PaperBLAST
PaperBLAST Hits for tr|Q9HZM8|Q9HZM8_PSEAE Ribonuclease E OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rne PE=1 SV=1 (1057 a.a., MKRMLINATQ...)
Show query sequence
>tr|Q9HZM8|Q9HZM8_PSEAE Ribonuclease E OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rne PE=1 SV=1
MKRMLINATQPEELRVALVDGQRLFDLDIESGAREQKKANIYKGRITRVEPSLEAAFVDF
GAERHGFLPLKEISREYFKKSPEGRINIKEVLSEGQEVIVQVEKEERGNKGAALTTFISL
AGRYLVLMPNNPRAGGISRRIEGEERNELREALNGLNAPADMGLIVRTAGLGRSTEELQW
DLDYLLQLWSAIKEASGERGAPFLIYQESNVIIRAIRDYLRQDIGEVLIDSIDAQEEALN
FIRQVMPQYASKVKLYQDSVPLFNRFQIESQIETAFQREVKLPSGGSIVIDPTEALVSID
INSARATKGGDIEETALQTNLEAAEEIARQLRLRDIGGLIVIDFIDMTPAKNQRAVEERV
REALEADRARVQVGRISRFGLLEMSRQRLRPSLGETSGIVCPRCNGQGIIRDVESLSLAI
LRLIEEEALKDRTAEVRARVPFQVAAFLLNEKRNAITKIELRTRARIFILPDDHLETPHF
EVQRLRDDSPELVAGQTSYEMATVEHEEAQPVSSTRTLVRQEAAVKTVAPQQPAPQHTEA
PVEPAKPMPEPSLFQGLVKSLVGLFAGKDQPAAKPAETSKPAAERQTRQDERRNGRQQNR
RRDGRDGNRRDEERKPREERAERQPREERAERPNREERSERRREERAERPAREERQPREG
REERAERTPREERQPREGREGREERSERRREERAERPAREERQPREGREERAERPAREER
QPREDRQARDAAALEAEALPNDESLEQDEQDDTDGERPRRRSRGQRRRSNRRERQREVSG
ELEGSEATDNAAAPLNTVAAAAAAGIAVASEAVEANVEQAPATTSEAASETTASDETDAS
TSEAVETQGADSEANTGETADIEAPVTVSVVRDEADQSTLLVAQATEEAPFASESVESRE
DAESAVQPATEAAEEVAAPVPVEVAAPSEPAATEEPTPAIAAVPANATGRALNDPREKRR
LQREAERLAREAAAAAEAAAQAAPAVEEIPAVASEEASAQEEPAAPQAEEITQADVPSQA
DEAQEAVQAEPEASGEGAADTEHAKKTEESETSRPHA
Running BLASTp...
Found 135 similar proteins in the literature:
PA2976 ribonuclease E from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
Kalia, mSphere 2024 - “...Conserved hypothetical protein 0.60057 Upregulated 0.480409 PA2830 Heat shock protein HtpX Upregulated 0.487969 Upregulated 1.124719 PA2976 Ribonuclease E Upregulated 0.68855 Upregulated 0.378461 PA3044 Two component sensor RocS2 0.81144 Upregulated 0.056449 PA3068 gdhB-NAD-dependent glutamate dehydrogenase Upregulated 0.628916 Upregulated 0.11409 PA3126 Heat shock protein IbpA Upregulated 0.061266 Upregulated...”
- Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
Ting, eLife 2022 - “...PA3861 1.00 1.10 PA4269 1.00 1.10 PA1092 0.95 0.78 PA0141 0.89 0.71 PA0963 0.84 1.27 PA2976 0.84 0.83 PA4260 0.84 0.69 PA4265 0.84 0.61 PA4270 0.84 1.04 PA1803 0.78 0.74 PA2151 0.78 0.77 PA3950 0.78 1.19 PA3001 0.73 1.10 PA3656 0.73 0.80 PA5173 0.73 0.76 PA5554...”
- “...PA4246 0.87 0.79 PA0090 0.85 0.53 PA1552 0.83 N.D. PA0077 0.81 5.33 PA2494 0.81 ND PA2976 0.72 0.71 PA0659 0.70 N.D. PA4761 0.70 0.44 PA4941 0.65 2.57 PA4265 0.63 0.46 PA3656 0.61 0.67 PA3794 0.61 N.D. PA2151 0.56 0.55 PA3821 0.56 N.D. * Proteins containing at...”
- The Quorum-Sensing Inhibitor Furanone C-30 Rapidly Loses Its Tobramycin-Potentiating Activity against Pseudomonas aeruginosa Biofilms during Experimental Evolution
Bové, Antimicrobial agents and chemotherapy 2021 (secret) - Differential transcription profiling of the phage LUZ19 infection process in different growth media
Brandão, RNA biology 2021 (secret) - RNase E Promotes Expression of Type III Secretion System Genes in Pseudomonas aeruginosa
Sharp, Journal of bacteriology 2019 (secret) - Extracellular DNA release, quorum sensing, and PrrF1/F2 small RNAs are key players in Pseudomonas aeruginosa tobramycin-enhanced biofilm formation
Tahrioui, NPJ biofilms and microbiomes 2019 - “...Noticeably, the proteome of tobramycin-exposed P. aeruginosa biofilm showed reduced accumulation of ribonucleases RNase E (PA2976), RNase R (PA4937), and PNPase (PA4740) (Supplementary Table 2 ; Fig. 3 ), suggesting a possible reduced catabolism of RNAs. Overall, these proteomic data revealing alterations in the abundance of...”
- Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome
Van, eLife 2016 - “...al., 2000 ). A Strep -tag II was fused to the C-terminus of RNase E (PA2976) by homologous recombination creating PAO1 rne::Strep II ( Lesic and Rahme, 2008 ). Three E. coli strains were used: E. coli TOP10 (Life Technologies, Carlsbad, CA) for cloning procedures, E....”
- Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa
Dettman, Genome biology and evolution 2014 - “...pirin-related protein PA3163 cmk , cytidylate kinase, pyrimidine metabolism PA2978 ptpA , phosphotyrosine protein phosphatase PA2976 rne , ribonuclease E PA2852 Hypothetical protein PA2839 ygiD , aromatic ring dioxygenase Not called Hypothetical protein (pseudogene) PA2573 Chemotaxis transducer, methyl-accepting chemotaxis protein Not called Hypothetical protein PA1930 Chemotaxis...”
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PSPTO_3841 ribonuclease, Rne/Rng family protein from Pseudomonas syringae pv. tomato str. DC3000
72% identity, 67% coverage
- Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity
Filiatrault, Journal of bacteriology 2010 - “...translational start codon (e.g., PSPTO_2030, PSPTO_3157, PSPTO_3836, PSPTO_3841, PSPTO3976, and PSPTO_5516). For PSPTO_ 2030, the predicted protein appears to...”
- “...P. syringae pv. syringae B728a, respectively. For PSPTO_3836, PSPTO_3841, PSPTO3976, and PSPTO_5516, conserved proteins are found in a number of the VOL. 192,...”
Psyr_1638 Ribonuclease E and G from Pseudomonas syringae pv. syringae B728a
77% identity, 61% coverage
- Involvement of rppH in thermoregulation in Pseudomonas syringae
Hockett, Journal of bacteriology 2014 - “...0.2 0.9 0.6 5.5 10.7 1.4 3.9 RNA degradation Psyr_1638 rne 0.4 0.8 2.0 1.0 Nitrogen metabolism Psyr_4817 glnA-1 0.3 0.8 2.0 0.8 Carbohydrate metabolism and...”
- “...in the rppH strain only at 30C. Intriguingly, RNase E (Psyr_1638) was more abundant in the rppH strain than in the wild-type strain at 30C but not at 20C....”
PP1905, PP_1905 ribonuclease E from Pseudomonas putida KT2440
85% identity, 56% coverage
- The world of ribonucleases from pseudomonads: a short trip through the main features and singularities
Apura, Microbial biotechnology 2021 - “...or rhlB ) and RhlE (PP_4980, or rhlE ), and ribonucleases, such as RNase E (PP_1905 or rne ), PNPase (PP_4708 or pnp ) and RNase D (PP_4591 or rnd ). It was also demonstrated that the growth rate of the rnr mutant strain at 10C...”
- Genomic analysis of the role of RNase R in the turnover of Pseudomonas putida mRNAs
Fonseca, Journal of bacteriology 2008 - “...were hardly affected (Fig. 2). Expression of RNase E (PP1905, or rne), PNPase (PP4708, or pnp), and RNase D (PP4591, or rnd) increased between 2- and 2.5-fold,...”
