growth
Zheng, Plant science : an international journal of experimental plant biology 2019 (PubMed)- “...< 0.01). Scale bar =5 mm. Fig. 1 Fig. 2 At1g32490 mutation is responsible for Glc-hypersensitive phenotype of gsm1 . (a) Schematic structure of the two...”
- “...been studied [9 ,30 ,31 ]. Studies of different At1g32490 mutant alleles were carried out previously [32 ,33 ]. Herr et al. found one At1g32490 mutant allele...”
- A temperature-sensitive allele of a putative mRNA splicing helicase down-regulates many cell wall genes and causes radial swelling in Arabidopsis thaliana
Howles, Plant molecular biology 2016 (PubMed)- “...The putative RNA helicase encoded by the Arabidopsis gene At1g32490 is a homolog of the yeast splicing RNA helicases Prp2 and Prp22. We isolated a...”
- “...deficient radial swelling mutant (rsw12) with a mutation in At1g32490 leading to a single amino acid change in a putative DExH box RNA helicase. Based on the...”
- RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants
Liu, Molecular plant 2016 - “...AT1g73840 3 end processing ( Herr et al., 2006 ) ESP3 ENHANCED SILENCING PHENOTYPE 3 AT1g32490 RNA splicing ( Herr et al., 2006 ) ESP4 ENHANCED SILENCING PHENOTYPE 4 AT5g01400 3 end processing ( Herr et al., 2006 ) ESP5 ENHANCED SILENCING PHENOTYPE 5 AT5g23880 3...”
- Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis
Zhu, Journal of experimental botany 2016 - “...these enzymes have not been determined, except for ENHANCED SILENCING PHENOTYPE 3/RADIAL SWELLING 12 (EPS3/RSW12; At1g32490), FASCIATED STEM 4 (AtFAS4; At1g33390), ABA OVERLY SENSITIVE 6 (ABO6; At5g04895), CLUMSY VEIN (CUV; At5g13010), and ROOT INITIATION DEFECTIVE 1 (RID1; At1g26370). EPS3 is a putative homolog of yeast PRP2,...”
- Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization
Zermiani, Annals of botany 2015 - “...At4g14900 At1g03750 At1g18450 At1g20960 At4g18465 At1g32490 At1g79950 At2g13370 At2g16390 At1g32750 At1g52740 At3g06400 At3g17590 At2g45640 At3g17310 At3g11540...”
- Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity
Monaghan, PLoS pathogens 2009 - “...- - - [24] AT1G20960 EMB1507; DEAD-box helicase U5-200kD Brr2p Brr2p [20] , [22] [25] AT1G32490 EMB2733/ESP3; DEAD-box like helicase hPrp2/DHX16 Prp2p Cdc28p [22] , [24] AT1G80070 SUS2/EMB177; embryogenesis U5-220kD Prp8p Cwf6p [20] , [22] [25] , [51] AT2G43770 WD-40 repeat family; nucleotide binding U5-40kD -...”
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DEAH8_ARATH / F4JMJ3 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH8; DEAH RNA helicase homolog PRP2; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G16680 RNA helicase, putative from Arabidopsis thaliana
36% identity, 51% coverage
- function: May be involved in pre-mRNA splicing.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - Transcriptomic profiling during the post-harvest of heat-treated Dixiland Prunus persica fruits: common and distinct response to heat and cold
Lauxmann, PloS one 2012 - “...EST from severe drought-stressed leaves ( Populus ). P-loop containing nucleoside triphosphate hydrolases superfamily protein. At4g16680 I7 JK845711 FJ752239 Monodehydroascorbate reductase ( M. domestica ). Putative monodehydroascorbate reductase, ATMDAR1. At3g52880 I8 JK845712 AY347830 LYTB-like protein mRNA ( M. domestica ). CLB6, ISPH, HDR (4-Hydroxy-3-methylbut-2-enyl Diphosphate Reductase)....”
- Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis
Herr, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...98 PRP22 Hs 71 ESP3 100 74 100 100 100 PRP22 Dm 99 At4g16680 99 99 100 100 PRP43 Sp MOG5 Ce 100 100 560 At3g26 22 Sp PRP43 Ce 100 97 PRP 0 231 PRP43-2 Ce At3g6...”
- “...4 B M Se R L St F G At1g32490 At2g35340 At4g16680 ESP1 ESP4 x x x x 5 At1g27590 At1g27595 Actin ESP1 rRNA D AtCstF64 RRM ESP1 hinge PC4/sub1/res1 hinge...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...Helicase_C, 1; HA2, 1 atPrp2-1b At2g35340 2 >1-2c DEAD, 1; Helicase_C, 1; HA2, 1 atPrp2-2 At4g16680 4 DEAD, 1; Helicase_C, 1; HA2, 1 Prp5 atPrp5-1a At3g09620 3 DEAD, 1; Helicase_C, 1 atPrp5-1b At1g20920 1 11 DEAD, 1; Helicase_C, 1 atPrp5-2 At2g47330 2 9 DEAD, 1; Helicase_C,...”
AFUA_2G07710, Afu2g07710 mRNA splicing factor RNA helicase (Cdc28), putative from Aspergillus fumigatus Af293
37% identity, 40% coverage
- Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus
Amich, PLoS pathogens 2013 - “...0,00023 AFUA_1G04110 C2H2 transcription factor, putative 0.410 3,2E-08 AFUA_7G04580 TBC domain protein, putative 0.451 5,9E-10 AFUA_2G07710 mRNA splicing factor RNA helicase 0.458 3,4E-09 AFUA_2G02520 cell polarity protein (Tea1), putative 0.465 8,2E-08 AFUA_4G07280 cAMP-mediated signaling protein Sok1, putative 0.503 5,5E-07 AFUA_3G10830 glutathione S-transferase GstA 0.503 2,9E-05 AFUA_5G11260...”
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...0.81 [0.91, 2.05] Afu2g02390 2.60 [2.01, 0.54] Afu3g12790 0.80 [1.21, 2.35] Afu4g11390 1.75 [2.26, 1.85] Afu2g07710 0.80 [1.21, 2.39] Afu1g09240 2.76 [2.08, 0.45] Afu4g01400 0.78 [1.20, 2.34] Afu3g02420 2.03 [1.84, 0.63] Afu2g12790 0.75 [1.20, 2.34] Afu6g09880 3.65 [1.70, 1.01] Afu1g09930 0.71 [1.79, 3.13] Afu6g10260 1.96 [2.20,...”
NP_956318 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 from Danio rerio
39% identity, 43% coverage
- The zebrafish maternal-effect gene mission impossible encodes the DEAH-box helicase Dhx16 and is essential for the expression of downstream endodermal genes
Putiri, Developmental biology 2011 - “...the dhx16 gene. (A) Amino acid sequence of the zebrafish DEAH Box Polypeptide 16, accession NP_956318 ( Amsterdam et al., 2004 ; Sambrook et al., 2005 ) shows four domains (denoted by I, II, III, and IV) predicted by Pfam ( http://pfam.sanger.ac.uk/ ; ( Finn et...”
- Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax
Sarropoulou, BMC genomics 2009 - “...c-type lectin BAE45333 Contig_1596 cu zn superoxide dismutase AAW29025 Contig_395 deah (asp-glu-ala-his) box polypeptide 16 NP_956318, AAH45393, AAI65206 Contig_2814 ets-1 transcript variant ets-1 delta(iii-vi) AAY19514 Contig_626 ferritin heavy chain NP_001117129, P49946, AAB34575 Contig_280 fth1 protein CAL92185 Contig_2392 g-protein couplededg6 NP_001112363 Contig_2662 heat shock 10 kda protein...”
LOC108227844 pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1 from Daucus carota subsp. sativus
31% identity, 53% coverage
- Complex population evolutionary history of four cold-tolerant Notopterygium herb species in the Qinghai-Tibetan Plateau and adjacent areas
Liu, Heredity 2019 - “...phylogenetic results, homologous sequences from Daucus carota L. subsp. sativus (Hoffm.) Arcang. (LOC108202681, LOC108225228, LOC108197207, LOC108227844, LOC108193745, LOC108227632, and LOC108210968), Heracleum moellendorffii Hance (LOC108225228), Pleurospermum franchetianum Hemsl. (LOC108995448), and Pleurospermum prattii H. Wolff (LOC108224998) were used as outgroups (Iorizzo et al. 2013 ; Xue et al....”
DHX16_CAEEL / O45244 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase mog-4; Masculinization of germline protein 4; Sex determination protein mog-4; EC 3.6.4.13 from Caenorhabditis elegans (see 5 papers)
37% identity, 44% coverage
- function: ATP-binding RNA helicase involved in pre-mRNA splicing (Probable). Operates during embryogenesis.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with mep-1 and smn-1.
disruption phenotype: Embryonic lethal. Defects in oocytogenesis and spermatogenesis. Approximately 80% of mutants have an abnormal somatic gonad and no vulva.
MAB_0056c ATP-dependent helicase HrpA from Mycobacterium abscessus ATCC 19977
40% identity, 34% coverage
H0VTB1 RNA helicase from Cavia porcellus
38% identity, 43% coverage
7qttN / O60231 Structural organization of a late activated human spliceosome (baqr, core region) (see paper)
38% identity, 53% coverage
8i0sX / O60231 8i0sX (see paper)
38% identity, 53% coverage
DHX16_HUMAN / O60231 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16; ATP-dependent RNA helicase #3; DEAH-box protein 16; EC 3.6.4.13 from Homo sapiens (Human) (see 7 papers)
O60231 RNA helicase (EC 3.6.4.13) from Homo sapiens (see paper)
NP_003578 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 1 from Homo sapiens
38% identity, 43% coverage
- function: Required for pre-mRNA splicing as a component of the spliceosome (PubMed:20423332, PubMed:20841358, PubMed:25296192, PubMed:29360106). Contributes to pre-mRNA splicing after spliceosome formation and prior to the first transesterification reaction. As a component of the minor spliceosome, involved in the splicing of U12- type introns in pre-mRNAs (Probable). Also plays a role in innate antiviral response by acting as a pattern recognition receptor sensing splicing signals in viral RNA (PubMed:35263596). Mechanistically, TRIM6 promotes the interaction between unanchored 'Lys-48'-polyubiquitin chains and DHX16, leading to DHX16 interaction with RIGI and ssRNA to amplify RIGI-dependent innate antiviral immune responses (PubMed:35263596).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of pre-catalytic spliceosome complexes (PubMed:20423332, PubMed:20841358, PubMed:25296192, PubMed:29360106). Component of the minor spliceosome, which splices U12-type introns (PubMed:33509932). Interacts with GPKOW. Interacts with TRIM6 (PubMed:35263596). Interacts with RIGI (PubMed:35263596). - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...EIF4A3 NP_055555 NP_649788 NP_566469 NP_010304 DDB0233740 RHA DHX9 NP_001348 NP_476641 NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413...”
- Molecular basis for the activation of human spliceosome.
Zhan, Nature communications 2024 - “...Expression and purification of PRP2 The cDNA sequences of human full-length PRP2 (DHX16, Uniprot ID: O60231), three truncated constructs (1-198, 1-305, 1-361), and four missense variants (R503A, T674M, L709A, R998A) were generated using PCR-based strategy, and individually subcloned into a pCAG vector with an N-terminal 3xFlag...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - L-Lactate dehydrogenase B may be a predictive marker for sensitivity to anti-EGFR monoclonal antibodies in colorectal cancer cell lines.
Nagamine, Oncology letters 2019 - Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...protein 15 DHX15 ATP-dependent RNA helicase #46 16 O60231 RNA helicase DHX16 17 Q92841 RNA helicase DDX17 DEAH-box protein 16 DHX16 ATP-dependent RNA helicase...”
- The Akt pathway regulates survival and homing in Waldenstrom macroglobulinemia.
Leleu, Blood 2007 - Gene expression pattern in Caco-2 cells following rotavirus infection
Cuadras, Journal of virology 2002 - “...O75822 O00303 P04765 Q9UNQ9 P49588 Q15046 Q9NSD9 P54577 P40562 O00571 O60231 Q64060 O15523 P38712 P06748 P09132 2.4 2.3 2.4 2.5 2.3 2.6 2.4 2.2 2.1 2.3 2.1 4.4...”
NP_001157711 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 2 from Homo sapiens
38% identity, 46% coverage
- Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
Hautakangas, Clinical genetics 2023 (PubMed)- GeneRIF: Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
- The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
Hage, Cell reports 2022 - GeneRIF: The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
- Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
Paine, American journal of human genetics 2019 - GeneRIF: Missense mutation in DHX16 gene is associated with neurodevelopmental disorder.
- GPKOW is essential for pre-mRNA splicing in vitro and suppresses splicing defect caused by dominant-negative DHX16 mutation in vivo.
Zang, Bioscience reports 2014 - GeneRIF: Data show that G patch domain and KOW motifs protein (GPKOW )interacted directly with the DEAH-box protein 16 (DHX16/hPRP2) and with RNA.
- Contribution of DEAH-box protein DHX16 in human pre-mRNA splicing.
Gencheva, The Biochemical journal 2010 - GeneRIF: DHX16 is required for human pre-mRNA splicing after the formation of a pre-catalytic spliceosome.
- A Large-scale genetic association study of esophageal adenocarcinoma risk.
Liu, Carcinogenesis 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein.
Gencheva, The Journal of biological chemistry 2010 - GeneRIF: Results suggest that mutant DHX16/hPRP2 causes a defective spliceosome to retain unspliced gene transcripts in the nuclei.
- High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
Barcellos, PLoS genetics 2009 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
PRP22_SCHPO / O42643 Pre-mRNA-splicing factor ATP-dependent RNA helicase prp22; EC 3.6.4.13 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
prp22 / RF|NP_593253.1 ATP-dependent RNA helicase Prp22 from Schizosaccharomyces pombe (see paper)
SPAC10F6.02c ATP-dependent RNA helicase Prp22 from Schizosaccharomyces pombe
37% identity, 39% coverage
- function: Acts late in the splicing of pre-mRNA. Required for the splicing of introns with a branch nucleotide to 3'-splice site distance greater or equal to 15. Mediates the release of the spliced mRNA from spliceosomes.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Belongs to the 40S cdc5-associated complex (or cwf complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least brr2, cdc5, cwf2/prp3, cwf3/syf1, cwf4/syf3, cwf5/ecm2, spp42/cwf6, cwf7/spf27, cwf8, cwf9, cwf10, cwf11, cwf12, prp45/cwf13, cwf14, cwf15, cwf16, cwf17, cwf18, cwf19, cwf20, cwf21, cwf22, cwf23, cwf24, cwf25, cwf26, cyp7/cwf27, cwf28, cwf29/ist3, lea1, msl1, prp5/cwf1, prp10, prp12/sap130, prp17, prp22, sap61, sap62, sap114, sap145, slu7, smb1, smd1, smd3, smf1, smg1 and syf2. - CharProtDB Source (per GeneDB): GeneDB_Spombe
- A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast
Bayne, Genome biology 2014 - “...cwf3 40.7 92.6 SPAC30D11.09 cwf19 35.0 74.4 SPBC31F10.11c cwf4 32.3 80.8 SPBC6B1.10 prp17 31.7 63.1 SPAC10F6.02c prp22 31.7 131.5 SPCC188.11 cwf13 28.7 62.7 SPBC13E7.01 cwf22 25.0 102.7 SPBP22H7.07 prp5 23.0 52.4 SPAC3A12.11c cwf2 19.3 44.3 SPCC550.02c cwf5 17.3 39.6 SPBC1289.11 spf38 16.3 37.4 SPAC29A4.08c prp19 15.0...”
- Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs
Ohi, Molecular and cellular biology 2002 - “...Yes Yes Yes Yes Yes 154 21 Yes Yes Prp22p (O42643) Cwf21p (O14161) 130 16 Yes No Cwc22p (P53333) Cwf22p (P78752) 67 Yes Cwc23p Cwc24p Cwc25p Cwc26p Cwc27p...”
NP_609946 lethal (2) 37Cb from Drosophila melanogaster
37% identity, 50% coverage
6i3pC / G0S700 Crystal structure of deah-box atpase prp22 with bound ssrna (see paper)
36% identity, 54% coverage
SCO2000 ATP-binding RNA helicase from Streptomyces coelicolor A3(2)
46% identity, 44% coverage
- Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives
Yagüe, FEMS microbiology letters 2013 - “...SCO0756 SCO1852 SCO3369 SCO4585 SCO5603 SCO6677 SCP1.136 SCO0824 SCO1966 SCO3370 SCO4620 SCO5633 SCO6683 SCP1.169 SCO1144 SCO2000 SCO3372 SCO4685 SCO5648 SCO6684 SCP1.205c SCO1147 SCO2257 SCO3418 SCO4797 SCO5668 SCO6719 SCP1.216Ac SCO1148 SCO2259 SCO3453 SCO4803 SCO5734 SCO6720 SCP1.290c SCO1152 SCO2324 SCO3526 SCO4909 SCO5750 SCO6742 SCP1.63 SCO1183 SCO2463 SCO3541 SCO4963...”
C4M5M5 RNA helicase from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_122790 helicase, putative from Entamoeba histolytica HM-1:IMSS
32% identity, 53% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U snRNAs and components of the post-catalytic/intron lariat spliceosome complexes (PILS in superscript) were described by Miranda et al. ( 1996 ), Hernandez-Rivas et...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...C4LZM8 Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U snRNAs and components of the post-catalytic/intron lariat spliceosome complexes (PILS in superscript) were described by Miranda et al. ( 1996 ), Hernandez-Rivas...”
6rm8A / G0SEG4 Crystal structure of the deah-box atpase prp2 in complex with spp2 and adp (see paper)
36% identity, 54% coverage
- Ligand: adenosine-5'-diphosphate (6rm8A)
B7PAK3 RNA helicase from Ixodes scapularis
36% identity, 40% coverage
HRPA_BORBU / O51767 ATP-dependent RNA helicase HrpA; EC 3.6.4.13 from Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31) (Borrelia burgdorferi) (see 2 papers)
BB0827 ATP-dependent helicase (hrpA) from Borrelia burgdorferi B31
33% identity, 51% coverage
- function: Has RNA-stimulated ATPase activity and RNA helicase activity (PubMed:24367266). Involved in global regulation of gene expression (PubMed:21814569). Could be involved in RNA processing and post- transcriptional gene regulation (PubMed:24367266). Essential for both tick transmission and mouse infection (PubMed:24367266).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Disruption of the gene results in the modulation of the expression of about 180 proteins and in a complete loss in the ability of the spirochetes to infect mice by needle inoculation. - Lyme Disease Pathogenesis
Coburn, Current issues in molecular biology 2021 - “...), and for dissemination within feeding tick ( Dunham-Ems et al., 2012 ) HrpA ( bb0827 ) chr ATP-dependent DEAH-box RNA helicase involved in RNA processing and global gene regulation ( Salman-Dilgimen et al., 2011 ; Salman-Dilgimen et al., 2013 ). Required for mouse infection and...”
- Temperature-dependent sRNA transcriptome of the Lyme disease spirochete
Popitsch, BMC genomics 2017 - “...of the B. burgdorferi life cycle and cell division, such as: bb0420 ( hk1 ), bb0827 ( hrpA ), bbb03 ( resT ), bbb17 ( guaB ), and bba66 [ 4 , 13 , 44 50 ]. Hk1 is the histidine kinase in the two-component system...”
- Borrelia burgdorferi HtrA: evidence for twofold proteolysis of outer membrane protein p66
Coleman, Molecular microbiology 2016 - “...that are relevant to p66 ( Samuels, 2011 ): Targeted disruption of RNA helicase HrpA (BB0827), results in the down regulation of expression of p66, along with varied effects on other B. burgdorferi genes ( Salman-Dilgimen et al. , 2011 , Salman-Dilgimen et al. , 2013...”
- HrpA, a DEAH-box RNA helicase, is involved in global gene regulation in the Lyme disease spirochete
Salman-Dilgimen, PloS one 2011 - “...work on antigenic variation in B. burgdorferi , we generated a disruption of the hrpA (bb0827) gene, which encodes a putative RNA helicase ( Fig. 1 ), to see if loss of this function would have an effect upon antigenic switching at the vlsE locus. Surprisingly,...”
- “...Results Construction of hrpA and bb0826 gene disruptions in B. burgdorferi Disruption of the hrpA (bb0827) gene in B. burgdorferi was accomplished by allelic exchange [36] . A knockout plasmid ( Fig. 2A ) was constructed in E. coli , in which the central 500 bp...”
- Genome-wide transposon mutagenesis of Borrelia burgdorferi for identification of phenotypic mutants
Stewart, Applied and environmental microbiology 2004 - “...BB0608 BBB18 BB0347 BBR41 BB0830 BB0562 BB0827 BBN16 BBD14/15 BBN26 BBO36 BB0102 Aminoacyl-histidine dipeptidase (putative) GuaA-GMP synthase Fibronectin...”
- Profiling of temperature-induced changes in Borrelia burgdorferi gene expression by using whole genome arrays
Ojaimi, Infection and immunity 2003 - “...BBS31 BB0308 BB0446 BB0812 BBH37 BBR17 BB0759 BB0832 BB0827 BBQ13 BBQ17 BB0216 BB0415 BB0431 BBO24 BB0819 BB0210 BBN21 BBM36 BBR19 Hypothetical protein Na/H...”
F6GT26 RNA helicase from Vitis vinifera
36% identity, 42% coverage
- Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid
Rattanakan, Horticulture research 2016 - “...actin remodeling, a component (F6HTW0) of the Cul4-RING E3 ubiquitin ligase complex, a DNA/RNA helicase (F6GT26), a protein involved in stability of Photosystem II (F6HVA4), a eukaryotic translation initiation factor (F6I2I6) and a ribosomal protein (A5AI30). ABA affects phosphoproteins in grapevine We utilized a new approach...”
- “...VIT_14s0030g01350 F6HTW0 Transducin/WD40 repeat-like superfamily protein 1.66 6.69E04 VGSAGNTSNsTRPR S18 Phospho VGSAGNTSNsTRPR S20 Phospho VIT_17s0000g06950 F6GT26 RNA helicase family protein 1.24 6.51E03 TSQDEDDDsELEEESLRDR S173 Phospho VITISV_031115 A5AI30 Ribosomal protein S21 family protein 1.83 1.17E02 NKKDDDEEDNWEVPEGELPF VITISV_013443 D7U6G6 Anthocyanidin reductase 1.54 1.23E02 YGIEEIYDESVEYFK VITISV_040194 A5BVL2 Hypothetical protein...”
MXAN_3177 ATP-dependent helicase HrpA from Myxococcus xanthus DK 1622
38% identity, 36% coverage
PA3297 probable ATP-dependent helicase from Pseudomonas aeruginosa PAO1
Q9HYU6 Probable ATP-dependent helicase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
38% identity, 34% coverage
- Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media
Belanger, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - Editorial: Antimicrobial Resistance and Virulence Common Mechanisms
Giraud, Frontiers in microbiology 2017 - “...counteract its killing and virulence-inhibitory effects. An interesting work by Tan et al. revealed that PA3297, a P. aeruginosa gene encoding a DEAH-box helicase, is involved in this response. Indeed, deficiency of this gene renders P. aeruginosa more susceptible to the killing and to virulence suppression...”
- Chitin Oligosaccharide (COS) Reduces Antibiotics Dose and Prevents Antibiotics-Caused Side Effects in Adolescent Idiopathic Scoliosis (AIS) Patients with Spinal Fusion Surgery
Qu, Marine drugs 2017 - “...in especially high demand for its increasing resistance to the antibiotic Azithromycin. The overexpression of PA3297 (a DEAH-box helicase; DEAH, Asp-Glu-Ala-His) was found to be caused by the interaction between Azithromycin and ribosomes. The mutant PA3297 will increase unprocessed 23TS-5S rRNA in the presence of Azithromycin,...”
- “...L. Weng Y. Chen R. Zhu F. Jin Y. Cheng Z. Jin S. Wu W. PA3297 Counteracts Antimicrobial Effects of Azithromycin in Pseudomonas aeruginosa Front. Microbiol. 2016 7 317 10.3389/fmicb.2016.00317 27014238 33. Garcia-Quintanilla M. Carretero-Ledesma M. Moreno-Martinez P. Martin-Pena R. Pachon J. McConnell M.J. Lipopolysaccharide loss...”
- PA3297 Counteracts Antimicrobial Effects of Azithromycin in Pseudomonas aeruginosa
Tan, Frontiers in microbiology 2016 - “...Microbiol Front. Microbiol. Frontiers in Microbiology 1664-302X Frontiers Media S.A. 4792872 10.3389/fmicb.2016.00317 Microbiology Original Research PA3297 Counteracts Antimicrobial Effects of Azithromycin in Pseudomonas aeruginosa Tan Hao 1 Zhang Lu 1 Weng Yuding 1 Chen Ronghao 1 Zhu Feng 1 Jin Yongxin 1 Cheng Zhihui 1 Jin...”
- “...to and counteracts the effects of AZM remain elusive. Here, we found that deficiency of PA3297, a gene encoding a DEAH-box helicase, intensified AZM-mediated bacterial killing, suppression of pyocyanin production and swarming motility, and hypersusceptibility to hydrogen peroxide. We demonstrated that expression of PA3297 is induced...”
- Use of phage display to identify potential Pseudomonas aeruginosa gene products relevant to early cystic fibrosis airway infections
Beckmann, Infection and immunity 2005 - “...PA2138 PA2305 PA2383 PA2600 PA2819 PA2928 PA3075 PA3297 narG PA4186 fptA pchF PA4601 tatB PA5384 PA5399 Probable two-component sensor Hypothetical protein...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...4922 Q9I688 595 Q9HUI2 1677 Q9HYU4 2759 Q9HVD9 3841 Q9I0I8 4923 Q9I695 596 Q9HUI8 1678 Q9HYU6 2760 Q9HVE1 3842 Q9I0K2 4924 Q9I6A2 597 Q9HUJ2 1679 Q9HYX5 2761 Q9HVE2 3843 Q9I0K3 4925 Q9I6A3 598 Q9HUJ4 1680 Q9HYX7 2762 Q9HVE3 3844 Q9I0K5 4926 Q9I6A4 599 Q9HUK8 1681 Q9HYX8...”
8c6jV / Q14562 8c6jV (see paper)
34% identity, 48% coverage
K7MP06 RNA helicase from Glycine max
36% identity, 38% coverage
- Quantitative Phosphoproteomic Analysis Provides Insights into the Sodium Bicarbonate Responsiveness of Glycine max
Li, Biomolecules 2023 - “...I1MR60, I1MC08, I1KKF7, K7N5A2, and I1K313) were involved in plantpathogen interactions (gmx04626), eight DEPs (I1KR32, K7MP06, I1JAI4, I1MRC7, C6T8C8, I1JAG0, I1MYV2, and I1LMC1) were involved in spliceosome (gmx03040), six DEPs (I1JAG0, I1MYV2, I1LQL7, I1LMC1, A0A368UGP3, and I1NGB7) were involved in nucleocytoplasmic transport (gmx03013), six DEPs (I1JAG0,...”
NP_001309148 ATP-dependent RNA helicase DHX8 isoform 6 from Homo sapiens
34% identity, 39% coverage
- Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.
Osterhoudt, RNA (New York, N.Y.) 2024 - GeneRIF: Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.
- Human gastric cancer progression and stabilization of ATG2B through RNF5 binding facilitated by autophagy-associated CircDHX8.
Wei, Cell death & disease 2024 - GeneRIF: Human gastric cancer progression and stabilization of ATG2B through RNF5 binding facilitated by autophagy-associated CircDHX8.
- Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release.
Felisberto-Rodrigues, The Biochemical journal 2019 (PubMed)- GeneRIF: This study provides an in-depth understanding of the activity of DHX8 and contributes insights into the RNA-unwinding mechanisms of the DEAH-box helicase family.
- A tandem duplication of BRCA1 exons 1-19 through DHX8 exon 2 in four families with hereditary breast and ovarian cancer syndrome.
Du, Breast cancer research and treatment 2018 (PubMed)- GeneRIF: The copy number variation initially recognized as duplication of exon 1-19 of the BRCA1 gene by MLPA analysis is a structural variation with breakpoints in the BRCA1 and DHX8 genes.
- Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.
Zanini, Journal of cell science 2017 (PubMed)- GeneRIF: cellular complexes comprising cactin, DHX8 and SRRM2 sustain precise chromosome segregation, genome stability and cell proliferation by allowing faithful splicing of specific pre-mRNAs.
- Structural analysis of the C-terminal domain of the spliceosomal helicase Prp22.
Kudlinzki, Biological chemistry 2012 (PubMed)- GeneRIF: structural and functional analysis of C-terminal domain of the spliceosomal helicase Prp22
- Crystallization and preliminary X-ray diffraction analysis of the C-terminal domain of the human spliceosomal DExD/H-box protein hPrp22.
Kudlinzki, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: Preliminary X-ray diffraction analysis of the crystals of the C-terminal domain of the human DExD/H-box protein hPrp22 at 2.1 A resolution, is reported.
DHX8_HUMAN / Q14562 ATP-dependent RNA helicase DHX8; DEAH box protein 8; RNA helicase HRH1; EC 3.6.4.13 from Homo sapiens (Human) (see 7 papers)
Q14562 RNA helicase (EC 3.6.4.13) from Homo sapiens (see paper)
NP_004932 ATP-dependent RNA helicase DHX8 isoform 1 from Homo sapiens
34% identity, 37% coverage
- function: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28076346, PubMed:28502770). Facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome (PubMed:8608946).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in the spliceosome C complex (PubMed:11991638, PubMed:28076346, PubMed:28502770). Interacts with ARRB2; the interaction is detected in the nucleus upon OR1D2 stimulation (PubMed:16820410). Interacts with SRRM2 (PubMed:28062851). Interacts with CACTIN (PubMed:28062851). - The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition
Guo, 2021 - Redox modifications of cysteine-containing proteins, cell cycle arrest and translation inhibition: Involvement in vitamin C-induced breast cancer cell death.
El, Redox biology 2019 - “...chromosome-associated kinesin KIF4A (accession number O95239 ), histone-binding protein RBBP4 (Q09028), ATP-dependent RNA helicase DHX8 (Q14562), U5 small nuclear ribonucleoprotein 40-kDa protein (Q96DI7), tRNA-splicing ligase RtcB homolog (Q9Y3I0), 26S proteasome non-ATPase regulatory subunit 3 (O43242), Cullin-4A (Q13619), E3 ubiquitin-protein ligase RING2 (Q99496), E3 ubiquitin-protein ligase UBR4...”
- Standardization of a protocol for shotgun proteomic analysis of saliva
Ventura, Journal of applied oral science : revista FOB 2018 - “...49.08 Q8N6M6 Aminopeptidase O 261.58 10.13 Q01484 Ankyrin-2 39.24 4.22 P02652 Apolipoprotein A-II 941.64 47.00 Q14562 ATP-dependent RNA helicase DHX8 365.21 7.38 Q8IYB8 ATP-dependent RNA helicase SUPV3L1_ mitochondrial 331.22 7.00 P04280 Basic salivary proline-rich protein 1 8867.97 44.39 P02812 Basic salivary proline-rich protein 2 54196.77 69.71...”
- Cellular fatty acid synthase is required for late stages of HIV-1 replication.
Kulkarni, Retrovirology 2017 - “...sequencing as the following: (1) Ubiquitin carboxyl terminal hydrolase (Q9Y4E8), (2) ATP-dependent RNA helicase DHX8 (Q14562), (3) FASN (P49327), (4) HSP90-beta (P08238), (5) GDP-L-fucose synthetase (Q13630), (6) L-lactate dehydrogenase (P07195) and pyridoxial kinase (O00764), (7) Argininosuccinate synthase (P00966), (8) Nucleoside diphosphate kinase-A (P15531) and, (9) Nucleoside...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...c i enc e. Donotdi s t r i but e. 9 Q14562 RNA helicase DHX8 RNA helicase HRH1 10 Q08211 RNA helicase A Nuclear DNA helicase II DHX9 NDH II DEAH-box protein 9...”
- Probing the efficiency of proteolytic events by positional proteomics.
Plasman, Molecular & cellular proteomics : MCP 2011 - Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate.
Coltri, PloS one 2011 - “...1 Second step factors: O95391 SLU7 Slu7p 68 2 O60508 PRP17 Prp17p 65 2 3 Q14562 DHX8 Prp22p 139 6 13 Recruited to C complex: O60306 AQR 171 5 52 Q9Y314 NOSIP 33 3 Q96BP3 PPWD1 74 2 Q9UJV9 DDX41 70 2 Q9H2H8 PPIL3 18 1...”
- More
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...XAB2 NP_064581 NP_610891 NP_198226 NP_010704 3C. Catalytic step II and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528...”
- Crystallization and preliminary X-ray diffraction analysis of the C-terminal domain of the human spliceosomal DExD/H-box protein hPrp22
Kudlinzki, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - “...of yPrp22 (hPrp22, DHX8, HRH1; NCBI accession No. NP_004932) has been identified (Ono et al., 1994) and further Acta Cryst. (2009). F65, 956-958 crystallization...”
T1IZH9 RNA helicase from Strigamia maritima
35% identity, 20% coverage
DEAH5_ARATH / Q38953 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5; DEAH RNA helicase homolog PRP22; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G26560 ATP-dependent RNA helicase, putative from Arabidopsis thaliana
NP_189288 ATP-dependent RNA helicase from Arabidopsis thaliana
35% identity, 39% coverage
- function: May be involved in pre-mRNA splicing.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - Proteomics approach to investigating osmotic stress effects on pistachio
Pakzad, Frontiers in plant science 2022 - “...family protein;HAB1, HYPERSENSITIVE TO ABA1;CSLD5, 1,4-beta-D-xylan synthase; AT5G14520, pescadillo-related protein; MST1, thiosulfate sulfurtransferase;COX1, cytochrome oxidase; AT3G26560, ATP-dependent RNA helicase DHX8/PRP22; RCAR1, abscisic acid receptor PYL9; RAD50, DNA repair protein RAD50; RBCL, ribulose-bisphosphate carboxylases;ATCSLC08, putative xyloglucan glycosyltransferase 8; GAUT3, galacturonosyltransferase 3; PGK1, phosphoglycerate kinase 1;PRH75, DEAD-box ATP-dependent...”
- Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components
Marondedze, Frontiers in molecular biosciences 2019 - “...AT2G43810 Small nuclear ribonucleoprotein family protein X X AT3G13570 SC35-like splicing factor 30A X X AT3G26560 ATP-dependent RNA helicase, putative X X AT5G48870 Small nuclear ribonucleoprotein family protein X X AT1G09770 Cell division cycle 5 X AT4G02840 Small nuclear ribonucleoprotein family protein X AT4G30330 Small nuclear...”
- Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions
Galla, Frontiers in plant science 2019 - “...encoded by AT2G32600, the pre-mRNA-splicing factor ISY1 (AT3G18790) and an ATP-dependent RNA helicase encoded by AT3G26560. Among these interactors, only the orthologous ISY1 (AT3G18790) was up-regulated in aposporous samples ( Supplementary Table S4 ; FDR p -value: 3.73e-3). However, several DEGs with the potential to interact...”
- Quantitative Phosphoproteomic Analysis Reveals Shared and Specific Targets of Arabidopsis Mitogen-Activated Protein Kinases (MAPKs) MPK3, MPK4, and MPK6
Rayapuram, Molecular & cellular proteomics : MCP 2018 - “...AT2G20960 AT2G25430 AT2G27100 AT3G05900 AT3G16420/AT3G16430 AT3G26560 AT3G55460 AT3G55460 AT3G63460 AT4G01290 AT4G27430 AT5G35200 AT5G45190 AT5G46750 AT5G57870...”
- “...connected to SKIP and the RNA helicase DHX8/PRP22 (AT3G26560) and phosphopeptides corresponding to SKIP and DHX8/PRP22 are missing in mpk4, suggesting that...”
- The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants
Gallie, Translation (Austin, Tex.) 2014 - “...by the A. thaliana genes, At1g48650 and At3g26560, exhibit limited homology with DHX29 (49.2%/54.9% and 50.7%/56.3% amino acid identity/similarity,...”
- Identification of novel in vivo MAP kinase substrates in Arabidopsis thaliana through use of tandem metal oxide affinity chromatography
Hoehenwarter, Molecular & cellular proteomics : MCP 2013 - “...unknown protein STPVRKPHTSTADLLTWSEVPPPDSP(ph)SSASR 1128.54 3 16E-05 0.626 1.0E-09 a 0.974 a 6.6 3.0 7.0 3.46E-02 AT3G26560 ATP-dependent RNA helicase, putative YSVDMS(ph)PVKIFK 747.35 2 76E-03 1 6.4E-12 1 1.8 1.1 1.2 1.03E-01 AT3G49590 Autophagy-related protein 13 IITDYVGS(ph)PATDPMR 858.38 2 20E-03 0.999 4.6E-03 0.976 1.9 2.1 2.1 3.63E-03...”
- Transcriptomic profiling during the post-harvest of heat-treated Dixiland Prunus persica fruits: common and distinct response to heat and cold
Lauxmann, PloS one 2012 - “...Hypothetical protein clone pPn31C7, and hypothetical transcription factor ( P. persica ). ATP-dependent RNA helicase. At3g26560 Expression pattern: 001111 I51 JK845755 CU223716 EST from leaves ( P. trichocarpa ). ACBP6 (Acyl-CoA-Binding Protein 6). At1g31812 I52 JK845756 XM_002523147 Nuclear transcription factor Y subunit A-7-like ( V. vinifera...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...At1g15200 1 9 AltA (1); Pinin/SDK/memA, 1; 2.7 Second step splicing factors Prp22 Prp22 atPrp22-1 At3g26560 3 11 DEAD, 1; Helicase_C, 1; S1, 1; HA2, 1; atPrp22-2 At1g26370 1 5 DEAD, 1; Helicase_C, 1; HA2, 1 atPrp22-3 At1g27900 1 15 DEAD, 1; Helicase_C, 1; HA2, 1...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_610891 NP_198226 NP_010704 3C. Catalytic step II and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...helicase (PFI0860c) 48 DHX16 DHX16 (LOC_Os03g17432) DHX8 (Q38953) PRP22 (P24384) RNA helicase (PF10_0294) 49 DHX29 DEAD/DEAH-box (LOC_Os04g35260) DHX8 (Q38953)...”
- “...helicase (PFI0860c) 52 DHX33 DHX8 (LOC_Os06g09280) DHX8 (Q38953) PRP22 (P24384) RNA helicase (PF10_0294) 53 DHX34 DEAD/DEAH-box (LOC_Os10g33275) DHX8 (Q38953)...”
Pfl01_1420 ATP-dependent helicase HrpA from Pseudomonas fluorescens Pf0-1
38% identity, 35% coverage
PRP16_HUMAN / Q92620 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16; ATP-dependent RNA helicase DHX38; DEAH box protein 38; EC 3.6.4.13 from Homo sapiens (Human) (see 5 papers)
NP_054722 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 from Homo sapiens
35% identity, 36% coverage
- function: Probable ATP-binding RNA helicase (Probable). Involved in pre-mRNA splicing as component of the spliceosome (PubMed:29301961, PubMed:9524131).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in the spliceosome C complex. - Hypoxia Alters the Proteome Profile and Enhances the Angiogenic Potential of Dental Pulp Stem Cell-Derived Exosomes.
Li, Biomolecules 2022 - “...1 PLOD1 1.216 0.002 up P08253 72 kDa type IV collagenase MMP2 1.399 0.002 up Q92620 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 DHX38 1.762 0.036 up P06576 ATP synthase subunit beta, mitochondrial ATP5B 1.221 0.002 up P35556 Fibrillin-2 FBN2 1.513 0.002 up P21810 Biglycan BGN 1.881...”
- Haptoglobin Induces a Specific Proteomic Profile and a Mature-Associated Phenotype on Primary Human Monocyte-Derived Dendritic Cells.
Torres, International journal of molecular sciences 2022 - “...and metal ion binding PCCB F8WBI9 Propionyl-CoA carboxylase beta chain, mitochondrial MA Ligase activity DHX38 Q92620 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 MA i. RNA and nucleic acid binding ii. Helicase and ATP hydrolisis activity HMGCS1 Q01581 Hydroxymethylglutaryl-CoA synthase MA Protein homodimerization activity PTPMT1 Q8WUK0-2 Phosphatidylglycerophosphatase...”
- Blood protein predictors of brain amyloid for enrichment in clinical trials?
Ashton, Alzheimer's & dementia (Amsterdam, Netherlands) 2015 - “...0.038 .081 0.044 .613 0.331 .021 0.671 .085 0.206 .164 0.191 .021 0.298 .039 3 Q92620 DEAH box protein 38 2 0.383 .351 0.046 .044 0.095 .207 0.223 .067 0.380 .351 0.046 .031 0.095 .208 0.243 .046 3 Q06033 ITI heavy chain H3 2 1.525 .027...”
- “...0.034 .783 0.148 .035 0.107 .351 0.445 .116 0.115 .475 0.156 .025 0.119 .300 2 Q92620 DEAH box protein 38 5 0.449 .199 0.123 .576 0.197 .038 0.144 .318 0.449 .199 0.123 .576 0.197 .038 0.144 .318 2 Q14624 ITI heavy chain H4 1 1.244 .041...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...AU-rich element ARE 36 Q8IY37 RNA helicase DHX37 37 Q92620 RNA helicase PRP16 DEAH-box protein 37 DHX37 RNA helicase DHX38 DHX38 DEAH-box protein 38 38 O00148...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520 3D. Exon junction complex proteins DDB0233615-o...”