U876_11735 ribonuclease E from Aeromonas hydrophila NJ-35
58% identity, 74% coverage
VC2030 ribonuclease E from Vibrio cholerae O1 biovar eltor str. N16961
58% identity, 64% coverage
- The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA
Kimura, Proceedings of the National Academy of Sciences of the United States of America 2019 - “...beginning of the C-terminal domain (CTD) of RNase E (VC2030) (Fig. 3C). The truncated protein retains RNase E's endonuclease domain, which is involved in rRNA...”
- Oligoribonuclease is the primary degradative enzyme for pGpG in Pseudomonas aeruginosa that is required for cyclic-di-GMP turnover
Orr, Proceedings of the National Academy of Sciences of the United States of America 2015 - “...expression of targets in E. coli. For example, RNase E (VC2030) is structurally similar to RNase G and possesses a 5 sensor pocket (67) and thus would be...”
- High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data
Chao, Nucleic acids research 2013 - “...the arginine-rich ribosomal binding site (ARBBS) and the scaffolding protein interaction domain were aligned to VC2030 and overlaid on the transposon-insertion sequencing data. In (D), transposon insertions are mapped across oriCII . The schematic spans the noncoding vca0001 ( rctA ), the intergenic region IG_vca0002 and...”
- “...several previous analyses of individual loci. For example, HMM identified essential and dispensable regions within VC2030, which encodes ribonuclease E, an essential enzyme required for 5S rRNA processing ( 32 ) and mRNA turnover ( 33 ). The highly homologous E. coli RneE has three domains:...”
- Mining regulatory 5'UTRs from cDNA deep sequencing datasets
Livny, Nucleic acids research 2010 - “...periplasmic oligopeptide-binding protein T-box(4), SAM(8) RLE0210(6) 8* VC1623 Carboxynorspermidine decarboxylase speF( 25 ), Lysine(17) 9 VC2030 Ribonuclease E rne5(32) 10* VC2108 Erythronate-4-phosphate dehydrogenase T-box(3), SAM(1) 11* VC2334 Hypothetical protein ykoK(3) RLE0310(6) 12 VC2356 Sodium/alanine symporter Glycine(118) 13 VC2439 Methyl-accepting chemotaxis protein GEMM RNA motif( 20 ),...”
- Genetic analysis of Vibrio cholerae monolayer formation reveals a key role for DeltaPsi in the transition to permanent attachment
Van, Journal of bacteriology 2008 - “...(glnE) (glutamine biosynthesis) 2 Transcription/translation VC1179 VC0369 VC2030 Pseudouridine synthase family 1 protein RplL ribosomal protein L9 RNase E 2 2...”
- Comparison of genome structures of vibrios, bacteria possessing two chromosomes
Tagomori, Journal of bacteriology 2002 - “...VC1220 VC1354 VC1486 VC1540 VC1623 VC1627 VC1751 VC1903 VC2030 VC2162 VC2174 VC2290 VC2305 VC2431 VC2560 Thiophene and furan oxidation protein ThdF Chromosomal...”
H16_A2580 Ribonuclease G and E from Ralstonia eutropha H16
H16_A2580 Rne/Rng family ribonuclease from Cupriavidus necator H16
57% identity, 66% coverage
SO2785 ribonuclease E from Shewanella oneidensis MR-1
60% identity, 60% coverage
- An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
Turse, PloS one 2010 - “...were observed from the S. oneidensis MR-1 cultures (SO0970, SO1127, SO1778, SO1779, SO2178, SO2361, SO2363, SO2785, SO3420, SO4048, SO4666), while only two were detected in the S. putrefaciens CN32 cultures (CN32_0905, CN32_1958) ( Table 2 ). The tetraheme cytochrome, fumarate reductase (SO0970 and CN32_0905) was observed...”
Q1ZS71 ribonuclease E (EC 3.1.26.12) from Photobacterium angustum S14 (see paper)
65% identity, 53% coverage
Q7MM07 ribonuclease E (EC 3.1.26.12) from Vibrio vulnificus (see paper)
64% identity, 56% coverage
YPK_1677 ribonuclease from Yersinia pseudotuberculosis YPIII
55% identity, 60% coverage
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...Colonization RhaS STM4048 LcrF pYV0076 96 22 Transcription Host defense Rnase E/rne STM1185 Rnase E YPK_1677 100 64 Translation Invasion, host defense RscC STM2271 RscC YPK_2844 99 58 TCS Colonization, invasion, host defense RtsA STM4315 NA NA NA Transcription Invasion RtsB STM4314 YPK_3033 62 41 Transcription...”
WP_002210926 ribonuclease E from Yersinia pestis biovar Orientalis str. BA200902009
YPO1590 ribonuclease E from Yersinia pestis CO92
55% identity, 59% coverage
NT01EI_2381 ribonuclease, RNaseE/RNaseG family , putative from Edwardsiella ictaluri 93-146
60% identity, 61% coverage
- Transposon mutagenesis and identification of mutated genes in growth-delayed Edwardsiella ictaluri
Kalindamar, BMC microbiology 2019 - “...NT01EI_3522 Selenate reductase, FAD-binding subunit 2.00E-73 23 Eis155 NT01EI_0725 Transcriptional regulator FruR 3.00E-134 43 Eis156 NT01EI_2381 Ribonuclease, RNaseE/RNaseG family 2.00E-04 72 Eis157 NT01EI_0144 Twin-arginine translocation protein subunit TatB 8.00E-07 13 Eis158 NT01EI_0022 Sulfurtransferase, TusA 8.00E-46 10 Eis171 NT01EI_3723 Magnesium-translocating P-type ATPase 0 71 Eis172 NT01EI_3786 Hypothetical...”
Q8ZQ17 ribonuclease E (EC 3.1.26.12) from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
STM1185 RNase E from Salmonella typhimurium LT2
NP_460156 RNase E from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
SL1344_1122, STMMW_11931 ribonuclease E from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
62% identity, 56% coverage
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...93 29 Transcription Colonization RhaS STM4048 LcrF pYV0076 96 22 Transcription Host defense Rnase E/rne STM1185 Rnase E YPK_1677 100 64 Translation Invasion, host defense RscC STM2271 RscC YPK_2844 99 58 TCS Colonization, invasion, host defense RtsA STM4315 NA NA NA Transcription Invasion RtsB STM4314 YPK_3033...”
- In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
Chao, Molecular cell 2017 - GeneRIF: In vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation.
- The virulence of Salmonella enterica Serovar Typhimurium in the insect model galleria mellonella is impaired by mutations in RNase E and RNase III.
Viegas, Applied and environmental microbiology 2013 - GeneRIF: Through the use of a galleria mellonella infection model, authors demonstrate a role for the main endoribonucleases RNase E and RNase III in Salmonella virulence.
- Temperature-sensitive mutants of RNase E in Salmonella enterica.
Hammarlöf, Journal of bacteriology 2011 - GeneRIF: RNase E mutants were defect in initial binding or subsequent cleavage of an mRNA critical for fast growth.
- Mutants of the RNA-processing enzyme RNase E reverse the extreme slow-growth phenotype caused by a mutant translation factor EF-Tu.
Hammarlöf, Molecular microbiology 2008 (PubMed)- GeneRIF: Suppressor mutations in RNase E can reverse the extreme slow-growth phenotype caused by a mutant translation factor EF-Tu.
- Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313
Ondari, Wellcome open research 2019 - “.... G796S 1200631 STMMW_11271 agp glucose-1-phosphatase precursor, secreted T C C . . L322P 1264174 STMMW_11931 rne ribonuclease E G T T . . R1062S 4277479 STMMW_40091 _ alcohol dehydrogenase T C C . . K78E 4390204 STMMW_41061 rpoB DNA-directed RNA polymerase, beta-subunit G A A...”
- The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression
Ramachandran, BMC genomics 2012 - “...First strand cDNA synthesis was performed using either random hexamers oligonucleotide primers (for SL1344_1204 and SL1344_1122) or gene-specific primers followed by PCR amplification with nested gene-specific primers and 5' Adaptor-specific DNA primer B6. Resulting PCR products were cloned into the pGEM -T Easy vector (Promega) and...”
SC1132 RNase E from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
62% identity, 56% coverage
- Temporal regulation of genes encoding the flagellar proximal rod in Caulobacter crescentus
Boyd, Journal of bacteriology 2001 - “...C. crescentus NA1000 LS2195 SC508 SC1032 SC1055 SC1131 SC1132 JG3108 JG3110 JG3111 Characteristics VOL. 183, 2001 727 antibodies as previously described (21)....”
- “...class II mutant, either SC1131 (fliM::Tn5) or SC1132 (flhA::Tn5), and assayed expression of fljL::lacZ in the resultant double-mutant background. We reasoned...”
- FlbT couples flagellum assembly to gene expression in Caulobacter crescentus
Mangan, Journal of bacteriology 1999 - “...SC1032 SC1137 SC1054 SC1055 SC1060 SC1066 SC1114 SC1132 SC2201 SC2204 SC3476 syn-1000 flgE806::Tn5-VB32 flbT650 flgE::IS511 fliQR153 flaF673 fla-674 syn-1000...”
- “...to Tn5-132 Transduction of SC1066 Phage SC3730 SC276 Phage SC1132 SC276 Phage SC1060 SC276 Phage SC1032 SC276 Phage SC1054 SC276 Phage SC2201 SC276 Phage SC2204...”
- A new class of Caulobacter crescentus flagellar genes
Leclerc, Journal of bacteriology 1998 - “...SC1029 SC1030 SC1032 SC1055 SC1066 SC1117 SC1127 SC1128 SC1132 SC1134 SC1135 SC2663 SC3090 SC3809 SC3898 SC3899 SC3971 SC3973 SC3975 SC4016 SC4250 Wild type...”
- “...flmA::cat flmC::cat flmE::cat flmG::cat SC1029 SC1032 SC1055 SC1066 SC1132 SC2663 SC3809 SC1117 SC1134 SC1135 SC1128 flhB (II) flbD (II) rpoN (II) fliL (II)...”
- A mutation that uncouples flagellum assembly from transcription alters the temporal pattern of flagellar gene expression in Caulobacter crescentus
Mangan, Journal of bacteriology 1995 - “...SC508 SC1029 SC1032 SC1042 SC1048 SC1055 SC1088 SC1131 SC1132 UC900 UC1010 UC1020 UC1030 UC1040 UC1041 UC1042 UC1043 UC1044 UC1045 UC1046 UC1047 UC1048 UC1049...”
- “...bfa SC508 (fliQR) SC1131 (fliLM) SC1048 (fliP) SC1029 (podW) SC1132 (flhA) UC2113 SC1055 (rpoN) SC1032 (flbD) NA1000 (wild type) fljL/lacZ flbG/lacZ 1 1 87 181...”
- Identification of the promoter and a negative regulatory element, ftr4, that is needed for cell cycle timing of fliF operon expression in Caulobacter crescentus
Van, Journal of bacteriology 1993 - “...triphosphates (dNTPs), and the CB15 CB15F SC511 SC1032 SC1132 E. coli HB101 DH5 a CJ236 Wild type Density variant of CB15 flaK155::IS511 flbDl98::TnS...”
- “...lane D, SC1032 (flbD198::TnS)/pRK2L1-SV4; lane E, SC1132 (flbF177::TnS)/pRK2L1-SV4; lanes F and G, Saccharomyces cerevisiae tRNAs. Nuclease S1 was...”
- Characterization of the Caulobacter crescentus flbF promoter and identification of the inferred FlbF product as a homolog of the LcrD protein from a Yersinia enterocolitica virulence plasmid
Sanders, Journal of bacteriology 1992 - “...Berkeley Strains C. crescentus CB15 SC1052 SC1032 SC1061 SC1132 E. coli HB101 DH5a RZ1032 Relevant characteristic 32P labeled with [-y-32P]ATP and T4...”
- “...motility defect in flbF mutant strains SC1061 and SC1132. (B) Restriction endonuclease map. Relevant restriction sites are shown. Abbreviations: A, AflII; B,...”
- Expression of an early gene in the flagellar regulatory hierarchy is sensitive to an interruption in DNA replication
Dingwall, Journal of bacteriology 1992 - “...and Genotype class Class I genes SC1032 SC1042 SC1132 SC1131 SC508 flbDl98::TnS flaO172::TnS flbF608::TnS flb0196::TnS flaSl53::TnS 160 143 180 130 300 Class II...”
- Timing of flagellar gene expression in the Caulobacter cell cycle is determined by a transcriptional cascade of positive regulatory genes
Ohta, Journal of bacteriology 1991 - “...PC5974 PC5978 PC5983 PC7812 SC298 SC511 SC1032 SC1132 SC1140 Wild type Wild type, density variant flaO172::TnS flaO172::TnS rec-526 flbD198::TnS rec-526...”
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YE1627 ribonuclease E from Yersinia enterocolitica subsp. enterocolitica 8081
63% identity, 49% coverage
S1168 ribonuclease E from Shigella flexneri 2a str. 2457T
62% identity, 56% coverage
- Addendum
, Open forum infectious diseases 2019
bglu_1g09400 Ribonuclease E from Burkholderia glumae BGR1
55% identity, 61% coverage
- Membrane Depolarization and Apoptosis-Like Cell Death in an Alkaline Environment in the Rice Pathogen Burkholderia glumae
Nam, Frontiers in microbiology 2021 - “...in QS mutants. The expression of genes encoding HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), ribonuclease E (BGLU_1G09400), and Hu-beta (BGLU_1G13530) was significantly elevated in QS mutants compared to that in wild-type BGR1, consistent with the degradation of cellular materials as observed under transmission electron microscopy (TEM). A...”
- “...), three genes encoding nucleic acid-degradation enzymes, HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), and ribonuclease E (BGLU_1G09400), and a gene encoding the chromosomal binding protein Hu-beta (BGLU_1G13530) were chosen for further analysis. The qRT-PCR results showed that the expression of these genes was higher in the QS...”
Q7NX09 Ribonuclease E from Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)
59% identity, 61% coverage
- GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
Lima, Scientific reports 2016 - “...213 Trigger factor GN= tig Protein folding Q7NYY5 211 186 Acetaldehyde dehydrogenase GN= adhE Glycolysis/Gluconeogenesis Q7NX09 196 194 Probable ribonuclease E GN=CV_1820 RNA degradation, Q7NY10 183 204 Polyribonucleotide nucleotidyltransferase GN= pnp Purine metabolism The proteins are represented in descending order. GN=Gene name. Table 2 Differentially abundant...”
- The influence of iron on the proteomic profile of Chromobacterium violaceum
Lima, BMC microbiology 2014 - “...28.3253877082137 0.2368 Protein kinase 30 Down-regulated Energetic metabolism Q7P0K7 10.238165245516 0.241 Glyceraldehyde-3-phosphate dehydrogenase (GapA) 18 Q7NX09 3.75399392335588 0.1019 Probable ribonuclease E 13 Stress response Q7NXP2 9.21434872096442 0.3333 Thioredoxin 7 Q7NXI3 2.18117433491428 0.2897 Chaperone protein DnaK 50 Q7NYF6 13.3096148191708 0.1268 Chaperone protein HtpG 12 Q7NQ87 13.3096148191708 0.3355...”
DR76_3839 ribonuclease E from Escherichia coli ATCC 25922
70% identity, 48% coverage
NP_309489 endoribonuclease from Escherichia coli O157:H7 str. Sakai
70% identity, 48% coverage
SmbB / b1084 ribonuclease E (EC 3.1.26.12) from Escherichia coli K-12 substr. MG1655 (see 7 papers)
rne / P21513 ribonuclease E (EC 3.1.26.12) from Escherichia coli (strain K12) (see 154 papers)
RNE_ECOLI / P21513 Ribonuclease E; RNase E; EC 3.1.26.12 from Escherichia coli (strain K12) (see 24 papers)
P21513 ribonuclease E (EC 3.1.26.12) from Escherichia coli (see 17 papers)
rne / GB|BAA35893.1 rne RNase E (1st module); EC 3.1.26.12 from Escherichia coli K12 (see 8 papers)
NP_415602 ribonuclease E from Escherichia coli str. K-12 substr. MG1655
b1084 fused ribonucleaseE: endoribonuclease/RNA-binding protein/RNA degradosome binding protein from Escherichia coli str. K-12 substr. MG1655
70% identity, 48% coverage
- function: Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Can also process other RNA species, such as RNAI, a molecule that controls the replication of ColE1 plasmid, and the cell division inhibitor DicF- RNA. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process. Required to initiate rRNA degradation during both starvation and quality control; acts after RNase PH (rph) exonucleolytically digests the 3'-end of the 16S rRNA (PubMed:27298395). Degradation of 16S rRNA leads to 23S rRNA degradation (PubMed:27298395). Processes the 3 tRNA(Pro) precursors immediately after the 3'-CCA to generate the mature ends (PubMed:27288443).
function: Prefers 5'-monophosphorylated substrates over 5'- triphosphorylated substrates (PubMed:10762247). 5'-monophosphate- assisted cleavage requires at least 2 and preferably 3 or more unpaired 5'-terminal nucleotides. The optimal spacing between the 5' end and the scissile phosphate appears to be 8 nucleotides. Any sequence of unpaired nucleotides at the 5'-end is tolerated (PubMed:26694614).