PF3D7_1030100 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative from Plasmodium falciparum 3D7
32% identity, 35% coverage
- Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages
Kaur, Scientific reports 2016 - “...protein L3 (RPL3) K3(Trimethyl) HILIC MDELNkEEIVDNINNEQAK PF3D7_1028400 nucleolar preribosomal assembly protein, putative K6(Trimethyl) HILIC LIVTSATLDAEk PF3D7_1030100 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22, putative (PRP22) C-Term(Methyl) HILIC SNSSDGSSSDGSSSDGSSSDGNSSDGSSSSSSNYk PF3D7_1032000 ribosome maturation factor RimM, putative (RimM) K35(Dimethyl) HILIC AYCNNGNMDnnTkSNSSDGSSSDGSSSDGSSSDGNSSDGSSSSSSNYk PF3D7_1032000 ribosome maturation factor RimM, putative (RimM) K13(Methyl); K48(Trimethyl)...”
- Fitness of artemisinin-resistant Plasmodium falciparum in vitro
Hott, The Journal of antimicrobial chemotherapy 2015 - “...susceptibility to artemisinin derivatives, increased copy number of Pf3D7_1030100 and an SNP in Pf3D7_0307600. An SNP conferring an E208K mutation in the kelch...”
- “...clone has only one copy of genes in this region.24 Pf3D7_1030100 is in the amplicon and C9 has two copies, whereas parental D6 maintains one copy. Therefore in...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...Helicase+DUF4217 PF3D7_0721300, PF3D7_1419100, PF3D7_1418900, PF3D7_0630900 Helicase+ZnF PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500 Helicase+HA2+S1 PF3D7_1030100 Helicase+HA2+OB fold PF3D7_1364300, PF3D7_1231600, PF3D7_0917600, PF3D7_0821300 Helicase+ZnF+DSHCT PF3D7_0909900 Helicase+rRNA proc-arch+DSHCT PF3D7_0602100 Helicase+HA2 PF3D7_0310500, PF3D7_1302700 Blue , pink and green boxes are used to denote transmembrane, low complexity, and coiled-coil regions,...”
- “...participate in ribosome biogenesis [ 26 ]. In P. falciparum , PF3D7_1364300, PF3D7_1231600, PF3D7_0917600 and PF3D7_1030100 all have a conserved DEAH domain and are classified as Prp (pre-mRNA processing) proteins. Similarly, almost all of the proteins classified under ribosome biogenesis (Fig. 2 and Additional file 6...”
OCU_RS37390 ATP-dependent RNA helicase HrpA from Mycobacterium intracellulare ATCC 13950
38% identity, 33% coverage
PF3D7_0917600 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43, putative from Plasmodium falciparum 3D7
34% identity, 50% coverage
- The Plasmodium falciparum Nuclear Protein Phosphatase NIF4 Is Required for Efficient Merozoite Invasion and Regulates Artemisinin Sensitivity
Zhu, mBio 2022 - “...<0.001 PF3D7_0802000 glutamate dehydrogenase, putative GDH3 1,000 <0.001 PF3D7_0823300 histone acetyltransferase GCN5 GCN5 1,000 <0.001 PF3D7_0917600 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43, putative PRP43 1,000 <0.001 PF3D7_1019400 60S ribosomal protein L30e, putative N/A 1,000 <0.001 PF3D7_1103100 60S acidic ribosomal protein P1, putative RPP1 1,000 <0.001 PF3D7_1220900...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...Helicase+ZnF PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500 Helicase+HA2+S1 PF3D7_1030100 Helicase+HA2+OB fold PF3D7_1364300, PF3D7_1231600, PF3D7_0917600, PF3D7_0821300 Helicase+ZnF+DSHCT PF3D7_0909900 Helicase+rRNA proc-arch+DSHCT PF3D7_0602100 Helicase+HA2 PF3D7_0310500, PF3D7_1302700 Blue , pink and green boxes are used to denote transmembrane, low complexity, and coiled-coil regions, respectively To further illustrate the...”
- “...DEAD helicases participate in ribosome biogenesis [ 26 ]. In P. falciparum , PF3D7_1364300, PF3D7_1231600, PF3D7_0917600 and PF3D7_1030100 all have a conserved DEAH domain and are classified as Prp (pre-mRNA processing) proteins. Similarly, almost all of the proteins classified under ribosome biogenesis (Fig. 2 and Additional...”
PSHAa1144 helicase, ATP-dependent from Pseudoalteromonas haloplanktis TAC125
36% identity, 34% coverage
XP_002663993 ATP-dependent RNA helicase DHX8 from Danio rerio
34% identity, 37% coverage
PVX_111220 RNA helicase, putative from Plasmodium vivax
32% identity, 37% coverage
- Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
Diez, PloS one 2017 - “...S2 Fig ). In addition, some helicases showed strong signals of selection ( PVX_088190 and PVX_111220 ) which were also detected in the same study [ 36 ] reinforcing the method used. Furthermore, we identified in South America a proximal region of selection (chr14: 1,414,1641,479,586) described...”
- “...199049199165 4.703 PVX_001850 hypothetical protein 6 605656608119 3.788 PVX_111260 hypothetical protein, conserved 6 635433635539 4.406 PVX_111220 RNA helicase, putative 6 661816 6.048 PVX_111180 28 kDa ookinete surface protein, (P28) 7 13969291396961 4.708 . Promoter region PVX_086903 7 1397181 4.700 PVX_086903 Plasmodium exported protein, unknown function 8...”
cgd6_1410 pre-mRNA splicing factor ATP-dependent RNA helicase from Cryptosporidium parvum Iowa II
34% identity, 45% coverage
NP_001121805 probable ATP-dependent RNA helicase DHX34 from Danio rerio
37% identity, 39% coverage
PRP2_YEAST / P20095 Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2; Pre-mRNA-processing protein 2; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 10 papers)
NP_014408 DEAH-box RNA-dependent ATPase PRP2 from Saccharomyces cerevisiae S288C
NP_014408, YNR011C Prp2p from Saccharomyces cerevisiae
34% identity, 51% coverage
- function: Involved in pre-mRNA splicing. Is required together with ATP and at least one other factor, for the first cleavage-ligation reaction. Functions as a molecular motor in the activation of the precatalytic spliceosome for the first transesterification reaction of pre-mRNA splicing by hydrolyzing ATP to cause the activation of the spliceosome without the occurrence of splicing. Capable of hydrolyzing nucleoside triphosphates in the presence of single-stranded RNAs such as poly(U).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts directly with pre-mRNA. According to PubMed:2251118, associated with spliceosomes prior to and throughout step 1 of the splicing reaction. According to PubMed:8943336, it leaves the spliceosome before reaction 1. Interacts with SPP2. - Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...DExH-box RNA helicases. The amino-acid sequence of ctPrp43 (G0RY84) was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...TCERG1 2JUC (212-266) 56-71 104-112 126-135 163-174 194-206 216-231 293-303 Known Splicing Factors Prp2 YNR011C P20095 99.8 876 0.18 0.25 0.30 0.23 1-6 DDX16 13-32 46-64 100-105 117-129 169-186 168-181 Cwc22 YGR278W P53333 67.3 577 0.19 0.28 0.37 0.24 462-471 KIAA1604 525-542 520-532 540-548 571-577 Cwc27...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...53 DHX34 DEAD/DEAH-box (LOC_Os10g33275) DHX8 (Q38953) PRP2 (P20095) RNA helicase (PF10_0294) 54 DHX35 DHX35 (LOC_Os01g11370) DHX8 (Q38953) PRP22 (P24384) RNA...”
- Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.
Bai, Science (New York, N.Y.) 2021 (PubMed)- GeneRIF: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.
- eIF4G is retained on ribosomes elongating and terminating on short upstream ORFs to control reinitiation in yeast.
Mohammad, Nucleic acids research 2021 - GeneRIF: eIF4G is retained on ribosomes elongating and terminating on short upstream ORFs to control reinitiation in yeast.
- Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2.
Hamann, Proceedings of the National Academy of Sciences of the United States of America 2020 - GeneRIF: The structural analysis unveils the role of conserved residues of the G-patch in the dynamic interaction mode of Spp2 with Prp2, which is vital to maintain the binding during the Prp2 domain movements needed for RNA translocation.
- The G-patch protein Spp2 couples the spliceosome-stimulated ATPase activity of the DEAH-box protein Prp2 to catalytic activation of the spliceosome.
Warkocki, Genes & development 2015 - GeneRIF: Spp2 plays a major role in coupling Prp2's ATPase activity to remodeling of the spliceosome into a catalytically active machine
- Link of NTR-mediated spliceosome disassembly with DEAH-box ATPases Prp2, Prp16, and Prp22.
Chen, Molecular and cellular biology 2013 - GeneRIF: NTR complex catalyzes the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome.
- Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS.
Ohrt, RNA (New York, N.Y.) 2012 - GeneRIF: The results suggest high cooperativity of multiple Prp2-mediated structural rearrangements at the spliceosome's catalytic core.
- The interaction of Prp2 with a defined region of the intron is required for the first splicing reaction.
Liu, Molecular and cellular biology 2012 - GeneRIF: propose that Prp2 is recruited to the spliceosome via interaction with Brr2 and is spatially positioned to interact with this specific region of the pre-mRNA, which stimulates the ATPase activity of Prp2 to promote progression of the first catalytic step
- Splicing factor Cwc22 is required for the function of Prp2 and for the spliceosome to escape from a futile pathway.
Yeh, Molecular and cellular biology 2011 - GeneRIF: In the absence of Cwc22, Prp2 can bind to the spliceosome but is dissociated upon ATP hydrolysis without promoting the release of SF3a/b.
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- Multi-source biological knowledge-guided hypergraph spatiotemporal subnetwork embedding for protein complex identification
Wang, Briefings in bioinformatics 2024 - “...YLR275W YLR117C YPR182W YKL173W YLR298C YMR125W YAL032C YLR424W YMR213W YGL128C YML049C YGR013W YPL178W YDL030W YPL151C YNR011C YPR178W YGR074W 6.62352e-35 GO:0005681 Spliceosomal Complex 3 YPR101W YGL122C YBL074C YLR424W YDL030W YMR288W YER172C YNR011C YLR117C YPR182W YPR152C YJR050W YAL032C YMR125W YML049C YLR275W YMR213W YDR473C 1.31311e-29 GO:0000398 mRNA Splicing, via...”
- Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Shen, BMC bioinformatics 2015 - “...ygr091w yhr019c yhr140w yjl013c yjl035c yjl124c yjr022w ykl173w ylr419w ylr438c-a ymr268c ynl092w ynl118c ynl147w ynl240c ynr011c yor308c ypr058w ypr178w Conclusions Protein functional module is a fundamental unit formed with highly connected proteins and often possesses specific biological functions [ 3 ]. While many algorithms have been...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...6-23 TCERG1 2JUC (212-266) 56-71 104-112 126-135 163-174 194-206 216-231 293-303 Known Splicing Factors Prp2 YNR011C P20095 99.8 876 0.18 0.25 0.30 0.23 1-6 DDX16 13-32 46-64 100-105 117-129 169-186 168-181 Cwc22 YGR278W P53333 67.3 577 0.19 0.28 0.37 0.24 462-471 KIAA1604 525-542 520-532 540-548 571-577...”
- Pre-messenger RNA processing factors in the Drosophila genome
Mount, The Journal of cell biology 2000 - “...E = 0 Cef1, NP_013940, 4E-49 CG10689 AAF53766 Prp2-like 37C NP_003578, E = 0 Prp2, NP_014408, E-172 CG8241 AAF58294 Prp22-like 50E HRH1, NP_004932, E = 0 Prp22, NP_010929, E = 0 CG1405 AAF48355 Prp16-like 12D1 NP_054722, E = 0 Prp16, NP_013012, E-160 CG6015 AAF55949 Prp17-like 93F14...”
NP_191790 RNA helicase family protein from Arabidopsis thaliana
AT3G62310 RNA helicase, putative from Arabidopsis thaliana
34% identity, 52% coverage
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520 3D....”
- Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)
Luo, Plants (Basel, Switzerland) 2021 - “...with PC2 may be involved in this process. The RNA helicase genes ( AT5G26742 and AT3G62310 ), RNA-binding protein gene AT1G13190 , and 3-5-exoribonuclease genes AT3G61620 genes enriched in mRNA surveillance pathway mediated the quality control mechanism by detecting and degrading abnormal mRNAs [ 45 ,...”
- “...DnaJ-domain superfamily protein PC3 104.85 BnaA09g39750D AT3G62200 Putative endonuclease or glycosyl hydrolase PC3 117.73 BnaA09g39790D AT3G62310 RNA helicase family protein PC3 148.6 BnaA09g39910D AT3G62470 Pentatricopeptide repeat-containing protein PC3 BnvaC0132342151 5.7 BnaC01g33060D AT3G19830 Calcium-dependent lipid-binding family protein PC3 BnvaC0320454520 0 BnaC03g33580D AT3G03960 T-complex protein PC3 2.46 BnaC03g33590D...”
- Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles
Fernández, Frontiers in plant science 2021 - “...nucleic acids, were reported: the emb1138, member of the DEAD-box ATPdependent RNA helicase 3, and At3G62310, a probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH2, which might be involved in pre-mRNA splicing. The DEAD-box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre-mRNA...”
- Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana
Wang, Nucleic acids research 2019 - “...intron lariats ( 24 , 25 ). The Arabidopsis genome encodes two putative PRP43 proteins, At3g62310 and At2g47250, hereafter referred to as PRP43a and PRP43b, respectively. In budding yeast ( Saccharomyces cerevisiae ), NTC-related protein 1 (NTR1) and NTR2 function as key co-factors of PRP43 (...”
- Function of Plant DExD/H-Box RNA Helicases Associated with Ribosomal RNA Biogenesis
Liu, Frontiers in plant science 2018 - “...S DDX56 Dbp9p OS03G0728800 H Zm00001d013358 AT4G34910 (AtRH16) C H DHX15 Prp43p OS03G0314100 D Zm00001d028923 AT3G62310 (DEAH2) Zm00001d047601 AT2G47250 (DEAH3) DHX37 Dhr1p OS02G0736600 Zm00001d017967 D AT1G33390 (DEAH13) C SkiV2L2 Mtr4p OS12G0279000 D H Zm00001d045590 D AT1G59760 (AtMTR4) The amino acid sequences of human and yeast DExD/H-box...”
- cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica
Xiao, Horticulture research 2016 - “...98 AB474615 230 AT5G14400 CYP724A1 Bra023464 BcCYP724A1 _A02 R x x x 99 AB474718 200 AT3G62310 AT3G62310 Bra007671 AT3G62310 _A09 R X X x 100 AB495003 1418 AT4G11260 EDM1 Bra035239 BcEDM1 _A09 R x X x x 101 AB474611 393 AT1G08540 SIG1 Bra030732 BcSIG1 _A08 R...”
- PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity
Feng, EMBO reports 2016 - “...transcription repressors; and several candidates (AT5G47210, AT4G09040, AT3G62310, and AT2G04420) are predicted to have RNA binding or helicase/ nuclease...”
- Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction
Amil-Ruiz, Frontiers in plant science 2016 - “...(9.10 1) 7.93E-03 M6A9 gene00185 AT5G67300 Transcription factor MYB44 Transcription factor 1.83 9.42E-03 M4C6 gene20572 AT3G62310 RNA helicase family protein RNA metabolism 1.79 9.42E-03 DIRECT DEFENSES M24B7# gene14817 AT4G16260 Glycosyl hydrolase superfamily protein Cell wall degradation, PR protein family 47.54 (30.54 16.25) 0 M16D12# gene02717 AT3G54420...”
- Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing
Sánchez-León, Journal of experimental botany 2012 - “...to five of these genes (At1g31760, At2g40880, At3g62310, At4g38150, and At5g13490) showed GUS expression restricted to cells of the female gametophyte...”
- “...female gametophyte exhibited GUS expression. In fusions with At3g62310, GUS expression was confined to the egg apparatus (synergids and egg cell), and with...”
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AT1G27900 RNA helicase, putative from Arabidopsis thaliana
34% identity, 54% coverage
- Selection on meiosis genes in diploid and tetraploid Arabidopsis arenosa
Wright, Molecular biology and evolution 2015 - “...Supplementary Material online) primarily in ZYP1b. Six genes (AT1G27900, MEI1, MSH2, PRD3, SMC3, and SMC6a) had weak patterns of differentiation that were...”
- Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
Krouk, Genome biology 2010 - “...response to NO 3 - (for example, At1g55120 , At3g50750 , At1g64370 , At4g16780 , At1g27900 , At1g22640 , At1g52060 , and At2g42200 ). While a second gene set is validated to be very early responsive genes (for example, At1g13300 , At1g49000 , At4g31910 , At5g15830...”
- A spatial dissection of the Arabidopsis floral transcriptome by MPSS
Peiffer, BMC plant biology 2008 - “...enriched expression were assayed as well. After staining, the promoter: GUS fusions for At1g07370 and At1g27900 were found to stain within the gynoecia as predicted (Figure 4fg ). MPSS predicted At1g33430 to be expressed in both reproductive organs. This result was substantiated through the histochemical assay,...”
- “...At2g42940 ( [D] and [E] ). MPSS-predicted stamen-enriched promoter: GUS . (F-G) At1g07370 [F] , At1g27900 [G] . MPSS-predicted carpel-enriched promoter: GUS . (H) At1g33430. MPSS-predicted stamen/carpel-enriched promoter: GUS . (I-J) At5g07550 [I] , At2g19070 [J] . MPSS-predicted stamen/petal-enriched promoter: GUS . (K) At1g07930. MPSS- ap3...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...S1, 1; HA2, 1; atPrp22-2 At1g26370 1 5 DEAD, 1; Helicase_C, 1; HA2, 1 atPrp22-3 At1g27900 1 15 DEAD, 1; Helicase_C, 1; HA2, 1 Prp17 Prp17p atPrp17-1 At1g10580 1 10 WD-40, 7; atPrp17-2 At5g54520 5 5 AltA (1); WD-40, 6; Prp18 Prp18 atPrp18-1 At1g03140 1 16...”
7dcpx / P20095 Cryo-em structure of the deah-box helicase prp2 and coactivator spp2 (see paper)
34% identity, 53% coverage
- Ligand: adenosine-5'-diphosphate (7dcpx)
NP_572947 pre-mRNA processing factor 16, isoform A from Drosophila melanogaster
35% identity, 37% coverage
AT2G47250 RNA helicase, putative from Arabidopsis thaliana
O22899 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH3 from Arabidopsis thaliana
34% identity, 52% coverage
- Phytohormonal regulation determines the organization pattern of shoot aerenchyma in greater duckweed (Spirodela polyrhiza)
Kim, Plant physiology 2024 - “...DREB2C (At2g40340), LTI65 (At5g52300), EIN3 (At3g20770), ERF3 (At1g50640), ERF9 (At5g44210), ERF104 (At5g61600), HRE1 (At1g72360), HRE2 (At2g47250), PAL2 (At3g53620), MES1 (At2g23620), PR1 (At2g14610), PDF2.1 (At2g02120), MC4 (At1g79340), ACD1 (At1g48420), LCB2 (At5g23670), BIR1 (At5g48380), EPF1 (At2g20875), EPF2 (At1g34245), PAD4 (At3g52430), and SAG101 (At5g14930). Supplementary Material kiae173_Supplementary_Data Acknowledgments We...”
- The genetic architecture ofArabidopsis thalianain response to native non-pathogenic leaf bacterial species revealed by GWA mapping in field conditions
Ramírez-Sánchez, 2022 - Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape (Brassica napus L.)
Liu, Molecular breeding : new strategies in plant improvement 2022 - “...al. 2016) --(Park et al. 2019) At1g65700 At1g07350 At2g47250 LSM8 SR45A --- Promote seed germination Required for proper splicing of FLC --Regulate flowering...”
- Light regulates alternative splicing outcomes via the TOR kinase pathway
Riegler, Cell reports 2021 - “...et al., 2014 ). Moreover, other splicing factors are also part of this set: At-PRP43b (AT2G47250), At-SR34a (AT3G49430), and At-RS41 (AT5G52040) ( Barta et al., 2010 ; Wang et al., 2019 ). We created a tool that allows visualization of splicing isoform schematics ( https://boxify.boku.ac.at/ )....”
- “...AT2G36320 A20/AN1-like zinc finger family protein ATNCER2 AT2G38010 neutral ceramidase 2, neutral/alkaline non-lysosomal ceramidase PRP43b AT2G47250 RNA helicase family protein ATMS2 AT3G03780 encodes a cytosolic methionine synthase, involved in methionine regeneration via the activated methyl cycle (or SAM cycle) - AT3G06530 armadillo (ARM) repeat superfamily protein,...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...from sexual accessions for MEM (AT5G39840 ) , in addition to the INO80 ortholog AT3G57300, AT2G47250, and AT2G35920 ( fig.3 B ). For other genes, including DCL2 ( AT3G03300 ) , RH1 ( AT4G15850), and RH5 ( AT1G31970 ) , mutations leading to premature stop were...”
- Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana
Wang, Nucleic acids research 2019 - “...( 24 , 25 ). The Arabidopsis genome encodes two putative PRP43 proteins, At3g62310 and At2g47250, hereafter referred to as PRP43a and PRP43b, respectively. In budding yeast ( Saccharomyces cerevisiae ), NTC-related protein 1 (NTR1) and NTR2 function as key co-factors of PRP43 ( 26 )....”
- Function of Plant DExD/H-Box RNA Helicases Associated with Ribosomal RNA Biogenesis
Liu, Frontiers in plant science 2018 - “...OS03G0728800 H Zm00001d013358 AT4G34910 (AtRH16) C H DHX15 Prp43p OS03G0314100 D Zm00001d028923 AT3G62310 (DEAH2) Zm00001d047601 AT2G47250 (DEAH3) DHX37 Dhr1p OS02G0736600 Zm00001d017967 D AT1G33390 (DEAH13) C SkiV2L2 Mtr4p OS12G0279000 D H Zm00001d045590 D AT1G59760 (AtMTR4) The amino acid sequences of human and yeast DExD/H-box RHs were BLAST-searched...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...1 atPrp43-2a At3g62310 3 17 AltA (1); >2-3 DEAD, 1; Helicase_C, 1; HA2, 1 atPrp43-2b At2g47250 2 14 >2-3 DEAD, 1; Helicase_C, 1; HA2, 1 SR140 atSR140-1 At5g25060 5 11 Surp, 1;RRM, 1;, 1;RPR, 1; atSR140-2 At5g10800 5 2 Surp, 1;RRM, 1;RPR, 1; SPF45 atSPF45 At1g30480...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...DEAD/DEAH-box (PFI0165c) 45 DHX8 DHX8 (LOC_Os06g09280) sf (O22899) PRP22 (P24384) RNA helicase (PF10_0294) 46 DHX9 DEAD/DEAH-box (LOC_Os10g33275) DHX15 (O22899)...”
- “...(continued) 47 DHX15 pre-mRNA sf (LOC_Os03g19960) DHX15 (O22899) RNA helicase (PFI0860c) 48 DHX16 DHX16 (LOC_Os03g17432) DHX8 (Q38953) PRP22 (P24384) RNA...”
C4M6S9 Helicase, putative from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_184530 helicase, putative from Entamoeba histolytica HM-1:IMSS
33% identity, 47% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...large subunit EHI_098300 C4LXB3 U2AF35 U2 snRNP auxiliary factor EHI_192500 C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373 Brr2...”
- Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters
Dorantes-Palma, International journal of molecular sciences 2024 - “...S1A ). The most frequent combination is Ehhsp100-Ehpgp5, present in 22 genes, including a helicase (EHI_184530), an EhHSTF (EHI_184530), and the chaperone clpB (EHI_155060). The second most common combination is Ehhsp100-Ehmlbp, found in 15 genes, which includes the DNA polymerase gene (EHI_132860), lipase (EHI_099800), and a...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...fact. large subunit EHI_098300 C4LXB3 U2AF35 U2 snRNP auxiliary factor EHI_192500 C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373...”
- A novel class of cysteine protease receptors that mediate lysosomal transport
Nakada-Tsukui, Cellular microbiology 2012 - “...EHI_164800 (CPBF1), 685-fold downregulation; EHI_179700 (hypothetical protein), 3-fold downregulation; EHI_194510 (DNA topoisomerase putative), 1.4-fold downregulation; EHI_184530 (hypothetical protein), 1.4-fold upregulation. These data reinforce gene-specific repression of CPBF1. We measured the CP activity in the cell and that secreted into the culture supernatant of the CPBF1 -silenced...”
Q7XIR8 Os07g0508000 protein from Oryza sativa subsp. japonica
34% identity, 35% coverage
DHX34_HUMAN / Q14147 Probable ATP-dependent RNA helicase DHX34; DEAH box protein 34; DExH-box helicase 34; EC 3.6.4.13 from Homo sapiens (Human) (see 4 papers)
Q14147 RNA helicase (EC 3.6.4.13) from Homo sapiens (see paper)
NP_055496 probable ATP-dependent RNA helicase DHX34 from Homo sapiens
36% identity, 39% coverage
- function: Probable ATP-binding RNA helicase required for nonsense- mediated decay (NMD) degradation of mRNA transcripts containing premature stop codons (PubMed:25220460, PubMed:33205750). Promotes the phosphorylation of UPF1 along with its interaction with key NMD pathway proteins UPF2 and EIF4A3 (PubMed:25220460). Interaction with the RUVBL1-RUVBL2 complex results in loss of nucleotide binding ability and ATP hydrolysis of the complex (PubMed:33205750). Negatively regulates the nucleotide binding ability and ATP hydrolysis of the RUVBL1-RUVBL2 complex via induction of N-terminus conformation changes of the RUVBL2 subunits (PubMed:33205750).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Forms a complex with RUVBL1 and RUVBL2 (PubMed:33205750). Part of a complex composed of SMG1, DHX34 and UPF1; within the complex DHX34 acts as a scaffolding protein to facilitate SMG1 phosphorylation of UPF1 (PubMed:26841701). Interacts with UPF1, MOV10, EIF4A3, XRN2, SMG6, SMG7, SMG9, UPF3A, UPF3B, CASC3/MLN51, XRN1, DIS3 and DCP1A; the interactions are RNA-independent (PubMed:25220460). Interacts with NCBP1/CPB80; the interaction is RNA-dependent (PubMed:25220460). Interacts (via C-terminus) with SMG1; the interaction is RNA- independent (PubMed:25220460, PubMed:26841701). - A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation.
Hug, RNA (New York, N.Y.) 2022 - GeneRIF: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation.
- Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM.
López-Perrote, eLife 2020 - GeneRIF: Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM.
- Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
Paine, American journal of human genetics 2019 - GeneRIF: Missense mutation in DHX34 gene is associated with neurodevelopmental disorder.
- The RNA helicase DHX34 functions as a scaffold for SMG1-mediated UPF1 phosphorylation.
Melero, Nature communications 2016 - GeneRIF: DHX34 activates nonsense-mediated mRNA decay by functioning as a scaffold for SMG1-mediated UPF1 phosphorylation via complex formation with SMG1 and UPF1.
- The RNA helicase DHX34 activates NMD by promoting a transition from the surveillance to the decay-inducing complex.
Hug, Cell reports 2014 - GeneRIF: DHX34 promotes mRNP remodeling and triggers the conversion from the SURF complex to the DECID complex resulting in NMD activation.
- DHX34 and NBAS form part of an autoregulatory NMD circuit that regulates endogenous RNA targets in human cells, zebrafish and Caenorhabditis elegans.
Longman, Nucleic acids research 2013 - GeneRIF: DHX34 and NBAS act in concert with core nonsense-mediated mRNA decay factors to co-regulate a large number of endogenous RNA targets.
- ITRAQ-based proteomics analysis of human ectopic endometrial stromal cells treated by Maqian essential oil.
Zhang, BMC complementary medicine and therapies 2023 - “...the top 20 up-regulated proteins in MQEQ-treated EESCs Accession Protein name Fold change P value Q14147 Probable ATP-dependent RNA helicase DHX34 3.347755422 0.03866958 Q7Z5H4 Vomeronasal type-1 receptor 5 2.844688021 0.01062212 P52823 Stanniocalcin-1 2.673433739 0.000512193 P08254 Stromelysin-1 2.639501666 0.0181334 O95500 Claudin-14 2.392929207 0.01584208 P02748 Complement component C9...”
- Learning peptide recognition rules for a low-specificity protein.
Wheeler, Protein science : a publication of the Protein Society 2020 - Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
Gao, Cancer biology & medicine 2015 - “...DDX51 OS=Homo sapiens GN=DDX51 PE=1 SV=3 - [DDX51_HUMAN] 1.20 1 1 1 666 72.4 8.16 Q14147 Probable ATP-dependent RNA helicase DHX34 OS=Homo sapiens GN=DHX34 PE=1 SV=2 - [DHX34_HUMAN] 0.70 1 1 1 1,143 128.0 7.56 Q7L775 EPM2A-interacting protein 1 OS=Homo sapiens GN=EPM2AIP1 PE=1 SV=1 - [EPMIP_HUMAN]...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...Q9H6R0 RNA helicase DHX33 DEAH-box protein 33 DHX33 33 Q14147 RNA helicase DHX34 DEAH-box protein 34 DHX34 34 Q9H5Z1 RNA helicase DHX35 DEAH-box protein 35...”
PRP16_ARATH / F4K2E9 Pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH7; DEAH RNA helicase homolog PRP16; Protein CLUMSY VEIN; Protein EMBRYO DEFECTIVE 3011; Protein PSR1-INTERACTING PROTEIN 1; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
EMB3011, NP_196805 RNA helicase family protein from Arabidopsis thaliana
34% identity, 36% coverage
- function: Involved in pre-mRNA splicing by mediating structural transitions of the spliceosome during the catalytic step. Facilitates expression of genes involved in auxin-mediated development including male-gametophyte transmission, apical-basal patterning of embryonic and gynoecium development, stamen development, phyllotactic flower positioning, and vascular development (PubMed:25384462). Also involved in root-meristem maintenance and planar polarity of root-hair positioning (PubMed:26237376). Acts as a component of RNA silencing that regulates distinct classes of endogenous small RNAs. Functions as a positive regulator of plant immunity (PubMed:25902521).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with the Phytophthora PSR1 protein.
disruption phenotype: Narrow rosette leaves with altered venation pattern. - QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules
Yamano, PloS one 2024 - “...MODERATE-impact variants, are homologs of the Arabidopsis genes AT5G50850 ( MAB1 ) and AT5G13010 ( EMB3011 / PINP1 ) associated with auxin transport and auxin-mediated organ development, respectively [ 44 , 45 ]. The gene g23617.t1 (Chr2_g000670.1) with a MODIFIER-impact variant was predicted to encode an...”
- “...03336 vs. 03009 and 03336 vs. NIL-M ( S13 Table ). Its Arabidopsis homolog (AT5G13010/ EMB3011 / PINP1 ) was previously shown to be associated not only with auxin-mediated organ development but also with plant immunity [ 44 , 65 ]. The genes annotated with the...”
- General Control Non-derepressible 1 (AtGCN1) Is Important for Flowering Time, Plant Growth, Seed Development, and the Transcription/Translation of Specific Genes in Arabidopsis
Cui, Frontiers in plant science 2021 - “...6.69 2.38 XIK AT5G13010 21.59 14.68 20.28 15.96 11.90 3.10 7.44 2.71 EMBRYO DEFECTIVE 3011 (EMB3011) AT4G30160 22.66 25.65 21.63 22.64 13.21 4.56 8.49 4.11 VILLIN 4 (VLN4) AT5G09810 315.39 290.08 252.95 253.12 151.60 148.71 100.92 142.14 ACTIN 7 (ACT7) AT5G43900 18.25 18.59 15.74 20.36 8.80...”
- SUMOylation in Phytopathogen Interactions: Balancing Invasion and Resistance
Sharma, Frontiers in cell and developmental biology 2021 - “...Virus AT1G65930 cICDH Cytosolic NADP+-dependent isocitrate dehydrogenase Bacteria AT1G55490 CPN60B Chaperonin 60 beta Fungi AT5G13010 EMB3011 RNA helicase family protein Fungi AT1G13440 GAPC2 Glyceraldehyde-3-phosphate dehydrogenase C2 Bacteria AT2G21660 GRP7 Cold, circadian rhythm, and RNA binding 2 AT4G39260 GRP8 Cold, circadian rhythm, and RNA binding 1 AT2G43910...”
- Integration of QTL Mapping and Gene Fishing Techniques to Dissect the Multi-Main Stem Trait in Rapeseed (Brassica napus L.)
Zhao, Frontiers in plant science 2019 - “...RR2 BnaC01g22110D AT1G27320 HK3 BnaC01g24570D AT3G46510 PUB13 BnaC01g26510D AT3G50070 CYCD3.3 BnaC01g26840D AT1G54990 AXR4 BnaC01g27460D AT5G13010 EMB3011 BnaC01g32740D AT3G20190 PRK4 BnaC01g33180D AT5G60440 AGL62 BnaC01g35230D AT3G16640 TCTP cqMMS.C3-3 BnaC03g13380D AT5G56600 PRF3 BnaC03g13120D AT5G57090 EIR1 cqMMS.C3-4 BnaC03g18890D AT1G78380 GSTU19 cqMMS.C3-5 BnaC03g25680D AT2G46310 CRF5 BnaC03g29310D AT4G11140 CRF1 BnaC03g26730D AT2G44080 ARL...”
- Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization
Zermiani, Annals of botany 2015 - “...034 066 068 055 058 At5g13010 At5g18830 At1g60200 EMB3011 (Embryo Defective 3011) SPL7 (Squamosa Promoter Binding Protein-Like 7) Splicing factor PWI domain/RNA...”
- Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis
Shi, PloS one 2012 - “...kinase 13 (CPK13) ppa018301m 8.86 CPR30 F-box and associated interaction domains-containing protein Metabolism ppa000615m 8.86 EMB3011 RNA helicase family protein ppa010131m 8.67 Peptidyl-tRNA hydrolase family protein ppa006743m 8.67 AGD2 Pyridoxal phosphate (PLP)-dependent transferases superfamily protein ppa006182m 8.86 Protein kinase superfamily protein ppa021659m 8.95 Dicer-like 3 (DCL3)...”
- “...in different kinds of metabolism, such as RNA, protein, pectin and fatty acid metabolism. The EMB3011 RNA helicase family protein [52] , peptidyl-tRNA hydrolase family protein [53] , DCL3 [54] , [55] and pre-mRNA-splicing factor CWC26 [56] , [57] are involved in RNA processing, including small...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520 3D. Exon junction complex proteins DDB0233615-o SRm160 e...”
- Integrating the genetic and physical maps of Arabidopsis thaliana: identification of mapped alleles of cloned essential (EMB) genes
Meinke, PloS one 2009 - “...HISN6A EMB3010 9 EMB163 No EMB1873 EMB2107 PAS2 9 EMB68 No PEX1 HISN6A EMB3010 EMB3135 EMB3011 CYL1 16 EMB262* Yes None 18 EMB269 Yes EMB2247 EMB3007 OEP80 20 EMB213 Yes EMB3138 EMB2247 EMB3007 EMB1379 23 EMB86* Yes None 27 EMB2 No EMB1379 CYL2 EMB1705 EMB1265 EMB3009...”
- More
VP1453 ATP-dependent RNA helicase HrpA from Vibrio parahaemolyticus RIMD 2210633
35% identity, 35% coverage
prh1 / RF|NP_593091.1 ATP-dependent RNA helicase Prh1 from Schizosaccharomyces pombe (see paper)
35% identity, 53% coverage
- CharProtDB Source (per GeneDB): GeneDB_Spombe
XP_969616 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 from Tribolium castaneum
35% identity, 38% coverage
E1BJ90 DExH-box helicase 34 from Bos taurus
36% identity, 40% coverage
AL538_RS17670 ATP-dependent RNA helicase HrpA from Vibrio harveyi
35% identity, 34% coverage
EHI_148930 helicase, putative from Entamoeba histolytica HM-1:IMSS
32% identity, 53% coverage
PRP22_YEAST / P24384 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_010929 DEAH-box ATP-dependent RNA helicase PRP22 from Saccharomyces cerevisiae S288C
NP_010929, YER013W DEAH-box RNA-dependent ATPase/ATP-dependent RNA helicase, associates with lariat intermediates before the second catalytic step of splicing; mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes from Saccharomyces cerevisiae
34% identity, 39% coverage
- function: Acts late in the splicing of pre-mRNA. Mediates the release of the spliced mRNA from spliceosomes.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Belongs to the CWC complex (or CEF1-associated complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2, RSE1 and YJU2. - No Chance to Survive: Mo-CBP3-PepII Synthetic Peptide Acts on Cryptococcus neoformans by Multiple Mechanisms of Action
Aguiar, Antibiotics (Basel, Switzerland) 2023 - “...proteins geranylgeranyltransferase component A P32864 Saccharomyces cerevisiae Nucleus 0.561076893 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 P24384 Saccharomyces cerevisiae Unknown 0.815963494 Autophagy-related protein 11 Q5AMN3 Candida albicans Vacuole 1.320278149 ADP-ribosylation factor GTPase-activating protein effector protein 2 P40529 Saccharomyces cerevisiae Cytoplasm/nucleus 0.909705632 Transferase E3 ubiquitin-protein ligase TOM1 Q03280...”
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...amino-acid sequence of ctPrp43 (G0RY84) was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values in parentheses indicate the...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...0.94 1.00 1.00 1-18 1-27 Srm300 44-66 99-116 96-106 117-123 Step 2 proteins Prp22 YER013W P24384 130.0 1.145 0.18 0.27 0.34 0.38 190-200 hPRP22 230-250 297-316 319-330 368-385 370-407 388-405 446-455 1115-1132 Prp16 YKR086W P15938 121.6 1.071 0.19 0.28 0.29 0.32 2-19 hPRP16 55-52 59-68 89-99...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...45 DHX8 DHX8 (LOC_Os06g09280) sf (O22899) PRP22 (P24384) RNA helicase (PF10_0294) 46 DHX9 DEAD/DEAH-box (LOC_Os10g33275) DHX15 (O22899) YLR419W (Q06698) RNA...”
- “...48 DHX16 DHX16 (LOC_Os03g17432) DHX8 (Q38953) PRP22 (P24384) RNA helicase (PF10_0294) 49 DHX29 DEAD/DEAH-box (LOC_Os04g35260) DHX8 (Q38953) YLR419W (Q06698) RNA...”
- Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs
Ohi, Molecular and cellular biology 2002 - “...Prp10p (Q10178) Sap145p (Q9UU13) Prp12p (Q9UTT2) (O43031) 39 40 Prp22p (P24384) Cwc21p (Q03375) 41 42 43 44 45 46 a b c Mol wt (kDa) (S. cerevisiae) Essential?b...”
- Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites.
Semlow, Cell 2016 - GeneRIF: At the catalytic stage of splicing, suboptimal splice sites are repressed by the DEAH-box ATPases Prp16 and Prp22. study shows that these ATPases function further by enabling the spliceosome to search for and utilize alternative branch sites and 3' splice sites.
- Link of NTR-mediated spliceosome disassembly with DEAH-box ATPases Prp2, Prp16, and Prp22.
Chen, Molecular and cellular biology 2013 - GeneRIF: NTR complex catalyzes the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome.
- Structural analysis of the C-terminal domain of the spliceosomal helicase Prp22.
Kudlinzki, Biological chemistry 2012 (PubMed)- GeneRIF: C-terminal domain of the spliceosomal helicase Prp22
- Characterization of the NTPase, RNA-binding, and RNA helicase activities of the DEAH-box splicing factor Prp22.
Tanaka, Biochemistry 2005 (PubMed)- GeneRIF: Prp22 unwinds duplexes with 3' overhangs; the 3' -> 5' directionality has implications for positioning of Prp22 on the RNA target
- Genomic markers on synthetic genomes
Zhao, Engineering in life sciences 2021 - “...the synthetic yeast chromosome V (synV), a Bsp HI restriction site TCATGA was introduced to YER013W gene by synonymously recoding TTATGA[9] (Figure 1D ). Short recoded sequences are generated by synonymous nucleotide alterations within ORFs [ 29 ]. The alterations make it possible to generate different...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...1.00 0.94 1.00 1.00 1-18 1-27 Srm300 44-66 99-116 96-106 117-123 Step 2 proteins Prp22 YER013W P24384 130.0 1.145 0.18 0.27 0.34 0.38 190-200 hPRP22 230-250 297-316 319-330 368-385 370-407 388-405 446-455 1115-1132 Prp16 YKR086W P15938 121.6 1.071 0.19 0.28 0.29 0.32 2-19 hPRP16 55-52 59-68...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_198226 NP_010704 3C. Catalytic step II and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18...”
- “...NP_566469 NP_010304 DDB0233740 RHA DHX9 NP_001348 NP_476641 NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287 DDB0233454...”
- Pre-messenger RNA processing factors in the Drosophila genome
Mount, The Journal of cell biology 2000 - “...= 0 Prp2, NP_014408, E-172 CG8241 AAF58294 Prp22-like 50E HRH1, NP_004932, E = 0 Prp22, NP_010929, E = 0 CG1405 AAF48355 Prp16-like 12D1 NP_054722, E = 0 Prp16, NP_013012, E-160 CG6015 AAF55949 Prp17-like 93F14 AAC39730, E = 0 Prp17, NP_010652, 1E-76 CG1420 AAF56845 Slu7-like 98F13 NP_006416,...”
- Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae
Ben-Yehuda, Genetics 2000 - “...function PRP8 YHR165c PRP16 SLU7 PRP22 YKR086w YDR088c YER013w SLT11 YBR065c Splicing factor involved in first and second steps Second step-splicing factor...”
LOC4350353 probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH4 from Oryza sativa Japonica Group
36% identity, 53% coverage
NP_001093527 ATP-dependent RNA helicase DHX33 from Danio rerio
36% identity, 53% coverage
DHX8_DROME / A1Z9L3 ATP-dependent RNA helicase DHX8; Peanuts; EC 3.6.4.13 from Drosophila melanogaster (Fruit fly) (see 2 papers)
NP_610928 peanuts from Drosophila melanogaster
34% identity, 36% coverage
- function: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:18981222, PubMed:24244416). Facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome (By similarity). Before and after egg-chamber formation, required for nurse-cell chromatin dispersal (NCCD) probably by playing a role in spliceosome localization to chromatin/interchromatin spaces (PubMed:24244416).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in the spliceosome C complex.
disruption phenotype: Lethal. RNAi-mediated knockdown in the germ line results in defective nurse cell morphology. - Spore Germination of the Obligate Biotroph Spongospora subterranea: Transcriptome Analysis Reveals Germination Associated Genes.
Balotf, Frontiers in microbiology 2021 - “...DNA excision repair protein ERCC-1 TCONS_00008936 P54211 Plasma membrane ATPase (EC 7.1.2.1) (Proton pump) TCONS_00014207 A1Z9L3 ATP-dependent RNA helicase DHX8 (EC 3.6.4.13) TCONS_00005711 Q10074 Vacuolar amino acid transporter 3 TCONS_00008752 Q43362 V-type proton ATPase 16 kDa proteolipid subunit TCONS_00008729 Q54CN8 Transcription initiation factor TFIID subunit 13...”
- Prp22 and spliceosome components regulate chromatin dynamics in germ-line polyploid cells.
Klusza, PloS one 2013 - GeneRIF: Prp22 and spliceosome components regulate chromatin dynamics in germ-line polyploid cells.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_064581 NP_610891 NP_198226 NP_010704 3C. Catalytic step II and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652...”
- “...NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287 DDB0233454 SKI2W SKIV2L NP_008860 NP_524465 NP_190280 NP_012485 Cyclophilins DDB0191208 CyPL1 PPIL1 NP_057143 NP_523874 NP_190046 NP_013633 DDB0233543 CyP60 PPIL2 NP_055152 NP_611113 NP_201554...”
SCO4092 ATP-dependent helicase from Streptomyces coelicolor A3(2)
36% identity, 34% coverage
- The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition
Lee, mBio 2020 - “...c RNA-seq fold change for WT+Tet/ wblC +Tet WblC regulon WT+Tet/WT WT+Tet/ wblC +Tet HrpA SCO4092 ATP-dependent RNA helicase 2.0 6.6 6.1 + SCO2532 SCO2532 PhoH-like protein, ortholog of E. coli YbeZ* 4.0 10.6 11.1 + HflX SCO5796 50S ribosomal subunit-associated GTPase 4.5 3.5 18.0 +...”
- DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
Šmídová, Nucleic acids research 2019 - “...total 85 (around 25%). The HrdB regulon contained genes such as DNA helicases (SCO1167, SCO3550, SCO4092, SCO5815), DNA topoisomerases (I-SCO3543, IV subunit betaSCO5822), subunits of DNA gyrase (ASCO3873, BSCO3874), DNA ligase SCO6707). Transcription In the HrdB regulon we revealed almost 26 genes that participate in the...”
- Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets
Świątek-Połatyńska, PloS one 2015 - “...SCO3679 + + - - - - - - - - 2 tgttgtctagtccaat -314 15.32 SCO4092 - - - - - - + + + + 4 SCO5239 + + - - - - - - - - 2 +, this paper agtggtctagtccaca -335 16.23 SCO5550...”
- “...upstream of SCO3679, to tRNA Met and to the tRNA Glu/Asp/Phe gene cluster upstream of SCO4092. Additionally, after 54 h of growth on MM agar plates, DasR binding was observed upstream of SCO2504 ( glyS ) encoding glycyl-tRNA synthetase ( Table 1 ). Finally, binding was...”
- Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
Hsiao, Antonie van Leeuwenhoek 2008 - “...III 0.05375 0.026053 0.328502 0.62343 SCO3879 chromosomal replication initiator protein (fragment) 1.25983 1.572531 0.731065 0.12482 SCO4092 ATP-dependent helicase 0.00752 0.055194 0.978098 0.21188 SCO4143 putative mutT-like protein 0.021035 0.435471 0.479161 0.28423 SCO4272 putative mutT-like protein 0.1352 0.016206 0.32968 0.527274 SCO4351 putative DNA invertase 1.26688 0.78144 1.29284 0.68489...”
CNAG_02303 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 from Cryptococcus neoformans var. grubii H99
35% identity, 33% coverage
AT5G13010 EMB3011 (embryo defective 3011); ATP binding / RNA helicase/ helicase/ nucleic acid binding from Arabidopsis thaliana
34% identity, 36% coverage
- QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules
Yamano, PloS one 2024 - “...HIGH- and MODERATE-impact variants, are homologs of the Arabidopsis genes AT5G50850 ( MAB1 ) and AT5G13010 ( EMB3011 / PINP1 ) associated with auxin transport and auxin-mediated organ development, respectively [ 44 , 45 ]. The gene g23617.t1 (Chr2_g000670.1) with a MODIFIER-impact variant was predicted to...”
- Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development
Jin, International journal of molecular sciences 2022 - “...HDA6 AT5G63110 ZmIMB3, ZmIMB4 (S) Zm00001d013330 S-0.639 PCN AT4G07410 Zm00001d033912 ZmIPO8 (S) Zm00001d006459 S-0.655 PRP16 AT5G13010 ZmIMB3, ZmIMB4 (S) Zm00001d030554 S-0.489 APUM23 AT1G72320 ZmIMP1/2/3/4 (P) Zm00001d037481 P-0.231 RPT5A AT3G05530 Zm00001d018409 (S) for Data analysis from STRING ( https://cn.string-db.org/ (accessed on 4 October 2022)), (P) for data...”
- General Control Non-derepressible 1 (AtGCN1) Is Important for Flowering Time, Plant Growth, Seed Development, and the Transcription/Translation of Specific Genes in Arabidopsis
Cui, Frontiers in plant science 2021 - “...(VCS) Root hair elongation 5 AT5G20490 22.26 22.51 17.87 21.14 11.36 2.94 6.69 2.38 XIK AT5G13010 21.59 14.68 20.28 15.96 11.90 3.10 7.44 2.71 EMBRYO DEFECTIVE 3011 (EMB3011) AT4G30160 22.66 25.65 21.63 22.64 13.21 4.56 8.49 4.11 VILLIN 4 (VLN4) AT5G09810 315.39 290.08 252.95 253.12 151.60...”
- SUMOylation in Phytopathogen Interactions: Balancing Invasion and Resistance
Sharma, Frontiers in cell and developmental biology 2021 - “...C2 Virus AT1G65930 cICDH Cytosolic NADP+-dependent isocitrate dehydrogenase Bacteria AT1G55490 CPN60B Chaperonin 60 beta Fungi AT5G13010 EMB3011 RNA helicase family protein Fungi AT1G13440 GAPC2 Glyceraldehyde-3-phosphate dehydrogenase C2 Bacteria AT2G21660 GRP7 Cold, circadian rhythm, and RNA binding 2 AT4G39260 GRP8 Cold, circadian rhythm, and RNA binding 1...”
- Integration of QTL Mapping and Gene Fishing Techniques to Dissect the Multi-Main Stem Trait in Rapeseed (Brassica napus L.)
Zhao, Frontiers in plant science 2019 - “...AT4G16110 RR2 BnaC01g22110D AT1G27320 HK3 BnaC01g24570D AT3G46510 PUB13 BnaC01g26510D AT3G50070 CYCD3.3 BnaC01g26840D AT1G54990 AXR4 BnaC01g27460D AT5G13010 EMB3011 BnaC01g32740D AT3G20190 PRK4 BnaC01g33180D AT5G60440 AGL62 BnaC01g35230D AT3G16640 TCTP cqMMS.C3-3 BnaC03g13380D AT5G56600 PRF3 BnaC03g13120D AT5G57090 EIR1 cqMMS.C3-4 BnaC03g18890D AT1G78380 GSTU19 cqMMS.C3-5 BnaC03g25680D AT2G46310 CRF5 BnaC03g29310D AT4G11140 CRF1 BnaC03g26730D AT2G44080...”
- Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis
Zhu, Journal of experimental botany 2016 - “...At1g32490), FASCIATED STEM 4 (AtFAS4; At1g33390), ABA OVERLY SENSITIVE 6 (ABO6; At5g04895), CLUMSY VEIN (CUV; At5g13010), and ROOT INITIATION DEFECTIVE 1 (RID1; At1g26370). EPS3 is a putative homolog of yeast PRP2, which is required for RNA processing and plays an important role in the regulation of...”
- Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection
Qiao, Proceedings of the National Academy of Sciences of the United States of America 2015 - “...in four independent experiments, and one protein (At5g13010) was repetitively identified. This protein was designated PSR1-Interacting Protein 1 (PINP1) (Fig....”
- Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization
Zermiani, Annals of botany 2015 - “...are in italics. 034 066 068 055 058 At5g13010 At5g18830 At1g60200 EMB3011 (Embryo Defective 3011) SPL7 (Squamosa Promoter Binding Protein-Like 7) Splicing...”
- More
8cntA / G0S0F9 Structure of the deah-box helicase prp16 in complex with adp (see paper)
34% identity, 53% coverage
- Ligand: adenosine-5'-diphosphate (8cntA)
ABO_1521 ATP-dependent helicase HrpA from Alcanivorax borkumensis SK2
37% identity, 34% coverage
HI1070 ATP-dependent RNA helicase HrpA from Haemophilus influenzae Rd KW20
34% identity, 38% coverage
5gm6Y / P20095 5gm6Y (see paper)
34% identity, 53% coverage
- Ligands: magnesium ion; adenosine-5'-diphosphate (5gm6Y)
DHX15_DROME / Q7K3M5 ATP-dependent RNA helicase DHX15 homolog; EC 3.6.4.13 from Drosophila melanogaster (Fruit fly) (see paper)
NP_610269 DEAH-box helicase 15, isoform A from Drosophila melanogaster
35% identity, 54% coverage
- function: RNA helicase involved in mRNA processing and antiviral innate immunity (By similarity). Acts as an activator of the p38 MAPK cascade (PubMed:24782566).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...II and late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520...”
XAC3122 ATP-dependent RNA helicase from Xanthomonas axonopodis pv. citri str. 306
38% identity, 33% coverage
XOO1725 ATP-dependent RNA helicase from Xanthomonas oryzae pv. oryzae KACC10331
38% identity, 33% coverage
HrpA / b1413 ATP-dependent RNA helicase HrpA from Escherichia coli K-12 substr. MG1655 (see 4 papers)
hrpA / P43329 ATP-dependent 3'→5' RNA helicase HrpA from Escherichia coli (strain K12) (see 5 papers)
P43329 ATP-dependent RNA helicase HrpA from Escherichia coli (strain K12)
NP_415931 ATP-dependent 3'->5' RNA helicase HrpA from Escherichia coli str. K-12 substr. MG1655
b1413 ATP-dependent helicase from Escherichia coli str. K-12 substr. MG1655
33% identity, 35% coverage
- Quantitative Shotgun Proteomic Analysis of Bacteria after Overexpression of Recombinant Spider Miniature Spidroin, MaSp1
Randene, International journal of molecular sciences 2024 - “...g-type lysozyme P76002 2.98 10 6 6.00 Inhibits g-type lysozyme hrpA ATP-dependent RNA helicase HrpA P43329 9.59 10 4 12.00 RNA helicase mglB D-galactose-binding periplasmic protein * P0AEE5 2.11 10 11 OLR Lactose metabolism rnpA Ribonuclease P protein component P0A7Y8 5.44 10 3 OLR tRNA processing...”
- Toward Single Bacterium Proteomics
Végvári, Journal of the American Society for Mass Spectrometry 2023 - “...[5258] [R].QSLDNVK.[A] 1262.74 631.87 +2 44.89 1 186.3 6.25% 242 ATP-dependent RNA helicase HrpA hrpA P43329 [10491063] [R].DSVAIKLFDNPLEQK.[Q] 2176.23 726.08 +3 91.39 7 104.31 25.00% putative permease PerM perM P0AFI9 [179188] [K].DKEQMLNAVR.[R] 1450.74 725.88 +2 53.56 4 172.05 18.75% 4-hydroxybenzoate octaprenyltransferase ubiA P0AGK1 [6179] [R].AAGCVVNDYADRKFDGHVK.[R] 2294.15...”
- “...P0A873 [6975] [R].DAIHAAK.[A] 1183.72 395.25 +3 31.52 2 214.27 12.50% ATP-dependent RNA helicase HrpA hrpA P43329 [988993] [R].SLQDLK.[D] 1162.71 581.86 +2 59.70 2 221.69 12.50% Transcriptional repressor PifC pifC P10030 [28] [M].LSQLNLR.[F] 1072.67 536.84 +2 54.13 1 195.86 6.25% histidinol-phphate aminotransferase hisC P06986 [170178] [R].TLLELTRGK.[A] 1488.95...”
- Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility
Grass, Proceedings of the National Academy of Sciences of the United States of America 2021 - “...Appendix , Table S1 ). Cloning. A DNA fragment encoding ec HrpA FL (Gene ID: P43329) was PCR-amplified from E. coli DH5- genomic DNA and inserted into the pETM-11 vector (EMBL Heidelberg) via sequence- and ligation-independent cloning ( 66 ), generating pETM-11- hrpA . DNA fragments...”
- A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12
Strader, Journal of proteome research 2013 - “...5 58 28.6 Ribosome maturation factor P0A7X6 RimM * 9 37 58.2 Ribosome maturation factor P43329 HrpA 43 312 41.4 ATP-dependent RNA helicase P69222 IF-1 4 27 94.4 Translation initiation factor P0A705 IF-2 * 44 475 59.8 Translation initiation factor P0A707 IF-3 * 14 568 77.2...”
- Identification of Erwinia amylovora genes induced during infection of immature pear tissue
Zhao, Journal of bacteriology 2005 - “...subunit NP_455812 ZP_00092789 ZP_00030390 NP_842492 P43329 NP_405343 P06223 AAL11450 Rso, 16 Acetolactate synthase III Amidophosphoribosyltransferase...”
- Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
Xin, Nucleic acids research 2024 - GeneRIF: Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013
c1840 ATP-dependent RNA helicase HrpA from Escherichia coli CFT073
33% identity, 35% coverage
cgd1_2650 hypothetical protein from Cryptosporidium parvum Iowa II
31% identity, 52% coverage
8ro1DX / Q20875 8ro1DX (see paper)
34% identity, 53% coverage
8po7A / P43329 Structure of escherichia coli hrpa in complex with adp and dinucleotide dcdc (see paper)
34% identity, 57% coverage
- Ligands: dna; adenosine-5'-diphosphate (8po7A)
Pnuc_1261 ATP-dependent helicase HrpA from Polynucleobacter sp. QLW-P1DMWA-1
35% identity, 34% coverage
- Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes
Srivastava, Frontiers in microbiology 2020 - “...changes p -Value Pnuc_1043 NADH-quinone oxidoreductase subunit I 5.38 0.020876 Pnuc_1177 tRNA-U16,U17-dihydrouridine synthase 5.12 0.000011 Pnuc_1261 ATP-dependent helicase HrpA 4.98 0.000004 Pnuc_1865 D , D -Heptose 1,7-bisphosphate phosphatase 4.58 0.000275 Pnuc_0332 Uncharacterized protein 4.57 0.000008 Pnuc_0167 MurG transferase 4.35 0.008714 Pnuc_1380 Uncharacterized protein 4.30 0.000007 Pnuc_1862...”
- “...related protein 1.72 0.000181 (D) 4C Locus tag Down-regulated proteins Log2 fold changes p -Value Pnuc_1261 ATP-dependent helicase HrpA 4.98 0.000004 Pnuc_0543 Protein tyrosine/serine phosphatase 4.27 0.000013 Pnuc_1718 SirA family protein 3.91 0.000000 Pnuc_1043 NADH-quinone oxidoreductase subunit I 2.46 0.000256 Pnuc_1407 Heavy metal translocating P-type ATPase...”
6zwwC / P43329 Crystal structure of e. Coli RNA helicase hrpa in complex with RNA (see paper)
33% identity, 54% coverage
6bk8P / P24384 S. Cerevisiae spliceosomal post-catalytic p complex (see paper)
34% identity, 54% coverage
NP_001108613 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 from Danio rerio
34% identity, 54% coverage
STM1641 ATP-dependent RNA helicase HrpA from Salmonella typhimurium LT2
34% identity, 35% coverage
- Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide
Kim, BMC microbiology 2010 - “...STM1567 Alcohol dehydrogenase adhP 35.49 5.8 42% STM1589 Putative NADP-dependent oxidoreductase yncB 39.2 5.6 23% STM1641 ATP-dependent helicase hrpA 148.71 8.22 15% STM1661 Putative universal stress protein ydaA 35.62 5.17 66% STM1682 Thiol peroxidase tpx 18.19 4.93 54% STM1714 DNA topoisomerase I topA 97.03 8.56 26%...”
- “...19 2% STM1567 Alcohol dehydrogenase adhP 9 2% STM1589 Putative NADP-dependent oxidoreductase yncB 12 2% STM1641 ATP-dependent helicase hrpA 20 3% STM1661 Putative universal stress protein ydaA 140 20% STM1682 Probable peroxidase tpx 19 2% STM1714 DNA topoisomerase I topA 17 4% STM1727 Tryptophan synthase trpA...”
cgd7_640 Prp16p pre-mRNA splicing factor. HrpA family SFII helicase from Cryptosporidium parvum Iowa II
33% identity, 43% coverage
D4AEG5 RNA helicase from Rattus norvegicus
33% identity, 54% coverage
- Construction of the experimental rat model of gestational diabetes
Chen, PloS one 2022 - “...B0BNJ4 ETHE1, persulfide dioxygenase Ethe1 0.00442 Down D3ZVB0 AP-5 complex subunit beta-1 Ap5b1 0.00184 Down D4AEG5 RNA helicase Dhx35 0.00668 Down D3ZPF2 Malonyl-CoA-acyl carrier protein transacylase Mcat 0.00361 Up D4A7B6 Transmembrane protein 87B Tmem87b 0.01044 Up F1LVX2 EH domain-binding protein 1 Ehbp1 0.02359 Down F1LPV2 Very...”
DIP1423 Putative ATP-dependent helicase from Corynebacterium diphtheriae NCTC 13129
35% identity, 35% coverage
DHX15_SCHPO / O42945 Probable pre-mRNA-splicing factor ATP-dependent RNA helicase prp43; EC 3.6.4.13 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
SPBC16H5.10c ATP-dependent RNA helicase Prp43 from Schizosaccharomyces pombe
36% identity, 50% coverage
- function: Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex
Weigt, Epigenetics & chromatin 2021 - “...E4 SPBC1861.04c Prp24 RNA-binding protein Prp24 (predicted) SPBC119.13c Prp31 U4/U6 U5 tri-snRNP complex subunit Prp31 SPBC16H5.10c Prp43 ATP-dependent RNA helicase Prp43 SPBP22H7.07 Prp5 WD repeat protein Prp5 SPAC227.12 Rna4 U4/U6 U5 tri-snRNP complex subunit Prp4 family, Rna4 SPAC19G12.07c Rsd1 RNA-binding protein Rsd1 (predicted) SPAC22A12.09c Sap114 U2...”
- Gene expression profiling data of Schizosaccharomyces pombe under nitrosative stress using differential display
Biswas, Data in brief 2016 - “...aminotransferase SPCC569.07 DNA replication factor C complex subunit Rfc3 SPAC27E2.10c ATP-dependent RNA helicase Prp43 (predicted) SPBC16H5.10c MBF transcription factor complex subunit Rep1 SPBC2D10.06 Thioredoxin reductase trr 1 SPBC3F6.03 Table 3 Validation of gene expression obtained from differential display by Real Time PCR. Table 3. Treatment with...”
- Php4 Is a Key Player for Iron Economy in Meiotic and Sporulating Cells
Brault, G3 (Bethesda, Md.) 2016 - “..., 386 SPAP8A3.05 ski7 + Ski complex interacting GTPase Ski7 2.481 2.641 586, 198, 126 SPBC16H5.10c prp43 + ATP-dependent RNA helicase Prp43 2.129 2.144 678, 671 a , 616 SPBC2F12.08c ceg1 + mRNA guanylyltransferase Ceg1 2.008 2.186 None Mitochondrial membrane-related SPBC3B9.19 mge1 + Mitochondrial GrpE domain...”
- Poly(A) tail-mediated gene regulation by opposing roles of Nab2 and Pab2 nuclear poly(A)-binding proteins in pre-mRNA decay
Grenier, Molecular and cellular biology 2013 - “...SPBC13E7.01 SPCC188.11 SPBC1289.11 SPAC27D7.07c SPBC16H5.10c SPAC26A3.08 SPBC19C2.14 SPBP22H7.07 SPBC1861.08c SPAC22A12.09c SPBC3E7.14 SPAC22F8.10c SPBC4B4.09...”
- Pre-spliceosome formation in S.pombe requires a stable complex of SF1-U2AF(59)-U2AF(23)
Huang, The EMBO journal 2002 - “...containing TAP-tagged SF1 (SPCC962.06c), U2AF59 (SPBC146.07), Prp43p (SPBC16H5.10c) or Prp5p (SPCC10H11.01) (lanes 2, 4, 6 and 8) were depleted of tagged...”
PF3D7_1364300 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 from Plasmodium falciparum 3D7
29% identity, 39% coverage
- Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum
Hollin, BMC genomics 2016 - “...putative RKSVHF PF3D7_1244500 conserved Plasmodium protein, unknown function RRKVNF PF3D7_1322100 variant-silencing SET protein (SETvs) KRNVSF PF3D7_1364300 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (PRP16) RKMVQF PF3D7_1366300 conserved Plasmodium protein, unknown function KKVVKF/KKKVQF PF3D7_1367500 NADH-cytochrome b5 reductase, putative KKHVHF PF3D7_1406200 conserved Plasmodium protein, unknown function KKMVSF PF3D7_1411500 conserved...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...PF3D7_1418900, PF3D7_0630900 Helicase+ZnF PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500 Helicase+HA2+S1 PF3D7_1030100 Helicase+HA2+OB fold PF3D7_1364300, PF3D7_1231600, PF3D7_0917600, PF3D7_0821300 Helicase+ZnF+DSHCT PF3D7_0909900 Helicase+rRNA proc-arch+DSHCT PF3D7_0602100 Helicase+HA2 PF3D7_0310500, PF3D7_1302700 Blue , pink and green boxes are used to denote transmembrane, low complexity, and coiled-coil regions, respectively To further...”
- “...processing, while DEAD helicases participate in ribosome biogenesis [ 26 ]. In P. falciparum , PF3D7_1364300, PF3D7_1231600, PF3D7_0917600 and PF3D7_1030100 all have a conserved DEAH domain and are classified as Prp (pre-mRNA processing) proteins. Similarly, almost all of the proteins classified under ribosome biogenesis (Fig. 2...”
NP_595890 ATP-dependent RNA helicase Prp16 from Schizosaccharomyces pombe
SPBC1711.17 ATP-dependent RNA helicase Prp16 from Schizosaccharomyces pombe
32% identity, 38% coverage
- Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features.
Vijayakumari, RNA biology 2019 - GeneRIF: The strength of splice sites - snRNA interactions in genome-wide transcripts determines whether the major Prp16 function in that organism is in splicing and/or gene silencing.
- The intron in centromeric noncoding RNA facilitates RNAi-mediated formation of heterochromatin.
Mutazono, PLoS genetics 2017 - GeneRIF: n, we demonstrate that the splicing factor spPrp16p is enriched at the centromere, and associates with Cid12p (a factor in the RNAi pathway) and the intron-containing dg ncRNA. Interestingly, removal of the dg intron, mutations of its splice sites, or replacement of the dg intron with an euchromatic intron significantly decreased H3K9 dimethylation
- The intron in centromeric noncoding RNA facilitates RNAi-mediated formation of heterochromatin
Mutazono, PLoS genetics 2017 - “...Complementation cloning of the prp14 + gene revealed that the mutation in prp14 resides in SPBC1711.17, which encodes an ATP-dependent RNA helicase homologous to Saccharomyces cerevisiae and human Prp16p (See S1 Text and S1 Fig ), indicating that the prp14 mutation is a prp16 allele. Hereafter,...”
BMA1750 ATP-dependent helicase HrpA from Burkholderia mallei ATCC 23344
35% identity, 31% coverage
PRP43_YEAST / P53131 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43; Helicase JA1; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 5 papers)
NP_011395, YGL120C Prp43p from Saccharomyces cerevisiae
NP_011395 DEAH-box ATP-dependent RNA helicase PRP43 from Saccharomyces cerevisiae S288C
33% identity, 53% coverage
- function: Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the NTR complex (NTC-related complex), composed of NTR1, NTR2 and PRP43. Interacts with NTR1 and NTR2. Interacts with SPP382. - DExD/H-box RNA helicases in ribosome biogenesis
Martin, RNA biology 2013 - “...DEVH JA1 - S MAK5 YJL050W DEAH - - L MTR4 YGL120C DEAD - hm, 66S PRP43 YGL171W DEAD - ROK1 YHR065C DEAD RRP3 YFL002C SPB4 Changes in precursor levels compared...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...28.4 251 0.43 0.38 0.34 0.46 1-14 hPRP18 1DVK (80-251) 12-29 23-37 Disassembly proteins Prp43 YGL120C P53131 87.6 767 0.15 0.39 0.34 0.23 1-9 hPRP43 2XAU (1-767) 17-32 42-54 81-89 106-112 339-345 385-391 Spp382 YLR424W Q06411 83.1 708 0.13 0.21 0.31 0.23 14-31 11-20 TFIP11 57-74...”
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...0.969321982 0.974163208 182396 + chr07 YGL163C 0.975825825 0.968348392 196409 chr07 YGL138C 0.971247145 0.983410766 249536 chr07 YGL120C 0.981452639 0.964320425 283943 chr07 YGL119W 0.986610225 0.981525372 284448 + chr07 YGL108C 0.961840326 0.985939242 304074 chr07 YGL058W 0.977732494 0.975176081 393992 + chr07 YGL056C 0.960426378 0.969119302 397624 chr07 YGL055W 0.964044825 0.969447792 398631...”
- “...YPR062W AFUA_1G05050 0.087018417 YDR497C AFUA_2G07910 0.078863767 YDR477W AFUA_2G01700 0.074801159 YLR378C AFUA_5G08130 0.074624328 YBR060C AFUA_5G08110 0.073589072 YGL120C AFUA_5G11620 0.069009268 YIL063C AFUA_2G10810 0.06328373 YOL157C AFUA_7G06380 0.06047767 YGL043W AFUA_3G07670 0.059398891 YMR027W AFUA_5G06710 0.058232831 YHR215W AFUA_8G01910 0.05787337 YDL247W AFUA_7G05190 0.05184022 YPR048W AFUA_5G07290 0.049809159 YBL051C AFUA_5G01940 0.048514144 YHR148W AFUA_2G08320 0.047441878 YJR160C...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...late-acting proteins DDB0233399 Prp22 DHX8 NP_004932 NP_610928 NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520 3D. Exon...”
- A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of saccharomyces cerevisiae mutants
Stefanini, The Journal of biological chemistry 2010 - “...complex disassembly (genes involved are SSB1, RSC3, TPA1, YGL120C, and RSC58) was up-regulated in BY4742 but pare the three experiments of this study with...”
- Uncovering the rules for protein-protein interactions from yeast genomic data
Wang, Proceedings of the National Academy of Sciences of the United States of America 2009 - “...YDL030W, YDL043C, YMR268C, YDR473C, YPR178W, YML046W, YDR243C, YGL120C, YGR006W, YGR075C, YGR091W, YHR165C, YJL203W, YKL012W, YLL036C, and YDR235W are premRNA...”
- Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data
Bryan, BMC genomics 2008 - “...(SGD) Functional Evidence Ribosomal RNA procesing (11.04.01) YBR271W Localizes to the cytoplasm S-adenosylmethionine-dependent methyltransferase. YCR016W YGL120C (PRP43) RNA helicase/maturation of rRNA, YPR135W (CTF4) Chromatin-associated protein YDL063C YPL131W (RPL5-Protein of (60S) ribosomal subunit) GO ribosome biogenesis & assembly (RCA) YDL167C (NRP1) GO ribosome biogenesis & assembly (RCA)...”
- “...assembly (RCA) YOR154W (SLP1) SUN like protein YOR252W (TMA16) YLR009W (RLP24) 60S ribosomal subunit biogenesis, YGL120C (PRP43) RNA helicase/maturation of rRNA YPL183C Negative regulation of transposition, RNA-mediated (IMP) DNA Topology (10.01.02) YBL112C Contained within telomere TEL02L, TEL02L-YP YEL076C Contained within telomere TEL05L, TEL05L-YP, YEL076C-A YER189W Contained...”
- An inventory of yeast proteins associated with nucleolar and ribosomal components
Staub, Genome biology 2006 - “...1 0 0 0 1 1 1 0.698 Casein kinase II catalytic alpha chain PRP43* YGL120C 1 1 1 0 1 1 0 0.695 Involved in spliceosome disassembly SUI3 YPL237W 1 0 0 0 1 1 0 0.721 Translation initiation factor eIF2 beta subunit DST1 YGL043W...”
- More
- The G-patch activators Pfa1 and PINX1 exhibit different modes of interaction with the Prp43 RNA helicase.
Mouffok, RNA biology 2021 - GeneRIF: The G-patch activators Pfa1 and PINX1 exhibit different modes of interaction with the Prp43 RNA helicase.
- Regulation of Prp43-mediated disassembly of spliceosomes by its cofactors Ntr1 and Ntr2.
Fourmann, Nucleic acids research 2017 - GeneRIF: Ntr1 and Ntr2 may act as 'doorkeepers' and both cofactors may inspect the RNP structure of spliceosomal complexes thereby targeting suboptimal spliceosomes for Prp43-mediated disassembly.
- Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding.
Robert-Paganin, Nucleic acids research 2017 - GeneRIF: Using Prp43 F357A mutants or pyrimidine nucleotides, we show that the lack of stacking of the nucleotide base to the F-motif decouples the NTPase and helicase activities of Prp43. In contrast the R159A mutant (R-motif) showed reduced ATPase and helicase activities.
- Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA.
He, RNA (New York, N.Y.) 2017 - GeneRIF: Study shows the crystal structure of Prp43p bound to single-stranded poly-uracil RNA and reveals differences with viral ATPases in the RecA1 domain but with striking similarities with viral ATPases in the RecA2 domain of the catalytic core, including both a prominent beta-hairpin that bookends the 5' end of the RNA stack and a dynamic motif Va that is implicated in mediating translocation.
- Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways.
Heininger, RNA biology 2016 - GeneRIF: Results show that Prp43 expression is regulated by Cmg1 which stimulates its RNA helicase activity.
- The target of the DEAH-box NTP triphosphatase Prp43 in Saccharomyces cerevisiae spliceosomes is the U2 snRNP-intron interaction.
Fourmann, eLife 2016 - GeneRIF: These data indicate that the U2 snRNP-intron interaction is Prp43's major target.
- Limited portability of G-patch domains in regulators of the Prp43 RNA helicase required for pre-mRNA splicing and ribosomal RNA maturation in Saccharomyces cerevisiae.
Banerjee, Genetics 2015 - GeneRIF: Prp43 differentially interacts with g-patch domains in Spp382, Sqs1, and Pxr1 G.
- Insights into the activation of the helicase Prp43 by biochemical studies and structural mass spectrometry.
Christian, Nucleic acids research 2014 - GeneRIF: This study investigated the activation of Prp43 by Ntr1 in the presence and absence of RNA substrate.
- More
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...all yeast DExH-box RNA helicases. The amino-acid sequence of ctPrp43 (G0RY84) was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698)....”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...251 0.43 0.38 0.34 0.46 1-14 hPRP18 1DVK (80-251) 12-29 23-37 Disassembly proteins Prp43 YGL120C P53131 87.6 767 0.15 0.39 0.34 0.23 1-9 hPRP43 2XAU (1-767) 17-32 42-54 81-89 106-112 339-345 385-391 Spp382 YLR424W Q06411 83.1 708 0.13 0.21 0.31 0.23 14-31 11-20 TFIP11 57-74 60-77...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...DHX32 pre-mRNA sf (LOC_Os03g19960) DHX15 (O22899) PRP43 (P53131) RNA helicase (PFI0860c) 52 DHX33 DHX8 (LOC_Os06g09280) DHX8 (Q38953) PRP22 (P24384) RNA...”
- “...and gene name for these DNA helicases. 134 PRP43 (P53131) Validation of helicases. Protein sequences of human RNA and DNA helicases are validated based on the...”
- Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
Pang, BMC genomics 2010 - “...regulator of transcription subunit 1 mR256 POL12 P38121 DNA polymerase alpha subunit B mK84 PRP43 P53131 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 dK662 PRT1 P06103 Eukaryotic translation initiation factor 3 subunit B mR572 PSD2 P53037 Phosphatidylserine decarboxylase proenzyme 2 precursor mR252 PYK1 P00549 Pyruvate kinase 1...”
- PIR pairwise alignment - a slip up for signal peptides.
Balaji, Bioinformation 2006 - “...O00160 Murinae Q9CQX8, P43687, Q60754, Q63356, P70248 Peloderinae Q09524 Phaseoleae P04145, P23233 Polygonaceae Q9XFM4 Saccharomycetaceae P53131, P38953, Q02555 Schizosaccharomycetaceae O14072, O14072 Solanaceae P23137, Q9XH42, Q9XH43 Suidae P98074, O62680 Triticeae P01543, P32032 Vicieae P13240 Virus P52358, P14979, P33495 Alphaherpesvirinae Geminiviridae Pneumovirinae Table 2 Percentage identities of SSEARCH...”
- “...21.5 43 32 1 3 Q9F7S4 + P14009 25.0 2 28 1 4 P70248 + P53131 20.2 88 32 1 5 P38953 + Q02555 17.8 32 24 1 6 O14072 + P91875 18.4 90 28 1 7 O14072 + Q8L7U5 20.7 24 24 1 8 O75030...”
- Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification
Dez, Molecular and cellular biology 2004 - “...A0, P20447 P53734 P36120 Q06218 P32892 Q03532 P38112 P53131 P25582 Q04660 P37838 P53261 P40991 P40010 Q08287 P36049 P38911 P35178 P53927 P33201 Q08962 Q12176...”
FTN_1432 HrpA-like helicase from Francisella tularensis subsp. novicida U112
35% identity, 32% coverage
3kx2B / P53131 Crystal structure of prp43p in complex with adp (see paper)
33% identity, 53% coverage
- Ligand: adenosine-5'-diphosphate (3kx2B)
6sh6A / O43143 Crystal structure of the human deah-helicase dhx15 in complex with the nkrf g-patch bound to adp (see paper)
35% identity, 52% coverage
- Ligand: adenosine-5'-diphosphate (6sh6A)
DHR2_YEAST / P36009 Probable ATP-dependent RNA helicase DHR2; DEAH box RNA helicase DHR2; Helicase JA2; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 4 papers)
NP_012845 RNA helicase from Saccharomyces cerevisiae S288C
YKL078W Dhr2p from Saccharomyces cerevisiae
34% identity, 52% coverage
- function: Probable ATP-binding RNA helicase. Required for 18S rRNA synthesis
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with NOP19 (PubMed:21941128). Interacts with UBP10 (PubMed:22902402, PubMed:26149687). - Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values in parentheses indicate the Uniprot accession numbers ( TheUniProtConsortium,...”
- The nucleolar protein Nop19p interacts preferentially with Utp25p and Dhr2p and is essential for the production of the 40S ribosomal subunit in Saccharomyces cerevisiae.
Choque, RNA biology - GeneRIF: Data show that Nop19p (renamed from YGR251W) interacts preferentially with the DEAH-box RNA helicase Dhr2p and Utp25p.
- Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
Kuppuswamy, Algorithms for molecular biology : AMB 2014 - “...YEL054C GO:0001510 18/20 YDR161W, YHR052W, YGR162W, YIL091C, YDR101C, YDL063C, YLR009W, YIL096C, YJR032W, YCR016W, YLR287C , YKL078W, YGR071C, YOL077C, YPL226W, YOR361C, YGR173W, YPL193W GO:0018193 17/20 YOR182C, YHR021C, YJL189W, YLR287C-A, YNL313C, YLR185W, YNL162W, YDL075W, YJL136C, YMR282C, YHR141C, YOL098C, YGR034W, YLR406C, YGR162W, YFR032C-A, YIL069C GO:0050790 18/20 YGR162W, YLR455W, YNL031C,...”
- DExD/H-box RNA helicases in ribosome biogenesis
Martin, RNA biology 2013 - “...DEAH red. 60S hm S YMR128W DEAH red. 40S S/L X a DHR1 YKL078W DEAD red. 40S L 45, 46 DHR2 YLL008W DEAD hm L X DRS1 YDR021W DEAD - hm S/L a X FAL1 YMR290C DEAD...”
- Systematic identification of novel, essential host genes affecting bromovirus RNA replication
Gancarz, PloS one 2011 - “...ADE13 46 57 YBR070C ALG14 11 14 YDL132W CDC53 8.4 6.3 YOR204W DED1 180 140 YKL078W DHR2 8.3 8.0 YLR129W DIP2 440 160 YMR128W ECM16 12 7.4 YLR274W MCM5 33 19 YGR103W NOP7 46 78 YGR119C NUP57 30 19 YOR122C PFY1 7.9 7.5 YLR196W PWP1 11...”
- “...19041 0.011 YGR251W N/A a 18945 0.014 YDR324C UTP4 18049 0.003 YLR196W PWP1 16541 0.011 YKL078W DHR2 16165 0.036 YGR103W NOP7 15521 0.011 YBR070C ALG14 15320 0.006 YGL044C RNA15 15316 0.003 YGR116W SPT6 15212 0.003 a ORF not annotated in Saccharomyces Genome Database. The 19 confirmed...”
- Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
Cheng, BMC bioinformatics 2008 - “...YPL240C 21 ribosome biogenesis and assembly 2.26E-04 1.26E-02 YAL025C, YBR238C, YBR267W, YDL031W, YDR083W, YDR184C, YIR026C, YKL078W 24 Glycolysis 3.40E-05 4.15E-03 YAL038W, YCR012W, YDR050C, YJR009C, YKL060C, YKL152C translational elongation 4.41E-09 5.38E-07 YAL003W, YBR118W, YDL081C, YDL130W, YDR382W, YDR385W, YLR249W, YLR340W, YOL039W regulation of translational fidelity 1.61E-08 1.97E-06 YBR048W,...”
- How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
Barriot, BMC bioinformatics 2007 - “...the missing elements. Here, the missing elements are the products of the genes YGL128c and YKL078w. YGL128c is annotated as 'Component of a complex containing Cef1p, putatively involved in pre-mRNA splicing'. It is currently annotated with 'biological process unknown' which explains why it is not found...”
- “...association to a complex containing Cef1p strongly suggests that YGL128c should be annotated with GO:0000398. YKL078w is annotated as 'Predominantly nucleolar DEAH-box RNA helicase, required for 18S rRNA synthesis'. It is annotated as GO:0007046 ribosome biogenesis of the biological process branch of the GO. This term...”
- A genome-wide survey and systematic RNAi-based characterization of helicase-like genes in Caenorhabditis elegans
Eki, DNA research : an international journal for rapid publication of reports on genes and genomes 2007 - “...21 uncharacterized genes including five essential genes YDL031W [ DBP10 ], YDL084W [ SUB2 ], YKL078W [ DHR2 ], YLR276C [ DBP9 ], and YMR128W [ ECM16 ], and YDL070W [ BDF2 ] and YGL150C [ INO80 ] were later shown to be non-essential. Some of...”
- Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
Caselle, BMC bioinformatics 2002 - “...-0.23 0.25 -0.92 -1.09 -1.69 -2.18 YJL033W HCA4 -0.06 0.01 0.21 -0.94 -0.36 -0.67 -0.62 YKL078W -0.04 -0.01 0.04 -1.12 -0.97 -0.71 -1.89 YKL172W EBP2 0.12 0.21 0.30 -0.74 -0.56 -0.42 -1.40 YLR276C DBP9 0.03 0.14 0.32 -0.62 -0.86 -0.67 -1.64 YLR401C -0.06 -0.07 0.07 -0.71...”
- Systematic identification, classification, and characterization of the open reading frames which encode novel helicase-related proteins in Saccharomyces cerevisiae by gene disruption and Northern analysis
Shiratori, Yeast (Chichester, England) 1999 (PubMed)- “...previously uncharacterized ORFs (YDL031w, YDL070w, YDL084w, YGL150c, YKL078w, YLR276c, and YMR128w) were identified by systematic gene disruption, to be...”
- “...YFR038w; YGL064c; YGL150c; YHR031c; YIR002c; YKL017c; YKL078w; YLR247c; YLR276c; YLR419w; YMR128w; YNL218w; YOL095c; YOR304w *Correspondence to: T. Eki,...”
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DHX15_MOUSE / O35286 ATP-dependent RNA helicase DHX15; DEAH box protein 15; EC 3.6.4.13 from Mus musculus (Mouse) (see 5 papers)
NP_031865 ATP-dependent RNA helicase DHX15 isoform 2 from Mus musculus
35% identity, 52% coverage
- function: RNA helicase involved in mRNA processing and antiviral innate immunity (PubMed:26494172, PubMed:34161762). Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA (By similarity). In cooperation with TFIP11 seem to be involved in the transition of the U2, U5 and U6 snRNP-containing IL complex to the snRNP-free IS complex leading to efficient debranching and turnover of excised introns (By similarity). Plays a key role in antiviral innate immunity by promoting both MAVS-dependent signaling and NLRP6 inflammasome (PubMed:26494172). Acts as an RNA virus sensor: recognizes and binds viral double stranded RNA (dsRNA) and activates the MAVS- dependent signaling to produce interferon-beta and interferon lambda-3 (IFNL3) (By similarity). Involved in intestinal antiviral innate immunity together with NLRP6: recognizes and binds viral dsRNA and promotes activation of the NLRP6 inflammasome in intestinal epithelial cells to restrict infection by enteric viruses (PubMed:26494172, PubMed:34161762, PubMed:34678144). The NLRP6 inflammasome acts by promoting maturation and secretion of IL18 in the extracellular milieu (PubMed:34161762). Also involved in antibacterial innate immunity by promoting Wnt-induced antimicrobial protein expression in Paneth cells (PubMed:33483420).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity). Identified in the Intron Large spliceosome complex (IL, also named intron lariat spliceosome), a post-mRNA release spliceosomal complex containing the excised intron, U2, U5 and U6 snRNPs, and splicing factors; the association may be transient (By similarity). The IL complex exists in two distinct conformations, one with the DHX15 (ILS2) and one without (ILS1) (By similarity). Interacts with TFIP11 (via G-patch domain); indicative for a recruitment to the IL complex (By similarity). Interacts with SSB/La (By similarity). Interacts with GPATCH2 (via G-patch domain); promoting the RNA helicase activity (By similarity). Interacts with NKRF (via G-patch domain); promoting the RNA helicase activity (By similarity). Interacts with NLRP6 (PubMed:26494172).
disruption phenotype: Conditional deletion in intestinal epithelial cells leads to impaired antiviral innate immunity, leading to lethality following infection by an RNA virus (PubMed:34161762). Conditional deletion in intestinal epithelial cells leads to impaired antibacterial immunity, characterized by susceptibility to infection by enteric bacteria C.rodentium (PubMed:33483420). Conditional deletion in Paneth cells leads to reduced expression of alpha-defensins and severe DSS (dextran sodium sulfate)-induced colitis (PubMed:33483420). - Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.
Zhu, Nature communications 2024 - GeneRIF: Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.
- Identification of Dhx15 as a Major Regulator of Liver Development, Regeneration, and Tumor Growth in Zebrafish and Mice.
Portolés, International journal of molecular sciences 2024 - GeneRIF: Identification of Dhx15 as a Major Regulator of Liver Development, Regeneration, and Tumor Growth in Zebrafish and Mice.
- The RNA helicase DHX15 is a critical regulator of natural killer-cell homeostasis and functions.
Wang, Cellular & molecular immunology 2022 - GeneRIF: The RNA helicase DHX15 is a critical regulator of natural killer-cell homeostasis and functions.
- The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells.
Wang, Proceedings of the National Academy of Sciences of the United States of America 2021 - GeneRIF: The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells.
- DHX15 is required to control RNA virus-induced intestinal inflammation.
Xing, Cell reports 2021 - GeneRIF: DHX15 is required to control RNA virus-induced intestinal inflammation.
- The loss of DHX15 impairs endothelial energy metabolism, lymphatic drainage and tumor metastasis in mice.
Ribera, Communications biology 2021 - GeneRIF: The loss of DHX15 impairs endothelial energy metabolism, lymphatic drainage and tumor metastasis in mice.
- Ceria nanoparticles enhance endochondral ossification-based critical-sized bone defect regeneration by promoting the hypertrophic differentiation of BMSCs via DHX15 activation.
Li, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019 (PubMed)- GeneRIF: ceria nanoparticles significantly promoted endochondral ossification-based bone regeneration by ensuring sufficient hypertrophic differentiation via the activation of the RNA helicase, DEAH (Asp-Glu-Ala-His) box helicase 15, and its downstream target, p38 MAPK.
- Nlrp6 regulates intestinal antiviral innate immunity.
Wang, Science (New York, N.Y.) 2015 - GeneRIF: These data demonstrate that Nlrp6 functions with Dhx15 as a viral RNA sensor to induce IFN-stimulated genes, and this effect is especially important in the intestinal tract.
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- The amyloid peptide β disrupts intercellular junctions and increases endothelial permeability in a NADPH oxidase 1-dependent manner.
Tarafdar, Redox biology 2022 - “...Protein synthesis and degradation Q9Z127 Large neutral amino acids transporter small subunit 1 Slc7a5 0.0000471 O35286 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 Dhx15 0.0001885 Q9R0P9 Ubiquitin carboxyl-terminal hydrolase isozyme L1 Uchl1 0.0005190 Q8CHW4 Translation initiation factor eIF-2B subunit epsilon Eif2b5 0.0009779 O89086 RNA-binding protein 3 Rbm3...”
- The RNA editing enzyme ADAR2 restricts L1 mobility.
Frassinelli, RNA biology 2021 - “...TOP1 DNA topoisomerase I Q969P6 TOP1M DNA topoisomerase I, mitochondrial P19338 NCL Nucleolin (Protein C23) O35286 DHX15 Putative pre-mRNA splicing factor RNA helicase (DEAH box protein 15) Q9C0E2 XPO4 Exportin 4 (Exp4) Q15233 NONO (p54 nrb) Non-POU domain containing octamer-binding protein P07910 HNRNPC1/C2 Heterogeneous nuclear ribonucleoproteins...”
- The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription.
Li, The Journal of biological chemistry 2016 - Neutrophil extracellular traps in sheep mastitis.
Pisanu, Veterinary research 2015 - “...1.89 Q3SZF8 Small nuclear ribonucleoprotein Sm D2 1.89 P60122 RuvB-like 1 1.87 P47845 Galectin-3 1.85 O35286 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 1.83 Q3T0D0 Heterogeneous nuclear ribonucleoprotein K 1.81 Q5EA36 RNA-binding protein 14 1.80 Q13247 Serine/arginine-rich splicing factor 6 1.69 P38646 Stress-70 protein, mitochondrial 1.66...”
- The adipogenic transcriptional cofactor ZNF638 interacts with splicing regulators and influences alternative splicing.
Du, Journal of lipid research 2014 - Association of SAP130/SF3b-3 with Cullin-RING ubiquitin ligase complexes and its regulation by the COP9 signalosome.
Menon, BMC biochemistry 2008 - “...transcription p100 (K)GFRQGPQPFTQQK (K)EATQTVAADTRP Un-assignable p95 (K)YYEQFSK HSP90, silkworm (BAB41209) Chaperon p82 (K)REVDDLGPEVGDIK (K)VYNPRIRVESLLVTAISK Ddx15/mDEAH9/prp43 (O35286) RNA splicing p72-77 (K)SQIHDIVLVGGSTRIPK (K)HWPFMVVNDAGRPK (K)LLQDFFNGK (K)TVQNAVITVPAYFNDSQRQATK Hsc70 family, Hspa8 (NP_112442) Chaperon p46 (K)LHREFHYGPDPQPVMQLDG (K)EGAVATRFHITKYPTLK CG9911 Drosophila (AAF48579) similar to mouse ERp44 oxidative protein folding in the ER p41 (K)FFENRANGQSK...”
D3ZD97 RNA helicase from Rattus norvegicus
35% identity, 52% coverage
A5D7D9 RNA helicase from Bos taurus
35% identity, 52% coverage
F1S5A8 RNA helicase from Sus scrofa
35% identity, 52% coverage
DHX15_HUMAN / O43143 ATP-dependent RNA helicase DHX15; ATP-dependent RNA helicase #46; DEAH box protein 15; Splicing factor Prp43; hPrp43; EC 3.6.4.13 from Homo sapiens (Human) (see 10 papers)
NP_001349 ATP-dependent RNA helicase DHX15 from Homo sapiens
35% identity, 52% coverage
- function: RNA helicase involved in mRNA processing and antiviral innate immunity (PubMed:19103666, PubMed:19432882, PubMed:24782566, PubMed:24990078, PubMed:32179686, PubMed:34161762). Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA (PubMed:19103666). In cooperation with TFIP11 seem to be involved in the transition of the U2, U5 and U6 snRNP-containing IL complex to the snRNP-free IS complex leading to efficient debranching and turnover of excised introns (PubMed:19103666). Plays a key role in antiviral innate immunity by promoting both MAVS-dependent signaling and NLRP6 inflammasome (PubMed:24782566, PubMed:24990078, PubMed:34161762). Acts as an RNA virus sensor: recognizes and binds viral double stranded RNA (dsRNA) and activates the MAVS-dependent signaling to produce interferon-beta and interferon lambda-3 (IFNL3) (PubMed:24782566, PubMed:24990078, PubMed:34161762). Involved in intestinal antiviral innate immunity together with NLRP6: recognizes and binds viral dsRNA and promotes activation of the NLRP6 inflammasome in intestinal epithelial cells to restrict infection by enteric viruses (PubMed:34161762). The NLRP6 inflammasome acts by promoting maturation and secretion of IL18 in the extracellular milieu (PubMed:34161762). Also involved in antibacterial innate immunity by promoting Wnt-induced antimicrobial protein expression in Paneth cells (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Identified in the Intron Large spliceosome complex (IL, also named intron lariat spliceosome), a post- mRNA release spliceosomal complex containing the excised intron, U2, U5 and U6 snRNPs, and splicing factors; the association may be transient (PubMed:19103666, PubMed:30728453). The IL complex exists in two distinct conformations, one with the DHX15 (ILS2) and one without (ILS1) (PubMed:30728453). Interacts with TFIP11 (via G-patch domain); indicative for a recruitment to the IL complex (PubMed:19103666). Interacts with SSB/La (PubMed:12458796). Interacts with GPATCH2 (via G- patch domain); promoting the RNA helicase activity (PubMed:19432882). Interacts with NKRF (via G-patch domain); promoting the RNA helicase activity (PubMed:32179686). Interacts with NLRP6 (PubMed:34161762). - GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.
Kanwal, Nucleic acids research 2024 - GeneRIF: GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.
- Unveiling the DHX15-G-patch interplay in retroviral RNA packaging.
Dostálková, Proceedings of the National Academy of Sciences of the United States of America 2024 - GeneRIF: Unveiling the DHX15-G-patch interplay in retroviral RNA packaging.
- Relationship between DHX15 expression and survival in colorectal cancer.
Fan, Revista espanola de enfermedades digestivas 2023 (PubMed)- GeneRIF: Relationship between DHX15 expression and survival in colorectal cancer.
- Splicing quality control mediated by DHX15 and its G-patch activator SUGP1.
Feng, Cell reports 2023 - GeneRIF: Splicing quality control mediated by DHX15 and its G-patch activator SUGP1.
- Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network.
Bohnsack, Nucleic acids research 2022 - GeneRIF: Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network.
- DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer.
Zhang, Proceedings of the National Academy of Sciences of the United States of America 2022 - GeneRIF: DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer.
- Dhx15 regulates zebrafish definitive hematopoiesis through the unfolded protein response pathway.
Cai, Cancer science 2021 - GeneRIF: Dhx15 regulates zebrafish definitive hematopoiesis through the unfolded protein response pathway.
- DHX15 is required to control RNA virus-induced intestinal inflammation.
Xing, Cell reports 2021 - GeneRIF: DHX15 is required to control RNA virus-induced intestinal inflammation.
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- CD147 Mediates the Metabolic Reprogramming of Cancer Associated Fibroblasts Induced by EVs Released by Differentiating Cancer Stem Cells.
Colella, Journal of extracellular biology 2025 - “...PRPF8 PremRNA processing factor 8 Q86XP3 DDX42 DEADbox helicase 42 P17844 DDX5 DEADbox helicase 5 O43143 DHX15 DEAHbox helicase 15 O75533 SF3B1 Splicing factor 3b subunit 1 Q9UMS4 PRPF19 PremRNA processing factor 19 Q09161 NCBP1 Nuclear cap binding protein subunit 1 Q96E39 RBMXL1 RBMX like 1...”
- An integrated approach using proximity labelling and chemical crosslinking to probe in situ host-virus protein-protein interactions.
Li, QRB discovery 2024 - “...Boruchowicz et al. ( 2020 ) BioID Single protein HBoV1 nuclear protein 1 300 DHX15 O43143 5XDR Wang et al. ( 2020 ) CPSF6 Q16630 3Q2S Proviral BioID Single protein HIV1 Vpr 352 APC1 Q9H1A4 4UI9 Proviral Barbosa et al. ( 2021 ) TurboID Single protein...”
- Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes.
Homma, Life science alliance 2024 - “...46.1 5.48 Splicing facotrs Early Q6P2Q9 Pre-mRNA-processing splicing factor 8 2229.28 28.18 43 273.4 8.84 O43143 Putative pre-mRNA splicing factor ATP-dependent RNA helicase DHX15 944.91 14.84 9 90.9 7.46 Late O75533 Splicing factor 3B subunit 1 1225.81 26.69 19 145.7 7.09 Q13435 Splicing factor 3B subunit...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Anti-U11/U12 Antibodies as a Rare but Important Biomarker in Patients with Systemic Sclerosis: A Narrative Review.
Fritzler, Diagnostics (Basel, Switzerland) 2023 - “...the molecular weight. Protein ID Molecular Weight ID Alternative Names/Protein Function hPrp43, DHX15 90 kDa O43143 ATP-dependent RNA helicase 46, DHX15 RNPC-3 65 kDa Q96LT9 RNA-Binding Region-Containing Protein 3 RNA-Binding Protein 40 U11/U12 Small Nuclear Ribonucleoprotein 65 kDa Protein PDCD7 59 kDa Q8N8D1 Programmed Cell Death...”
- Splicing quality control mediated by DHX15 and its G-patch activator SUGP1.
Feng, Cell reports 2023 - An Improved Model for Circular RNA Overexpression: Using the Actin Intron Reveals High Circularization Efficiency.
Li, Advanced genetics (Hoboken, N.J.) 2023 - “...Q07955 (+2) SRSF1 28kDa 3 3 10 3 Q6P2Q9 PRPF8 274kDa 5 6 5 2 O43143 DHX15 91kDa 4 5 3 3 P84103 (+1) SRSF3 19kDa 2 4 7 2 Q9UHX12 PUF60 58kDa 2 2 Q13435 SF3B2 100kDa 3 1 3 2 Q13243 SRSF5 31kDa 2...”
- Tocotrienol-Rich Fraction and Levodopa Regulate Proteins Involved in Parkinson's Disease-Associated Pathways in Differentiated Neuroblastoma Cells: Insights from Quantitative Proteomic Analysis
Magalingam, Nutrients 2022 - “...complex subunit 2 PSME2 27,402 0.005 0.967 P35637 RNA-binding protein FUS FUS 53,426 0.003 0.885 O43143 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 90,933 0.010 0.666 P49321 Nuclear autoantigenic sperm protein NASP 85,238 0.026 0.618 P05386 60S acidic ribosomal protein P1 RPLP1 11,514 0.006 0.484 P14174 Macrophage...”
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AGABI2DRAFT_79146 hypothetical protein from Agaricus bisporus var. bisporus H97
33% identity, 53% coverage
Bm1_47285 putative ATP-dependent helicase DHX35, putative from Brugia malayi
35% identity, 51% coverage
- DEAD/DExH-Box RNA Helicases in Selected Human Parasites
Marchat, The Korean journal of parasitology 2015 - “...a smaller N-terminal region when compared to its human counterpart DDX4; another example is the Bm1_47285 whose helicase domains lacks motif IV [ 29 ]. These data suggest that DEAD/DExH-box RNA helicases could be utilized as rational biochemical targets for developing new anti-parasite treatments and overcome...”
B4E0S6 RNA helicase from Homo sapiens
35% identity, 52% coverage
DHX33_MOUSE / Q80VY9 ATP-dependent RNA helicase DHX33; DEAH box protein 33; EC 3.6.4.13 from Mus musculus (Mouse) (see 4 papers)
NP_848144 ATP-dependent RNA helicase DHX33 from Mus musculus
34% identity, 53% coverage
- function: Implicated in nucleolar organization, ribosome biogenesis, protein synthesis and cytoplasmic dsRNA sensing (By similarity) (PubMed:21930779). Stimulates RNA polymerase I transcription of the 47S precursor rRNA. Associates with ribosomal DNA (rDNA) loci where it is involved in POLR1A recruitment (PubMed:21930779). In the cytoplasm, promotes elongation-competent 80S ribosome assembly at the late stage of mRNA translation initiation (PubMed:26100019). Senses cytosolic dsRNA mediating NLRP3 inflammasome formation in macrophages and type I interferon production in myeloid dendritic cells (By similarity). Required for NLRP3 activation induced by viral dsRNA and bacterial RNA (By similarity). In dendritic cells, required for induction of type I interferon production induced by cytoplasmic dsRNA via the activation of MAPK and NF-kappa-B signaling pathways (PubMed:24037184).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with UBTF (PubMed:21930779). Interacts with DDX3X, EIF3G and EIF3H; the interaction is independent of RNA (PubMed:26100019). Interacts (via HA2 region and Helicase C-terminal domain) with the components of the large ribosomal subunit RPL3, RPL7, RPL26 and RPL27 (PubMed:26100019). Binds to mRNA (PubMed:26100019). Interacts (via the helicase C-terminal domain) with MAVS (PubMed:24037184). Binds to double-stranded RNA (via the helicase C- terminal domain) (PubMed:24037184). - Dhx33 promotes B-cell growth and proliferation by controlling activation-induced rRNA upregulation.
He, Cellular & molecular immunology 2023 - GeneRIF: Dhx33 promotes B-cell growth and proliferation by controlling activation-induced rRNA upregulation.
- Function of DHX33 in promoting Warburg effect via regulation of glycolytic genes.
Peng, Journal of cellular physiology 2021 (PubMed)- GeneRIF: Function of DHX33 in promoting Warburg effect via regulation of glycolytic genes.
- Targeting RNA helicase DHX33 blocks Ras-driven lung tumorigenesis in vivo.
Wang, Cancer science 2020 - GeneRIF: Targeting RNA helicase DHX33 blocks Ras-driven lung tumorigenesis in vivo.
- Recombinant DHX33 Protein Possesses Dual DNA/RNA Helicase Activity.
Wang, Biochemistry 2019 (PubMed)- GeneRIF: DHX33 hydrolyzes ATP in the presence of DNA/RNA duplexes.DHX33 protein possesses unwinding activity toward DNA and RNA duplexes.
- Loss of the deubiquitinase USP36 destabilizes the RNA helicase DHX33 and causes preimplantation lethality in mice.
Fraile, The Journal of biological chemistry 2018 - GeneRIF: Usp36 is essential for cell and organism viability because of its role in ribosomal RNA processing and protein synthesis, which is mediated, at least in part, by regulating DHX33 stability.
- Alternative translation initiation from two in-frame start codons in DHX33 gene.
Wang, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: DHX33 doublet is due to alternative translation initiation by two in-frame initiation codons. DHX33 translation initiation from either AUG codon happens at equal efficiency. Short DHX33 protein has similar cellular location and functions with full-length DHX33. Leaky scanning normally occurs in DHX33 mRNA translation, which may serve as a safeguard mechanism to ensure optimal DHX33 translation efficiency.
- P19ARF and RasV¹² offer opposing regulation of DHX33 translation to dictate tumor cell fate.
Zhang, Molecular and cellular biology 2013 - GeneRIF: results directly implicate DHX33 as a crucial player in establishing rRNA synthesis rates in the face of Ras(V12) or ARF signals, adjusting ribosome biogenesis to match the appropriate growth or antigrowth signals
AFUA_1G03820 mRNA splicing factor RNA helicase (Prp16), putative from Aspergillus fumigatus Af293
34% identity, 49% coverage
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...AFUA_5G04040 0.47610876 YIL129C AFUA_6G11010 0.473123981 YDR300C AFUA_2G07570 0.469287567 YOL156W AFUA_7G00950 0.46726022 YGL201C AFUA_5G10890 0.462753539 YKR086W AFUA_1G03820 0.461061937 YPL157W AFUA_6G08610 0.460257721 YIL046W AFUA_2G14110 0.45798838 YGL048C AFUA_4G04660 0.457664607 YHR216W AFUA_2G03610 0.456902272 YDR424C AFUA_1G04850 0.455530713 YPR141C AFUA_2G14280 0.452133975 YLR427W AFUA_1G07150 0.444534443 YHL004W AFUA_1G06570 0.439699159 YLL002W AFUA_5G09540 0.431520497 YKR052C AFUA_6G12550...”
DHX35_HUMAN / Q9H5Z1 Probable ATP-dependent RNA helicase DHX35; DEAH box protein 35; EC 3.6.4.13 from Homo sapiens (Human) (see paper)
NP_068750 probable ATP-dependent RNA helicase DHX35 isoform 1 from Homo sapiens
33% identity, 54% coverage
- function: May be involved in pre-mRNA splicing
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in the spliceosome C complex. - The RNA helicase DHX35 functions as a co-sensor for RIG-I-mediated innate immunity.
Qiao, PLoS pathogens 2024 - GeneRIF: The RNA helicase DHX35 functions as a co-sensor for RIG-I-mediated innate immunity.
- DRH1 - a novel blood-based HPV tumour marker.
Weiland, EBioMedicine 2020 - GeneRIF: DRH1 - a novel blood-based HPV tumour marker.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_001348 NP_476641 NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287 DDB0233454 SKI2W SKIV2L NP_008860 NP_524465 NP_190280...”
- Identification of a novel human DDX40gene, a new member of the DEAH-box protein family.
Xu, Journal of human genetics 2002 (PubMed)- GeneRIF: human DDX40gene, a new member of the DEAH-box protein family shares 53% and 43% amino acid identity with human DDX8 and yeast Drh1.DDX40 may play roles in pre-mRNA splicing, ribosome biogenesis and other RNA processing functions
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Rose, Molecular medicine (Cambridge, Mass.) - GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - [Quantitative analysis of differential proteins in liver tissues of patients with non-alcoholic steatohepatitis using iTRAQ technology]
Zhu, Nan fang yi ke da xue xue bao = Journal of Southern Medical University 2021 (secret) - Growth inhibition by bacterial Cas2Em proteins expressed in mammalian cells
Yu, American journal of translational research 2020 (secret) - Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...Q14147 RNA helicase DHX34 DEAH-box protein 34 DHX34 34 Q9H5Z1 RNA helicase DHX35 DEAH-box protein 35 DHX35 35 Q9H2U1 RNA helicase DHX36 DEAH-box protein 36...”
Afu1g09240 ATP dependent RNA helicase, putative from Aspergillus fumigatus Af293
36% identity, 50% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...2.60 [2.01, 0.54] Afu3g12790 0.80 [1.21, 2.35] Afu4g11390 1.75 [2.26, 1.85] Afu2g07710 0.80 [1.21, 2.39] Afu1g09240 2.76 [2.08, 0.45] Afu4g01400 0.78 [1.20, 2.34] Afu3g02420 2.03 [1.84, 0.63] Afu2g12790 0.75 [1.20, 2.34] Afu6g09880 3.65 [1.70, 1.01] Afu1g09930 0.71 [1.79, 3.13] Afu6g10260 1.96 [2.20, 1.41] Afu5g01550 0.69 [0.56,...”
cgd8_4100 PRP43 involved in spliceosome disassembly mRNA splicing from Cryptosporidium parvum Iowa II
33% identity, 52% coverage
GRMZM2G300375 ATP-dependent RNA helicase DHX8 from Zea mays
34% identity, 54% coverage
DHX30_MOUSE / Q99PU8 ATP-dependent RNA helicase DHX30; DEAH box protein 30; EC 3.6.4.13 from Mus musculus (Mouse) (see paper)
36% identity, 35% coverage
- function: RNA-dependent helicase (PubMed:25219788). Plays an important role in the assembly of the mitochondrial large ribosomal subunit (By similarity). Required for optimal function of the zinc-finger antiviral protein ZC3HAV1 (By similarity). Associates with mitochondrial DNA (By similarity). Involved in nervous system development and differentiation through its involvement in the up-regulation of a number of genes which are required for neurogenesis, including GSC, NCAM1, neurogenin, and NEUROD (PubMed:25219788).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in a complex with TFAM and SSBP1. Interacts (via N- terminus) with ZC3HAV1 (via N-terminal domain) in an RNA-independent manner. Found in a complex with GRSF1, DDX28, FASTKD2 and FASTKD5. - Purification and proteomics of pathogen-modified vacuoles and membranes.
Herweg, Frontiers in cellular and infection microbiology 2015 - “...P51659 P51660 Q9NKW1 + + + + 7 DHX30 Putative ATP-dependent RNA helicase DHX30 Q7L2E3 Q99PU8 + + 8 EF1B Elongation factor 1-beta P24534 O70251 Q9GRF8 + + + 9 EF1G Elongation factor 1-gamma P26641 Q9D8N0 + + + 10 EF2 Elongation factor 2 P13639 P58252...”
- The adipogenic transcriptional cofactor ZNF638 interacts with splicing regulators and influences alternative splicing.
Du, Journal of lipid research 2014
DHX33_HUMAN / Q9H6R0 ATP-dependent RNA helicase DHX33; DEAH box protein 33; EC 3.6.4.13 from Homo sapiens (Human) (see 3 papers)
NP_064547 ATP-dependent RNA helicase DHX33 isoform 1 from Homo sapiens
33% identity, 53% coverage
- function: Implicated in nucleolar organization, ribosome biogenesis, protein synthesis and cytoplasmic dsRNA sensing (By similarity) (PubMed:21930779, PubMed:23871209, PubMed:26100019). Stimulates RNA polymerase I transcription of the 47S precursor rRNA. Associates with ribosomal DNA (rDNA) loci where it is involved in POLR1A recruitment (PubMed:21930779). In the cytoplasm, promotes elongation-competent 80S ribosome assembly at the late stage of mRNA translation initiation (PubMed:26100019). Senses cytosolic dsRNA mediating NLRP3 inflammasome formation in macrophages and type I interferon production in myeloid dendritic cells (PubMed:23871209). Required for NLRP3 activation induced by viral dsRNA and bacterial RNA (PubMed:23871209). In dendritic cells, required for induction of type I interferon production induced by cytoplasmic dsRNA via the activation of MAPK and NF-kappa-B signaling pathways (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with UBTF (PubMed:21930779). Interacts with DDX3X, EIF3G and EIF3H; the interaction is independent of RNA (PubMed:26100019). Interacts (via HA2 region and Helicase C-terminal domain) with the components of the large ribosomal subunit RPL3, RPL7, RPL26 and RPL27 (PubMed:26100019). Interacts (via DEAH box) with NLRP3 (via NACHT domain) (PubMed:23871209). Binds to mRNA (PubMed:26100019). Binds to double-stranded RNA (via the helicase C-terminal domain) (PubMed:23871209). Interacts (via the helicase C-terminal domain) with MAVS (By similarity). - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077 NP_010929 DDB0233432 SF3b125 DDX42 NP_031398 NP_648413 NP_566099 NP_014287 DDB0233454 SKI2W SKIV2L NP_008860 NP_524465 NP_190280 NP_012485 Cyclophilins DDB0191208 CyPL1 PPIL1 NP_057143 NP_523874 NP_190046 NP_013633 DDB0233543 CyP60 PPIL2 NP_055152 NP_611113...”
- DHX33 Interacts with AP-2β To Regulate Bcl-2 Gene Expression and Promote Cancer Cell Survival
Wang, Molecular and cellular biology 2019 (secret) - miR-193a-3p interaction with HMGB1 downregulates human endothelial cell proliferation and migration.
Khoo, Scientific reports 2017 - “...41.81 P62304 SNRPE 1 5.34E-06 6.75 6191.37 917.68 P28289 TMOD1 1 0.000119239 5.64 36804.73 6522.19 Q9H6R0 DHX33 1 8.58E-05 5.55 2326.65 419.27 Q9UHY1 NRBP1 1 8.81E-06 5.35 726.59 135.78 Q8IVL6 LEPREL2 2 6.52E-10 5.23 1394.90 266.83 Q8WUM0 NUP133 1 0.003479238 5.20 779.99 149.88 Q9NQW7 XPNPEP1 2...”
- Heme-binding-mediated negative regulation of the tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) by IDO2.
Lee, Experimental & molecular medicine 2014 - “...protein sel-1 homolog 1 1.594 Q9UPN9 TRIM33 Isoform alpha of E3 ubiquitin-protein ligase TRIM33 1.589 Q9H6R0 DHX33 Highly similar to putative ATP-dependent RNA helicase DHX33 1.583 O95453 PARN Poly(A)-specific ribonuclease PARN 1.572 P11021 GRP78 78kDa glucose-regulated protein 1.571 Q9NXE4 SMPD4 Isoform 4 of sphingomyelin phosphodiesterase 4...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...helicase-like protein 1 (DHLP1) DEAD/H box 32 HuDDX32 32 Q9H6R0 RNA helicase DHX33 DEAH-box protein 33 DHX33 33 Q14147 RNA helicase DHX34 DEAH-box protein 34...”
NP_001239611 ATP-dependent RNA helicase DHX30 isoform 1 from Mus musculus
36% identity, 36% coverage
WP_017099829 helicase-related protein from Vibrio sp. FF59
37% identity, 54% coverage
DHX30_RAT / Q5BJS0 ATP-dependent RNA helicase DHX30; DEAH box protein 30; EC 3.6.4.13 from Rattus norvegicus (Rat) (see paper)
36% identity, 36% coverage
- function: RNA-dependent helicase (By similarity). Plays an important role in the assembly of the mitochondrial large ribosomal subunit (By similarity). Associates with mitochondrial DNA (By similarity). Required for optimal function of the zinc-finger antiviral protein ZC3HAV1 (PubMed:21204022). Involved in nervous system development and differentiation through its involvement in the up-regulation of a number of genes which are required for neurogenesis, including GSC, NCAM1, neurogenin, and NEUROD (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in a complex with TFAM and SSBP1 (By similarity). Interacts (via N-terminus) with ZC3HAV1 (via N-terminal domain) in an RNA-independent manner. Found in a complex with GRSF1, DDX28, FASTKD2 and FASTKD5 (By similarity).
G0RY84 RNA helicase (EC 3.6.4.13) from Chaetomium thermophilum (see paper)
36% identity, 50% coverage
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43
Tauchert, eLife 2017 - “...MLE from D. melanogaster to all yeast DExH-box RNA helicases. The amino-acid sequence of ctPrp43 (G0RY84) was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639),...”
5d0uA / G0RY84 Crystal structure of the RNA-helicase prp43 from chaetomium thermophilum bound to adp (see paper)
36% identity, 50% coverage
- Ligand: adenosine-5'-diphosphate (5d0uA)
LOC101860724 putative pre-mRNA-splicing factor ATP-dependent RNA helicase PRP1 from Aplysia californica
34% identity, 52% coverage
- In search of the Aplysia immunome: an in silico study
Kron, BMC genomics 2022 - “...role in the immune response of vertebrates, including DDX1 (LOC101857175), DDX41(LOC101864496), DHX9 (LOC101848799), and DHX15 (LOC101860724). Furthermore, the Aplysia genome contains 12 DEAD-box OB fold, also called domain of unknown function 1605, containing DExD/H-box helicases. This group contains other known vertebrate immune-associated genes including DHX29/30/33/36 and...”
NP_055781 ATP-dependent RNA helicase DHX30 isoform 2 from Homo sapiens
36% identity, 37% coverage
- DHX30-Associated Neurodevelopmental Disorder with Severe Motor Impairment and Absent Language: First Korean Case in Two Siblings and Literature Review.
Park, Annals of clinical and laboratory science 2023 (PubMed)- GeneRIF: DHX30-Associated Neurodevelopmental Disorder with Severe Motor Impairment and Absent Language: First Korean Case in Two Siblings and Literature Review.
- Conformational change of RNA-helicase DHX30 by ALS/FTD-linked FUS induces mitochondrial dysfunction and cytosolic aggregates.
Hikiami, Scientific reports 2022 - GeneRIF: Conformational change of RNA-helicase DHX30 by ALS/FTD-linked FUS induces mitochondrial dysfunction and cytosolic aggregates.
- Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders.
Mannucci, Genome medicine 2021 - GeneRIF: Genotype-phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders.
- De novo pathogenic DHX30 variants in two cases.
Miyake, Clinical genetics 2021 (PubMed)- GeneRIF: De novo pathogenic DHX30 variants in two cases.
- A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus.
Chen, Nucleic acids research 2020 - GeneRIF: A double-stranded RNA is required for the interaction between a host restriction factor DHX30 and the NS1 protein of influenza A virus.
- Nutlin-Induced Apoptosis Is Specified by a Translation Program Regulated by PCBP2 and DHX30.
Rizzotto, Cell reports 2020 - GeneRIF: Nutlin-Induced Apoptosis Is Specified by a Translation Program Regulated by PCBP2 and DHX30.
- De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder.
Lessel, American journal of human genetics 2017 - GeneRIF: Provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.
- The packaging of human immunodeficiency virus type 1 RNA is restricted by overexpression of an RNA helicase DHX30.
Zhou, Virology 2008 (PubMed)- GeneRIF: Here, we provide evidence that overexpression of an RNA helicase named DHX30 enhances HIV-1 gene expression, but leads to the generation of viruses that package significantly low levels of viral RNA and exhibit severely decreased infectivity.
- More
DHX30_HUMAN / Q7L2E3 ATP-dependent RNA helicase DHX30; DEAH box protein 30; EC 3.6.4.13 from Homo sapiens (Human) (see 6 papers)
36% identity, 36% coverage
- function: RNA-dependent helicase (PubMed:29100085). Plays an important role in the assembly of the mitochondrial large ribosomal subunit (PubMed:25683715, PubMed:29100085). Required for optimal function of the zinc-finger antiviral protein ZC3HAV1 (By similarity). Associates with mitochondrial DNA (PubMed:18063578). Involved in nervous system development and differentiation through its involvement in the up- regulation of a number of genes which are required for neurogenesis, including GSC, NCAM1, neurogenin, and NEUROD (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Identified in a complex with TFAM and SSBP1. Interacts with AGO1 and AGO2. Interacts (via N-terminus) with ZC3HAV1 (via N-terminal domain) in an RNA-independent manner (By similarity). Found in a complex with GRSF1, DDX28, FASTKD2 and FASTKD5 (PubMed:25683715). - The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Mitochondria-derived vesicles and their potential roles in kidney stone disease.
Chaiyarit, Journal of translational medicine 2023 - “...B) (PFK-B) (Phosphohexokinase) 43 CLPX O76031 ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial 44 DHX30 Q7L2E3 ATP-dependent RNA helicase DHX30 (EC 3.6.4.13) (DEAH box protein 30) 45 YME1L1 Q96TA2 ATP-dependent zinc metalloprotease YME1L1 (EC 3.4.24.-) (ATP-dependent metalloprotease FtsH1) (Meg-4) (Presenilin-associated metalloprotease) (PAMP) (YME1-like protein 1) 46...”
- Synergistic Interactions of Cannabidiol with Chemotherapeutic Drugs in MCF7 Cells: Mode of Interaction and Proteomics Analysis of Mechanisms.
Alsherbiny, International journal of molecular sciences 2021 - “...mitochondrial 1.36 Q8N565 MREG Melanoregulin 1.33 Q14802 FXYD3 FXYD domain-containing ion transport regulator 3 1.33 Q7L2E3 DHX30 ATP-dependent RNA helicase DHX30 1.32 Q12767 TMEM94 Transmembrane protein 94 1.31 Q8N0X2 SPAG16 Sperm-associated antigen 16 protein 1.30 P14854 COX6B1 Cytochrome c oxidase subunit 6B1 1.30 Q92820 GGH Gamma-glutamyl...”
- Cigarette smoke extract stimulates bronchial epithelial cells to undergo a SUMOylation turnover.
Zhou, BMC pulmonary medicine 2020 - “...Splicing factor, proline- and glutamine-rich 2.843 Up SFPQ P04183 Thymidine kinase, cytosolic 2.84 Up TK1 Q7L2E3 Putative ATP-dependent RNA helicase DHX30 2.773 Up DHX30 P31689 DnaJ homolog subfamily A member 1 2.667 Up DNAJA1 P11142 Heat shock cognate 71kDa protein 2.584 Up HSPA8 Q6NZI2 Polymerase I...”
- Global Interactomics Connect Nuclear Mitotic Apparatus Protein NUMA1 to Influenza Virus Maturation.
Rahim, Viruses 2018 - “...Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 5 - 28 22 8.66 - 46.27 40.65 Q7L2E3 DHX30# Putative ATP-dependent RNA helicase DHX30 2 9 53 59 3.05 17.57 87.85 100.67 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 3 3 5 3 4.52 6.14 10.8 6.18 Q5QJE6...”
- Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Retinal and Choroidal Vascular Endothelial Cells: Potential Targets for New Biologic Drugs.
Smith, American journal of ophthalmology 2018 - “...Mediator of DNA damage checkpoint protein 1 Q14676 2.59 1.9333E-02 Putative ATP-dependent RNA helicase DHX30 Q7L2E3 2.56 1.1716E-02 Sister chromatid cohesion protein PDS5 homolog B Q9NTI5 2.53 1.7867E-02 AspartatetRNA ligase, mitochondrial Q6PI48 2.47 3.8611E-02 SH2 domain-containing protein 3C Q8N5H7 2.45 1.7371E-02 Histone H2AX (H2a/x) P16104 2.31...”
- β-Catenin Knockdown Affects Mitochondrial Biogenesis and Lipid Metabolism in Breast Cancer Cells
Vergara, Frontiers in physiology 2017 - “...protein SCaMC-1 Q6NUK1 21 59.7 CDC73 Parafibromin Q6P1J9 7 14.3 DHX30 Putative ATP-dependent RNA helicase Q7L2E3 21 22.8 RBM45 RNA-binding protein 45 Q8IUH3 3 8 LPCAT1 Lysophosphatidylcholine acyltransferase 1 Q8NF37 15 31.5 BRIX1 Ribosome biogenesis protein BRX1 homolog Q8TDN6 13 48.7 DDX17 Probable ATP-dependent RNA helicase...”
- Immunoprecipitation and mass spectrometry defines an extensive RBM45 protein-protein interaction network
Li, Brain research 2016 - “...+ 1 1 P35637 FUS RNA-binding protein FUS 12 + + + + 1 1 Q7L2E3 DHX30 Putative ATP-dependent RNA helicase DHX30 12 + + + + 1 1 Q6PKG0 LARP1 La-related protein 1 11 + + + + 1 1 Q9Y6M1 IGF2BP 2 Insulin-like growth...”
- More
H7BXY3 ATP-dependent RNA helicase DHX30 from Homo sapiens
36% identity, 36% coverage
Smp_147330 putative atp-dependent RNA helicase from Schistosoma mansoni
32% identity, 36% coverage
- Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites
Kincaid-Smith, Genome biology and evolution 2018 - “...3 XLOC_009689 (1017639510178030) 1 10177131 Biased Endonuclease-reverse transcriptase Smp_169030 1 17479792 Biased Probable asparaginetRNA mitochondrial Smp_147330 1 19943769 Biased Probable ATP-dependent RNA helicase dhx34 Chr_2.SC_0193 1 Smp_171530 1 63337 Biased Beta Parvin related Chr_3.SC_0083 1 Smp_168560 1 661857 Biased Steroid dehydrogenase Chr_4 3 Smp_149950 1 3351765...”
- “...paternally expressed SNPs were identified. Among those, we pinpointed the putative ATP-dependent RNA helicase dhx34 (Smp_147330) protein-coding gene, which is part of the DEAD box proteins family, conserved in metazoan they are known for their implication in embryogenesis, spermatogenesis, cellular growth, and division ( Godbout and...”
NGO1196 putative ATP-dependent DNA helicase related protein from Neisseria gonorrhoeae FA 1090
35% identity, 48% coverage
CG3225 uncharacterized protein from Drosophila melanogaster
34% identity, 54% coverage
- Quantitative MNase-seq accurately maps nucleosome occupancy levels
Chereji, Genome biology 2019 - “...track in Fig. 3 shows the identified nucleosomes in the corresponding region near the gene CG3225 . After we identified the well-positioned nucleosomes and normalized the nucleosome counts using the spike-in levels from each sample, we were able to study the evolution of the number of...”
- Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster
Hernández, Molecular and cellular biology 2013 - “...(CG9677), pMT-eIF3f (CG9769), pMT-eIF3h (CG9124), and pMT-CG3225 (CG3225) were created by subcloning the respective coding regions in frame with the V5...”