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits and are essential for homotetramerization and catalytic activity, but not for RNA binding. In the absence of zinc, the protein dissociates into inactive dimers.)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Within the RNA degradosome, RNase E assembles into a homotetramer formed by a dimer of dimers. Tetramerization is essential for catalytic activity, but not for RNA-binding. Interacts with RhlB, PNPase (pnp) and enolase (eno). Interacts with DeaD at reduced temperature.
disruption phenotype: Essential, it cannot be deleted. In a temperature sensitive mutant at non-permissive temperature, slow processing of the 17S rRNA precursor to 16S rRNA; a double rne-rng mutated strain no longer processes the 17S rRNA precursor. - Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...P0A9H9 CHEZ Function unknown Cytoplasm 85 P05055 PNP Translation, ribosomal structure and biogenesis Cytoplasm 86 P21513 RNE Translation, ribosomal structure and biogenesis Cytoplasm 87 P0A80 YJGA Function unknown Cytoplasm 88 P39406 RSMC Translation, ribosomal structure and biogenesis Cytoplasm 89 P00962 SYQ Translation, ribosomal structure and biogenesis...”
- Multi-scale ensemble properties of the Escherichia coli RNA degradosome
Dendooven, Molecular microbiology 2022 - “...across RNA degradosome components Protein or segment Identification code uniprot Isoelectric point, protomer RNase E P21513 5.47 RNase E catalytic domain 1-529, and with membrane interaction site 1-602 P21513 6.16, 6.01 RNase E RNA binding region 603-850; PNPase interaction segment 851-1063 P21513 10.67 , 4.11 RhlB,...”
- The Protein Interactome of Glycolysis in Escherichia coli
Chowdhury, Proteomes 2021 - “...7 GpmI P37689 GpmA P62707 Rajagopala/Lasserre [ 2 , 32 ] 8 Eno P0A6P9 Rne P21513 Hu/Rajagopala/Shatsky [ 3 , 2 , 27 ] 8 Eno P0A6P9 Pnp P05055 Hu/Shatsky [ 3 , 27 ] 9 PykA P21599 PflB P09373 Hu/Rajagopala [ 3 , 2 ]...”
- Exploiting bacterial outer membrane vesicles as a cross-protective vaccine candidate against avian pathogenic Escherichia coli (APEC)
Hu, Microbial cell factories 2020 - “...18 P0AFG8 aceE Pyruvate dehydrogenase E1 component Cytoplasmic Energy production and conversion 99.667 6.63E+08 19 P21513 rne Ribonuclease E Cytoplasmic Translation, ribosomal structure and biogenesis 118.2 6.48E+08 20 P00968 carB Carbamoyl-phosphate synthase subunit beta Periplasmic Membrane biogenesis/synthesize carbamoyl phosphate 117.842 4.28E+08 MOMVs represents multi-serogroup outer membrane...”
- Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder
Machulin, International journal of molecular sciences 2019 - “...0 36 26 Ribonuclease R E. coli P21499 13 6 27 Ribonuclease E E. coli P21513 0 20 26 Tex-like protein N-terminal domain protein Kingella denitrificans F0F1S0 0 0 13 ijms-20-02377-t003_Table 3 Table 3 Ratio of regions connecting elements of the secondary structure according to the...”
- A structural and biochemical comparison of Ribonuclease E homologues from pathogenic bacteria highlights species-specific properties
Mardle, Scientific reports 2019 - “...amino acid sequences were downloaded from UniProtKB using the following accession codes: Ec RNase E (P21513), Yp RNase E (Q74TC3), Ft RNase E (Q5NFK7), Bp RNase E (A0A0H3HN63) and Ab RNase E (A0A0B9WR03). The sequences were aligned in MOE (Molecular Operating Environment, 2013.08; Chemical Computing Group...”
- Modulation of RNase E activity by alternative RNA binding sites
Kim, PloS one 2014 - “...of RNA substrates [1] [4] . In Escherichia coli , RNase E (UniProt KB no., P21513) is an essential protein with a mass of 118.2 kDa and a subunit structure that consists of two distinct halves. The N-terminal domain (NTD; amino acid residues 1529) contains the...”
- SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method.
Zhang, Journal of biomolecular structure & dynamics 2012 - “...human p53, E. coli RNase E, measles virus nucleoprotein, and axin, UniProt IDs: Q13541, P04637, P21513, P10050, and O15169, respectively). In all plots, disorder scores (the probability of a given residue being disordered) are shown as a function of residue index. Red, blue and green curves...”
- “...C-terminal binding motif. Figure 5C shows that PONDR-FIT outperformed SPINE-D in the case RNase E (P21513) and was similar to the PONDRVLXT outputs for this protein. On the other hand, Figure 5D illustrates that SPINE-D can detect a C-terminal binding site in the measles virus nucleoprotein...”
- More
- Unraveling the interplay between a small RNA and RNase E in bacteria.
Vigoda, Nucleic acids research 2024 - GeneRIF: Unraveling the interplay between a small RNA and RNase E in bacteria.
- Graded impact of obstacle size on scanning by RNase E.
Richards, Nucleic acids research 2023 - GeneRIF: Graded impact of obstacle size on scanning by RNase E.
- The C nucleotide at the mature 5' end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3' terminus as well as functionality.
Mohanty, Nucleic acids research 2022 - GeneRIF: The C nucleotide at the mature 5' end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3' terminus as well as functionality.
- Escherichia coli RNase E can efficiently replace RNase Y in Bacillus subtilis.
Laalami, Nucleic acids research 2021 - GeneRIF: Escherichia coli RNase E can efficiently replace RNase Y in Bacillus subtilis.
- Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E.
Ali, Nucleic acids research 2020 - GeneRIF: we have examined RNase E variants bearing extended C-terminal truncations in combination with substitutions in the active site or 5'-sensor pocket. We show that intragenic or allelic complementation occurs in RNase E, whereby enzyme activity is restored and strains are rendered viable when pairs of individually inactive mutant proteins are mixed together or co-expressed
- Stem-loops direct precise processing of 3' UTR-derived small RNA MicL.
Updegrove, Nucleic acids research 2019 - GeneRIF: Moreover, our assays of MicL, ArcZ and CpxQ showed that sRNAs exhibit differential sensitivity to RNase E, likely a consequence of a hierarchy of sRNA features recognized by the endonuclease.
- Obstacles to Scanning by RNase E Govern Bacterial mRNA Lifetimes by Hindering Access to Distal Cleavage Sites.
Richards, Molecular cell 2019 - GeneRIF: These findings suggest that RNase E searches for cleavage sites by scanning linearly from the 5'-terminal monophosphate along single-stranded regions of RNA and that its progress is impeded by structural discontinuities encountered along the way.
- Feedback regulation of small RNA processing by the cleavage product.
Durica-Mitic, RNA biology 2019 - GeneRIF: accumulation of GlmZ* prevents complete GlmZ turnover. This mechanism may serve to adjust a robust glmS basal expression level that is buffered against fluctuations in RapZ availability.
- More
- Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
Chhabra, PloS one 2011 - “...in messenger RNA processing and is composed of the following additional proteins: Ribonuclease E (Rne, b1084), RNA helicase (RhlB, b3780), polyphosphate kinase (Ppk, b2501) and enolase (Eno, b2779). The suggested component stoichiometries in the complex are [(Ppk) 4 ][(Rne) 4 ][(RhlB) 2 ][(Pnp) 3 ][(Eno) 2...”
- “...multiple sequence alignment of Rne from D. vulgaris (DVU3055) and its E. coli K12 counterpart (b1084) confirmed that only the N-terminal portion of Rne exhibits conservation (42% sequence identity) between the two species. Even though the D. vulgaris Hildenborough genome encodes several homologs to components of...”
- Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
Thiele, Biophysical journal 2010 - “...eigen-reaction consisted of the gene synthesis reaction for b1084 (Rne), a component of the multiprotein complex degradosome, which is responsible for mRNA...”
- “...eigen-reaction consists of the synthesis of b2794 (QueF) and b1084 (Rne). QueF is a protein involved in the synthesis of pre_Q0, a precursor to queuosine that...”
Q65S31 Ribonuclease E from Mannheimia succiniciproducens (strain KCTC 0769BP / MBEL55E)
61% identity, 60% coverage
- Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction
Xue, International journal of molecular sciences 2010 - “...MoRF region N of RNase E is highly conserved among five different proteins, where CafA (Q65S31) is also a member of RNase family. As indicated by the prediction in Figure 2(a) , this segment in all five molecules is flanked by disordered regions. Although the specific...”
- “...RNase E was also shown to interact with enolase. As shown by Figure 2(c) , Q65S31, A5UA75, and A4NVQ3 all have RNaseE-C3-like segment within a disordered region. The alignment and disorder prediction indicate that these three proteins may also interact with enolase. Actually, as indicated by...”
RNE_HAEIN / P44443 Ribonuclease E; RNase E; EC 3.1.26.12 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
HI0413 ribonuclease E from Haemophilus influenzae Rd KW20
64% identity, 56% coverage
- function: Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs.