- “...protein that binds RNA, eIF4Es, eIF3, and CG3225. (A) Schematic representation of the domain structure and interactions of Mextli, Saccharomyces cerevisiae...”
- A small genomic region containing several loci required for gastrulation in Drosophila
Mathew, PloS one 2009 - “...? + ? + + + + CG15629 ? + ? + + + + CG3225 PCR +++ +++ +++ +++ + + + 5-HA-1531 + + ? + + + + CG15628 + + ? + + + + + CG2976 + + ? +...”
- “...Representative single embryo PCR with primers for dumpy (dp), N-Cadherin (NCad) CG15631, CG11929, CG15436 and CG3225 on embryos from the Df(2L)dp-h28 (A) and Df(2L)dp-h24 stocks (B). NCad is the positive control, dp, CG11929, CG15631 and CG3225 the candidate genes tested. In embryos 4, 9 and 10...”
- Conservation of the protein composition and electron microscopy structure of Drosophila melanogaster and human spliceosomal complexes
Herold, Molecular and cellular biology 2009 - “...gi17977678 gi21355805 gi24652559 CG8241 CG1866 CG8833 CG1676 CG3225 CG14637 CG6015 CG12343 pea Moca-cyp GPTC1 cactin EJC/mRNP eIF4AIII Y14 gi24645031 gi24651979...”
- A genetic screen for suppressors of Drosophila NSF2 neuromuscular junction overgrowth
Laviolette, Genetics 2005 - “...respectively. PCR primers locations are indicated by yellow squares for CG3225 ; by yellow diamonds for polo ; by blue diamonds for snap ; by a yellow triangle...”
AT4G18465 RNA helicase, putative from Arabidopsis thaliana
33% identity, 52% coverage
- Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants
Omondi, Ecology and evolution 2024 - “...root hair elongation 2,3 Chr8_85565240 MTWeQ CYP80G2 Secondary metabolite biosynthetic process 4 Chr9_1078596 Silt, cec At4g18465 May be involved in premRNA splicing 5 Chr9_18066040 Wind HCR90 Response to fungal pathogen 7 Chr9_19520528 Nitrogen, wind Unknown Protein of unknown function Chr9_46071667 Nitrogen TIC110 Involved in protein precursor...”
- Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization
Zermiani, Annals of botany 2015 - “...At4g02020 At4g14900 At1g03750 At1g18450 At1g20960 At4g18465 At1g32490 At1g79950 At2g13370 At2g16390 At1g32750 At1g52740 At3g06400 At3g17590 At2g45640 At3g17310...”
- Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa
Xu, PloS one 2013 - “...rosette, young rosette, seedling and germinated seed. AT2G44980 , AT3G19760 , AT3G53110 ( LOS4 ), AT4G18465 , AT5G11200 and AT5G51280 were highly expressed in senescence stage. Our results showed that the most RNA helicase genes were expressed in more than 20 tissues in Arabidopsis with different...”
AFUA_5G11620 pre-mRNA splicing factor RNA helicase (Prp43), putative from Aspergillus fumigatus Af293
36% identity, 50% coverage
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...AFUA_1G05050 0.087018417 YDR497C AFUA_2G07910 0.078863767 YDR477W AFUA_2G01700 0.074801159 YLR378C AFUA_5G08130 0.074624328 YBR060C AFUA_5G08110 0.073589072 YGL120C AFUA_5G11620 0.069009268 YIL063C AFUA_2G10810 0.06328373 YOL157C AFUA_7G06380 0.06047767 YGL043W AFUA_3G07670 0.059398891 YMR027W AFUA_5G06710 0.058232831 YHR215W AFUA_8G01910 0.05787337 YDL247W AFUA_7G05190 0.05184022 YPR048W AFUA_5G07290 0.049809159 YBL051C AFUA_5G01940 0.048514144 YHR148W AFUA_2G08320 0.047441878 YJR160C AFUA_7G05190...”
VC83_08625 DEAH-box ATP-dependent RNA helicase prp43 from Pseudogymnoascus destructans
35% identity, 50% coverage
7b9vQ C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound (see paper)
34% identity, 51% coverage
VV1465 HrpA-like helicase from Vibrio vulnificus YJ016
33% identity, 66% coverage
C4LWD6 RNA helicase from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_096230 helicase, putative from Entamoeba histolytica HM-1:IMSS
33% identity, 53% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373 Brr2 PILC B-B act ; C-Post splicing EhDExH10/U5 snRNP-specific 200kd EHI_045170...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...EHI_192500 C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373 Brr2 PILC B-B act ; C-Post splicing EhDExH10/U5 snRNP-specific 200kd...”
Q6PE54 Probable ATP-dependent RNA helicase DHX40 from Mus musculus
31% identity, 54% coverage
C4M435 DEAD/DEAH box helicase, putative from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_033720 DEAD/DEAH box helicase, putative from Entamoeba histolytica HM-1:IMSS
31% identity, 54% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...MGC13125 PILC EF-hand calcium-binding EHI_150550 C4M234 Complex B act Prp2 B act -B* EhDExH4 EHI_033720 C4M435 Complex C Abstrakt EhDEAD1 EHI_175030 C4LZM8 Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U snRNAs...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...complex MGC13125 PILC EF-hand calcium-binding EHI_150550 C4M234 Complex B act Prp2 B act -B* EhDExH4 EHI_033720 C4M435 Complex C Abstrakt EhDEAD1 EHI_175030 C4LZM8 Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U...”
TP0526 ATP-dependent helicase (hrpA) from Treponema pallidum subsp. pallidum str. Nichols
33% identity, 51% coverage
- The binary protein interactome of Treponema pallidum--the syphilis spirochete
Titz, PloS one 2008 - “...in translational and cell division PI (tRNA-synthetases, DNA primase); GBAA (translation); GT (rod-shape determining proteins) TP0526 (b) transcription termination/antitermination PI (nusA) TP0561 (c) Membrane protein chaperone PI (with membrane proteins), DOM (SsgA, sporulation, cell division) TP0580 (e) ABC transporter, polysaccharide (antigen) synthesis (dTMP sugar) PI (uridylate...”
5vheA / Q05B79 Dhx36 in complex with thE C-myc g-quadruplex (see paper)
31% identity, 52% coverage
DHX40_HUMAN / Q8IX18 Probable ATP-dependent RNA helicase DHX40; DEAH box protein 40; Protein PAD; EC 3.6.4.13 from Homo sapiens (Human) (see paper)
31% identity, 54% coverage
PRP16_YEAST / P15938 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
NP_013012, YKR086W Prp16p from Saccharomyces cerevisiae
NP_013012 DEAH-box RNA helicase PRP16 from Saccharomyces cerevisiae S288C
33% identity, 40% coverage
- function: Influences the fidelity of branchpoint recognition in yeast splicing. This is RNA-dependent ATPase which is essential for viability. It may mediate one of the many ATP-requiring steps of spliceosome assembly and that accuracy of branchpoint recognition may be coupled to ATP binding and/or hydrolysis.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand
Blount, 2022 - Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...0.18 0.27 0.34 0.38 190-200 hPRP22 230-250 297-316 319-330 368-385 370-407 388-405 446-455 1115-1132 Prp16 YKR086W P15938 121.6 1.071 0.19 0.28 0.29 0.32 2-19 hPRP16 55-52 59-68 89-99 119-137 166-183 178-185 197-203 284-290 353-360 1064-1071 Prp17 YDR364C P40968 52.1 455 0.23 0.23 0.57 0.28 1-9 hPRP17...”
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...0.954392373 0.96688713 533106 chr11 YKR082W 0.962931616 0.991018501 592467 + chr11 YKR084C 0.953228662 0.976903834 598532 chr11 YKR086W 0.952006608 0.976533657 599499 + chr12 YLL050C 0.976179673 0.990695339 40413 chr12 YLL002W 0.972688874 0.981122544 146290 + chr12 YLR001C 0.966206724 0.98012374 153976 chr12 YLR012C 0.956516633 0.962463803 170280 chr12 YLR013W 0.978873849 0.985557204 171338...”
- “...YLR104W AFUA_5G04040 0.47610876 YIL129C AFUA_6G11010 0.473123981 YDR300C AFUA_2G07570 0.469287567 YOL156W AFUA_7G00950 0.46726022 YGL201C AFUA_5G10890 0.462753539 YKR086W AFUA_1G03820 0.461061937 YPL157W AFUA_6G08610 0.460257721 YIL046W AFUA_2G14110 0.45798838 YGL048C AFUA_4G04660 0.457664607 YHR216W AFUA_2G03610 0.456902272 YDR424C AFUA_1G04850 0.455530713 YPR141C AFUA_2G14280 0.452133975 YLR427W AFUA_1G07150 0.444534443 YHL004W AFUA_1G06570 0.439699159 YLL002W AFUA_5G09540 0.431520497 YKR052C...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_189288 NP_010929 DDB0233403 Prp43 DHX15 NP_001349 NP_610269 NP_191790 NP_011395 DDB0191460 Prp16 DHX38 NP_054722 NP_572947 NP_196805 NP_013012 DDB0233423 MCG9280 SLU7 NP_006416 NP_651659 NP_564859 NP_010373 DDB0233421 Prp17 CDC40 NP_056975 NP_651005 NP_172528 NP_010652 DDB0233422 Prp18 PRPF18 NP_003666 NP_650776 NP_563676 NP_011520 3D. Exon junction complex proteins DDB0233615-o SRm160 e SRRM1...”
- Pre-messenger RNA processing factors in the Drosophila genome
Mount, The Journal of cell biology 2000 - “...0 Prp22, NP_010929, E = 0 CG1405 AAF48355 Prp16-like 12D1 NP_054722, E = 0 Prp16, NP_013012, E-160 CG6015 AAF55949 Prp17-like 93F14 AAC39730, E = 0 Prp17, NP_010652, 1E-76 CG1420 AAF56845 Slu7-like 98F13 NP_006416, E-128 Slu7, NP_010373, 1E-12 Prp18 (CG6011) AAF55627 Prp18-like 91E4 NP_003666, 4E-93 Prp18, NP_011520,...”
- Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae
Ben-Yehuda, Genetics 2000 - “...name Gene function PRP8 YHR165c PRP16 SLU7 PRP22 YKR086w YDR088c YER013w SLT11 YBR065c Splicing factor involved in first and second steps Second step-splicing...”
- An ATP-independent role for Prp16 in promoting aberrant splicing.
Chung, Nucleic acids research 2023 - GeneRIF: An ATP-independent role for Prp16 in promoting aberrant splicing.
- A central role of Cwc25 in spliceosome dynamics during the catalytic phase of pre-mRNA splicing.
Tseng, RNA (New York, N.Y.) 2017 - GeneRIF: In the process of pre-mRNA splicing, Cwc25 binds tightly to the spliceosome after the reaction and is then removed from the spliceosome, which normally requires Prp16 and ATP hydrolysis, to allow the occurrence of the second reaction.
- Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites.
Semlow, Cell 2016 - GeneRIF: At the catalytic stage of splicing, suboptimal splice sites are repressed by the DEAH-box ATPases Prp16 and Prp22. study shows that these ATPases function further by enabling the spliceosome to search for and utilize alternative branch sites and 3' splice sites.
- Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2.
Hogg, Nucleic acids research 2014 - GeneRIF: Results indicate that the prp16-302 mutation in Prp16 stabilizes Cwc2 interactions with U6 snRNA and destabilizes Cwc2 interactions with pre-mRNA, indicating antagonistic functions of Cwc2 and Prp16.
- Link of NTR-mediated spliceosome disassembly with DEAH-box ATPases Prp2, Prp16, and Prp22.
Chen, Molecular and cellular biology 2013 - GeneRIF: NTR complex catalyzes the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome.
- A weak spliceosome-binding domain of Yju2 functions in the first step and bypasses Prp16 in the second step of splicing.
Chiang, Molecular and cellular biology 2013 - GeneRIF: In the absence of the C domain, Yju2-N domain is not stably associated with the spliceosome after lariat formation, and thus bypasses the need for Prp16.
- The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing.
Koodathingal, Molecular cell 2010 - GeneRIF: The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing.
- The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing.
Villa, Genes & development 2005 - GeneRIF: Prp16 remodels an interaction involving Isy1 in the transition between two steps of splicing
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...helicases. The amino-acid sequence of ctPrp43 (G0RY84) was aligned to scPrp43 (P53131), scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values in parentheses...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...0.27 0.34 0.38 190-200 hPRP22 230-250 297-316 319-330 368-385 370-407 388-405 446-455 1115-1132 Prp16 YKR086W P15938 121.6 1.071 0.19 0.28 0.29 0.32 2-19 hPRP16 55-52 59-68 89-99 119-137 166-183 178-185 197-203 284-290 353-360 1064-1071 Prp17 YDR364C P40968 52.1 455 0.23 0.23 0.57 0.28 1-9 hPRP17 17-34...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...57 DHX38 PRP16 (LOC_Os07g32430) DHX8 (Q38953) PRP16 (P15938) 58 DHX40 PRP16 (LOC_Os07g32430) DHX8 (Q38953) PRP22 (P24384) RNA helicase (PFI0860c) 59 DHX57...”
- Two novel conserved motifs in the hepatitis C virus NS3 protein critical for helicase action
Lam, The Journal of biological chemistry 2003 - “...not known; spliceosome component prp16 (NCBI accession P15938), nuclear DNA helicase II (NCBI accession O70133), the cockayne syndrome-linked protein ERCC-6...”
- The mammalian homologue of Prp16p is overexpressed in a cell line tolerant to Leflunomide, a new immunoregulatory drug effective against rheumatoid arthritis
Ortlepp, RNA (New York, N.Y.) 1998 - “...aligned with Prp16p from S. cerevisiae (accession no+ P15938) using the CLUSTAL algorithm+ Identical amino acids are boxed in black, whereas conserved residues...”
PRP22_ARATH / F4IE66 Pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH10; DEAH RNA helicase homolog PRP22; Protein ROOT INITIATION DEFECTIVE 1; EC 3.6.4.13 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_173961 RNA helicase family protein from Arabidopsis thaliana
AT1G26370 RNA helicase, putative from Arabidopsis thaliana
33% identity, 53% coverage
- function: Involved in pre-mRNA splicing. Plays a role during development in processes such as meristem maintenance, leaf morphogenesis and root morphogenesis.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Defects in female gametophyte development. - Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis.
Zhu, Journal of experimental botany 2016 - GeneRIF: interaction with GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development
- Arabidopsis root initiation defective1, a DEAH-box RNA helicase involved in pre-mRNA splicing, is essential for plant development.
Ohtani, The Plant cell 2013 - GeneRIF: Data indicate that RID1 was identified as At1g26370 encoding a DEAH-box RNA helicase implicated in pre-mRNA splicing.
- Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis
Zhu, Journal of experimental botany 2016 - “...OVERLY SENSITIVE 6 (ABO6; At5g04895), CLUMSY VEIN (CUV; At5g13010), and ROOT INITIATION DEFECTIVE 1 (RID1; At1g26370). EPS3 is a putative homolog of yeast PRP2, which is required for RNA processing and plays an important role in the regulation of embryo development, flowering, and temperature-sensitive seedling growth...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...Prp22 Prp22 atPrp22-1 At3g26560 3 11 DEAD, 1; Helicase_C, 1; S1, 1; HA2, 1; atPrp22-2 At1g26370 1 5 DEAD, 1; Helicase_C, 1; HA2, 1 atPrp22-3 At1g27900 1 15 DEAD, 1; Helicase_C, 1; HA2, 1 Prp17 Prp17p atPrp17-1 At1g10580 1 10 WD-40, 7; atPrp17-2 At5g54520 5 5...”
- Analysis of the myosins encoded in the recently completed Arabidopsis thaliana genome sequence
Reddy, Genome biology 2001 - “...protein database [ 58 ]. Two are not full-length myosins. One is a putative helicase (At1g26370) with no myosin motor domain and one is a possible pseudogene (At1g42680) with only 162 amino acids that have some similarity to the myosin motor domain. MIPS does not list...”
BIF_01186 ATP-dependent RNA helicase HrpA from Bifidobacterium animalis subsp. lactis BB-12
32% identity, 32% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...93268 TA Intergenic(+46/+3) BIF_01365 / BIF_02171 93270 +AT Intergenic(+48/+1) BIF_01365 / BIF_02171 103949 4bp22bp Intergenic(+18/+56) BIF_01186 / BIF_02012 103961 CA Intergenic(+30/+47) BIF_01186 / BIF_02012 103963 1bp Intergenic(+32/+45) BIF_01186 / BIF_02012 112686 +25bp Intergenic(226/+31) BIF_00107 / BIF_00801 132978 5bp19bp Intergenic(+14/185) BIF_01865 / BIF_02174 132990 +G Intergenic(+26/177) BIF_01865...”
XP_002110272 uncharacterized protein from Trichoplax adhaerens
32% identity, 46% coverage
8szqA / M3WPI7 Cat dhx9 bound to adp (see paper)
30% identity, 52% coverage
- Ligands: adenosine-5'-diphosphate; magnesium ion (8szqA)
6hyuC / Q14562 Crystal structure of dhx8 helicase bound to single stranded poly- adenine RNA (see paper)
33% identity, 53% coverage
FVEG_08023 hypothetical protein from Fusarium verticillioides 7600
34% identity, 32% coverage
8pjbA / P24785 Cryo-em structure of mle in complex with uuc RNA and adp (see paper)
32% identity, 46% coverage
- Ligands: rna; adenosine-5'-diphosphate (8pjbA)
L9KLP8 Complement component 1 Q subcomponent-binding protein, mitochondrial from Tupaia chinensis
35% identity, 32% coverage
DHX33_DROME / Q9VL25 ATP-dependent RNA helicase DHX33; DEAH box protein 33 homolog; Protein athos; EC 3.6.4.13 from Drosophila melanogaster (Fruit fly) (see paper)
29% identity, 63% coverage
- function: Part of a translational control module, also containing pths/DDX47 and ais/DDX52, which coordinates germline stem cell differentiation with ribosome biogenesis during oogenesis. This module allows for coregulation of ribosomal proteins and non1/GTPBP4, a p53 repressor, preventing p53 stabilization, cell cycle arrest and loss of stem cell differentiation.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Conditional RNAi-mediated knock-down in germline cells results in hypotrophy of the nucleolus.
NP_001260639 RHAU helicase, isoform B from Drosophila melanogaster
NP_610056 RHAU helicase, isoform A from Drosophila melanogaster
32% identity, 45% coverage
- RNAi-mediated knockdown of the Rhau helicase preferentially depletes proteins with a Guanine-quadruplex motif in the 5'-UTR of their mRNA.
Vester, Biochemical and biophysical research communications 2019 (PubMed)- GeneRIF: This indicates that in an unexpectedly small set of genes, in which G-quadruplex motifs are unusually common in the 5'-UTR of their mRNAs, Rhau helicase is responsible for the regulation of their expression.
- Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.
Chen, Structure (London, England : 1993) 2018 (PubMed)- GeneRIF: The crystal structures of DHX36 in complex with RNA and DNA, revealing that G-rich tracts are specifically recognized by the helicase. The negatively charged G-quadruplex is recognized and destabilized by a positively charged binding cage and then unfolded via ATP-dependent ssDNA translocation activity. On the basis of these results, a conceptual G4 DNA-resolving mechanism is proposed.
- RHAU helicase stabilizes G4 in its nucleotide-free state and destabilizes G4 upon ATP hydrolysis.
You, Nucleic acids research 2017 - GeneRIF: The study provides the first evidence that the unfolding kinetics of a G-quadruplex can be modulated by different nucleotide-bound states of the RHAU helicase (CG9323).
- Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU.
Lattmann, Nucleic acids research 2010 - GeneRIF: CG9323 is the true ortholog of the human RHAU/DHX36 DEAH-box RNA helicase. CG9323 possesses guanine quadruplex-RNA binding and resolving activities.
- Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU
Lattmann, Nucleic acids research 2010 - “...tropicalis , ENSXETP00000016958), zebrafish ( Danio rerio , NP_001122016), fruit fly ( Drosophila melanogaster , NP_610056), blood fluke ( Schistosoma mansoni , XP_002577014), placozoan ( Trichoplax adhaerens , XP_002110272), choanoflagellate ( Monosiga brevicollis , XP_001747335). ( B ) Gel mobility shift assay for G4-RNA binding: radio-labelled...”
- “...metabolism and merits future investigation of its potential roles in different biological contexts. ACCESSION NUMBER NP_610056. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. FUNDING Novartis Research Foundation. Funding for open access charge: Novartis Research Foundation. Conflict of interest statement . None declared. Supplementary Material...”
- Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain
Chalupníková, The Journal of biological chemistry 2008 - “...CAM56669), fruit fly (Drosophila melanogaster, NP_610056), trematoda (Schistosoma japonicum, AAW25528), and choanoflagellate (Monosiga brevicollis, EDQ87802)....”
5n9dB / Q8SWT2 Crystal structure of drosophila dhx36 helicase in complex with gggttagggt (see paper)
32% identity, 49% coverage
XP_021445207 ATP-dependent RNA helicase A isoform X1 from Oncorhynchus mykiss
29% identity, 33% coverage
YK16_SCHPO / Q9HDY4 Putative ATP-dependent RNA helicase PB1A10.06c; EC 3.6.4.13 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAPB1A10.06c ATP-dependent RNA helicase Dhr1 (predicted) from Schizosaccharomyces pombe
27% identity, 49% coverage
6zqgJD / Q04217 structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C (see paper)
32% identity, 51% coverage
ECU09_0150 pre-mRNA splicing factor from Encephalitozoon cuniculi GB-M1
29% identity, 73% coverage
NP_586183 PRE-mRNA SPLICING FACTOR from Encephalitozoon cuniculi GB-M1
31% identity, 53% coverage
- ESTs from the microsporidian Edhazardia aedis
Gill, BMC genomics 2008 - “...POLYADENYLATE-BINDING PROTEIN 2 Encephalitozoon cuniculi NP_586226 POLYPROTEIN Sorghum bicolor AAD27571 PRE-mRNA SPLICING FACTOR Encephalitozoon cuniculi NP_586183 PROTEIN KINASE B-LIKE PROTEIN Plasmodium falciparum AAT06260 PROTEIN TRANSPORT PROTEIN SEC23 HOMOLOG (COPII COAT) Encephalitozoon cuniculi NP_586385 PUTATIVE HYDROLASE-LIKE PROTEIN Antonospora locustae AAU11090 PUTATIVE ZINC FINGER PROTEIN Encephalitozoon cuniculi NP_597297...”
- “...rich pre-mRNA splicing factor ( NP_597487 in E. cuniculi ), a pre-mRNA splicing factor ( NP_586183 in E. cuniculi ) and a U5 associated snRNP ( NP_586393 in E. cuniculi ). These genes comprise 2.2% of the total unique genes found. Hsp70 Roughly 28% of total...”
C4M8N6 ATP-dependent helicase, putative from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_077640 ATP-dependent helicase, putative from Entamoeba histolytica HM-1:IMSS
32% identity, 47% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...Complex C Abstrakt EhDEAD1 EHI_175030 C4LZM8 Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U snRNAs and components of the post-catalytic/intron lariat spliceosome complexes (PILS in superscript) were described by Miranda et...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...C4M435 Complex C Abstrakt EhDEAD1 EHI_175030 C4LZM8 Step 2 factors Prp22 PILC Post splicing-ILS EhDExH3 EHI_077640 C4M8N6 Prp16 C-Post splicing EhDExH5 EHI_122790 C4M5M5 a AmoebaDB. E. histolytica splicing factors, U snRNAs and components of the post-catalytic/intron lariat spliceosome complexes (PILS in superscript) were described by Miranda...”
K7GND3 RNA helicase from Sus scrofa
29% identity, 32% coverage
- Proteomic Characterization of PAMs with PRRSV-ADE Infection.
Xu, Viruses 2022 - “...0.000015 J7FJH8 Interferon-induced protein with tetratricopeptide repeats 2 (IFIT2)/Interferon-stimulated gene 54 (ISG54) IFIT2/ISG54 0.551217726 0.004211 K7GND3 DExH-box protein 9 (DHX9) DHX9 1.509146168 0.003557 K7GS53 DExH-box protein 58 (DHX58) DHX58 0.428630681 0.000008 Q59HI8 Toll-like receptor 2 (TLR2) TLR2 1.24016114 0.027161 Q5S3G4 Cytochrome coxidase subunit 5B (COX-5B) COX-5B...”
- Protein profiling of testicular tissue from boars with different levels of hyperactive sperm motility.
van, Acta veterinaria Scandinavica 2022 - “...protein USP39 F2Z5T8 Uncharacterized protein MOBKL3 A0A287B5H5 Tubulin alpha chain TUBA8 F1SFI7 Alpha-2-HS-glycoprotein AHSG Perseus K7GND3 ATP-dependent RNA helicase A DHX9 A0A287BE52 LEDGF domain-containing protein PSIP1 F1S5S7 Inactive hydroxysteroid dehydrogenase-like protein 1 isoform X1 HSDL1 A0A287AIE8 Uncharacterized protein SUGP2 I3LDD5 Pribosyltran domain-containing protein PRTFDC1 Common proteins...”
AT2G35920 helicase domain-containing protein from Arabidopsis thaliana
32% identity, 44% coverage
- Proteomic analysis of haem-binding protein from Arabidopsis thaliana and Cyanidioschyzon merolae
Shimizu, Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2020 - “...peak 8 1946.958 2.516 338352 DL C KVLRE C NAEDLK AspGluAlaAsp (DEAD)-box ATP-dependent RNA helicase At2g35920 nucleus 111.0 23.9 peak 2 613.332 56.41 370374 DLLPR peak 3 718.295 57.469 128133 ADLDER peak 4 842.52 43.806 150156 KLGSLLK peak 8 1946.958 68.106 674691 ALQPPDALAVENAIELLK calcium-dependent protein kinase...”
- “...The second group is AspGluAlaAsp (DEAD)-box ATP-dependent RNA helicases (DBRHs): one protein from A. thaliana (At2g35920) and one protein from Cy. merolae (CML137C). The DBRH family participates in broad aspects of RNA metabolism, such as transcription, translation, RNA decay and miRNA processing. This is also involved...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...fig. S5 , Supplementary Material online). Unlike the homologs of RECQ4A (AT1G10930), RH5 ( AT1G31970), AT2G35920, and AT3G02060 that even showed lower selection pressure on allelic variants of sexual accessions as compared with apomicts, only for ESP3 and AT1G58060 higher rates of mutation accumulation were identified...”
- “...accessions for MEM (AT5G39840 ) , in addition to the INO80 ortholog AT3G57300, AT2G47250, and AT2G35920 ( fig.3 B ). For other genes, including DCL2 ( AT3G03300 ) , RH1 ( AT4G15850), and RH5 ( AT1G31970 ) , mutations leading to premature stop were identified in...”
- Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena
Aronica, Genes & development 2008 - “...and XP_001423262 in Paramecium, DHX57 and DHX36 in human, AT2G35920 in Arabidopsis, and GH07148p in the fruit fly. DHX36 was recently identified as an AGO1- and...”
7ajuJD / Q04217 structure of the 90S-exosome super-complex (state Post-A1-exosome) (see paper)
30% identity, 60% coverage
W5QCQ4 RNA helicase from Ovis aries
30% identity, 34% coverage
- Teladorsagia Circumcincta Galectin-Mucosal Interactome in Sheep
Hafidi, Veterinary sciences 2021 - “...receptor class B member 2 49.78 439 5 22.38 9 0 N Lysosome Binding function W5QCQ4 DHX9 DExH-box helicase 9 142.13 1289 9 22.36 7 29 N Nucleus Regulatory function W5Q436 SLC25A5 Mitochondrial carrier protein 29.33 263 3 22.34 1 0 N Mitochondria Regulatory function W5PPJ0...”
SPAC20H4.09 ATP-dependent RNA helicase, spliceosomal (predicted) from Schizosaccharomyces pombe
28% identity, 59% coverage
- Defining the Functional Interactome of Spliceosome-Associated G-Patch Protein Gpl1 in the Fission Yeast Schizosaccharomyces pombe
Selicky, International journal of molecular sciences 2022 - “...protein Gpl1 of the fission yeast S. pombe mediates interactions between putative RNA helicase Gih35 (SPAC20H4.09) and WD repeat protein Wdr83, and ensures their binding to the spliceosome. Furthermore, RT-qPCR analysis of the splicing efficiency of deletion mutants indicated that the absence of any of the...”
- Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast Schizosaccharomyces pombe
Cipakova, Cell cycle (Georgetown, Tex.) 2019 - “...factors including a possible functional interaction between G-patch domain-containing protein Gpl1 and putative RNA helicase SPAC20H4.09. Results and discussion In our previous study, we used tandem affinity purification (TAP) protocol followed by mass-spectrometry analysis to identify proteins associated with Nrl1. We found that splicing factors Ntr1,...”
- “...processing [ 10 , 12 , 13 ]. Interestingly, we found that Gpl1-TAP co-purified with SPAC20H4.09 ( Figure 1(c ), Table S1), an uncharacterized RNA helicase that shares similarities with human DHX35 [ 14 ]. Previous observations that both Gpl1 and SPAC20H4.09 co-purify with splicing factors...”
- Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence
Diament, Nucleic acids research 2017 - “...not in S. cerevisiae . These genes include the RNA helicases PRP16, PRP22, PRP43, CDC28, SPAC20H4.09 , involved in spliceosome assembly/disassembly, and the RNA binding SPBC13G1.14c . This re-organization is expected, since the transcriptome of S. pombe contains 5061 introns, including over 1000 multiple-intron genes, whereas...”
- A genome-wide screen of genes involved in cadmium tolerance in Schizosaccharomyces pombe
Kennedy, Toxicological sciences : an official journal of the Society of Toxicology 2008 - “...ADE12/YNL220W None YDR071C SNL1/YIL016W ubp14 SPAC20H4.09 SPBC6B1.06c None UBP14/YBR058C SPBC30B4.03c SPAC12B10.03 SPCC162.02c SPBC21D10.07 YDL233W None None...”
- Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
Schmidt, Molecular systems biology 2007 - “...SPAC23G3.12c Serine protease R.Y#VEVCGAKFHNLSYQLAR.Q 2.6886 0.1181 2177.5 643.3 0.412 K.K@GT#ALVLDKDKGLAVT#S#R.S 3.0538 0.1095 2225.3 809 0.5 SPAC20H4.09 ATP-dependent RNA helicase R.T#LS#T#DLLLGVLK.R 3.0509 0.1078 1513.53 268 0.545 SPAPB2B4.04c p-type calcium ATPase R.T#EGQAT#PLQLRLS#R.V 2.789 0.1696 1809.92 257.4 0.462 SPBC342.02 Glutaminyl-Trna synthetase R.LMFLPDPIKVTLENLDDS#Y#R.E 2.6182 0.1042 2540.22 574.3 0.447 cek1 Serine/threonine...”
NP_776461 ATP-dependent RNA helicase A from Bos taurus
Q28141 ATP-dependent RNA helicase A from Bos taurus
30% identity, 34% coverage
Krad_3104 ATP-dependent RNA helicase HrpA from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
36% identity, 31% coverage
6h57A / Q04217 Crystal structure of s. Cerevisiae deah-box RNA helicase dhr1, essential for small ribosomal subunit biogenesis (see paper)
32% identity, 51% coverage
- Ligand: magnesium ion (6h57A)
UCP12_SCHPO / O94536 Putative ATP-dependent RNA helicase ucp12; EC 3.6.4.13 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
30% identity, 33% coverage
- function: Probable ATP-binding RNA helicase.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
GL50803_17539 putative RNA helicase from Giardia intestinalis
34% identity, 50% coverage
NP_724440 maleless, isoform C from Drosophila melanogaster
30% identity, 47% coverage
- Interaction of MLE with CLAMP zinc finger is involved in proper MSL proteins binding to chromosomes in Drosophila.
Tikhonova, Open biology 2024 - GeneRIF: Interaction of MLE with CLAMP zinc finger is involved in proper MSL proteins binding to chromosomes in Drosophila.
- Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless.
Jagtap, Molecular cell 2023 (PubMed)- GeneRIF: Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless.
- MLE Helicase Is a New Participant in the Transcription Regulation of the ftz-f1 Gene Encoding Nuclear Receptor in Higher Eukaryotes.
Nikolenko, Doklady. Biochemistry and biophysics 2021 (PubMed)- GeneRIF: MLE Helicase Is a New Participant in the Transcription Regulation of the ftz-f1 Gene Encoding Nuclear Receptor in Higher Eukaryotes.
- Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila.
Lv, Nucleic acids research 2019 - GeneRIF: our research provides structural insights into the interactions between MLE dsRBDs and R2H1 and facilitates a deeper understanding of the mechanism by which MLE tandem dsRBDs play an indispensable role in specific recognition of roX and the assembly of the MSL-DCC in Drosophila dosage compensation.
- Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless.
Ankush, Nucleic acids research 2019 - GeneRIF: Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless has been reported.
- Multifunctional ENY2 Protein Interacts with RNA Helicase MLE.
Nikolenko, Doklady. Biochemistry and biophysics 2019 (PubMed)- GeneRIF: ENY2 Protein Interacts with RNA Helicase MLE
- The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts.
Cugusi, PLoS genetics 2016 - GeneRIF: MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location
- Drosophila maleless gene counteracts X global aneuploid effects in males.
Bhadra, The FEBS journal 2016 (PubMed)- GeneRIF: We have employed a systems biology approach (microarray) to investigate the global aneuploid effect of the maleless (mle) mutation that disrupts the binding of male specific lethal (MSL) proteins that function in dosage compensation.
- More
5aorA / P24785 Structure of mle RNA adp alf4 complex (see paper)
30% identity, 44% coverage
- Ligands: rna; adenosine-5'-diphosphate; tetrafluoroaluminate ion (5aorA)
MLE_DROME / P24785 Dosage compensation regulator mle; Protein male-less; Protein maleless; Protein no action potential; EC 3.6.4.13 from Drosophila melanogaster (Fruit fly) (see 10 papers)
NP_476641 maleless, isoform A from Drosophila melanogaster
30% identity, 34% coverage
- function: RNA helicase component of the male-specific lethal (MSL) histone acetyltransferase complex, a multiprotein complex essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation) (PubMed:1653648, PubMed:25158899, PubMed:26545078). Within the MSL complex, the helicase activity of mle remodels roX non-coding RNA (roX1 and roX2)s to promote assembly of the MSL complex (PubMed:23870142, PubMed:26545078, PubMed:30649456, PubMed:30805612). Able to unwind blunt-ended RNA duplexes and has specificity for uridine-rich nucleotides (PubMed:26545078).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the male-specific lethal (MSL) histone acetyltransferase complex, composed of mof, mle, msl-1, msl-2 and msl-3 proteins, as well as roX1 and roX2 non-coding RNAs (PubMed:10679323, PubMed:11014199, PubMed:23870142). Interacts with Unr; promoting association between mle and roX2 non-coding RNA (PubMed:25158899). Interacts with Top2 (PubMed:23989663). - Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...scPrp2 (P20095), scPrp16 (P15938), scPrp22 (P24384), scDhr1 (Q04217) and scDhr2 (P36009). The sequence of dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values in parentheses indicate the Uniprot accession numbers ( TheUniProtConsortium, 2015 ). The alignment was...”
- Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research
Andere, BMC genomics 2016 - “...of protein sequences of the sex determining gene maleless of P. regina and D. melanogaster (P24785). Sequence similarities between the male and female P. regina is 100%, and the similarity to D. melanogaster is 72.27%. (JPG 1574kb) Additional file 19: Figure S8. Multiple amino acid sequence...”
- Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases
Gibson, Nucleic acids research 1994 - “...Z30423 Helicase A em:Hsrnahela L13848 11 Maleless Mle_Drome P24785 Notch Notc_Drome2 NGG1 Histone I B Nggl-Yeast2 H IB StrPu2 P07207 P32494 P15869 12 13...”
- The biology of DHX9 and its potential as a therapeutic target
Lee, Oncotarget 2016 - “...B. taurus ) (NP_776461), mouse ( M. musculus ) (NP_031868), Drosophila ( D. melanogaster ) (NP_476641), C. elegans (NP_495890), and Arabidopsis ( A. thaliana ) (NP_850154). Red text indicates residues that are identical in all species. Blue text indicates residues with high similarity amongst species. The...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_057306 NP_524220 NP_199941 NP_014287 DDB0191511 NMP265 EIF4A3 NP_055555 NP_649788 NP_566469 NP_010304 DDB0233740 RHA DHX9 NP_001348 NP_476641 NP_178223 NP_013523 DDB0233398 Prp2 DHX16 NP_003578 NP_609946 NP_181077 NP_010929 DDB0233419 DDX 35 DHX35 NP_068750 NP_609946 NP_174527 NP_010929 DDB0233453 fSAP118 SKIV2L2 NP_056175 NP_524929 NP_565338 NP_012485 DDB0233404 FLJ21972 DHX33 NP_064547 NP_610928 NP_181077...”
AT5G10370 helicase domain-containing protein / IBR domain-containing protein / zinc finger protein-related from Arabidopsis thaliana
33% identity, 24% coverage
- The plant-unique protein DRIF1 coordinates with sorting nexin 1 to regulate membrane protein homeostasis
Zhu, The Plant cell 2023 (PubMed)- “...a premature stop codon or a missense mutation in AT5G10370, 41 respectively. This gene was named DEAH and RING domain-containing protein as 42 FREE1 suppressor...”
- “...A N U SC RI PT a missense mutation, respectively, in AT5G10370, named as DEAH and RING M 137 RESULTS 139 sof10 and sof641 can rescue the seedling lethality of...”
- Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Ruchika,, Cells 2021 - “...5 AT3G02515 - 41 20795012 69 64 AT3G56040 UDP-glucose pyrophosphorylase 3 42 3264804 0 2 AT5G10370 helicase domain-containing protein/IBR domain-containing protein/zinc finger protein-related 43 9633752 0 2 AT5G27330 Prefoldin chaperone subunit family protein 44 12108844 0 9 AT5G32481 - 45 15644809 0 4 AT5G39090 HXXXD-type acyl-transferase...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...[ 18 , 56 59 ] AT3G47890, AT3G53500, AT3G53500, AT5G51660, AT3G56825, AT3G57570, AT3G19515, AT3G19630, AT3G13290, AT5G10370, AT4G02970, AT5G62600, AT3G55220, AT3G10070 Proteolysis or protein synthesis AT1G67120, AT1G67550, AT2G40930, AT4G26510, AT5G35620, AT5G58200, AT5G23110, AT1G28350, AT5G49030, AT5G27700, AT3G47060, AT2G07715, AT2G24640, AT2G25740 [ 18 ] Protein located in mitochondria or...”
- “...[ 18 , 56 59 ] AT3G47890, AT3G53500, AT3G53500, AT5G51660, AT3G56825, AT3G57570, AT3G19515, AT3G19630, AT3G13290, AT5G10370, AT4G02970, AT5G62600, AT3G55220, AT3G10070 a Suggests the function of RNA itself, for example, rRNA, or the functions in its expressed proteins b The functions of many transcripts were inferred by...”
- Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa
Xu, PloS one 2013 - “...seedling, inflorescence, silique, shoot and roots. Forty-four genes were highly expressed in sperm cells and AT5G10370 and AT5G61140 were only highly expressed in primary root tissue ( Figure 4 ). 10.1371/journal.pone.0078982.g004 Figure 4 The expression profiles of 145 RNA helicase genes in Arabidopsis . The expression...”
- Evolution of plant HECT ubiquitin ligases
Marín, PloS one 2013 - “...(II B) 0.36 0.27 0.46 0.26 0.80 AT3g53690 (II C) 0.09 0.18 0.50 0.40 0.47 AT5g10370 (HEL) 0.81 0.79 0.57 0.63 0.33 AT1g32340 (ARA54) 0.12 0.18 0.62 0.50 0.80 AT2g16090 (ARI A) 0.68 0.59 0.10 0.19 0.13 AT4g34370 (ARI A) 0.26 0.47 0.78 0.78 0.29 AT1g05890...”
- Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
Kosarev, Genome biology 2002 - “...spacing Cellulose synthase At5g05170 Wrong ligand spacing Cellulose synthase At5g09870 Wrong ligand spacing Cellulose synthase At5g10370 Incomplete Protein contains one RING variant domain At5g15790 Incomplete Protein contains one RING-H2 domain At5g17420 Wrong ligand spacing Cellulose synthase At5g23110 Incomplete Protein contains one RING-HC domain At5g25560 Incomplete Protein...”
- “...- - - - Cluster 3.6 AT4g01020 - - - - Second motif in protein AT5g10370 - - - - Cluster 3.7 At2g25360 - - - - AT3g45470 - - - - Unique At1g11100 - - - - RUSH1 alpha-like protein At1g32340 - - - -...”
YG65_SCHPO / O60114 Uncharacterized helicase C15C4.05; EC 3.6.4.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
31% identity, 31% coverage
L7MCS1 RNA helicase (Fragment) from Rhipicephalus pulchellus
31% identity, 51% coverage
- Proteomic Analysis of Exosome-Like Vesicles Isolated From Saliva of the Tick Haemaphysalis longicornis
Nawaz, Frontiers in cellular and infection microbiology 2020 - “...dehydrogenase V5H108 DNA-directed RNA polymerase III subunit A0A293MQS4 NADPH-dependent diflavin oxidoreductase 1 B7Q0Z1 GTPase, putative L7MCS1 Putative mrna splicing factor atp-dependent rna helicase B7Q2U6 Nicotinamide N-methyltransferase, putative Q4R1A6 Metalloprotease B7QCU5 Sulfotransferase, putative Q86GZ5 Midgut cysteine proteinase 2 A0A131YGI5 RHIAP Angiotensin-converting enzyme V5HY02 Putative tick metalloprotease L7S6B3...”
Q869Z1 RNA helicase from Dictyostelium discoideum
30% identity, 31% coverage
- Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein
Meier, PLoS genetics 2016 - “...RNA binding domain protein B (RbdB) DDB_G0269426 Q55FS1 Double stranded RNase B (DrnB) DDB_G0268410 [drnB] Q869Z1 DEAD/DEAH box helicase (Dhx9) DDB_G0275313[dhx9] Q86L44 DEAD/DEAH box Helicase HelF DDB_G0294407[helF] Q95ZG5 Double stranded RNase A (DrnA) DDB_G0273051[drnA-1] We eliminated proteins which are involved in translation or ribosomal proteins and...”
AT4G01020 helicase domain-containing protein / IBR domain-containing protein / zinc finger protein-related from Arabidopsis thaliana
32% identity, 24% coverage
- Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis
Zhou, Nature communications 2024 - “...one, was selected. The phylogenetic tree was annotated using iTOL (similarly, hereinafter). The Arabidopsis DCS4 (AT4G01020, AtDEAH11 of the DEAH/RHA family) protein sequence was used as a query to perform a BLASTP search. All of the sequences with an E-value of less than 1e3 and with...”
- Functions and mechanisms of RNA helicases in plants
Li, Journal of experimental botany 2023 - “...zinc finger domain, such as AT5G26742 (RH3) and AT4G01020. In contrast, Ski2-like RHs have multiple additional extensions in the C-terminal regions, including...”
- Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing
Sun, Biomolecules 2019 - “...N csa-mir013 XM_004143155.2 chitin elicitor receptor kinase 1-like - N csa-mir013 XM_004137239.2 putative uncharacterized protein At4g01020 - N csa-mir013 XM_004135249.2 signal recognition particle subunit SRP72-like - 1800 csa-mir013 XM_004133898.2 ent-kaurenoic acid oxidase 1 - N Note: log 2 (Fold Change) indicates log 2 (Fold_change) of miRNA...”
- Expression of ROS-responsive genes and transcription factors after metabolic formation of H(2)O(2) in chloroplasts
Balazadeh, Frontiers in plant science 2012 - “...GARP-ARR-B 0.21 0.10 At3g55980 C3H 0.90 3.97 At5g07210 GARP-ARR-B 1.57 0.85 At4g00305 C3H 0.46 0.93 At4g01020 C3H 0.93 0.40 At4g29190 C3H 0.72 1.36 At1g13300 GARP-G2-like 1.44 0.56 At3g50650 GRAS 0.15 0.27 At4g29940 HB 0.07 0.46 At3g54220 GRAS 0.61 0.37 At4g32040 HB 0.01 0.84 At3g60630 GRAS 0.16...”
- Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
Kosarev, Genome biology 2002 - “...Incomplete Protein contains one RING-H2 domain At3g62970 Incomplete Protein contains one RING-H2 domain At4g00070 Incomplete At4g01020 Incomplete Protein contains one RING-HC and One RING-variant domain At4g10940 Incomplete At4g12150 Incomplete Protein contains one RING-variant domain, Which is part of a RING-H2 cluster At4g26400 Incomplete Protein contains one...”
- “...+ + - AT3g29270 + + + - Cluster 1.10 At1g01350 + + + + AT4g01020 + + + + Second motif in protein AT5g06420 + + + + Cluster 1.11 At1g30860 + + + + At2g34920 + + + + AT5g44690 + + + -...”
REH2_TRYB2 / Q581T1 RNA editing associated helicase 2; ATP-dependent RNA helicase REH2; EC 3.6.4.13 from Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (see 4 papers)
30% identity, 20% coverage
- function: ATP-dependent RNA helicase that unwinds RNA in a 3' to 5' direction and that plays an important role in mitochondrial mRNA editing, a process involving the addition and deletion of uridine (U) nucleotides in the pre-mRNA (PubMed:19850921, PubMed:26769962, PubMed:31034523). As part of the RET2-containing gRNA-binding (RET2- GRBC) complex, acts as a scaffold for the assembly of mRNA-gRNA hybrids and the recruitment of the RNA editing core (RECC) complex (PubMed:25928631, PubMed:26769962). Regulates several steps of mRNA editing by the MRBC3010/GRBC6 containing gRNA-binding (MRBC3010-GRBC) complex including loading of unedited mRNA, editing in the first sequence block and subsequent editing progression across multiple sequence blocks (PubMed:25928631). Also, regulates the RNA substrate content of the MRBC3010-GRBC complex as well as the association of this complex with mitoribosomes (PubMed:25928631).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the REH2-associated complex (REH2C) composed of helicase REH2, associated factors H2F1 and H2F2, and mRNAs at various editing stages; the formation of the complex is RNA-independent (PubMed:26769962, PubMed:31034523). Within the complex, interacts with H2F1; the interaction is direct (PubMed:26769962, PubMed:31034523). Interacts transiently, in a RNA-dependent manner, with various editing complexes including the RNA editing core (RECC) complex, the gRNA- binding (GRBC) complex (also known as the MRB1 complex) and the RNA editing mediator (REMC) complex (PubMed:19850921, PubMed:25928631, PubMed:26769962, PubMed:31034523). Interacts with GAP1/GRBC2 via RNA forming a variant of the GRBC complex known as REH2-GRBC complex (PubMed:19850921, PubMed:25928631, PubMed:26769962, PubMed:31034523). Interacts with mitochondrial ribosomes (PubMed:19850921).
disruption phenotype: RNAi-mediated knockdown at the procyclic stage causes a loss of RNA unwinding activity (PubMed:26769962). Reduces association of H2F1 and abolishes H2F2 association with components of various editing complexes (PubMed:26769962). RNAi-mediated knockdown at the procyclic stage inhibits editing at early 3' sites on pre-mRNA substrates without affecting the interactions between MRB3010/GRBC6, GAP1/GRBC2, RGG2, REL1 and gRNA (PubMed:25928631). Decreases the ratio of unedited mRNA substrates in the MRB3010/GRBC6-MRB complex and the association of never-edited mRNA and 9SrRNA with the MRB3010-MRB complex (PubMed:25928631). Also, causes a decrease in the steady-state levels of guide RNA (gRNA) (PubMed:19850921).
DHX9_CAEEL / Q22307 ATP-dependent RNA helicase A; Nuclear DNA helicase II; NDH II; EC 3.6.4.13 from Caenorhabditis elegans (see paper)
NP_495890 ATP-dependent RNA helicase A from Caenorhabditis elegans
31% identity, 34% coverage
- function: Multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and that plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. Requires a 3'-single-stranded tail as entry site for acid nuclei unwinding activities as well as the binding and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide triphosphates (NTPs). Binds to DNA, RNA and small interfering siRNA. Plays a role in DNA replication at origins of replication and cell cycle progression (By similarity). Plays a role as a transcriptional coactivator acting as a bridging factor between polymerase II holoenzyme and transcription factors or cofactors (PubMed:15817227). Plays several roles in post-transcriptional regulation of gene expression. Promotes pre-mRNA alternative splicing activities of a subset of genes. As component of a large PER complex, is involved in the negative regulation of 3' transcriptional termination of circadian target genes. Component of the coding region determinant (CRD)-mediated complex that promotes cytoplasmic MYC mRNA stability. Plays a role in mRNA translation. Also plays a role in the RNA-induced silencing complex (RISC) loading complex (RLC) assembly, and hence functions in the RISC-mediated gene silencing process. Mediates the attachment of heterogeneous nuclear ribonucleoproteins (hnRNPs) to actin filaments in the nucleus (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the coding region determinant (CRD)-mediated complex. Identified in mRNP granule complexes containing untranslated mRNAs. Associates with the RISC complex. Associates with the SMN complex. Associates with polysomes. - RNA helicase A is important for germline transcriptional control, proliferation, and meiosis in C. elegans.
Walstrom, Mechanisms of development 2005 (PubMed)- GeneRIF: RHA-1 is a conserved transcription regulation protein that controls germline proliferation and development in C. elegans
7mqaNS / Q8IY37 structure of the human SSU processome, state post-A1 (see paper)
34% identity, 53% coverage
AFUA_2G16140 RNA helicase from Aspergillus fumigatus Af293
32% identity, 33% coverage
YL419_YEAST / Q06698 Putative ATP-dependent RNA helicase YLR419W; EC 3.6.4.13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
NP_013523, YLR419W Putative helicase with limited sequence similarity to human Rb protein; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YLR419W is not an essential gene from Saccharomyces cerevisiae
28% identity, 30% coverage
- function: Probable ATP-binding RNA helicase.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065) - YLR419W is the homolog of the mammalian translation initiation factor DHX29
Fromont-Racine, microPublication biology 2024 - “...Biology 2578-9430 Caltech Library 10997966 10.17912/micropub.biology.001112 New Finding Interaction Data Expression Data S. Cerevisiae Human YLR419W is the homolog of the mammalian translation initiation factor DHX29 Fromont-Racine Micheline 1 2 Khanna Varun 3 Jacquier Alain 1 2 Badis Gwenael 1 2 1 Cytoplasmic mRNA surveillance in...”
- “...and DHX57 as three putative homologs of the yeast Ylr419wp. Functional studies first linked the Ylr419w protein to the translating ribosome and cross-linking and analysis of cDNA (CRAC) experiments determined the precise region of Ylr419wp in contact with the ribosome. It corresponds to the loop of...”
- Core promoter activity contributes to chromatin-based regulation of internal cryptic promoters
Lee, Nucleic acids research 2021 - “...during the second galactose exposure (Figure 5E ). A converse case is the gene called YLR419W ( 28 ). It has at least three cryptic promoters ( Supplementary Figure S5A ) and, compared to HXT5 , shows the opposite response to the carbon source shifts. In...”
- An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana
Helderman, Viruses 2021 - “...metabolism NbS00027624g0003.1 P38929 PMC1 Calcium-transporting ATPase 2 KOG0204 Inorganic ion transport and metabolism NbS00037522g0005.1 Q06698 YLR419W Putative ATP-dependent RNA helicase KOG0920 Replication, recombination, and repair NbS00036611g0008.1 P32481 GCD11 Eukaryotic translation initiation factor 2 KOG0466 Translation, ribosomal structure, and biogenesis NbS00009889g0007.1 P35723 YET1 Endoplasmic reticulum transmembrane protein...”
- Heterologous Hsp90 promotes phenotypic diversity through network evolution
Koubkova-Yu, PLoS biology 2018 - “...We excluded genes with uncharacterized function or dubious open reading frames, including YLR345W, YEL034C-A, YMR102C, YLR419W, YOL166C, and Q0182. To understand the functional relationship between the mutated genes and Hsp90, we constructed the functional network between them. The genetic and physical interactions of Hsp90 were first...”
- ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
Jain, eLife 2018 - “...not find clear matches to the YTHDC2 architecture in fungi. The closest Saccharomyces cerevisiae homolog (YLR419W) lacks the diagnostic ARD insertion between the helicase core domains, has N-terminal UBA (ubiquitin-associated) and RWD domains rather than an R3H domain, and lacks a YTH domain. YLR419W thus more...”
- “...human DHX57 ( Figure 8figure supplement 1A ), which is indeed the top hit when YLR419W is used as the query in a BLASTP search against the human genome (GenBank accession AAH65278.1; 29% identity, E-value 210 110 ). Data availability Reagents and mouse strains are available...”
- Regulation of DEAH/RHA helicases by G-patch proteins
Robert-Paganin, BioMed research international 2015 - “...Prp2, Prp16, Prp22, and Prp43 (resp., DHX16, DHX38, DHX8, and DHX15 in human) and of YLR419w (DHX29), Dhr1 (DHX37), and Dhr2 (DHX32). Other members of the family have no known homologues in yeast, such as DHX35, DHX9 (RNA helicase A), DHX57, DHX36, DHX30, DHX33, DHX40, and...”
- “...of DEAH/RHA helicases in translation initiation has mostly been investigated for the human homologue of YLR419w (DHX29) and DHX9. The DHX29 helicase is essential in translation initiation during the formation of the 43S complex, composed of the eIF2/GTP/Met-tRNAi Met complex, initiation factors, and the ribosomal 40S...”
- Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Shen, BMC bioinformatics 2015 - “...ydr473c yel015w yer112w yer146w yer172c ygl068w ygl173c ygr091w yhr019c yhr140w yjl013c yjl035c yjl124c yjr022w ykl173w ylr419w ylr438c-a ymr268c ynl092w ynl118c ynl147w ynl240c ynr011c yor308c ypr058w ypr178w Conclusions Protein functional module is a fundamental unit formed with highly connected proteins and often possesses specific biological functions [...”
- Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
Kuppuswamy, Algorithms for molecular biology : AMB 2014 - “...YNL031C, YMR124W, YLR019W, YGL140C, YEL025C, YMR031C, YBR079C, YFR016C, YJL084C, YBL002W, YJR056C, YDR334W, YPL282C, YNL301C, YMR144W, YLR419W, YKL219W GO:0009966 18/20 YHR155W, YJL084C, YDR520C, YHL004W, YER033C, YNL289W, YKR104W, YKL209C, YBR071W, YGR162W, YOR077W, YIR016W, YHL029C, YGR054W, YDL123W, YCR030C, YOR166C, YNL208W Table shows the fraction of the genes correctly predicted...”
- More
- An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana
Helderman, Viruses 2021 - “...and metabolism NbS00027624g0003.1 P38929 PMC1 Calcium-transporting ATPase 2 KOG0204 Inorganic ion transport and metabolism NbS00037522g0005.1 Q06698 YLR419W Putative ATP-dependent RNA helicase KOG0920 Replication, recombination, and repair NbS00036611g0008.1 P32481 GCD11 Eukaryotic translation initiation factor 2 KOG0466 Translation, ribosomal structure, and biogenesis NbS00009889g0007.1 P35723 YET1 Endoplasmic reticulum transmembrane...”
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Tauchert, eLife 2017 - “...dmMLE (P24785) was aligned to scMtr4 (P47047), scSki2 (P35207), scBrr2 (P32639), scSlh1 (P53327) and scYL419 (Q06698). The values in parentheses indicate the Uniprot accession numbers ( TheUniProtConsortium, 2015 ). The alignment was visualized with ESPript 3.0 ( Robert and Gouet, 2014 ). The Hook-Turn and Hook-Loop...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...DEAD/DEAH-box (LOC_Os10g33275) DHX15 (O22899) YLR419W (Q06698) RNA helicase (PFI0860c) www.landesbioscience.com Communicative & Integrative Biology 133 Table...”
- “...DHX29 DEAD/DEAH-box (LOC_Os04g35260) DHX8 (Q38953) YLR419W (Q06698) RNA helicase (PFI0860c) 50 DHX30 DEAD/DEAH-box (LOC_Os10g33275) DHX15 (O22899) YLR419W...”
NP_001186628 ATP-dependent RNA helicase DHX33 isoform 2 from Homo sapiens
33% identity, 41% coverage
LOC25501139 DExH-box ATP-dependent RNA helicase DExH3 from Medicago truncatula
31% identity, 39% coverage
- Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)
Gutiérrez, Frontiers in plant science 2023 - “...- MTR_3g075100 Telomere length regulation protein TEL2 homolog Chr3: 37,598,521 - 37,609,730 AX-181183872 11.7 VF4 LOC25501139 - MTR_8g044260 DExH-box ATP-dependent RNA helicase DExH3 Chr8:16,827,348 - 16,850,409 AX-181483303 8.4 VF0 LOC11434981 - MTR_1g045510 28 kDa ribonucleoprotein, chloroplastic Chr1: 17,459,568 - 17,462,374 AX-181167806 5.9 VF6 LOC25494322 - MTR_4g133952...”
BMEI1817 ATP-DEPENDENT HELICASE HRPB from Brucella melitensis 16M
44% identity, 27% coverage
- Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Boggiatto, BMC molecular biology 2018 - “...N No change Slight repress BMEI0828 Phosphatidate cytidyltransferase 2101 95 5.9 N Activated Slight repress BMEI1817 ATP-dependent helicase HrpB 3100 1291 6.6 N Repressed No change BMEI1896 Hypothetical protein 2953 17 2.8 N Repressed No change BMEII0111 ICC protein family 2227 136 3.2 N Activated No...”
- “...family 3.4 No BMEI0171 Ribosomal protein L11 methyltransferase 3.4 No BMEI1926 Hydroxymethylglutaryl-CoA lyase 3.4 No BMEI1817 ATP_dependent helicase HrpB 3.3 No BMEI0173 Ycil-like protein 3.3 No BMEI1925 Acetyl-CoA carboxylase alpha chain/propionyl-CoA carboxylase alpha chain 3.3 No BMEII0564 Bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase ( putA ) 3.2 No...”
AT5G04895 DEA(D/H)-box RNA helicase family protein from Arabidopsis thaliana
30% identity, 38% coverage
- Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression
Mizrahi, International journal of molecular sciences 2024 - “...early plant development, as heterozygous T-DNA insertional lines found within the coding region of the AT5G04895 locus are unable to produce homozygous progeny. The growth and developmental defect phenotypes, and reduced levels of various organellar nad mRNA transcripts in abo6 mutants, are likely associated with altered...”
- “...[ 45 ] SUV3 S000005950 S.c. Nucleolysis (degredosomal factor) [ 46 , 47 ] ABO6 At5g04895 A.t. Splicing (group II introns) [ 48 ] ISE1/EMB1586 At1g12770 A.t. T.B.D. * 2 , affects mitochondria biogenesis [ 49 ] DExH18 At5g39840 A.t. T.B.D., predicted to the mitochondria *...”
- Abscisic acid increases hydrogen peroxide in mitochondria to facilitate stomatal closure
Postiglione, Plant physiology 2023 - “...under the accession numbers: PYR1 (At4g17870), PYL1 (At5g46790), PYL4 (At2g38310), PYL5 (At5g05440), PYL8 (At5g53160), ABO6 (At5g04895), RBOHD (At5g47910), RBOHF (At1g64060). Supplemental data The following materials are available in the online version of this article. Supplemental Figure S1 . Abscisic acid (ABA) increases dichlorofluorescein (DCF) fluorescence when...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...AT1G72730 ( VASL ), CHR12 (AT3G06010), CHR11 (AT3G06400), ABA OVERLY SENSITIVE 6 ( ABO6 ; AT5G04895), and others being under strong purifying selection, whereas SNF2-RING-HELICASE LIKE5 (FRG5) (AT1G11100) and CHR40 (AT3G24340) showed relatively high -values pointing toward near neutral evolution. Furthermore, -values averaged for alleles of...”
- Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis
Zhu, Journal of experimental botany 2016 - “...3/RADIAL SWELLING 12 (EPS3/RSW12; At1g32490), FASCIATED STEM 4 (AtFAS4; At1g33390), ABA OVERLY SENSITIVE 6 (ABO6; At5g04895), CLUMSY VEIN (CUV; At5g13010), and ROOT INITIATION DEFECTIVE 1 (RID1; At1g26370). EPS3 is a putative homolog of yeast PRP2, which is required for RNA processing and plays an important role...”
- Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds
McKeown, BMC plant biology 2011 - “...At4g29450 Leucine-rich repeat protein kinase, putative At4g33450 Myb domain protein 69 (AtMYB69) At4g37530 Peroxidase, putative At5g04895 ATP binding/helicase/nucleic acid binding protein At5g16620 Pigment defective embryo (PDE120) chloroplast import (Tic40) At5g17080 Cathepsin-related protein At5g35730 EXS family protein/ERD1/XPR1/SYG1 family protein At5g35737 Unknown protein At5g38320 Unknown protein At5g39510 VESICLE...”
- “...was used. The following genes did not have probes: At1g12420, At1g55320, At2g45315, At3g21465, At4g01000, At4g25315, At5g04895, At5g35737 and At5g40240. Probes for At4g37530 and At1g14880 also matched another gene so were omitted from the analysis due to the possibility of ambiguous results. LCM Siliques of emasculated and...”
- SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex
Pouch-Pélissier, PLoS genetics 2008 - “...dsRBP involved in transcriptional regulation [44] , while two other dsRBPs of unknown function (At1g48650, at5g04895) contain a helicase domain. Therefore SB1 RNA potentially affects basic cellular processes other than RNAi, and this in turn could affect plant development. Based on our in vitro studies, we...”
FPRO_08166 uncharacterized protein from Fusarium proliferatum ET1
31% identity, 29% coverage
Q7QCW2 Probable ATP-dependent RNA helicase spindle-E from Anopheles gambiae
30% identity, 30% coverage
GL50803_13200 putative RNA helicase from Giardia intestinalis
31% identity, 46% coverage
- DEAD/DExH-Box RNA Helicases in Selected Human Parasites
Marchat, The Korean journal of parasitology 2015 - “...]. In Giardia , the antigenic variation process is associated to the up-regulation of the GL50803_13200 and GL50803_17387 proteins, which have high homology with the human DEAH-box helicase RHA (DHX9) involved in remodeling RNA-induced silencing complex to allow dsRNA loading onto this complex, and the GL50803_2098...”
- Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts
Gargantini, BMC microbiology 2012 - “...: Figure S3, the 5 helicases present the eight characteristic motifs, with the exception of GL50803_13200, which was incomplete in its N-terminal region, missing Motif I. As with the missing motif of DEAD-box helicase GL50803_34684, a new database search showed a homologous gene, GL50581_4549 from the...”
- “...this complex [ 52 ], has a high homology with the G. lamblia DEAH-box helicase GL50803_13200, which presents a later up-regulation during antigenic variation, in agreement with the Giardia Ago expression (34 h post induction). Another G. lamblia DEAH-box helicase found to have high homology with...”
GL50803_6616 putative RNA helicase from Giardia intestinalis
30% identity, 58% coverage
XP_971741 probable ATP-dependent RNA helicase spindle-E from Tribolium castaneum
28% identity, 32% coverage
LOC123671460 probable ATP-dependent RNA helicase spindle-E from Harmonia axyridis
28% identity, 31% coverage
- Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird
Li, BMC biology 2023 - “...Obs F ST P -value Location Protein Original_scaffold_1348 5,014,802 6747 0.202924 0.882225 0.00E+00 Downstream of LOC123671460 Probable ATP-dependent RNA helicase spindle-E FragScaff_scaffold_198 4,590,085 4739 0.211016 0.875361 1.05E299 Unknown Unknown Original_scaffold_540 399,348 6068 0.190675 0.854398 1.05E273 Downstream of LOC123686084 piggyBac transposable element-derived protein 3-like FragScaff_scaffold_198 4,755,908 4743...”
- “...Procathepsin L-like (LOC123685704), transcript variant X2, mRNA Original_scaffold_1348 1,942,409 6691 0.23695 0.79731 1.57E208 Downstream of LOC123671460 Probable ATP-dependent RNA helicase spindle-E Original_scaffold_1348 3,619,473 6711 0.226716 0.773365 8.86E184 Downstream of LOC123671460 Probable ATP-dependent RNA helicase spindle-E Original_scaffold_1348 4,905,076 6744 0.221071 0.76982 3.08E180 No match No match FragScaff_scaffold_60...”
EHI_090040 helicase, putative from Entamoeba histolytica HM-1:IMSS
C4MA27 Helicase, putative from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
27% identity, 36% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...U2AF35 U2 snRNP auxiliary factor EHI_192500 C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373 Brr2 PILC B-B act ;...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...U2 snRNP auxiliary factor EHI_192500 C4M1H0 Prp43 ILS-disassembly EhDExH9 EHI_184530 C4M6S9 Prp43 ILS-disassembly EhDExH13 EHI_090040 C4MA27 Prp43 ILS-disassembly EhDExH7 EHI_096230 C4LWD6 Prp5 E-A (U2-3'ss) EhDEAD3 EHI_013960 C4LXN8 U5 snRNP U5 snRNA Snu114 PILC B-B act U5 snRNP subunit EHI_021380 B1N373 Brr2 PILC B-B act ; C-Post...”
LOC109750189 DExH-box ATP-dependent RNA helicase DExH3 from Aegilops tauschii subsp. strangulata
28% identity, 36% coverage
- Chlorophyll Fluorescence in Wheat Breeding for Heat and Drought Tolerance
Abdullaev, Plants (Basel, Switzerland) 2024 - “...significant SNPs (IWB60417 and IWB11846), associated with candidate genes (DExH-box ATP-dependent RNA helicase DExH3-like ( LOC109750189 ) and the fructose-1,6-bisphosphate aldolase 1 ( FBA1 ), respectively) were identified for F v /F m on chromosome 3A [ 135 ]. The first gene is involved in plant...”
B8AMY3 RNA helicase from Oryza sativa subsp. indica
30% identity, 42% coverage
SPNE_DROME / Q9VF26 Probable ATP-dependent RNA helicase spindle-E; Protein homeless; EC 3.6.4.13 from Drosophila melanogaster (Fruit fly) (see 14 papers)
NP_476741 spindle E from Drosophila melanogaster
29% identity, 30% coverage
- function: Probable ATP-binding RNA helicase which plays a central role during spermatogenesis and oogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi and govern the methylation and subsequent repression of transposons. Involved in the repression of LTR retrotransposon copia. Also involved in telomere regulation by repressing specialized telomeric retroelements HeT-A, TAHRE, and TART; Drosophila telomeres being maintained by transposition of specialized telomeric retroelements. Involved in telomeric trans- silencing, a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located in euchromatin. Involved in the repression of testis-expressed Stellate genes by the homologous Su(Ste) repeats. Required for anteroposterior and dorsoventral axis formation during oogenesis. Key component of the perinuclear meiotic nuage, an electron dense structure involved in the post-transcriptional regulation of transposons and mRNAs; required for recruitment of other nuage comonents including vas, krimp, aub and mael (PubMed:17428915). May have a role in production of piwi-interacting RNA (piRNA) (PubMed:17428915).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
disruption phenotype: Egg chambers for females lacking spn-E display startmispositioned oocytes. At a low frequency, females generate early egg chambers in which the oocyte is positioned incorrectly within the cyst. At a high frequency, late-stage egg chambers exhibit a ventralized chorion. Flies show transposable elements derepression, an aberrant piRNA profile and a reduction of H3 'Lys-9' methylation and delocalization of HP1 and HP2. - E2F/Dp inactivation in fat body cells triggers systemic metabolic changes
Zappia, eLife 2021 - “...) TMT-MS intensities showing protein levels of Dp (Uniprot Q24318), E2F2/DP target protein Arp53 (Uniprot Q9VF26), SpnE (Uniprot P455891), and dATM (Uniprot Q5EAK6) in fat bodies and muscles. Data are represented as individual intensity value for each replicate, n= 3 per genotype in fat body and...”
- The South American Fruit Fly: An Important Pest Insect With RNAi-Sensitive Larval Stages
Dias, Frontiers in physiology 2019 - “...bits = 1164 50 Homeless (spindle-E) TRINITY_DN31966_c0_g1_i1 ATP-dependent RNA helicase spindle-E ( Drosophila melanogaster ) Q9VF26 E = 0.0; bits = 1281 48 Maelstrom TRINITY_DN28061_c2_g2_i5 Protein maelstrom ( Drosophila yakuba ) B4PIP5 E = 6e-085; bits = 279 38 HEN1 TRINITY_DN27986_c1_g1_i3 Small RNA 2- O -methyltransferase...”
- RNA helicase Spn-E is required to maintain Aub and AGO3 protein levels for piRNA silencing in the germline of Drosophila.
Ryazansky, European journal of cell biology 2016 (PubMed)- GeneRIF: The lack of Spn-E caused a significant drop of protein levels of key ping-pong participants, Aubergine (Aub) and AGO3 proteins of PIWI subfamily, in the germline of both males and females, but did not disrupt of their assembly in nuage granules.
- The DExH box helicase domain of spindle-E is necessary for retrotransposon silencing and axial patterning during Drosophila oogenesis.
Ott, G3 (Bethesda, Md.) 2014 - GeneRIF: DExH box domain of Spindle-E is necessary for its function in the piRNA pathway and retrotransposon silencing during oogenesis and embryonic patterning.
- Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery.
Pal-Bhadra, Science (New York, N.Y.) 2004 (PubMed)- GeneRIF: mutations in piwi, aubergine, or spindle-E which encode RNAi components result in reduction of H3 Lys9 methylation and delocalization of HP1 and HP2
- RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E.
Kennerdell, Genes & development 2002 - GeneRIF: RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E.
YL540_MIMIV / Q5UQ96 Putative ATP-dependent RNA helicase L540; EC 3.6.4.13 from Acanthamoeba polyphaga mimivirus (APMV) (see paper)
MIMI_L540 VVI8 helicase from Acanthamoeba polyphaga mimivirus
28% identity, 50% coverage
Q3MHU3 ATP-dependent RNA helicase TDRD9 from Rattus norvegicus
27% identity, 33% coverage
XP_006720082 ATP-dependent RNA helicase TDRD9 isoform X1 from Homo sapiens
27% identity, 33% coverage
- Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers.
Mo, Pathology oncology research : POR 2020 (PubMed)- GeneRIF: Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers.
- Testicular expression of TDRD1, TDRD5, TDRD9 and TDRD12 in azoospermia.
Babakhanzadeh, BMC medical genetics 2020 - GeneRIF: Here we evaluate gene and protein expression levels of four key TDRDs (TDRD1, TDRD5, TDRD9 and TDRD12) in testicular biopsy samples obtained from men with obstructive azoospermia (OA, n = 29), as controls, and various types of non-obstructive azoospermia containing hypospermatogenesis (HP, 28), maturation arrest (MA, n = 30), and Sertoli cell-only syndrome (SCOS, n = 32) as cases.
- Mutation in TDRD9 causes non-obstructive azoospermia in infertile men.
Arafat, Journal of medical genetics 2017 (PubMed)- GeneRIF: first report of a recessive deleterious mutation in TDRD9 in humans; study demonstrates that non-obstructive azoospermia can be caused by a mutation in TDRD9
- Family-based association study for bipolar affective disorder.
Secolin, Psychiatric genetics 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Genome-wide searching of rare genetic variants in WTCCC data.
Feng, Human genetics 2010 - GeneRIF: Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
- Findings from bipolar disorder genome-wide association studies replicate in a Finnish bipolar family-cohort.
Ollila, Molecular psychiatry 2009 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
XP_017170707 ATP-dependent RNA helicase TDRD9 isoform X7 from Mus musculus
26% identity, 54% coverage
TDRD9_HUMAN / Q8NDG6 ATP-dependent RNA helicase TDRD9; Tudor domain-containing protein 9; EC 3.6.4.13 from Homo sapiens (Human) (see paper)
27% identity, 33% coverage
- function: ATP-binding RNA helicase required during spermatogenesis (PubMed:28536242). Required to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Acts downstream of piRNA biogenesis: exclusively required for transposon silencing in the nucleus, suggesting that it acts as a nuclear effector in the nucleus together with PIWIL4.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with piRNA-associated proteins PIWIL1 and PIWIL4. - A Novel Compound Heterozygous Mutation in TDRD9 Causes Oligozoospermia.
Wang, Reproductive sciences (Thousand Oaks, Calif.) 2024 - “...the structure of the TDRD9 mutant protein, and PyMOL software ( http://www.pymol.org ) (PDB ID: Q8NDG6) was used to visualize the structure of theTDRD9 protein. Results Clinical Characteristics The patient was 29years old and was diagnosed with oligozoospermia. No sperm were found during routine examination of...”
TDRD9_MOUSE / Q14BI7 ATP-dependent RNA helicase TDRD9; Tudor domain-containing protein 9; EC 3.6.4.13 from Mus musculus (Mouse) (see 4 papers)
26% identity, 33% coverage
- function: ATP-binding RNA helicase which plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity (PubMed:20059948, PubMed:28633017). Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons (PubMed:20059948, PubMed:28633017). Acts downstream of piRNA biogenesis: exclusively required for transposon silencing in the nucleus, suggesting that it acts as a nuclear effector in the nucleus together with PIWIL4 (PubMed:28633017).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with piRNA-associated proteins PIWIL1 and PIWIL4.
disruption phenotype: Mice are viable but show male sterility with chromosome synapsis failure. In fetal testes, LINE-1 (L1) transposable elements derepression and an aberrant piRNA profile in prospermatogonia, followed by cognate DNA demethylation are observed.
AO090701000118 uncharacterized protein from Aspergillus oryzae RIB40
38% identity, 17% coverage
NIH_ARATH / F4IDQ6 DExH-box ATP-dependent RNA helicase DExH2; DEIH-box RNA/DNA helicase; EC 3.6.4.13; EC 3.6.4.12 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G06670 NIH (NUCLEAR DEIH-BOXHELICASE); DNA binding / DNA helicase from Arabidopsis thaliana
35% identity, 15% coverage
NP_178223 ATP binding / ATP-dependent helicase/ RNA binding / double-stranded RNA binding / helicase/ nucleic acid binding from Arabidopsis thaliana
37% identity, 21% coverage
DHX36_MOUSE / Q8VHK9 ATP-dependent DNA/RNA helicase DHX36; DEAD/H box polypeptide 36; DEAH box protein 36; MLE-like protein 1; RNA helicase associated with AU-rich element ARE; EC 3.6.4.13 from Mus musculus (Mouse) (see 5 papers)
NP_082412 ATP-dependent DNA/RNA helicase DHX36 from Mus musculus
35% identity, 24% coverage
- function: Multifunctional ATP-dependent helicase that unwinds G- quadruplex (G4) structures (PubMed:25611385). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (PubMed:21590736, PubMed:21703541). G4 structures correspond to helical structures containing guanine tetrads (By similarity). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-DNA and G4-RNA) (By similarity). Plays a role in genomic integrity (By similarity). Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (By similarity). Plays a role in transcriptional regulation. Resolves G4-DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (By similarity) (PubMed:25611385). Plays a role in post-transcriptional regulation (By similarity). Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre-mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (By similarity). Binds to the precursor-microRNA-134 (pre-miR- 134) terminal loop and regulates its transport into the synapto- dendritic compartment (By similarity). Involved in the pre-miR-134- dependent inhibition of target gene expression and the control of dendritic spine size (By similarity). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability (By similarity). Binds to both G4-RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression (By similarity). Binds to both G4-RNA structure in the 5'-UTR and AU-rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1-dependent manner, respectively (By similarity). Also binds to ARE sequences present in several mRNAs mediating exosome- mediated 3'-5' mRNA degradation (By similarity). Involved in cytoplasmic urokinase-type plasminogen activator (uPA) mRNA decay (By similarity). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1 (PubMed:21703541). Required for the early embryonic development and hematopoiesis (PubMed:22422825). Involved in the regulation of cardioblast differentiation and proliferation during heart development (PubMed:26489465). Involved in spermatogonia differentiation (PubMed:25611385). May play a role in ossification (PubMed:21590736).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
cofactor: Mg(2+)
subunit: Found in a multi-helicase-TICAM1 complex at least composed of DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells with or without dsRNA poly(I:C) ligand stimulation (PubMed:21703541). Interacts (via C-terminus) with TICAM1 (via TIR domain) (PubMed:21703541). Interacts (via C-terminus) with DDX21; this interaction serves as bridges to TICAM1 (PubMed:21703541). Interacts with TERT; this interaction is dependent on the ability of DHX36 to bind to the G-quadruplex RNA (G4-RNA) structure present in the telomerase RNA template component (TERC). Interacts with DKC1; this interaction is dependent on the ability of DHX36 to bind to the G4-RNA structure present in TERC. Interacts with PARN; this interaction stimulates PARN to enhance uPA mRNA decay. Interacts with EXOSC3; this interaction occurs in a RNase-insensitive manner. Interacts with EXOSC10; this interaction occurs in a RNase-insensitive manner. Interacts with ILF3; this interaction occurs in a RNA-dependent manner. Interacts with ELAVL1; this interaction occurs in an RNA-dependent manner. Interacts with DDX5; this interaction occurs in a RNA-dependent manner. Interacts with DDX17; this interaction occurs in a RNA- dependent manner. Interacts with HDAC1; this interaction occurs in a RNA-dependent manner (By similarity) (PubMed:21590736). Interacts with HDAC3; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with HDAC4 (PubMed:21590736). Interacts with AGO1. Interacts with AGO2 (By similarity). Interacts with ERCC6 (By similarity).
disruption phenotype: Mice die at around embryonic 7 days post-coitum (dpc). Conditional knockout mice in the hematopoeitic system leads to hemolytic anemia, a reduction in blood platelet and erythroblast development (PubMed:22422825). Cardiac progenitor-cell-specific knockout mice die around 12.5 dpc and lead to abnormal cardiovascular development with a reduction in cardiomyocyte proliferation. Mice display increased NKX2-5 mRNA but decreased NKX2-5 protein levels, respectively, in the heart at 12.5 dpc compared to wild-type mice (PubMed:26489465). Male germ-cell-specific knockout mice lead to testicular hypoplasia development, due to spermatogonia differentiation block, meiosis initiation arrest as early as meiosis I stage and an absence of mature sperm in the epididymis (PubMed:25611385). Mice show several alteration in meiosis-related gene expression such as the differentiating spermatogonia markers KIT/c-kit (PubMed:25611385). - Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU
Lattmann, Nucleic acids research 2010 - “...RHAU orthologues listed are: human ( Homo sapiens , NP_065916), mouse ( Mus musculus , NP_082412), chicken ( Gallus gallus , XP_422834), frog ( Xenopus tropicalis , ENSXETP00000016958), zebrafish ( Danio rerio , NP_001122016), fruit fly ( Drosophila melanogaster , NP_610056), blood fluke ( Schistosoma mansoni...”
- Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain
Chalupníková, The Journal of biological chemistry 2008 - “...(Homo sapiens, NP_065916), mouse (Mus musculus, NP_082412), chicken (Gallus gallus, XP_422834), frog (Xenopus tropicalis, ENSXETP00000016953), zebrafish (Danio...”
- Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells.
Frohn, Molecular & cellular proteomics : MCP 2012
DHX36_BOVIN / Q05B79 ATP-dependent DNA/RNA helicase DHX36; DEAD/H box polypeptide 36; DEAH-box protein 36; G4-resolvase-1; G4R1; MLE-like protein 1; RNA helicase associated with AU-rich element protein; EC 3.6.4.12; EC 3.6.4.13 from Bos taurus (Bovine) (see paper)
NP_001073720 ATP-dependent DNA/RNA helicase DHX36 from Bos taurus
34% identity, 24% coverage
- function: Multifunctional ATP-dependent helicase that unwinds G- quadruplex (G4) structures (PubMed:29899445). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (By similarity). G4 structures correspond to helical structures containing guanine tetrads (PubMed:29899445). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-DNA and G4- RNA) (By similarity) (PubMed:29899445). Plays a role in genomic integrity. Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (By similarity). Plays a role in transcriptional regulation. Resolves G4-DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (By similarity). Plays a role in post-transcriptional regulation. Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre- mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (By similarity). Binds to the precursor-microRNA-134 (pre-miR-134) terminal loop and regulates its transport into the synapto-dendritic compartment (By similarity). Involved in the pre-miR-134-dependent inhibition of target gene expression and the control of dendritic spine size (By similarity). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability (By similarity). Binds to both G4-RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression (By similarity). Binds to both G4-RNA structure in the 5'-UTR and AU-rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1- dependent manner, respectively (By similarity). Also binds to ARE sequences present in several mRNAs mediating exosome-mediated 3'-5' mRNA degradation (By similarity). Involved in cytoplasmic urokinase- type plasminogen activator (uPA) mRNA decay (By similarity). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro- inflammatory cytokines via the adapter molecule TICAM1 (By similarity). Required for the early embryonic development and hematopoiesis. Involved in the regulation of cardioblast differentiation and proliferation during heart development. Involved in spermatogonia differentiation. May play a role in ossification (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
cofactor: Mg(2+)
subunit: Found in a multi-helicase-TICAM1 complex at least composed of DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells with or without dsRNA poly(I:C) ligand stimulation. Interacts (via C- terminus) with TICAM1 (via TIR domain). Interacts (via C-terminus) with DDX21; this interaction serves as bridges to TICAM1 (By similarity). Interacts with TERT; this interaction is dependent on the ability of DHX36 to bind to the G-quadruplex RNA (G4-RNA) structure present in the telomerase RNA template component (TERC). Interacts with DKC1; this interaction is dependent on the ability of DHX36 to bind to the G4-RNA structure present in TERC. Interacts with PARN; this interaction stimulates PARN to enhance uPA mRNA decay. Interacts with EXOSC3; this interaction occurs in a RNase-insensitive manner. Interacts with EXOSC10; this interaction occurs in a RNase-insensitive manner. Interacts with ILF3; this interaction occurs in a RNA-dependent manner. Interacts with ELAVL1; this interaction occurs in an RNA-dependent manner. Interacts with DDX5; this interaction occurs in a RNA-dependent manner. Interacts with DDX17; this interaction occurs in a RNA- dependent manner. Interacts with HDAC1; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with HDAC3; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with HDAC4 (By similarity). Interacts with AGO1. Interacts with AGO2 (By similarity). Interacts with ERCC6 (By similarity). - Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36.