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer.)
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Within the RNA degradosome, RNase E assembles into a homotetramer formed by a dimer of dimers. - Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries
Jenkins, Genome biology 2002 - “...6.00E-14 Bacillus subtilis (O34526) B Miscellaneous F3 BH001162 Ribonuclease E (RNase E) 1.00E-38 Haemophilus influenzae (P44443) B H6 BH001163 Inter-alpha-trypsin inhibitor heavy chain H2 precursor 2.00E-06 Mus musculus (Q61703) E pl2-D4 BH001164 Putative methionine aminopeptidase B (MAP) peptidase M 3.00E-08 Rickettsia prowazekii (Q9ZCD3) B Hypothetical proteins...”
- Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis
Gmuender, Genome research 2001 - “...hi1125 hi0250 hi0113 hi0256 hi0079 hi0872 hi0970 hi1384 hi0413 hi1742 hi0602 hi0717 hi1447 hi0411 hi0287 hi0331 hi0991 hi0622 hi0206 hi0603 hi1325 hi0993 hi0865...”
NMV_0215 Rne/Rng family ribonuclease from Neisseria meningitidis 8013
58% identity, 58% coverage
BP0475 ribonuclease E from Bordetella pertussis Tohama I
57% identity, 59% coverage
Q9R5Y8 Ribonuclease G (Fragment) from Escherichia coli
72% identity, 46% coverage
5f6cA / P21513 The structure of e. Coli rnase e catalytically inactive mutant with RNA bound (see paper)
70% identity, 48% coverage
- Ligands: rna; magnesium ion; zinc ion (5f6cA)
NGO1785 Rne from Neisseria gonorrhoeae FA 1090
58% identity, 58% coverage
- Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae
Ducey, Microbial pathogenesis 2009 - “...metabolism [ 18 ]. The gonococcus has homologs for both Hfq (NGO0326) and RNase E (NGO1785), suggesting that in conjunction with these loci, NrrF may enhance degradation of mRNA encoding for iron containing proteins during times of iron depletion. We also have utilized a single reaction,...”
BCAL0982 putative ribonuclease E from Burkholderia cenocepacia J2315
BCAL2888 ribonuclease E 1 from Burkholderia cenocepacia J2315
63% identity, 51% coverage
- The Essential Genome of Burkholderia cenocepacia H111
Higgins, Journal of bacteriology 2017 - “...B. cenocepacia J2315, with each functional copy being designated BCAL0982 and BCAL2888. Image taken from the LB data set. amine (PRA) using the ammonia group...”
- The Essential Genome of Burkholderia cenocepacia H111
Higgins, Journal of bacteriology 2017 - “...J2315, with each functional copy being designated BCAL0982 and BCAL2888. Image taken from the LB data set. amine (PRA) using the ammonia group from L-glutamine...”
- Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
Sass, Scientific reports 2017 - “...of genes known to harbour cis-regulatory structures in other bacterial species, e.g. ribonuclease E 34 (BCAL2888), a proline-betaine transporter 35 (BCAL1252), ribosomal proteins 36 (BCAL0115, BCAL2091, BCAL2765, BCAL2714, BCAL3348), carA 37 (BCAL1260) and tRNA-synthetases 36 (BCAL3373, BCAL3436). Attenuation, observed for many short 5UTRs, is indicative of...”
E6MW75 Ribonuclease E from Neisseria meningitidis serogroup B / serotype 15 (strain H44/76)
58% identity, 57% coverage
Varpa_1519 Rne/Rng family ribonuclease from Variovorax paradoxus EPS
63% identity, 46% coverage
- Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation
Fredendall, Access microbiology 2020 - “...in the V. paradoxus EPS genome, consisting of polynucleotide phosphorylase (PNPase, Varpa_4029), enolase (Varpa_2167), RNaseE/R (Varpa_1519, Varpa_3333) and helicases (DEAD/DEAH box, Varpa_4256, Varpa_0178, Varpa_2773), along with the RNA 5 pyrophosphohydrolase RppH (Varpa_4825) and the Rho transcription termination factor (Varpa_2500). Varpa_1640 was not identified in the KEGG...”
NE1457 Ribonucleases G and E from Nitrosomonas europaea ATCC 19718
60% identity, 51% coverage
ACIAD0438 ribonuclease E (RNase E): endoribonuclease for rRNA processing and mRNA degradation from Acinetobacter sp. ADP1
60% identity, 45% coverage
2c0bL / P21513 Catalytic domain of e. Coli rnase e in complex with 13-mer RNA (see paper)
68% identity, 48% coverage
- Ligands: rna; zinc ion (2c0bL)
CBU_0486 ribonuclease, Rne/Rng family from Coxiella burnetii RSA 493
62% identity, 48% coverage
ABUW_3478 Rne/Rng family ribonuclease from Acinetobacter baumannii
ABAYE3375 ribonuclease E (RNase E): endoribonuclease for rRNA processing and mRNA degradation from Acinetobacter baumannii AYE
63% identity, 43% coverage
WP_015444149 ribonuclease E/G from Legionella pneumophila
50% identity, 62% coverage
Q5NFK7 Ribonuclease E from Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
53% identity, 47% coverage
WP_032731480 ribonuclease E/G from Francisella tularensis subsp. tularensis
53% identity, 47% coverage
FTL_0717 Ribonuclease E from Francisella tularensis subsp. holarctica
FTH_0719 ribonuclease E from Francisella tularensis subsp. holarctica OSU18
53% identity, 47% coverage
- Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA
Miller, BMC microbiology 2014 - “...start FTL_0539 ( lpxA ) UDP-N-acetylglucosamine acyltransferase T36N 522331 Unique to S102 107bp from start FTL_0717 ( rne ) Ribonuclease E K38T 709489 ripA , and S102 114bp from start FTL_1388 ( nadB ) L-aspartate oxidase A93T 1317802 wt, ripA , and S102 278bp from start...”
- “...leading to the missense A93T mutation. The ripA strain contained an additional missense mutation in FTL_0717, ribonuclease E, K38T. The missense mutation in ribonuclease E does not contribute the growth defect of the ripA strain, because the growth defect in this, and all other ripA strains,...”
- Possible links between stress defense and the tricarboxylic acid (TCA) cycle in Francisella pathogenesis
Dieppedale, Molecular & cellular proteomics : MCP 2013 - “...FTL_1866 FTL_0552 FTL_1138 FTL_1426 FTL_0068 FTL_0717 FTL_0690 FTL_0113/FTL_1159 FTL_0906 FTL_0673 FTL_0539 FTL_0427 FTL_0421 FTL_1541 AMP-binding protein...”
- Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
Horák, Soft matter 2012 - “...Conserved hypothetical protein 4.51/8.90 cyt TMH FTH_0689 Probable multidrug resistance efflux pump 37.83/9.36 ? cyt FTH_0719 Ribonuclease E 95.95/7.12 cyt cyt FTH_0799 Bifunctional 1-pyrroline-5-carboxylate dehydrogenase/proline dehydrogenase 150.39/7.97 cyt cyt FTH_0800 APC family amino acidpolyamine-organocation transporter 55.00/9.27 CM TMH FTH_0836 Preprotein translocase subunit 12.87/10.55 CM SPI FTH_0837...”
- “...Conserved hypothetical protein 14.93/8.92 ? SPII FTH_0689 Probable multidrug resistance efflux pump 37.83/9.36 ? cyt FTH_0719 Ribonuclease E 95.95/7.12 cyt cyt FTH_0792 Type IV pilus assembly protein 23.00/9.58 ? SPI FTH_0799 Bifunctional 1-pyrroline-5-carboxylate dehydrogenase/proline dehydrogenase 150.39/7.97 cyt cyt FTH_0800 APC family amino acid-polyamine-organocation transporter 55.00/9.27 CM...”
- Multimethodological approach to identification of glycoproteins from the proteome of Francisella tularensis, an intracellular microorganism
Balonova, Journal of proteome research 2010 - “...identified proteins contain this extended glycosylation motif, with proteins dTDP-glucose 4,6-dehydratase (FTH_0592) and ribonuclease E (FTH_0719) having two of these motifs. The proteins with no predicted N-glycosylation site are most likely modified through O-glycosylation, or, possibly, they could be part of the non-glycosylated proteome that was,...”
- “...11.54 0 - cyt - FTH_1764 ConA, DSA, SNA 25.20 6.95 0 - cyt - FTH_0719 DSA, PNA, SBA 95.95 7.12 6 DVN 302 SS ETN 791 QT cyt - FTH_0232 DSA, PNA, SBA 22.55 10.29 0 - ? - FTH_1691 DSA, SBA, SNA 43.39 4.87...”
OOM_1576 ribonuclease E/G from Francisella orientalis
52% identity, 46% coverage
SMc01336 PROBABLE RIBONUCLEASE E PROTEIN from Sinorhizobium meliloti 1021
50% identity, 39% coverage
A0A2J0Z3F8 ribonuclease E (EC 3.1.26.12) from Sinorhizobium meliloti (see paper)
50% identity, 39% coverage
RSP_2131 Ribonuclease E from Rhodobacter sphaeroides 2.4.1
51% identity, 38% coverage
WP_002964041 ribonuclease E from Brucella abortus 90-1280
BAB1_0930 Ribonuclease E and G from Brucella melitensis biovar Abortus 2308
49% identity, 38% coverage
- The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus.
Sheehan, Journal of bacteriology 2020 - GeneRIF: The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus.
- The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus
Sheehan, Journal of bacteriology 2020 (secret) - Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
Roset, Scientific reports 2017 - “...NO 1.54 0.11 GI:82699769 BAB1_0918 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B C NO 1.41 0.15 GI:82699781 BAB1_0930 ribonuclease E and G C NO 1.36 0.11 GI:82699998 BAB1_1181 frr ribosome recycling factor C NO 0.79 0.04 GI:82700035 BAB1_1223 alaS alanyl-tRNA synthetase C NO 1.33 0.04 GI:82700083 BAB1_1271 ef_Tu...”
- A 6-Nucleotide Regulatory Motif within the AbcR Small RNAs of Brucella abortus Mediates Host-Pathogen Interactions
Sheehan, mBio 2017 - “...could be constructed in B.abortus (Xavier DeBolle, personal communication). Therefore, to determine if RNase E (BAB1_0930) is responsible for AbcR sRNA-mRNA degradation in B.abortus , a chromosomal B.abortus Rnase E gene mutant was constructed which lacked the C-terminal domain. Northern blot analysis of the AbcR sRNAs,...”
- Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308
Caswell, Molecular microbiology 2012 - “...possible that a similar mechanism is in place in Brucella . In fact, the gene BAB1_0930 in the B. abortus 2308 genome is annotated as ribonuclease E and G and exhibits 45% identity and 64% similarity at the amino acid level to RNase E of E....”
Q98NB6 Ribonuclease E from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
49% identity, 38% coverage
- Cyclic Isothiocyanate Goitrin Impairs Lotus japonicus Nodulation, Affects the Proteomes of Nodules and Free Mesorhizobium loti, and Induces the Formation of Caffeic Acid Derivatives in Bacterial Cultures
Jeong, Plants (Basel, Switzerland) 2024 - “...were upregulated. In F1, only two proteins were significantly reduced: 5-nucleotidase Q98H62 and ribonuclease E (Q98NB6) acting in 5S and 16S rRNAs and the majority of tRNAs maturation and in mRNA degradation. Five proteins have an insignificantly lower abundance, among them, (anti)termination protein NusG, GMP synthetase,...”
- “...is only known for water-soluble quinone oxidoreductases [ 102 ]. The significantly downregulated ribonuclease E (Q98NB6) for t-RNAs maturation and mRNA degradation together, with the imbalance in ribosomal proteins encloses malfunctions in translation processes. The many unchanged or downregulated glutathione-S-transferases being candidates for goitrin complex formation...”
BMEI1057 RIBONUCLEASE E / ZINC METALLOPROTEASE from Brucella melitensis 16M
49% identity, 38% coverage
Atu1339 ribonuclease E from Agrobacterium tumefaciens str. C58 (Cereon)
48% identity, 38% coverage
- α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies
Al-Husini, Molecular cell 2018 - “...E-YFP fusion was generated by cloning the last 915 bp of the RNase E gene (Atu1339) lacking a stop codon into pYFPC-4 ( Thanbichler et al., 2007 ). First the last 915 bp of the RNase E gene were amplified by PCR from the C58 genome...”
- “...by Gibson assembly. This was done by PCR amplifying the last 861bp Atu -CTD fragment (Atu1339 ) lacking stop codon using the following DNA primers: j5_00398_(Atu_CTD)_forward GGAAGAAGAAGACGACGACGATATCGTCATCGAGGTGGAAGAGGAC j5_00399_(Atu_CTD)_reverse CGCGTAACGTTCGAATTGAAGAAGCCTTTGCGCTGCCACC We also PCR opened the pVRNE(NTD)-YFPC-4 plasmid using the following primers: j5_00396_(CC_NTD_Correct)_forward GCGCAAAGGCTTCTTCAATTCGAACGTTACGCGTCACCGGT j5_00397_(CC_NTD_Correct)_reverse CGATGACGATATCGTCGTCGTCTTCTTCTTCCTCGTCGTCGTAGG The resultant...”
bll4305 ribonuclease E from Bradyrhizobium japonicum USDA 110
47% identity, 39% coverage
CC1877 ribonuclease, Rne/Rng family protein from Caulobacter crescentus CB15
CCNA_01954 ribonuclease E from Caulobacter crescentus NA1000
48% identity, 38% coverage
- Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome
Voss, Nucleic acids research 2014 - “...RNA degradosome by co-immunopurification, and have shown that this complex is comprised of RNase E (cc1877), the DEAD-box protein cc1847, the exoribonuclease polynucleotide phosphorylase (PNPase/cc0034) and the tricarboxylic acid cycle enzyme aconitase (cc3667) ( 7 ). The binding sites for PNPase and aconitase in RNase E...”
- Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly
Hardwick, Open biology 2012 - “...codes 4AM3, 4AID and 4AIM. 3.5. Construction of Caulobacter crescentus strains DNA sequences upstream of cc1877 ( rne ), a triple-flag sequence, and the beginning of the rne gene were PCR amplified using the primer pairs 3713_SpeI-700upcc1877-fw and 3714_Upcc1877-3xflag-rv, 3715_Upcc1877-3xflag-fw and 3746_3xflag-cc1877-rv, or 3716_3xflag-cc1877-fw and 3718_700cc1877-NheI-rv,...”
- An RNA degradosome assembly in Caulobacter crescentus
Hardwick, Nucleic acids research 2011 - “...at 125kDa is the full-length RNase E (16 unique proteolytic peptides identified, protein identification code CC1877). Like its E. coli homologue ( 38 ), C. crescentus RNase E runs at a higher than expected position on a denaturing gel, with an apparent mass of 125kDa by...”
- α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies
Al-Husini, Molecular cell 2018 - “...RNase E-YFP fusion was generated by cloning the last 534bp of the RNase E gene (CCNA_01954) lacking a stop codon into pYFPC-1 ( Thanbichler et al., 2007 ). First the last 534bp of the RNase E gene were amplified by PCR from the NA1000 genome using...”
CKC_RS00790 ribonuclease E/G from Candidatus Liberibacter solanacearum CLso-ZC1
47% identity, 38% coverage
- Interactions "Candidatus Liberibacter solanacearum"-Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses
Yao, Frontiers in cellular and infection microbiology 2016 - “...involved in DNA repair and DNA restriction and modification ( CKC_RS00225 , CKC_RS01855 , and CKC_RS00790 ). Table 5 List of predicted effector genes identify by S4TE (threshold score > 5) . Gene Protein description S4TE score CKC_RS05675 Hypothetical protein 8 CKC_RS00980 Hypothetical protein 8 CKC_RS04080...”
- “...Hypothetical protein 5 CKC_RS05560 Hypothetical protein 5 CKC_RS01855 Type I restriction-modification system, M subunit 5 CKC_RS00790 Ribonuclease E 5 CKC_RS00820 Glycyl-tRNA synthetase subunit alpha: glyQ 5 CKC_RS00375 30S ribosomal protein S20 5 Evaluation of S4TE-predicted effector gene expression by qPCR To evaluate the S4TE-predicted effectors gene...”
A4NVQ3 23S rRNA pseudouridylate synthase C from Haemophilus influenzae 22.4-21
55% identity, 34% coverage
- Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction
Xue, International journal of molecular sciences 2010 - “...also shown to interact with enolase. As shown by Figure 2(c) , Q65S31, A5UA75, and A4NVQ3 all have RNaseE-C3-like segment within a disordered region. The alignment and disorder prediction indicate that these three proteins may also interact with enolase. Actually, as indicated by STRING 8.2, Q65S31...”
- “...can also interact with enolase with a score of 0.829. Although the interaction network of A4NVQ3 is missing in STRING 8.2, due to the high sequence identity between A4NVQ3 and Q65S31, it is very likely that A4NVQ3 will also interact with enolase. The p53-N-like segment was...”
Dde_0537 Ribonuclease E (rne) from Desulfovibrio desulfuricans G20
41% identity, 44% coverage
DVU3055 ribonuclease, Rne/Rng family from Desulfovibrio vulgaris Hildenborough
43% identity, 43% coverage
NCgl2281 translation initiation factor IF-2 N-terminal domain-containing protein from Corynebacterium glutamicum ATCC 13032
42% identity, 38% coverage
CAB780 Rne/Rng family ribonuclease from Chlamydia abortus S26/3
36% identity, 46% coverage
ECH_0470 ribonuclease, Rne/Rng family from Ehrlichia chaffeensis str. Arkansas
43% identity, 35% coverage
CT808 Axial Filament Protein from Chlamydia trachomatis D/UW-3/CX
37% identity, 46% coverage
S3BLZ2 Rne/Rng family ribonuclease from Streptomyces sp. HPH0547
39% identity, 26% coverage
SCO2599 hypothetical protein from Streptomyces coelicolor A3(2)
38% identity, 31% coverage
- Streptomyces RNases - Function and impact on antibiotic synthesis
Jones, Frontiers in microbiology 2023 - “...1997 ). Lee and Cohen identified the gene encoding the enzyme responsible for that activity, sco2599 ( rns ) and overexpressed and characterized the gene product, designating it RNase ES ( Lee and Cohen, 2003 ). S. coelicolor RNase ES is even larger that RNase E...”
- “...essential in E. coli ( Apirion and Lassar, 1978 ) but the corresponding gene ( sco2599 , rns ) could be disrupted in S. coelicolor with only minimal impact on the physiology of the null mutant ( Lee and Cohen, 2003 ). Lee and Cohen noted...”
- A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing
Romero, Molecular microbiology 2014 - “...the 3 end ( Table S4 ). S. coelicolor has homologues of both RNase E (SCO2599) and tRNase Z (SCO2547), which could cut on the 3 side of tRNAs. These cleavages presumably allow 3 to 5 exonucleolytic trimming of the tail prior to addition of the...”
- Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor
Alam, BMC research notes 2011 - “...0.52 2.38E-06 37 5 7 SCO5787 hypothetical protein 27 26 0.12 5.88E-06 44 3 7 SCO2599 hypothetical protein 27.5 25 0.13 4.17E-07 44 1 1 SCO5711 hypothetical protein 29.5 30 0.12 8.65E-06 44 5 5 The proteins are prioritized according to their conservation across actinomycetes, bacteria...”
- High precision multi-genome scale reannotation of enzyme function by EFICAz
Arakaki, BMC genomics 2006 - “...mtu Rv1500 16257960 2.4.1.- 2.4.1.- 3 Bacteria mtu Rv3225c 12715873 2.7.1.- 2.7.1.- 3 Bacteria sco SCO2599 12951512 3.1.4.- 3.1.4.- 3 Bacteria spn SP1051 12571357 2.7.1.- 2.7.1.- 3 Archaea sto ST0071 15212797 3.1.1.- 3.1.1.- 3 Archaea sto ST0723 16618099 1.5.1.30 1.5.1.- 3 Bacteria ttj TTHA1280 16511182 2.1.1.-...”
HMPREF0004_2445 ribonuclease G from Achromobacter piechaudii ATCC 43553
39% identity, 42% coverage
AXYL_02095 ribonuclease G from Achromobacter xylosoxidans A8
38% identity, 44% coverage
SACE_1406 ribonuclease, Rne/Rng family from Saccharopolyspora erythraea NRRL 2338
38% identity, 39% coverage
MAB_1607 Possible ribonuclease E Rne from Mycobacterium abscessus ATCC 19977
38% identity, 38% coverage
MAB_1607 ribonuclease E/G from Mycobacteroides abscessus ATCC 19977
38% identity, 38% coverage
KYC_17547 ribonuclease G from Achromobacter arsenitoxydans SY8
38% identity, 42% coverage
MAP2267c Rne from Mycobacterium avium subsp. paratuberculosis str. k10
40% identity, 37% coverage
RNE_MYCS2 / A0R152 Ribonuclease E; RNase E; EC 3.1.26.12 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see 2 papers)
MSMEG_4626 ribonuclease, Rne/Rng family protein from Mycobacterium smegmatis str. MC2 155
MSMEG_4626, MSMEI_4509 Rne/Rng family ribonuclease from Mycolicibacterium smegmatis MC2 155
39% identity, 37% coverage
- function: Endoribonuclease that plays a central role in RNA processing and decay. Plays a major role in pre-16S rRNA maturation, probably generating the mature 5'-end, and a minor role in pre-5S and pre-23S rRNA maturation (PubMed:22014150). Probably also processes tRNA (By similarity). RNase E and HupB jointly contribute to cellular adaptation to changing growth conditions and survival during antibiotic treatment. Overexpression or depletion leads to changes in gene expression; overexpression induces metabolic slowdown and cell stress while depleted strains grow less well than induced strains (PubMed:35521527).
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits.)
subunit: Assembles into a homotetramer formed by a dimer of dimers (By similarity). Interacts with DNA-binding protein HhupB (Probable) (PubMed:35521527).
disruption phenotype: Essential, it cannot be deleted. Depletion experiments show decreased processing of furA-katG operon mRNA, altered processing of pre-16S rRNA, minor effects on pre-23S rRNA processing. A double rnj-rne depletion mutant has decreased amounts of mature 5S rRNA (PubMed:22014150). Depletion experiments show a decrease in growth rate and decreased expression levels of many transcripts, and suggests rne and hupB are coregulated (PubMed:35521527). - Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...0.02 A0QS66 rpoC , MSMEG_1368, MSMEI_1329 DNA-directed RNA polymerase subunit beta 0.45 0.57 0.36 0.29 A0R152 rne , MSMEG_4626, MSMEI_4509 Ribonuclease E (RNase E) (EC 3.1.26.12) 0.21 0.18 0.09 0.06 A0QSL8 rpoA , MSMEG_1524, MSMEI_1488 DNA-directed RNA polymerase subunit alpha 0.05 0.02 A0QVQ5 pnp , gpsI...”
- Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage.
Ganief, Emerging microbes & infections 2018 - “...A0R218 rho Transcription termination factor Rho (EC 3.6.4.-) (ATP-dependent helicase Rho) 3.6.4.- 0.25 Protein expression A0R152 rne Ribonuclease E (RNase E) (EC 3.1.26.12) 3.1.26.12 0.46 Protein expression Q59560 recA Protein RecA (recombinase A) N/A 0.33 Protein expression A0R7F4 MSMEG_6892 Replicative DNA helicase (EC 3.6.4.12) 3.6.4.12 0.58...”
- Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs
Zhou, The Journal of biological chemistry 2023 - “...model. We therefore constructed an M.smegmatis strain in which we could repress transcription of rne (msmeg_4626), the gene encoding RNase E. Replacement of the native rne promoter and 5 UTR ( 17 ) with the P766(8G) promoter and associated 5 UTR ( 19 ) produced a...”
- “...driven by promoter ptb38, L5 integrating, kan R mc 2 155 in which the rne (msmeg_4626) promoter and UTR (nt346 through1 relative to the rne start codon) were replaced by the P766(8G) promoter and associated 5 UTR ( 19 ). In addition, the hyg R gene...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “..., MSMEG_1368, MSMEI_1329 DNA-directed RNA polymerase subunit beta 0.45 0.57 0.36 0.29 A0R152 rne , MSMEG_4626, MSMEI_4509 Ribonuclease E (RNase E) (EC 3.1.26.12) 0.21 0.18 0.09 0.06 A0QSL8 rpoA , MSMEG_1524, MSMEI_1488 DNA-directed RNA polymerase subunit alpha 0.05 0.02 A0QVQ5 pnp , gpsI , MSMEG_2656, MSMEI_2593...”
- RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness
Griego, iScience 2022 - “...pAG214 attB::rne-linker-mKate2_attT::infA-linker-mCitrine This paper AGS15 AGS13 pAG216 attB::rne-linker-mKate2_attT::hupB-linker-mCitrine This paper AGS17 ATCC700084 pGM255; rne ( MSMEG_4626 ) CRISPRi/dCas9 This paper mc 2 155/pGM255 ATCC700084 pGM257; scrambled CTsgRNA/dCas9 This paper mc 2 155/pGM257 AGS2 pAG216; attT :: hupB -linker-mCitrine This paper AGS33 mc 2 155/pGM255 - pAG216;...”
- “...gene silencing, Km R Addgene ( Rock etal., 2017 ) # 115163 pMYC rne ( MSMEG_4626 ), acetamide-inducible Rne-6xHist tag This paper pAG202 pMV361-based integrative vector, containing attB phage attachment site, Km R Lab collection ( Pea etal., 1996 ) pND200 pND200 expressing mCherry wt from...”
- mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacterium smegmatis
Vargas-Blanco, mBio 2019 - “...( 84 ) and contained 1kb of the sequence upstream and downstream of the rne (msmeg_4626) start codon, with the sequence encoding 6His-3FLAG-TEV-4Gly inserted after the start codon. Constructs were built using NEBuilder HiFi (E2621). Integrants were selected with 200g/ml hygromycin and confirmed by sequencing. Counterselection...”
- “.... doi: 10.1111/j.1348-0421.2005.tb03697.x . 16301812 30. Csanadi A , Faludi I , Miczak A 2009 MSMEG_4626 ribonuclease from Mycobacterium smegmatis . Mol Biol Rep 36 : 2341 2344 . doi: 10.1007/s11033-009-9454-1 . 19153821 31. Tamura M , Moore CJ , Cohen SN 2013 Nutrient dependence of...”
- MSMEG_4626 ribonuclease from Mycobacterium smegmatis
Csanadi, Molecular biology reports 2009 (PubMed)- “...MSMEG_4626 ribonuclease from Mycobacterium smegmatis Agnes Csanadi AE Ildiko Faludi AE Andras Miczak Received: 30 September 2008 / Accepted: 7 January 2009 /...”
- “...2009 O Springer Science+Business Media B.V. 2009 Abstract The MSMEG_4626 gene was cloned from Mycobacterium smegmatis MC2 155. It codes for a protein of 1,037...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...MSMEG_1368, MSMEI_1329 DNA-directed RNA polymerase subunit beta 0.45 0.57 0.36 0.29 A0R152 rne , MSMEG_4626, MSMEI_4509 Ribonuclease E (RNase E) (EC 3.1.26.12) 0.21 0.18 0.09 0.06 A0QSL8 rpoA , MSMEG_1524, MSMEI_1488 DNA-directed RNA polymerase subunit alpha 0.05 0.02 A0QVQ5 pnp , gpsI , MSMEG_2656, MSMEI_2593 Polyribonucleotide...”
OFBG_00227 ribonuclease G from Oxalobacter formigenes OXCC13
38% identity, 40% coverage
- Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
Ellis, Journal of proteomics & bioinformatics 2016 - “...with degradation of stable RNA were also increased in stationary phase relative to log phase (OFBG_00227, OFBG_01664). The processing of nucleotides and degradation of stable RNA has been shown to occur in stationary phase and other forms of starvation in many bacterial species, and would appear...”
HEAR0551 RNase G (ribonuclease G) from Herminiimonas arsenicoxydans
38% identity, 40% coverage
- The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons
Hickey, Frontiers in microbiology 2012 - “...phage BcepC6B 60 BcepC6B_gp25 NA Burkholderia sp. CCGE1002 52 BC1002_6580 NA Herminiimonas arsenicoxydans 47 HEAR0550 HEAR0551 Burkholderia pseudomallei 305 46 BURPS305_2640 BURPS305_2639 Burkholderia sp. CCGE1001 45 BC1001_1032 BC1001_1033 Burkholderia pseudomallei K96243 45 BPSL1157 BPSL1158 Burkholderia thailandensis TXDOH 45 BthaT_010100019559 BthaT_010100019564 Burkholderia sp. 383 44 Bcep18194_A5642 NA...”
RNE_MYCTU / P71905 Ribonuclease E; RNase E; EC 3.1.26.12 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Rv2444c POSSIBLE RIBONUCLEASE E RNE from Mycobacterium tuberculosis H37Rv
NP_216960 ribonuclease E from Mycobacterium tuberculosis H37Rv
39% identity, 36% coverage
- function: Endoribonuclease that plays a central role in RNA processing and decay. Plays a major role in pre-16S rRNA maturation, probably generating the mature 5'-end, and a minor role in pre-5S and pre-23S rRNA maturation. Probably also processes tRNA (By similarity). RNase E and HupB jointly contribute to cellular adaptation to changing growth conditions and survival during antibiotic treatment and in the host (PubMed:35521527).
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits.)
subunit: Assembles into a homotetramer formed by a dimer of dimers (By similarity). Interacts with DNA-binding protein HU (hupB) (Probable) (PubMed:35521527).
disruption phenotype: Essential, it cannot be deleted. Depletion experiments show a decrease in growth rate, decreased processing of furA-katG operon mRNA and decreased expression levels of many transcripts, accounting for the metabolic decrease. Cells are more sensitive to isoniazid (INH). Murine macrophage infection is impaired. - RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness
Griego, iScience 2022 - “...the pLJR965 empty vector ( ct_rne , A), or the ATC-inducible sgRNA-dCas9 repression system against rv2444c ( si_rne , B). See also Video S4 . ATC, INH, and days are indicated. Phase-contrast (magenta) and sfGFP fluorescence (green) are merged and scaled to the brightest frame. Arrows...”
- “...This paper pAG216 pGM218 expressing P native - rne- linker- mCherry , Hyg R ( rv2444c ) This paper pGM301 pJG1100-based vector for chromosomal knock-in of gfp-linker fused in frame to rpsJ ( rv0700 ) start codon This paper pGM213 pTTP1A expressing P native -hupB- linker-...”
- Small RNAs Asserting Big Roles in Mycobacteria
Coskun, Non-coding RNA 2021 - “...cleavage of RNA, removing extra 3 nucleotides from tRNA precursor, generating 3 termini of tRNAs. rv2444c Rne M. bovis, Mtb, M. leprae, M. marinum, M. smegmatis Putative RNase E. Plays a central role in the maturation of 5S and 16S rRNAs and the majority of tRNAs....”
- A Phenotypic Characterization of Two Isolates of a Multidrug-Resistant Outbreak Strain of Mycobacterium tuberculosis with Opposite Epidemiological Fitness
Bei, BioMed research international 2020 - “...unknown functions (Rv3221c and Rv2081c), a GCN5-related N-acetyltransferase (Eis, Rv2416c), and a putative ribonuclease E (Rv2444c). Rv2057c, Rv2058c, Rv2154c, and Rv0290 showed a higher accumulation in Mp. Rv2057c and Rv2058c are ribosomal proteins, whereas Rv2154c is the peptidoglycan glycosyltransferase FtsW, which seems to participate in the...”
- “...-2.19 6.70 E -03 N-acetyltransferase Eis Rv2081c Rv2081c -2.16 1.20 E -02 Uncharacterized protein Rne Rv2444c -2.06 3.90 E -03 Possible ribonuclease E RpmB2 Rv2058c 2.03 2.40 E -03 50S ribosomal protein FtsW Rv2154c 2.07 1.00 E -02 Probable peptidoglycan glycosyltransferase EccDE Rv0290 2.22 5.90 E...”
- Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics
Gupta, High-throughput 2018 - “...Del 539586 Non-essential Glutamine-dependent NAD(+) synthetase Rv2438c Figure S12 1aa Del 584641 Essential ribonuclease E Rv2444c Figure S13 3aa Ins 219269 Essential putative folylpolyglutamate synthase protein (FolC) Rv2447c Figure S14 3aa Ins 111170 Essential DNA topoisomerase I TOPA (omega-protein) Rv3646c Figure S15 3aa Ins 392440 Essential...”
- Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis.
Płociński, Nucleic acids research 2019 - GeneRIF: degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J (RNase J) are major components of the RNA degradosome complexes in the transcriptome of Mycobacterium tuberculosis
ML1468 possible ribonuclease from Mycobacterium leprae TN
39% identity, 36% coverage
MT2520 cytoplasmic axial filament protein, putative from Mycobacterium tuberculosis CDC1551
39% identity, 36% coverage
HMPREF0675_3891 Rne/Rng family ribonuclease from Cutibacterium acnes SK137
37% identity, 39% coverage
TWT474 ribonuclease G from Tropheryma whipplei str. Twist
38% identity, 38% coverage
MAE_15200 ribonuclease E from Microcystis aeruginosa NIES-843
41% identity, 35% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...PCC 7421 gvip208 gvip371 glr4180 * glr1019 gll1616 gll1448 gvip129 glr4144 gll3149 Microcystis aeruginosa NIES-843 MAE_15200 MAE_31570 MAE_60800 MAE_28410 * MAE_62670 MAE_23880 MAE_46880 MAE_53390 Prochlorococcus marinus pastoris CCMP 1986 PMM1501 PMM1603 PMM0949 * PMM1652 PMM0868 PMM0847 PMM1191 Synechococcus elongatus PCC 7942 Synpcc7942_0878 Synpcc7942_1645 Synpcc7942_2120 * Synpcc7942_1846...”
FTL_1968 Ribonuclease G from Francisella tularensis subsp. holarctica
38% identity, 40% coverage
- Francisella tularensis: FupA mutation contributes to fluoroquinolone resistance by increasing vesicle secretion and biofilm formation
Siebert, Emerging microbes & infections 2019 - “...lyase 4.3.2.2 76,329 0,00290404 2,93821586 1,470,10 FTL_1274 Biotin synthesis protein BioC 