Chen, Nature 2018 - GeneRIF: co-crystal structure of bovine DHX36 bound to a DNA with a G-quadruplex and a 3' single-stranded DNA segment; the N-terminal DHX36-specific motif folds into a DNA-binding-induced alpha-helix that, together with the OB-fold-like subdomain, selectively binds parallel G-quadruplexes
DQX1_MOUSE / Q924H9 ATP-dependent RNA helicase DQX1; DEAQ box polypeptide 1; EC 3.6.4.12 from Mus musculus (Mouse) (see paper)
30% identity, 57% coverage
- catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
DHX36_HUMAN / Q9H2U1 ATP-dependent DNA/RNA helicase DHX36; DEAD/H box polypeptide 36; DEAH-box protein 36; G4-resolvase-1; G4R1; MLE-like protein 1; RNA helicase associated with AU-rich element protein; EC 3.6.4.12; EC 3.6.4.13 from Homo sapiens (Human) (see 20 papers)
NP_065916 ATP-dependent DNA/RNA helicase DHX36 isoform 1 from Homo sapiens
36% identity, 24% coverage
- function: Multifunctional ATP-dependent helicase that unwinds G- quadruplex (G4) structures (PubMed:16150737, PubMed:18854321, PubMed:20472641, PubMed:21586581). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (PubMed:14731398, PubMed:18279852, PubMed:21993297, PubMed:22238380, PubMed:25579584). G4 structures correspond to helical structures containing guanine tetrads (By similarity). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-DNA and G4-RNA) (PubMed:16150737, PubMed:18842585, PubMed:20472641, PubMed:21586581, PubMed:24369427, PubMed:26195789). Plays a role in genomic integrity (PubMed:22238380). Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (PubMed:20472641, PubMed:21149580, PubMed:21846770, PubMed:22238380, PubMed:24151078, PubMed:25579584). Plays a role in transcriptional regulation (PubMed:21586581, PubMed:21993297). Resolves G4-DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (PubMed:21993297). Plays a role in post-transcriptional regulation (PubMed:27940037). Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre- mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (PubMed:27940037). Binds to the precursor-microRNA-134 (pre-miR-134) terminal loop and regulates its transport into the synapto-dendritic compartment (By similarity). Involved in the pre-miR-134-dependent inhibition of target gene expression and the control of dendritic spine size (By similarity). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability (PubMed:24369427, PubMed:26489465). Binds to both G4-RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression (PubMed:24369427). Binds to both G4-RNA structure in the 5'-UTR and AU- rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1- dependent manner, respectively (PubMed:26489465). Also binds to ARE sequences present in several mRNAs mediating exosome-mediated 3'-5' mRNA degradation (PubMed:14731398, PubMed:18279852). Involved in cytoplasmic urokinase-type plasminogen activator (uPA) mRNA decay (PubMed:14731398). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1 (By similarity). Required for early embryonic development and hematopoiesis. Involved in the regulation of cardioblast differentiation and proliferation during heart development. Involved in spermatogonia differentiation. May play a role in ossification (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
cofactor: Mg(2+)
subunit: Found in a multi-helicase-TICAM1 complex at least composed of DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells with or without dsRNA poly(I:C) ligand stimulation (By similarity). Interacts (via C-terminus) with TICAM1 (via TIR domain) (By similarity). Interacts (via C-terminus) with DDX21; this interaction serves as bridges to TICAM1 (By similarity). Interacts with TERT; this interaction is dependent on the ability of DHX36 to bind to the G- quadruplex RNA (G4-RNA) structure present in the telomerase RNA template component (TERC) (PubMed:21846770). Interacts with DKC1; this interaction is dependent on the ability of DHX36 to bind to the G4-RNA structure present in TERC (PubMed:21846770). Interacts with PARN; this interaction stimulates PARN to enhance uPA mRNA decay (PubMed:14731398). Interacts with EXOSC3; this interaction occurs in a RNase-insensitive manner (PubMed:14731398). Interacts with EXOSC10; this interaction occurs in a RNase-insensitive manner (PubMed:14731398). Interacts with ILF3; this interaction occurs in a RNA-dependent manner (PubMed:14731398). Interacts with ELAVL1; this interaction occurs in an RNA-dependent manner (PubMed:14731398, PubMed:26489465). Interacts with DDX5; this interaction occurs in a RNA-dependent manner (PubMed:18279852). Interacts with DDX17; this interaction occurs in a RNA-dependent manner (PubMed:18279852). Interacts with HDAC1; this interaction occurs in a RNA-dependent manner (PubMed:18279852). Interacts with HDAC3; this interaction occurs in a RNA-dependent manner (PubMed:18279852). Interacts with HDAC4 (By similarity). Interacts with AGO1 (PubMed:17932509). Interacts with AGO2 (PubMed:17932509). Interacts with ERCC6 (PubMed:26030138). - Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures
Ban, Nucleic acids research 2024 - “...Heterogeneous nuclear ribonucleoprotein D0 ( 53 ) Q16666 IFI16 Gamma-interferon-inducible protein 16 ( 54 ) Q9H2U1 DHX36 ATP-dependent DNA/RNA helicase DHX36 ( 55 ) a G4BPs found in area vii in Figure 3C are summarized. Although the known iMBPs are properly enriched with the FiTE strategy,...”
- Unite and Conquer: Association of Two G-Quadruplex Aptamers Provides Antiproliferative and Antimigration Activity for Cells from High-Grade Glioma Patients
Pavlova, Pharmaceuticals (Basel, Switzerland) 2024 - “...= Homo sapiens OX = 9606 GN = PARP1 PE = 1 SV = 4 Q9H2U1 DHX36_HUMAN 211.11 28 1.44 10 8 47 47 101 114,760 ATP-dependent DNA/RNA helicase DHX36 OS = Homo sapiens OX = 9606 GN = DHX36 PE = 1 SV = 2...”
- Longitudinal Assessment of Nasopharyngeal Biomarkers Post-COVID-19: Unveiling Persistent Markers and Severity Correlations.
Redondo-Calvo, Journal of proteome research 2024 - “...ran-binding protein 9 2.61 2.17 RANBP9 Q96S59 DHX36 ATP-dependent DNA/RNA helicase DHX36 2.96 2.22 DHX36 Q9H2U1 COG3# conserved oligomeric Golgi complex subunit 3 2.10 2.24 COG3 Q96JB2 ACSA acetyl-coenzyme A synthetase, cytoplasmic 1.98 2.24 ACSS2 Q9NR19 DEOC deoxyribose-phosphate aldolase 2.00 2.24 DERA Q9Y315 RN5A 25A-dependent ribonuclease...”
- Prediction of Human Papillomavirus-Host Oncoprotein Interactions Using Deep Learning.
Santa, Bioinformatics and biology insights 2024 - “...0.8672 1 0.95859158 1 HPV31L2_S P17389 TIM50_HUMAN Q3ZCQ8 0.85303 1 0.548475564 1 HPV31L1_S P17388 DHX36_HUMAN Q9H2U1 0.84899 1 0.607559264 1 HPV31L1_S P17388 HNRL2_HUMAN Q1KMD3 0.82506 1 0.626150787 1 HPV31L2_S P17389 KANK2_HUMAN Q63ZY3 0.81256 1 0.530457973 1 HPV31L2_S P17389 C1QBP_HUMAN Q07021 0.76217 1 0.756749749 1 Table 2....”
- Comparative transcriptome of normal and cancer-associated fibroblasts.
Abikar, BMC cancer 2024 - “...O00425 protein ENSG00000163364 LINC01116 CRNKL1 Q9BZJ0 protein ENSG00000163364 LINC01116 IGF2BP1 Q9NZI8 protein ENSG00000163364 LINC01116 DHX36 Q9H2U1 protein ENSG00000163364 LINC01116 EZH2 A0A090N8E9 protein ENSG00000223485 LINC01615 IGF2BP3 O00425 protein NONHSAG099482 LINC01301 A1CF Q9NQ94 protein NONHSAG099482 LINC01301 A1CF Q9NQ94 protein NONHSAG099482 LINC01301 TRIM25 Q14258 protein NONHSAG099482 LINC01301 ZC3HAV1 Q7Z2W4...”
- “...Q12905 protein NONHSAG099482 LINC01301 IGF2BP1 Q9NZI8 protein NONHSAG099482 LINC01301 AGO2 Q9UKV8 protein NONHSAG099482 LINC01301 DHX36 Q9H2U1 protein NONHSAG099482 LINC01301 DHX36 Q9H2U1 protein NONHSAG016089 LINC02298 DMD A0A075B6G3 protein NONHSAG016089 LINC02298 TRIM25 Q14258 protein NONHSAG016089 LINC02298 IGF2BP3 O00425 protein NONHSAG016089 LINC02298 SOX2 P48431 protein NONHSAG016089 LINC02298 IGF2BP1 Q9NZI8...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.
Meier, Nucleic acids research 2018 - “...of human DHX36(53-105) peptide (residues 53-105 of ATP-dependent RNA helicase DHX36, UniProtKB ( 43 ) Q9H2U1 or DHX36_HUMAN) by hanging drop vapour diffusion with drop sizes of 2+2 l in 2.5 M NaCl, 10% (v/v) ethanol, 0.1 M sodium cacodylate, pH 6.5 at 20C. Crystals emerged...”
- Probing the prostate tumour microenvironment II: Impact of hypoxia on a cell model of prostate cancer progression
Tonry, Oncotarget 2017 - “...v AI Up 2 Q14938-5 NFIX_HUMAN 4.1 11.9 8 Hour AS v AI Up 2 Q9H2U1 DHX36_HUMAN 14.8 13.1 8 Hour AS v AI Down 2 O15355 PPM1G_HUMAN 20.2 15.2 AMPK Down 2 P30837 AL1B1_HUMAN 3.6 15.8 8 Hour AS v AI Down 2 Q05639 EF1A2_HUMAN...”
- More
- Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU
Lattmann, Nucleic acids research 2010 - “...underneath. Species and accession numbers of RHAU orthologues listed are: human ( Homo sapiens , NP_065916), mouse ( Mus musculus , NP_082412), chicken ( Gallus gallus , XP_422834), frog ( Xenopus tropicalis , ENSXETP00000016958), zebrafish ( Danio rerio , NP_001122016), fruit fly ( Drosophila melanogaster ,...”
- Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain
Chalupníková, The Journal of biological chemistry 2008 - “...numbers are as follows: human (Homo sapiens, NP_065916), mouse (Mus musculus, NP_082412), chicken (Gallus gallus, XP_422834), frog (Xenopus tropicalis,...”
DHX36_RAT / D4A2Z8 ATP-dependent DNA/RNA helicase DHX36; DEAD/H box polypeptide 36; DEAH-box protein 36; G4-resolvase-1; G4R1; MLE-like protein 1; RNA helicase associated with AU-rich element protein; EC 3.6.4.12; EC 3.6.4.13 from Rattus norvegicus (Rat) (see paper)
NP_001101148 ATP-dependent DNA/RNA helicase DHX36 from Rattus norvegicus
35% identity, 24% coverage
- function: Multifunctional ATP-dependent helicase that unwinds G- quadruplex (G4) structures (By similarity). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (PubMed:23651854). G4 structures correspond to helical structures containing guanine tetrads (By similarity). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-DNA and G4-RNA) (By similarity). Plays a role in genomic integrity. Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (By similarity). Plays a role in transcriptional regulation. Resolves G4- DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (By similarity). Plays a role in post-transcriptional regulation. Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre-mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (By similarity). Binds to the precursor-microRNA-134 (pre- miR-134) terminal loop and regulates its transport into the synapto- dendritic compartment (PubMed:23651854). Involved in the pre-miR-134- dependent inhibition of target gene expression and the control of dendritic spine size (PubMed:23651854). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability. Binds to both G4- RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression. Binds to both G4-RNA structure in the 5'-UTR and AU-rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1- dependent manner, respectively. Also binds to ARE sequences present in several mRNAs mediating exosome-mediated 3'-5' mRNA degradation. Involved in cytoplasmic urokinase-type plasminogen activator (uPA) mRNA decay (By similarity). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1. Required for the early embryonic development and hematopoiesis. Involved in the regulation of cardioblast differentiation and proliferation during heart development. Involved in spermatogonia differentiation. May play a role in ossification (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
cofactor: Mg(2+)
subunit: Found in a multi-helicase-TICAM1 complex at least composed of DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells with or without dsRNA poly(I:C) ligand stimulation. Interacts (via C- terminus) with TICAM1 (via TIR domain). Interacts (via C-terminus) with DDX21; this interaction serves as bridges to TICAM1 (By similarity). Interacts with TERT; this interaction is dependent on the ability of DHX36 to bind to the G-quadruplex RNA (G4-RNA) structure present in the telomerase RNA template component (TERC). Interacts with DKC1; this interaction is dependent on the ability of DHX36 to bind to the G4-RNA structure present in TERC. Interacts with PARN; this interaction stimulates PARN to enhance uPA mRNA decay. Interacts with EXOSC3; this interaction occurs in a RNase-insensitive manner. Interacts with EXOSC10; this interaction occurs in a RNase-insensitive manner. Interacts with ILF3; this interaction occurs in a RNA-dependent manner. Interacts with ELAVL1; this interaction occurs in an RNA-dependent manner. Interacts with DDX5; this interaction occurs in a RNA-dependent manner. Interacts with DDX17; this interaction occurs in a RNA- dependent manner. Interacts with HDAC1; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with HDAC3; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with HDAC4 (By similarity). Interacts with AGO1. Interacts with AGO2 (By similarity). Interacts with ERCC6 (By similarity). - The DEAH-box helicase DHX36 mediates dendritic localization of the neuronal precursor-microRNA-134.
Bicker, Genes & development 2013 - GeneRIF: DHX36 is required for dendritic localization of pre-miR-134 in hippocampal neurons
- Proteomic Analysis of the Amygdala Reveals Dynamic Changes in Glutamate Transporter-1 During Progression of Complete Freund's Adjuvant-Induced Pain Aversion.
Wu, Molecular neurobiology 2023 - “...(glial high affinity glutamate transporter), member 2 Amyotrophic lateral sclerosis (ALS) Glutamatergic synapse 2.214674084 0.401431656 D4A2Z8 DEAH (Asp-Glu-Ala-His) box polypeptide 36 ATP-dependent RNA helicase DHX36 RNA degradation 0.809824354 0.805031089 Q3KRE3 Guanine nucleotide-binding protein subunit gamma guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-10 Cholinergic synapse Morphine addiction PI3K-Akt...”
- “...and day 15 groups, including Q641Y7, D4A7X5, Q8R4T5, D4ADD7, A0A0G2JTL7, M0RCA3, D3ZGY4, M0R6D6, F1M378, Q8R462, D4A2Z8, Q3KRE3, and Q6IFV3 (Table 3 ). These DEPs were involved in glutamatergic, cholinergic, and GABAergic synapses, morphine addiction, PI3K-Akt signalling pathway, as well as dopaminergic and serotonergic synapses. We used...”
- Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons
Al, The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 (secret) - Identification of differentially expressed proteins involved in fetal scarless wound healing using a rat model of cleft lip.
Yan, Molecular medicine reports 2021 - “...homolog 4 0.043 0.557 F1M754 Map4k4 Mitogen-activated protein kinase kinase kinase kinase 4 0.022 0.526 D4A2Z8 Dhx36 Probable ATP-dependent RNA helicase DHX36 0.009 0.522 P31430 Dpep1 Dipeptidase 1 0.010 0.513 Q6AXY8 Dhrs1 Dehydrogenase/reductase SDR family member 1 0.019 0.495 D4A414 Cox15 COX15 homolog 0.031 0.476 D4ABV5...”
M3VK01 RNA helicase from Sus scrofa
34% identity, 24% coverage
Afu6g04330 DEAH-box RNA helicase (Dhr1), putative from Aspergillus fumigatus Af293
38% identity, 17% coverage
DHX9_MOUSE / O70133 ATP-dependent RNA helicase A; DEAH box protein 9; mHEL-5; Nuclear DNA helicase II; NDH II; RNA helicase A; RHA; EC 3.6.4.13 from Mus musculus (Mouse) (see 8 papers)
O70133 RNA helicase (EC 3.6.4.13) from Mus musculus (see paper)
35% identity, 17% coverage
- function: Multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and that plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. Requires a 3'-single-stranded tail as entry site for acid nuclei unwinding activities as well as the binding and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide triphosphates (NTPs). Unwinds numerous nucleic acid substrates such as double-stranded (ds) DNA and RNA, DNA:RNA hybrids, DNA and RNA forks composed of either partially complementary DNA duplexes or DNA:RNA hybrids, respectively, and also DNA and RNA displacement loops (D- and R-loops), triplex-helical DNA (H-DNA) structure and DNA- and RNA-based G-quadruplexes. Binds dsDNA, single-stranded DNA (ssDNA), dsRNA, ssRNA and poly(A)-containing RNA. Also binds to circular dsDNA or dsRNA of either linear and/or circular forms and stimulates the relaxation of supercoiled DNAs catalyzed by topoisomerase TOP2A. Plays a role in DNA replication at origins of replication and cell cycle progression. Plays a role as a transcriptional coactivator acting as a bridging factor between polymerase II holoenzyme and transcription factors or cofactors, such as BRCA1, CREBBP, RELA and SMN1. Binds to the CDKN2A promoter. Plays several roles in post-transcriptional regulation of gene expression. In cooperation with NUP98, promotes pre-mRNA alternative splicing activities of a subset of genes (By similarity). As component of a large PER complex, is involved in the negative regulation of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms (PubMed:22767893). Also acts as a nuclear resolvase that is able to bind and neutralize harmful massive secondary double-stranded RNA structures formed by inverted-repeat Alu retrotransposon elements that are inserted and transcribed as parts of genes during the process of gene transposition (PubMed:28355180). Involved in the positive regulation of nuclear export of constitutive transport element (CTE)- containing unspliced mRNA. Component of the coding region determinant (CRD)-mediated complex that promotes cytoplasmic MYC mRNA stability. Plays a role in mRNA translation. Positively regulates translation of selected mRNAs through its binding to post-transcriptional control element (PCE) in the 5'-untranslated region (UTR). Involved with LARP6 in the translation stimulation of type I collagen mRNAs for CO1A1 and CO1A2 through binding of a specific stem-loop structure in their 5'- UTRs. Stimulates LIN28A-dependent mRNA translation probably by facilitating ribonucleoprotein remodeling during the process of translation. Also plays a role as a small interfering (siRNA)-loading factor involved in the RNA-induced silencing complex (RISC) loading complex (RLC) assembly, and hence functions in the RISC-mediated gene silencing process. Binds preferentially to short double-stranded RNA, such as those produced during rotavirus intestinal infection (PubMed:28636595). This interaction may mediate NLRP9 inflammasome activation and trigger inflammatory response, including IL18 release and pyroptosis (PubMed:28636595). Finally, mediates the attachment of heterogeneous nuclear ribonucleoproteins (hnRNPs) to actin filaments in the nucleus (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (By similarity). The large PER complex involved in the repression of transcriptional termination is composed of at least PER2, CDK9, DDX5, DHX9, NCBP1 and POLR2A (active) (PubMed:22767893). Associates (via DRBM domains) with the RISC complex; this association occurs in a small interfering (siRNA)-dependent manner. Associates with the SMN complex; this association induces recruitment of DHX9 to the RNA polymerase II. Associates with polysomes in a LIN28A-dependent manner. Interacts (via C-terminus) with ACTB; this interaction is direct and mediates the attachment to nuclear ribonucleoprotein complexes (By similarity). Interacts with ADAR isoform 1; this interaction occurs in a RNA-independent manner (PubMed:28355180). Interacts (via DRBM domains) with AGO2 (via middle region); this interaction promotes active RISC assembly by promoting the association of siRNA with AGO2. Interacts (via NTD domain) with AKAP8L (via N- terminus). Interacts with BRCA1 (via C-terminus); this interaction is direct and links BRCA1 to the RNA polymerase II holoenzyme. Interacts (via N-terminus) with CREBBP; this interaction mediates association with RNA polymerase II holoenzyme and stimulates CREB-dependent transcriptional activation (By similarity). Interacts (via N-terminus) with EIF2AK2/PKR; this interaction is dependent upon the activation of the kinase (PubMed:19229320). Interacts (via DRBM domains) with DICER1. Interacts with H2AX; this interaction is direct, requires phosphorylation of histone H2AX on 'Ser-140' by PRKDC and promotes binding of DHX9 to transcriptionally stalled sites on chromosomal DNA in response to genotoxic stress. Interacts with HNRNPC; this interaction is direct, enhanced probably by their concomitant binding to RNA and mediates the attachment to actin filaments. Interacts (via NTD domain) with PRMT1. Interacts with IGF2BP1. Interacts with IGF2BP2, IGF2BP3. Interacts (via DRBM domains) with ILF3; this interaction occurs in a RNA-independent manner. Interacts with Importin alpha/Importin beta receptor. Interacts with LARP6 (via C-terminus); this interaction occurs in a mRNA-independent manner. Interacts (via N- and C-terminus) with LIN28A (via C-terminus); this interaction occurs in a RNA-independent manner. Interacts with LMX1B. Interacts (via helicase C-terminal domain, HA2 and OB-fold regions) with MAVS (via CARD domain); this interaction occurs in both resting and double- stranded RNA poly(I:C)-induced cells. Interacts with MBD2; this interaction stimulates transcriptional activation in a CREB-dependent manner. Interacts (via H2A and OB-fold regions) with MYD88 (via TIR domain); this interaction is direct. Interacts with NLRP9 upon rotavirus infection; this interaction may trigger NLRP9 inflammasome activation and inflammatory response. Interacts (via DRBM, OB-fold and RGG regions) with NUP98 (via N-terminus); this interaction occurs in a RNA-dependent manner and stimulates DHX9-mediated ATPase activity and regulates transcription and splicing of a subset of genes. Interacts (via N-terminus) with NXF1 (via N-terminus); this interaction is direct and negatively regulates NXF1-mediated nuclear export of constitutive transport element (CTE)-containing cellular mRNAs. Interacts with RELA; this interaction is direct and activates NF-kappa-B-mediated transcription. Interacts (via MTAD region) with RNA polymerase II holoenzyme; this interaction stimulates transcription activation in a CREB-dependent manner. Interacts (via RGG region) with SMN1; this interaction links SMN1 to the RNA polymerase II holoenzyme (By similarity). Interacts with SP7 (PubMed:17303075). Interacts (via DRBM domains) with TARBP2 (via DRBM first and second domains); this interaction occurs in a small interfering (siRNA)-dependent manner. Interacts with TOP2A; this interaction occurs in a E2 enzyme UBE2I- and RNA-dependent manner, negatively regulates DHX9-mediated double- stranded DNA and RNA duplex helicase activity and stimulates TOP2A- mediated supercoiled DNA relaxation activity. Interacts (via DRBM domains and C-terminus) with WRN (via 3'-5' exonuclease domain); this interaction inhibits the DNA-dependent NTPase and DNA helicase activities of DHX9 and stimulates the 3'-5' exonuclease activity of WRN. Interacts with XRCC5; this interaction occurs in a RNA-dependent manner (By similarity). Interacts with ZIC2 (via C2H2-type domain 3) (PubMed:17251188). Interacts with MCM3AP (By similarity).
disruption phenotype: Mice are viable but have behavioral and neurological abnormalities. They exhibit hypoactivity in novel environments, tremor, and sensorineural hearing loss. - Hemopexin reverses activation of lung eIF2α and decreases mitochondrial injury in chlorine-exposed mice.
Matalon, American journal of physiology. Lung cellular and molecular physiology 2024 - RNF128 regulates neutrophil infiltration and myeloperoxidase functions to prevent acute lung injury
Liu, Cell death & disease 2023 - “...NHP2-like protein 1 OS=Mus musculus OX=10090 GN=Snu13 PE=1 SV=4 - [NH2L1_MOUSE] Snu13 179.43 66.69 2.690508322 O70133 ATP-dependent RNA helicase A OS=Mus musculus OX=10090 GN=Dhx9 PE=1 SV=2[DHX9_MOUSE] Dhx9 292.4390632 111.8318968 2.614987955 P63276 40S ribosomal protein S17 OS=Mus musculus OX=10090 GN=Rps17 PE=1 SV=2[RS17_MOUSE] Rps17 156.7504083 61.14 2.563794706 P27546...”
- Peroxiredoxin 5 regulates osteogenic differentiation through interaction with hnRNPK during bone regeneration
Cho, eLife 2023 - “...Space 2.311 2.063 1.278 H3BJS5 Melanoma inhibitory activity protein 2 (Fragment) Mia2 Cytoplasm 0.863 0.541 O70133 ATP-dependent RNA helicase A Dhx9 Nucleus 0.157 0.197 P24369 Peptidyl-prolyl cis - trans isomerase B Ppib Cytoplasm 13.511 10.12 12.063 F6T9C3 Translation initiation factor eIF-2B subunit (Fragment) Eif2b5 Cytoplasm 1.959...”
- “...Collagen -1(VIII) chain Col8a1 Extracellular space 0.202 Q61510 E3 ubiquitin/ISG15 ligase TRIM25 Trim25 Cytoplasm 0.202 O70133 ATP-dependent RNA helicase A Dhx9 Nucleus 0.177 Figure 6. Heterogeneous nuclear ribonucleoprotein K (hnRNPK) interacts with peroxiredoxin 5 (Prdx5) in osteoblasts. ( A ) To determine co-localization, osteoblasts were stained...”
- Doublecortin facilitates the elongation of the somatic Golgi apparatus into proximal dendrites.
Li, Molecular biology of the cell 2021 - “...3.47 10 0.35 P26040 Ezrin 3.47 9 0.39 Q8K3G9 DCC-interacting protein 13-beta 6.95 18 0.39 O70133 ATP-dependent RNA helicase A 17.37 44 0.39 Q501J6 Probable ATP-dependent RNA helicase DDX17 11.58 29 0.4 P02089 Hemoglobin subunit beta-2 31.26 78 0.4 Q08509 Epidermal growth factor receptor kinase substrate...”
- The Long Linker Region of Telomere-Binding Protein TRF2 Is Responsible for Interactions with Lamins.
Travina, International journal of molecular sciences 2021 - “...PRP8 Q99PV0 Pre-mRNA-processing-splicing factor 8 1 H0V9E4 H0V9E4 Probable ATP-dependent RNA helicase DDX5 4 DHX9 O70133 ATP-dependent RNA helicase A (DHX9) 7 E9PV04 E9PV04 Eukaryotic translation initiation factor 4A3-like 1 1 TOP1 Q04750 DNA topoisomerase I 2 HSP7C P63017 Heat shock cognate 71 kDa protein 3...”
- Vascular permeability disruption explored in the proteomes of mouse lungs and human microvascular cells following acute bromine exposure
Addis, American journal of physiology. Lung cellular and molecular physiology 2020 (secret) - Alport syndrome: Proteomic analysis identifies early molecular pathway alterations in Col4a3 knock out mice.
Nicolaou, Nephrology (Carlton, Vic.) 2020 - “...P17809 GTR1 2.83E03 0.5 NN MM Solute carrier family 2, facilitated glucose transporter member 1 O70133 DHX9 1.61E03 0.5 NN MM ATPdependent RNA helicase A O88322 NID2 4.49E03 0.5 NN MM Nidogen2 Q8CIE6 COPA 2.24E02 0.5 NN MM Coatomer subunit alpha O70456 1433S 4.88E02 0.5 NN...”
- Stat3-mediated alterations in lysosomal membrane protein composition.
Lloyd-Lewis, The Journal of biological chemistry 2018 - “...Q80VQ0 Aldh3b1 Aldehyde dehydrogenase family 3 member B1 P35821 Ptpn1 Tyrosine-protein phosphatase non-receptor type 1 O70133 Dhx9 ATP-dependent RNA helicase A Q9DBG3 Ap2b1 AP-2 complex subunit P14901 Hmox1 Heme oxygenase 1 Q6P9J9 Ano6 Anoctamin-6 Q8BTM8 Flna Filamin-A Q61739 Itga6 Integrin -6 P97384 Anxa11 Annexin A11 Q62261...”
- More
An15g01160 uncharacterized protein from Aspergillus niger
31% identity, 24% coverage
- The Effect of Cyclosporin A on Aspergillus niger and the Possible Mechanisms Involved
Li, Foods (Basel, Switzerland) 2023 - “...eleven variable categories of biological processes ( Figure 5 C). ATP-dependent RNA helicases (An08g07790, An01g09040, An15g01160, and An02g06750) were involved in multiple rRNAs or in pre-rRNA formation. The keys to tRNA processing and maturation were the methyltransferases of structural modification of tRNA (An01g09640, TRM82, An01g00070, and...”
- Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy
Hagiwara, BMC genomics 2016 - “...ribosomal subunit L7, putative Afu2g02150 An07g06760 AO090011000490 15.5 20.0 12.7 S10a Ribosomal protein S10 Afu6g04330 An15g01160 AO090701000118 15.1 35.8 12.0 - DEAH-box RNA helicase (Dhr1), putative Afu1g05390 An18g04220 AO090009000405 14.8 28.8 10.6 - Mitochondrial ADP,ATP carrier protein (Ant), putative Afu1g11710 An08g03910 AO090038000249 13.9 16.2 13.2 -...”
D4A9D6 RNA helicase from Rattus norvegicus
35% identity, 20% coverage
- Proteomic analysis of spinal dorsal horn in prior exercise protection against neuropathic pain.
Chen, Scientific reports 2025 - “...to the CCI group. A total of 13 overlapping DEPs (protein accession: B1H216, B0BNN3, O55158, D4A9D6, P17475, Q63910, Q62669, P06866, A0A0G2JU, P06399, P02091, P02680 and P02770) were upregulated after CCI and downregulated in prior exercise (Fig. 2 C and Table 1 ). Table 1 shows the...”
- “...Carbonic anhydrase 1 Ca1 212.15 0.00564 0.0030593 0.00544 O55158 Tetraspanin Tspan8 6.1912 0.00332 0.45608 0.00840 D4A9D6 RNA helicase Dhx9 3.9999 0.01312 0.2689 0.01153 P17475 Alpha-1-antiproteinase Serpina1 206.69 1.64E-08 0.0031391 1.05E-08 Q63910 Globin c1 Hba-a2 89.312 3.86E-09 0.11579 0.00263 Q62669 Globin a1 Hbb-b1 8.9919 0.00090 0.4045 0.04458...”
- Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons
Al, The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 (secret) - Long-term evaluation of safety and biological effects of Korean Red Ginseng (Panax Ginseng): a long-term in vivo study.
Park, BMC complementary medicine and therapies 2022 - “...-1.515 0.039 Complement C8 beta chain P55314 C8B ES other -1.561 0.037 DExH-box helicase 9 D4A9D6 DHX9 Nucleus enzyme -1.655 0.040 ATP synthase F1 subunit beta P10719 ATP5F1B Cytoplasm transporter -1.731 0.032 Lactate dehydrogenase A P04642 Ldha/RGD1562690 Cytoplasm enzyme -1.756 0.003 40S ribosomal protein S26 A0A0G2JY64...”
- Hyperbaric Oxygen Therapy-Induced Molecular and Pathway Changes in a Rat Model of Spinal Cord Injury: A Proteomic Analysis.
Li, Dose-response : a publication of International Hormesis Society 2022 - “...FGG .82 Down B3AT 1.27 Up LAMB1 .82 Down G3V7W1 1.27 Up OGN .82 Down D4A9D6 1.33 Up ERMN 1.21 Up D3ZVB7 1.41 Up HBB2 1.43 Up LEG5 1.49 Up Q62669 1.49 Up HBA 1.59 Up Figure 2. Identification and quantitation of differentially expressed proteins by...”
XP_019677306 ATP-dependent RNA helicase A isoform X1 from Felis catus
35% identity, 18% coverage
E9QNN1 RNA helicase from Mus musculus
35% identity, 17% coverage
Q5R874 ATP-dependent RNA helicase A from Pongo abelii
36% identity, 18% coverage
PF3D7_0821300 ATP-dependent RNA helicase DHX36, putative from Plasmodium falciparum 3D7
28% identity, 27% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500 Helicase+HA2+S1 PF3D7_1030100 Helicase+HA2+OB fold PF3D7_1364300, PF3D7_1231600, PF3D7_0917600, PF3D7_0821300 Helicase+ZnF+DSHCT PF3D7_0909900 Helicase+rRNA proc-arch+DSHCT PF3D7_0602100 Helicase+HA2 PF3D7_0310500, PF3D7_1302700 Blue , pink and green boxes are used to denote transmembrane, low complexity, and coiled-coil regions, respectively To further illustrate the conservation...”
- “...5 ). Of the 48 RNA helicases, five genes are upregulated in ookinetes (PF3D7_1459000, PF3D7_1021500, PF3D7_0821300, PF3D7_0602100 and PF3D7_0508700), whereas others conform to the general transcriptional program with reduced transcription at schizont stage. Fig. 5 A heatmap of the expression profiles of PfRBPs throughout the blood...”
DHX9_HUMAN / Q08211 ATP-dependent RNA helicase A; DEAH box protein 9; DExH-box helicase 9; Leukophysin; LKP; Nuclear DNA helicase II; NDH II; RNA helicase A; EC 3.6.4.13 from Homo sapiens (Human) (see 58 papers)
Q08211 RNA helicase (EC 3.6.4.13) from Homo sapiens (see 4 papers)
NP_001348 ATP-dependent RNA helicase A from Homo sapiens
36% identity, 18% coverage
- function: Multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and that plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing (PubMed:11416126, PubMed:12711669, PubMed:15355351, PubMed:16680162, PubMed:17531811, PubMed:20669935, PubMed:21561811, PubMed:24049074, PubMed:24990949, PubMed:25062910, PubMed:28221134, PubMed:9111062, PubMed:37467750). Requires a 3'- single-stranded tail as entry site for acid nuclei unwinding activities as well as the binding and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide triphosphates (NTPs) (PubMed:1537828). Unwinds numerous nucleic acid substrates such as double-stranded (ds) DNA and RNA, DNA:RNA hybrids, DNA and RNA forks composed of either partially complementary DNA duplexes or DNA:RNA hybrids, respectively, and also DNA and RNA displacement loops (D- and R-loops), triplex-helical DNA (H-DNA) structure and DNA and RNA-based G-quadruplexes (PubMed:20669935, PubMed:21561811, PubMed:24049074). Binds dsDNA, single-stranded DNA (ssDNA), dsRNA, ssRNA and poly(A)-containing RNA (PubMed:10198287, PubMed:9111062). Also binds to circular dsDNA or dsRNA of either linear and/or circular forms and stimulates the relaxation of supercoiled DNAs catalyzed by topoisomerase TOP2A (PubMed:12711669). Plays a role in DNA replication at origins of replication and cell cycle progression (PubMed:24990949). Plays a role as a transcriptional coactivator acting as a bridging factor between polymerase II holoenzyme and transcription factors or cofactors, such as BRCA1, CREBBP, RELA and SMN1 (PubMed:11038348, PubMed:11149922, PubMed:11416126, PubMed:15355351, PubMed:28221134, PubMed:9323138, PubMed:9662397). Binds to the CDKN2A promoter (PubMed:11038348). Plays several roles in post-transcriptional regulation of gene expression (PubMed:28221134, PubMed:28355180). In cooperation with NUP98, promotes pre-mRNA alternative splicing activities of a subset of genes (PubMed:11402034, PubMed:16680162, PubMed:28221134, PubMed:28355180). As component of a large PER complex, is involved in the negative regulation of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms (By similarity). Also acts as a nuclear resolvase that is able to bind and neutralize harmful massive secondary double-stranded RNA structures formed by inverted-repeat Alu retrotransposon elements that are inserted and transcribed as parts of genes during the process of gene transposition (PubMed:28355180). Involved in the positive regulation of nuclear export of constitutive transport element (CTE)-containing unspliced mRNA (PubMed:10924507, PubMed:11402034, PubMed:9162007). Component of the coding region determinant (CRD)-mediated complex that promotes cytoplasmic MYC mRNA stability (PubMed:19029303). Plays a role in mRNA translation (PubMed:28355180). Positively regulates translation of selected mRNAs through its binding to post-transcriptional control element (PCE) in the 5'-untranslated region (UTR) (PubMed:16680162). Involved with LARP6 in the translation stimulation of type I collagen mRNAs for CO1A1 and CO1A2 through binding of a specific stem-loop structure in their 5'-UTRs (PubMed:22190748). Stimulates LIN28A- dependent mRNA translation probably by facilitating ribonucleoprotein remodeling during the process of translation (PubMed:21247876). Plays also a role as a small interfering (siRNA)-loading factor involved in the RNA-induced silencing complex (RISC) loading complex (RLC) assembly, and hence functions in the RISC-mediated gene silencing process (PubMed:17531811). Binds preferentially to short double- stranded RNA, such as those produced during rotavirus intestinal infection (PubMed:28636595). This interaction may mediate NLRP9 inflammasome activation and trigger inflammatory response, including IL18 release and pyroptosis (PubMed:28636595). Finally, mediates the attachment of heterogeneous nuclear ribonucleoproteins (hnRNPs) to actin filaments in the nucleus (PubMed:11687588).
function: (Microbial infection) Plays a role in HIV-1 replication and virion infectivity (PubMed:11096080, PubMed:19229320, PubMed:25149208, PubMed:27107641). Enhances HIV-1 transcription by facilitating the binding of RNA polymerase II holoenzyme to the proviral DNA (PubMed:11096080, PubMed:25149208). Binds (via DRBM domain 2) to the HIV-1 TAR RNA and stimulates HIV-1 transcription of transactivation response element (TAR)-containing mRNAs (PubMed:11096080, PubMed:9892698). Involved also in HIV-1 mRNA splicing and transport (PubMed:25149208). Positively regulates HIV-1 gag mRNA translation, through its binding to post-transcriptional control element (PCE) in the 5'-untranslated region (UTR) (PubMed:16680162). Binds (via DRBM domains) to a HIV-1 double-stranded RNA region of the primer binding site (PBS)-segment of the 5'-UTR, and hence stimulates DHX9 incorporation into virions and virion infectivity (PubMed:27107641). Also plays a role as a cytosolic viral MyD88-dependent DNA and RNA sensors in plasmacytoid dendritic cells (pDCs), and hence induce antiviral innate immune responses (PubMed:20696886, PubMed:21957149). Binds (via the OB-fold region) to viral single-stranded DNA unmethylated C-phosphate-G (CpG) oligonucleotide (PubMed:20696886).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (PubMed:19029303). Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1 (PubMed:19029303). Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (PubMed:17289661). The large PER complex involved in the repression of transcriptional termination is composed of at least PER2, CDK9, DDX5, DHX9, NCBP1 and POLR2A (active) (By similarity). Associates (via DRBM domains) with the RISC complex; this association occurs in a small interfering (siRNA)-dependent manner (PubMed:17531811, PubMed:23361462). Associates with the SMN complex; this association induces recruitment of DHX9 to the RNA polymerase II (ref.8). Associates with polysomes in a LIN28A-dependent manner (PubMed:16680162, PubMed:21247876). Interacts (via C-terminus) with ACTB; this interaction is direct and mediates the attachment to nuclear ribonucleoprotein complexes (PubMed:11687588). Interacts with ADAR isoform 1; this interaction occurs in a RNA-independent manner (PubMed:28355180). Interacts (via DRBM domains) with AGO2 (via middle region); this interaction promotes active RISC assembly by promoting the association of siRNA with AGO2 (PubMed:17531811, PubMed:23361462). Interacts (via RGG region) with AKAP8L (via N-terminus) (PubMed:11402034). Interacts with BRCA1 (via C-terminus); this interaction is direct and links BRCA1 to the RNA polymerase II holoenzyme (PubMed:9662397). Interacts (via N-terminus) with CREBBP; this interaction mediates association with RNA polymerase II holoenzyme and stimulates CREB-dependent transcriptional activation (PubMed:9323138). Interacts (via N-terminus) with EIF2AK2/PKR; this interaction is dependent upon the activation of the kinase (PubMed:19229320). Interacts (via DRBM domains) with DICER1 (PubMed:17531811). Interacts with H2AX; this interaction is direct, requires phosphorylation of histone H2AX on 'Ser-140' by PRKDC and promotes binding of DHX9 to transcriptionally stalled sites on chromosomal DNA in response to genotoxic stress (PubMed:15613478, PubMed:17498979). Interacts with HNRNPC; this interaction is direct, enhanced probably by their concomitant binding to RNA and mediates the attachment to actin filaments (PubMed:11687588). Interacts (via RGG region) with PRMT1 (PubMed:15084609). Interacts with IGF2BP1 (PubMed:17289661, PubMed:23640942). Interacts with IGF2BP2, IGF2BP3 (PubMed:23640942). Interacts (via DRBM domains) with ILF3; this interaction occurs in a RNA-independent manner (PubMed:12946349). Interacts with Importin alpha/Importin beta receptor (PubMed:16375861). Interacts with LARP6 (via C-terminus); this interaction occurs in a mRNA-independent manner (PubMed:22190748). Interacts (via N- and C- terminus) with LIN28A (via C-terminus); this interaction occurs in a RNA-independent manner (PubMed:21247876). Interacts with LMX1B (PubMed:23308148). Interacts (via helicase C-terminal domain, HA2 and OB-fold regions) with MAVS (via CARD domain); this interaction occurs in both resting and double-stranded RNA poly(I:C)-induced cells (PubMed:21957149). Interacts with MBD2; this interaction stimulates transcriptional activation in a CREB-dependent manner (PubMed:12665568). Interacts (via H2A and OB-fold regions) with MYD88 (via TIR domain); this interaction is direct (PubMed:20696886). Interacts with NLRP9 upon rotavirus infection; this interaction may trigger NLRP9 inflammasome activation and inflammatory response (PubMed:28636595). Interacts (via DRBM, OB-fold and RGG regions) with NUP98 (via N-terminus); this interaction occurs in a RNA-dependent manner and stimulates DHX9-mediated ATPase activity and regulates transcription and splicing of a subset of genes (PubMed:28221134). Interacts (via N-terminus) with NXF1 (via N-terminus); this interaction is direct and negatively regulates NXF1-mediated nuclear export of constitutive transport element (CTE)-containing cellular mRNAs (PubMed:10924507). Interacts with RELA; this interaction is direct and activates NF-kappa-B-mediated transcription (PubMed:15355351). Interacts (via MTAD region) with RNA polymerase II holoenzyme; this interaction stimulates transcription activation in a CREB-dependent manner (PubMed:11149922, PubMed:11416126, PubMed:9323138). Interacts (via RGG region) with SMN1; this interaction links SMN1 to the RNA polymerase II holoenzyme (PubMed:11149922). Interacts with SP7 (PubMed:17303075). Interacts (via DRBM domains) with TARBP2 (via DRBM first and second domains); this interaction occurs in a small interfering (siRNA)-dependent manner (PubMed:17531811, PubMed:23361462). Interacts with TOP2A; this interaction occurs in a E2 enzyme UBE2I- and RNA-dependent manner, negatively regulates DHX9- mediated double-stranded DNA and RNA duplex helicase activity and stimulates TOP2A-mediated supercoiled DNA relaxation activity (PubMed:12711669). Interacts (via DRBM domains and C-terminus) with WRN (via 3'-5' exonuclease domain); this interaction inhibits the DNA- dependent NTPase and DNA helicase activities of DHX9 and stimulates the 3'-5' exonuclease activity of WRN (PubMed:15995249). Interacts with XRCC5; this interaction occurs in a RNA-dependent manner (PubMed:14704337). Interacts with ZIC2 (via C2H2-type domain 3) (PubMed:17251188). Interacts with MCM3AP isoform GANP (PubMed:23652018).
subunit: (Microbial infection) Interacts with Chikungunya virus non- structural protein 3 (via C-terminus); this interaction allows the recruitment of DHX9 to the plasma membrane, where it associates with viral replication complexes and may play a role in the translation-to- replication switch.
subunit: (Microbial infection) Interacts with Epstein-Barr virus (EBV) mRNA export factor ICP27 homolog/SM protein; this interaction may have an inhibitory effect on virion production. - ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress.
Liu, Nucleic acids research 2024 - GeneRIF: ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress.
- The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma.
Chellini, Oncogene 2024 (PubMed)- GeneRIF: The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma.
- Complex interplay between FMRP and DHX9 during DNA replication stress.
Chakraborty, The Journal of biological chemistry 2024 - GeneRIF: Complex interplay between FMRP and DHX9 during DNA replication stress.
- AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer.
Huang, Cancer research 2024 - GeneRIF: AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer.
- Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells.
Cottrell, Cancer research communications 2024 - GeneRIF: Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells.
- DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells.
Ren, Nature communications 2024 - GeneRIF: DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells.
- AURKB targets DHX9 to promote hepatocellular carcinoma progression via PI3K/AKT/mTOR pathway.
Zhu, Molecular carcinogenesis 2024 (PubMed)- GeneRIF: AURKB targets DHX9 to promote hepatocellular carcinoma progression via PI3K/AKT/mTOR pathway.
- The pseudogene GBP1P1 suppresses influenza A virus replication by acting as a protein decoy for DHX9.
Yu, Journal of virology 2024 - GeneRIF: The pseudogene GBP1P1 suppresses influenza A virus replication by acting as a protein decoy for DHX9.
- More
- Comparative Analysis of Acquired Resistance to Bortezomib in Prostate Cancer Cells Using Proteomic and Bioinformatic Tools.
Seker, Journal of cellular and molecular medicine 2025 - “...3_ mitochondrial 13 3.983 2.472 79234.165 Q14247 CTTN Src substrate cortactin 4 3.968 2.634 61757.287 Q08211 DHX9 ATPdependent RNA helicase A 25 3.925 2.215 142270.353 P00492 HPRT1 Hypoxanthineguanine phosphoribosyltransferase 7 3.914 0.733 24807.545 O60841 EIF5B Eukaryotic translation initiation factor 5B 3 3.878 1.858 139283.262 P31942 HNRNPH3...”
- Proteomic Profiling Identifies Candidate Diagnostic Biomarkers of Hydrosalpinx in Endometrial Fluid: A Pilot Study
Gonzalez-Martin, International journal of molecular sciences 2024 - “...kDa phosphohistidine phosphatase 0.038 2.27 P0DMV9 HS71B Heat shock 70 kDa protein 1B 0.014 2.33 Q08211 DHX9 ATP-dependent RNA helicase A 0.024 2.33 P00966 ASSY Argininosuccinate synthase 0.038 2.63 O14773 TPP1 Tripeptidyl-peptidase 1 0.020 2.63 O94760 DDAH1 N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 0.040 3.03 Q96TA1 NIBA2 Protein Niban...”
- “...1.61 P15169 CBPN Carboxypeptidase N catalytic chain 0.025 1.79 P30085 KCY UMP-CMP kinase 0.037 2.00 Q08211 DHX9 ATP-dependent RNA helicase A 0.038 2.08 Q86Z20 CC125 Coiled-coil domain-containing protein 125 0.040 2.08 Q99536 VAT1 Synaptic vesicle membrane protein VAT-1 homolog 0.026 2.22 Q15582 BGH3 Transforming growth factor-beta-induced...”
- An engineered niche delineates metastatic potential of breast cancer.
Orbach, Bioengineering & translational medicine 2024 - “...of the genes are reported to have primarily procancer functions. Dhx9 (DExHBox Helicase 9; UniProt Q08211), Dusp12 (Dual Specificity Phosphatase 12; UniProt Q9UNI6), and Spon2 (Spondin 2; UniProt Q9BUD6) act as oncogenes and are strongly associated with tumorigenesis. 58 , 59 , 60 Ifitm1 (Interferon Induced...”
- Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes.
Homma, Life science alliance 2024 - “...RNA helicases Early O75643 U5 small nuclear ribonucleoprotein 200-kD helicase 3349.71 34.97 52 244.4 6.06 Q08211 ATP-dependent RNA helicase A 2466.37 31.42 27 140.9 6.84 Late O00571 ATP-dependent RNA helicase DDX3X 1340.82 31.42 15 73.2 7.18 P60842 Eukaryotic initiation factor 4A-I 1266.42 39.66 12 46.1 5.48...”
- The Effect of a Nature-Based Gel on Gingival Inflammation and the Proteomic Profile of Crevicular Fluid: A Randomized Clinical Trial.
Figueiredo, Gels (Basel, Switzerland) 2024 - “...1 subunit beta protein folding chaperone protein folding Q00688 Peptidyl-prolyl cis-trans isomerase FKBP3 rna binding Q08211 ATP-dependent RNA helicase A atp-dependent activity regulation of dna-templated transcription Q13155 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 molecular adaptor activity programmed cell death Q8WUM4 Programmed cell death 6-interacting protein...”
- The Effect of Citrus aurantium on Non-Small-Cell Lung Cancer: A Research Based on Network and Experimental Pharmacology
Yao, BioMed research international 2023 - “...42 mRNA of protein-tyrosine phosphatase, nonreceptor type 1 PTPN22 Q9Y2R2 43 DNA topoisomerase II DHX9 Q08211 44 Estrogen receptor beta PDGFRB P09619 45 Dipeptidyl peptidase IV DPP4 P27487 46 Serine/threonine-protein kinase Chk1 CDK1 P06493 47 Trypsin-1 PRSS1 P07477 48 Calcium-activated potassium channel subunit alpha 1 KCNMA1...”
- Ectopic pregnancy: search for biomarker in salivary proteome
Priya, Scientific reports 2023 - “...1 1 79. Q05639 Elongation factor 1-alpha 2 EEF1A2 463 50,470 9.11 1 1 80. Q08211 ATP-dependent RNA helicase A DHX9 1270 140,958 6.41 1 1 81. Q13231 Chitotriosidase-1 CHIT1 466 51,681 6.55 1 1 82. Q13490 Baculoviral IAP repeat-containing protein 2 BIRC2 618 69,900 6.27...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - More
K9FUM5 RNA helicase from Penicillium digitatum (strain PHI26 / CECT 20796)
37% identity, 18% coverage
E1B9N7 ATP-dependent RNA helicase DHX29 from Bos taurus
35% identity, 18% coverage
XP_001747335 uncharacterized protein from Monosiga brevicollis MX1
36% identity, 22% coverage
Q6PGC1 ATP-dependent RNA helicase DHX29 from Mus musculus
36% identity, 18% coverage
DHX29_HUMAN / Q7Z478 ATP-dependent RNA helicase DHX29; DEAH box protein 29; Nucleic acid helicase DDXx; EC 3.6.4.13 from Homo sapiens (Human) (see 2 papers)
NP_061903 ATP-dependent RNA helicase DHX29 isoform 1 from Homo sapiens
35% identity, 18% coverage
- function: ATP-binding RNA helicase involved in translation initiation. Part of the 43S pre-initiation complex that is required for efficient initiation on mRNAs of higher eukaryotes with structured 5'-UTRs by promoting efficient NTPase-dependent 48S complex formation. Specifically binds to the 40S ribosome near the mRNA entrance. Does not possess a processive helicase activity.
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Part of the 43S pre-initiation complex (PIC) that contains at least Met-tRNA, EIF1, EIF1A (EIF1AX or EIF1AY), EIF2S1, EIF2S2, EIF2S3, EIF3A, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L, EIF3M, DHX29 and the 40S ribosomal subunit. - 5q11.2 deletion syndrome revisited-Further narrowing of the smallest region of overlap for the main clinical characteristics of the syndrome.
Bayat, American journal of medical genetics. Part A 2021 (PubMed)- GeneRIF: 5q11.2 deletion syndrome revisited-Further narrowing of the smallest region of overlap for the main clinical characteristics of the syndrome.
- Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs.
Sweeney, Nucleic acids research 2021 - GeneRIF: Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs.
- DHX29 functions as an RNA co-sensor for MDA5-mediated EMCV-specific antiviral immunity.
Zhu, PLoS pathogens 2018 - GeneRIF: A critical role for DHX29 in innate immune response; molecular insights into the mechanisms by which DHX29 recognizes 5' structured EMCV RNA and interacts with MDA5 for potent type I interferon signaling and antiviral immunity.
- DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context.
Pisareva, Nucleic acids research 2016 - GeneRIF: DHX29 is another example of an initiation factor contributing to start codon selection.
- DHX29 and eIF3 cooperate in ribosomal scanning on structured mRNAs during translation initiation.
Pisareva, RNA (New York, N.Y.) 2016 - GeneRIF: DHX29 and eIF3 cooperate in scanning on structured mRNAs. Our findings support previous genetic data on the role of eIF3 during scanning
- Helicase proteins DHX29 and RIG-I cosense cytosolic nucleic acids in the human airway system.
Sugimoto, Proceedings of the National Academy of Sciences of the United States of America 2014 - GeneRIF: Helicase proteins DHX29 and RIG-I cosense cytosolic nucleic acids in the human airway system.
- Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs.
Dhote, Proceedings of the National Academy of Sciences of the United States of America 2012 - GeneRIF: Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs.
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- More
- The difference in serum proteomes in schizophrenia and bipolar disorder
Smirnova, BMC genomics 2019 - “...X-linked protein 4 ARMCX4 370,518 5,322,898 Q6UB98 Ankyrin repeat domain-containing protein 12 ANKRD12 4,403,913 594,308 Q7Z478 ATP-dependent RNA helicase DHX29 DHX29 4,348,332 458,995 Q8TE73 Dynein heavy chain 5, axonemal DNAH5 3,785,117 6,673,067 Q96BK5 PIN2/TERF1-interacting telomerase inhibitor 1 PINX1 5,743,424 6,480,803 Q96KN2 Beta-Ala-His dipeptidase CNDP1 4,732,742 6,322,812...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...helicase DDX28 Mitochondrial DEAD-box protein 28 DDX28 28 Q7Z478 RNA helicase DHX29 DEAH-box protein 29 DHX29 Nucleic acid helicase DDXx 29 Q7L2E3 RNA helicase...”
HVT1_ARATH / F4INY4 DExH-box ATP-dependent RNA helicase DExH6; Protein HELICASE IN VASCULAR TISSUE AND TAPETUM; EC 3.6.4.13; EC 3.6.4.12 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G30800, NP_850154 HVT1 (HELICASE IN VASCULAR TISSUE AND TAPETUM); ATP binding / helicase/ nucleic acid binding from Arabidopsis thaliana
37% identity, 14% coverage
PF3D7_1231600 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative from Plasmodium falciparum 3D7
32% identity, 20% coverage
- Combining IP3 affinity chromatography and bioinformatics reveals a novel protein-IP3 binding site on Plasmodium falciparum MDR1 transporter
Alves, Current research in microbial sciences 2023 - “...ABCE1, ABC transporter E family member 1 (PF3D7_1,368,200). PRP2, pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2 (PF3D7_1231600). PF11_0488, serine/threonine protein kinase (PF3D7_1148000). DDX1, ATP-dependent RNA helicase DDX1 (PF3D7_0521700). SEC13, protein transport protein SEC13 (PF3D7_1230700). SEC24A, transport protein Sec24A (PF3D7_1361100). EIF2GAMMA, eukaryotic translation initiation factor 2 subunit gamma...”
- Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages
Kaur, Scientific reports 2016 - “...unknown function K5(Methyl) HILIC NKYYkDNIYDGNNICDGNnIYCNNNNICCNNNNICCNNNNIYCNNNNIYDNNTCDk PF3D7_1227400 conserved Plasmodium protein, unknown function K5(Dimethyl); K56(Dimethyl) HILIC ELnTSYDnnSPTDSTYk PF3D7_1231600 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative (PRP2) C-Term(Methyl) IP TVYLFDIFLNEqSk PF3D7_1232000 phenylalaninetRNA ligase (aFRS) C-Term(Methyl) HILIC GMESDnINEMVSDNINEMASDNINEMVSDNINEMTSDNINkMANQMNYEQNTDGIIIk PF3D7_1233600 asparagine and aspartate rich protein 1 (AARP1) K41(Dimethyl); C-Term(Methyl) IP LNVqRDKTFnEEDnIk...”
- Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum
Hollin, BMC genomics 2016 - “...(MSP9) QDO/A (1) TDO/A (1) PF3D7_1229400 macrophage migration inhibitory factor (MIF) QDO/A (1) TDO/A (1) PF3D7_1231600 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP2, putative (PRP2) TDO/A (1) PF3D7_1234600 conserved Plasmodium protein, unknown function TDO/A (1) PF3D7_1234900 conserved Plasmodium protein, unknown function TDO/A (1) PF3D7_1240600 erythrocyte membrane protein...”
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...PF3D7_0630900 Helicase+ZnF PF3D7_0527900, PF3D7_0909900, PF3D7_1313400 Helicase+UPF_Zn PF3D7_1005500 Helicase+Sec63 PF3D7_1439100, PF3D7_0422500 Helicase+HA2+S1 PF3D7_1030100 Helicase+HA2+OB fold PF3D7_1364300, PF3D7_1231600, PF3D7_0917600, PF3D7_0821300 Helicase+ZnF+DSHCT PF3D7_0909900 Helicase+rRNA proc-arch+DSHCT PF3D7_0602100 Helicase+HA2 PF3D7_0310500, PF3D7_1302700 Blue , pink and green boxes are used to denote transmembrane, low complexity, and coiled-coil regions, respectively To further illustrate...”
- “...while DEAD helicases participate in ribosome biogenesis [ 26 ]. In P. falciparum , PF3D7_1364300, PF3D7_1231600, PF3D7_0917600 and PF3D7_1030100 all have a conserved DEAH domain and are classified as Prp (pre-mRNA processing) proteins. Similarly, almost all of the proteins classified under ribosome biogenesis (Fig. 2 and...”
G1U383 ATP-dependent RNA helicase DHX29 from Oryctolagus cuniculus
35% identity, 18% coverage
AT1G58060 helicase domain-containing protein from Arabidopsis thaliana
36% identity, 16% coverage
- Aux/IAA14 Regulates microRNA-Mediated Cold Stress Response in Arabidopsis Roots
Aslam, International journal of molecular sciences 2020 - “...(AT2G41570, AT1G35990), clathrin heavy chain (AT3G11130) miR396b-3p MYB76 (AT5G07700), ATBTAF1 (AT3G54280), RNA helicase family protein (AT1G58060) miR398a-5p SETH2, UDP-glycosyltransferase superfamily protein (AT3G45100); alpha/beta-hydrolases superfamily protein (AT3G48080); ARM repeat superfamily protein (AT5G06120) miR399a PHO2/UBC24 (AT2G33770), CYP705A30 (AT3G20940), terpenoid cyclases family protein (AT1G78500), sodium bile acid symporter family...”
- Organismal benefits of transcription speed control at gene boundaries
Leng, EMBO reports 2020 - “...significant reduction in expression (Fig 4 F) that we visualized for internal exons of the AT1G58060 and AT3G05680 genes (Fig 4 G). In contrast, we detected a stronger decrease for DE introns in NRPB2 Y732F mutant compared to NRPB2 WT (Fig 4 H). We next tested...”
- Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera
Kiefer, Genome biology and evolution 2020 - “...pressure on allelic variants of sexual accessions as compared with apomicts, only for ESP3 and AT1G58060 higher rates of mutation accumulation were identified for alleles from apomictic accessions. As higher ploidy is commonly perceived as a strategy to buffer the effect of deleterious mutations, we tested...”
- Assortment of Flowering Time and Immunity Alleles in Natural Arabidopsis thaliana Populations Suggests Immunity and Vegetative Lifespan Strategies Coevolve
Glander, Genome biology and evolution 2018 - “...pools (log2-fold change > 1.5) using RT-PCR. We followed standard protocols and used RNA Helicase (AT1G58060), Protein Phosphatase 2A Subunit A3 (PP2AA3) and transcript AT5G12240 as control genes. Gene expression based on RNA sequencing and RT-PCR were strongly correlated (Pearson correlation, 0.58<R<0.96, max P <0.01). Supplementary...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...acid binding, DNA repair, DNA/RNA synthesis AT1G02990, AT1G08840, AT1G12930, AT1G50840, AT2G20000, AT2G32000, AT1G17580, AT3G54280, AT1G20920, AT1G58060, AT2G19520, AT3G23780, AT3G48190, AT3G61240, AT4G09680, AT4G25880, AT5G05560, AT5G16630, AT5G22010, AT2G03070, AT3G23780, AT3G53500, AT1G07705, AT4G00060, AT4G16280, AT4G32200, AT1G33390, AT3G54460 [ 18 , 40 43 ] Regulation of transcription AT1G07470, AT2G20330, AT2G35110,...”
- Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting
Coker, Frontiers in plant science 2015 - “...MAP65-7 AT3G45850 AT1G48650 AT4G21270 ATK1, KATAP AT1G27385 AT3G54190 AT1G54820 AT4G22930 PYR4, DHOASE AT1G35780 AT3G60840 MAP65-4 AT1G58060 AT4G30610 BRS1, SCPL24 AT1G48600 AtPMEAMT AT4G37080 AT1G63630 AT4G34210 ASK11, SK11 AT1G53560 AT5G01015 AT1G66510 AT4G37110 AT1G70370 PG2 AT5G15310 ATMYB16, ATMIXTA, AT2G21380 AT5G17220 GST26, TT19, GSTF12 AT1G71695 AT5G15740 AT2G22330 CYP79B3 AT5G17410 AT1G79200...”
Q8BZS9 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX32 from Mus musculus
NP_001272960 putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX32 isoform a from Mus musculus
26% identity, 53% coverage
B2RD71 cDNA, FLJ96486, highly similar to Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 32 (DHX32), mRNA from Homo sapiens
26% identity, 46% coverage
Q6P158 Putative ATP-dependent RNA helicase DHX57 from Homo sapiens
42% identity, 12% coverage
- SARS-CoV-2 nsp13 suppresses hepatitis B virus replication by targeting cccDNA transcription.
Li, Journal of virology 2024 - Snapshot imprinting as a tool for surface mapping and identification of novel biomarkers of senescent cells.
Piletska, Nanoscale advances 2022 - “...0.00 A0A087WYL6; A0A087WZG6 Partitioning defective 3 homolog B 6748 735 27 16 A0A087X1S9; Q587I4; Q8TEW8 Q6P158; A0A087WZ11; B4DKW2 Putative ATP-dependent RNA helicase DHX57 11675 660 2150 238 Shaving approach P04908; P0C0S8; P0C0S9; P20671; Q16777; Q3ZBX9; Q6FI13; Q7L7L0; Q93077; Q96KK5; Q99878; Q9BTM1; P0C0S4; P0C0S5; P16104; Q32LA7; Q71UI9;...”
- Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication.
Cai, The Journal of biological chemistry 2021 - “...proteins within SARS-CoV-2 N interactome ID Name RNA binding Q14444 CAPRIN1 Yes Q8TDD1 DDX54 Yes Q6P158 DHX57 Yes Q08211 DHX9 Yes Q01844 EWSR1 Yes Q9NZB2 FAM120A Yes Q8NCA5 FAM98A Yes P22087 FBL Yes P51114 FXR1 Yes Q13283 G3BP1 Yes Q9UN86 G3BP2 Yes O14979 HNRNPDL Yes Q9BUJ2...”
- Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Retinal and Choroidal Vascular Endothelial Cells: Potential Targets for New Biologic Drugs.
Smith, American journal of ophthalmology 2018 - “...regulator of chromatin subfamily D member 1 Q96GM5 2.94 8.9858E-02 Putative ATP-dependent RNA helicase DHX57 Q6P158 2.92 7.0378E-02 Cysteine and glycine-rich protein 2 Q16527 2.89 9.6375E-02 Peptidyl-prolyl cis-trans isomerase G (PPIase G; Peptidyl- prolyl isomerase G) Q13427 2.70 8.6633E-02 Lysine-specific histone demethylase 1A O60341 2.69 6.6003E-02...”
- Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer
Xu, Oncotarget 2016 - “...1.0 1.0 1.5 1.6 ND ND ND ND ND ND ND ND ND ND 78.1 Q6P158 Putative ATP-dependent RNA helicase DHX57 GN=DHX57 2.0 0.0 0.8 0.8 1.0 1.1 1.9 1.7 1.0 0.6 0.7 0.8 ND ND ND ND ND ND 155.5 Q96CU9 FAD-dependent oxidoreductase domain-containing protein...”
- A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases
Muller, PLoS pathogens 2015 - “...2 4 0 10 0 NPM1 * P06748 Nucleophosmin 7 0 6 0 DHX57 * Q6P158 DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57 5 0 8 0 ZC3HAV1 * Q7Z2W4 Zinc finger CCCH-type antiviral 1 10 0 3 0 ILF2 Q12905 Interleukin enhancer-binding factor 2 5 0 7...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...61 kDa nucleolar RNA helicase DEAD-box protein 21 54 Q6P158 RNA helicase DHX57 DEAH-box protein 57 DHX57 55 O95786 RNA helicase DDX58 DEAD-box protein 58 DDX58...”
- Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to preribosome particles
Yoshikawa, Molecular & cellular proteomics : MCP 2011 - “...117 118 119 120 121 122 123 124 Q6P158 Q69YN4 Q9BX40 Q9Y520 Q9ULL5 Q96DN6 Q9UNF1 Q9NXS2 Q96SL8 Q68CQ4 Q9H0W5 DHX57_HUMAN VIR_HUMAN LS14B_HUMAN BA2L2_HUMAN...”
- More
XP_004993066 uncharacterized protein from Salpingoeca rosetta
30% identity, 25% coverage
B4DKW2 cDNA FLJ56001, highly similar to Putative ATP-dependent RNA helicase DHX57 (Fragment) from Homo sapiens
42% identity, 18% coverage
YTDC2_MOUSE / B2RR83 3'-5' RNA helicase YTHDC2; Keen to exit meiosis leaving testes under-populated protein; Ketu; YTH domain-containing protein C2; mYTHDC2; EC 3.6.4.13 from Mus musculus (Mouse) (see 7 papers)
NP_001156485 3'-5' RNA helicase YTHDC2 from Mus musculus
30% identity, 20% coverage
- function: 3'-5' RNA helicase that plays a key role in the male and female germline by promoting transition from mitotic to meiotic divisions in stem cells (PubMed:28380054, PubMed:28809393, PubMed:29033321, PubMed:29087293, PubMed:29360036, PubMed:32470506). Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non- coding RNAs that plays a role in the efficiency of RNA processing and stability (PubMed:29360036). Essential for ensuring a successful progression of the meiotic program in the germline by regulating the level of m6A-containing RNAs (PubMed:29033321). Acts by binding and promoting degradation of m6A-containing mRNAs: the 3'-5' RNA helicase activity is required for this process and RNA degradation may be mediated by XRN1 exoribonuclease (PubMed:29033321). Required for both spermatogenesis and oogenesis (PubMed:28809393, PubMed:29033321).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with MEIOC; binds transcripts that regulate the mitotic cell cycle inhibiting progression into metaphase, thereby allowing meiotic prophase to proceed normally (PubMed:28380054, PubMed:29087293). Interacts (via ANK repeats) with XRN1 (By similarity). Interacts with ZCCHC4 (By similarity). Associates with the small ribosomal subunit (By similarity). Interacts with RBM46 (PubMed:36001654).
disruption phenotype: Mice are viable and reach adulthood (PubMed:28809393, PubMed:29033321, PubMed:29087293). However, both male and female mice are infertile; male mice have smaller testes, and female mice have smaller ovaries and show progressive loss of germ cells (PubMed:28809393, PubMed:29033321, PubMed:29087293). Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs (PubMed:29033321, PubMed:29087293). Mutant testes reveal an up-regulation of N6-methyladenosine (m6A)- enriched transcripts (PubMed:29033321). - YTHDC2 control of gametogenesis requires helicase activity but not m6A binding.
Saito, Genes & development 2022 - “...( Sievers et al. 2011 ) of YTH domains (gray highlight) from mouse YTHDC2 (Uniprot B2RR83) and all five human YTH domain-containing proteins: YTHDC2 (Uniprot Q9H6S0), YTHDC1 (Uniprot Q96MU7), YTHDF1 (Uniprot Q9BYJ9), YTHDF2 (Uniprot Q9Y5A9), and YTHDF3 (Uniprot Q7Z739). Pink boxes indicate positions of m 6...”
- Tandem mass tag-based quantitative proteomic analysis of effects of multiple sevoflurane exposures on the cerebral cortex of neonatal and adult mice.
Feng, Frontiers in neurology 2022 - Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver.
Klinge, Environmental epigenetics 2021 - “...YTHDF2 ENSMUSG00000040025 Q91YT7 YTHDF3 ENSMUSG00000047213 0.65 Q8BYK6 m1A m6A YTHDC1 ENSMUSG00000035851 E9Q5K9 YTHDC2 ENSMUSG00000034653 0.80 B2RR83 m6A HNRNPA2B1 ENSMUSG00000004980 O88569 m6A IGFBP1 ENSMUSG00000020429 P47876 IGFBP2 ENSMUSG00000039323 0.62 0.98 P47877 IGFBP3 ENSMUSG00000020427 P47878 m6A PRRC2A ENSMUSG00000024393 0.73 Q7TSC1 FMR1 ENSMUSG00000000838 0.67 0.87 P35922 0.67 0.66 ELAVL1 ENSMUSG00000040028...”
- The m6A reader YTHDC2 maintains visual function and retinal photoreceptor survival through modulating translation of PPEF2 and PDE6B.
Yang, Journal of genetics and genomics = Yi chuan xue bao 2024 (PubMed)- GeneRIF: The m[6]A reader YTHDC2 maintains visual function and retinal photoreceptor survival through modulating translation of PPEF2 and PDE6B.
- The m6A reader YTHDC2 promotes SIRT3 expression by reducing the stabilization of KDM5B to improve mitochondrial metabolic reprogramming in diabetic peripheral neuropathy.
Jiao, Acta diabetologica 2023 (PubMed)- GeneRIF: The m[6]A reader YTHDC2 promotes SIRT3 expression by reducing the stabilization of KDM5B to improve mitochondrial metabolic reprogramming in diabetic peripheral neuropathy.
- Mettl3-mediated m6 A modification of Lrp2 facilitates neurogenesis through Ythdc2 and elicits antidepressant-like effects.
Xu, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2022 (PubMed)- GeneRIF: Mettl3-mediated m(6) A modification of Lrp2 facilitates neurogenesis through Ythdc2 and elicits antidepressant-like effects.
- N6 -Methyladenosine Reader Protein YT521-B Homology Domain-Containing 2 Suppresses Liver Steatosis by Regulation of mRNA Stability of Lipogenic Genes.
Zhou, Hepatology (Baltimore, Md.) 2021 (PubMed)- GeneRIF: N(6) -Methyladenosine Reader Protein YT521-B Homology Domain-Containing 2 Suppresses Liver Steatosis by Regulation of mRNA Stability of Lipogenic Genes.
- YTHDC2 is essential for pachytene progression and prevents aberrant microtubule-driven telomere clustering in male meiosis.
Liu, Cell reports 2021 - GeneRIF: YTHDC2 is required for meiotic progression through the pachytene stage. Inducible inactivation of YTHDC2 causes a massively dysregulated transcriptome in pachytene cells and altered transcripts in YTHDC2-deficient cells encode microtubule network proteins. Depletion of YTHDC2 leads to telomere clustering in pachytene cells.
- Critical roles of mRNA m6A modification and YTHDC2 expression for meiotic initiation and progression in female germ cells.
Zeng, Gene 2020 (PubMed)- GeneRIF: Results suggest that mRNA m(6)A modification and YTHDC2 expression are essential for meiotic initiation and progression in female germ cells.
- ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2.
Jain, eLife 2018 - GeneRIF: The authors propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
- Meioc maintains an extended meiotic prophase I in mice
Soh, PLoS genetics 2017 - GeneRIF: We conclude that when the meiotic chromosomal program is initiated, Meioc is simultaneously induced so as to extend meiotic prophase. Specifically, MEIOC, together with YTHDC2, promotes a meiotic (as opposed to mitotic) cell cycle program via post-transcriptional control of their target transcripts.
- “...verterbrates. Alignment of electronic predictions of YTHDC2 orthologs. We searched for homologs of mouse YTHDC2 (NP_001156485) by querying the RefSeq protein database by blastp. We restricted the search to the following representative species: Mus musculus , Rattus norvegicus , Canis familiaris , Monodelphis domestica , Homo...”
- More
NP_001414131 probable ATP-dependent RNA helicase YTHDC2 from Rattus norvegicus
30% identity, 20% coverage
DHX32_HUMAN / Q7L7V1 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX32; DEAD/H box 32; DEAD/H helicase-like protein 1; DHLP1; DEAH box protein 32; HuDDX32; EC 3.6.4.13 from Homo sapiens (Human) (see 4 papers)
NP_060650 putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX32 from Homo sapiens
26% identity, 46% coverage
- catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
- Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
Vieira, BMC genomics 2011 - “...cell antigen CD34 precursor Cell-cell or cell-matrix adhesion. Role in early haematopoiesis. SAPD06600 2.263 0.013 NP_060650 DEAD/H Asp-Glu-Ala-Asp/His box polypeptide 32 RNA metabolism, gene regulation. SAPD01688 2.233 0.023 Q6PH41 Glutathione S-transferase, theta 3 Antioxidant, stress protein. The "Top 20 known genes" were taken from 45 transcripts...”
- Genome-wide comprehensive analysis of human helicases
Umate, Communicative & integrative biology 2011 - “...Q9H8H2 RNA helicase DDX31 DEAD-box protein 31 DDX31 31 Q7L7V1 RNA helicase DHX32 DEAH-box protein 32 DHX32 DEAD/H helicase-like protein 1 (DHLP1) DEAD/H box 32...”
AT1G58050 helicase domain-containing protein from Arabidopsis thaliana
35% identity, 17% coverage
- The MADS-box gene XAANTAL1 participates in Arabidopsis thaliana primary root growth and columella stem cell patterns in response to ROS, via direct regulation of PEROXIDASE 28 and RETINOBLASTOMA-RELATED genes
Zluhan-Martínez, Journal of experimental botany 2025 - “...2024 ). Relative mRNA transcript accumulation was quantified using the comparative Ct method, with RNAH (AT1G58050), PDF2 (AT1G13320), and UPL7 (AT3G53090) as reference genes ( Czechowski et al ., 2005 ; Hong et al ., 2010 ), and the WT as a control line. For RTqPCR...”
- SYP72 interacts with the mechanosensitive channel MSL8 to protect pollen from hypoosmotic shock during hydration
Zhou, Nature communications 2022 - “...20s, extension at 72C for 30s) on a CFX Connect TM Real-Time System (Bio-Rad, USA). AT1G58050 , AT1G13320 , and AT4G34270 were selected as reference genes. RT-qPCR data were analysed using the Bio-Rad CFX Manager v.3.1. Primers for RT-qPCR are listed in Supplementary Table 2 ....”
- Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time
Williams, The Plant cell 2022 - “...et al., 2014 ): FLC_F: AGCCAAGAAGACCGAACTCA, and FLC_R: TTTGTCCAGCAGGTGACATC. Reactions were normalized to reference gene AT1G58050 ( Czechowski et al., 2005 ). All qPCR reactions were performed with technical triplicates. Cycling conditions were as follows: 95C for 20 s followed by 40 cycles of 95C for...”
- Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7
Schulten, The Plant cell 2022 - “...( MIR860a ), At1g19371 ( MIR169H ), At5g60390 ( EF1 ), At3g13920 ( EIF4A1 ), At1g58050 ( HEL ) . At4g05320 ( UBQ10 ), At5g62700 ( TUB3 ), and At5g09810 ( ACT7 ). Supplemental data The following materials are available in the online version of this...”
- A variably imprinted epiallele impacts seed development
Pignatta, PLoS genetics 2018 - “...was calculated using the ddCt method as described [ 48 ]. The reference gene was AT1G58050 [ 49 ]. For allele-specific expression in Col-Cvi crosses, a multiplex TaqMan assay was developed by designing primers and PrimeTime Double-quenched Custom Probes with online tool http://www.idtdna.com/pages/products/gene-expression/custom-qpcr-probes . Cycling conditions...”
- Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana
Simon, Nucleic acids research 2018 - “...sequence of the 5S rRNA by the average coverage along 16 reference genes ( At1g13320, At1g58050, At1g59830, At2g28390, At2g32170, At3g01150, At3g53090, At4g26410, At4g27960, At4g33380, At4g34270, At4g38070, At5g08290, At5g15710, At5g46630 and At5g55840 ( 25 )), in addition to the genes At2g36060 and At4g29130 used for qPCR normalization...”
- Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit
Williams, Nature communications 2017 - “...PCR system (Applied Biosystems). Primers were designed as previously specified 13 . The reference gene AT1G58050 was used to normalize all reactions, as described 28 (Supplementary Table 2 ). All reactions were performed in technical triplicate, except for the data in Fig. 1d , which were...”
- Transgenic cotton expressing Cry10Aa toxin confers high resistance to the cotton boll weevil
Ribeiro, Plant biotechnology journal 2017 - “...component-id pbi12694 cover-date August 2017 details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:5.1.4 mode:remove_FC converted:19.07.2017 Accession numbers (GenBank): AtRNAH : At1g58050 (TAIR); Atpp2a : At1g13320 (TAIR); Cry1Ac: P05068; Cry2Aa: P0A377; cry10Aa : AAA22614.1; Ghubq14 : DW505546; Ghpp2a1 : DT545658; uceA1.7 : JN887312. Introduction Cotton ( Gossypium hirsutum ) production is highly...”
- More
YTDC2_HUMAN / Q9H6S0 3'-5' RNA helicase YTHDC2; YTH domain-containing protein 2; hYTHDC2; EC 3.6.4.13 from Homo sapiens (Human) (see 5 papers)
30% identity, 21% coverage
- function: 3'-5' RNA helicase that plays a key role in the male and female germline by promoting transition from mitotic to meiotic divisions in stem cells (PubMed:26318451, PubMed:29033321, PubMed:29970596). Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs that plays a role in the efficiency of RNA processing and stability (PubMed:26318451, PubMed:29033321). Essential for ensuring a successful progression of the meiotic program in the germline by regulating the level of m6A-containing RNAs (By similarity). Acts by binding and promoting degradation of m6A- containing mRNAs: the 3'-5' RNA helicase activity is required for this process and RNA degradation may be mediated by XRN1 exoribonuclease (PubMed:29033321). Required for both spermatogenesis and oogenesis (By similarity).
catalytic activity: ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)
subunit: Interacts with MEIOC; binds transcripts that regulate the mitotic cell cycle inhibiting progression into metaphase, thereby allowing meiotic prophase to proceed normally (By similarity). Interacts (via ANK repeats) with XRN1 (PubMed:29033321, PubMed:29970596). Interacts with ZCCHC4 (PubMed:31799605). Associates with the small ribosomal subunit (PubMed:29970596). Interacts with RBM46 (By similarity). - Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain.
Miller, Computational and structural biotechnology journal 2023 - “...with orange cartoon). Apo structure not yet experimentally resolved. E) AlphaFold model of YTHDC2 (UniProt Q9H6S0) superimposed on YTHDC2 apo structure (PDB: 6k6u) and YTHDC1 holo structure bound to GG(m 6 A)CU 5mer RNA (PDB: 4r3i, YTHDC1 domain shown with cyan cartoon). F) AlphaFold model of...”
- Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.
McGlacken-Byrne, JCI insight 2022 - “...p.P856R variant YTHDC2. The human YTHDC2 protein sequence was retrieved from the UniProt database (UniProt Q9H6S0) ( 48 ). Sequence searches were conducted to identify conserved domain signatures using PFAM ( 37 ). Blastp against the PDB database ( 82 ) identified the structures of the...”
- YTHDC2 control of gametogenesis requires helicase activity but not m6A binding.
Saito, Genes & development 2022 - “...highlight) from mouse YTHDC2 (Uniprot B2RR83) and all five human YTH domain-containing proteins: YTHDC2 (Uniprot Q9H6S0), YTHDC1 (Uniprot Q96MU7), YTHDF1 (Uniprot Q9BYJ9), YTHDF2 (Uniprot Q9Y5A9), and YTHDF3 (Uniprot Q7Z739). Pink boxes indicate positions of m 6 A-binding residues. ( B ) Fluorescence anisotropy binding curves for...”
- Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.
Yu, Nucleic acids research 2021 - “...The protein fragments used are YTHDC1 residues 345509 of UniProtKB/Swiss-Prot Q96MU7, YTHDC2 residues 12681430 of Q9H6S0, YTHDF1 residues 370559 of Q9BYJ9 and YTHDF2 residues 391579 of Q9Y5A9 and YTHDF3 residues 400585 of Q7Z739. The YTH fragments as GST-tagged fusion in a pGEX-4T1 vector were synthesized by...”
- Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.
Lygirou, Journal of translational medicine 2018 - “...2.28 8.28E02 P54317 Pancreatic lipase-related protein 2 2 0.01 4.51E03 3 Only in controls 9.96E02 Q9H6S0 Probable ATP-dependent RNA helicase YTHDC2 3 5.23 4.60E03 6 2.31 1.21E01 P01266 Thyroglobulin 3 0.33 9.90E03 4 0.46 1.21E01 P08185 Corticosteroid-binding globulin 2 2.65 3.26E02 4 3.35 1.21E01 [ 80...”
- YTH Domain: A Family of N6-methyladenosine (m6A) Readers.
Liao, Genomics, proteomics & bioinformatics 2018 - “...Domain architecture of human YTH domain-containing proteins: YTHDC1 (UniProt ID: Q96MU7 ), YTHDC2 (UniProt ID: Q9H6S0 ), YTHDF1 (UniProt ID: Q9BYJ9 ), YTHDF2 (UniProt ID: Q9Y5A9 ), and YTHDF3 (UniProt ID: Q7Z739 ). B. Sequence alignment of the YTH domains of human YTHDC1, YTHDC2, YTHDF13, budding...”
- A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases
Muller, PLoS pathogens 2015 - “...** Q12771 heterogeneous nuclear ribonucleoprotein Dalso known as AUF1 8 0 6 1 YTHDC2 * Q9H6S0 YTH domain containing 2 4 0 10 0 NPM1 * P06748 Nucleophosmin 7 0 6 0 DHX57 * Q6P158 DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57 5 0 8 0 ZC3HAV1 *...”
- Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery
Freibaum, Journal of proteome research 2010 - “...P43243 14 9 10 0 0 0 * Probable ATP-dependent RNA helicase YTHDC2 YTHDC2 160 Q9H6S0 14 6 5 0 0 0 * Non-POU domain-containing octamer-binding protein NONO 54 Q15233 14 9 25 12 7 22 1.2 ELAV-like protein 1 ELAVL1 36 Q15717 13 5 15...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory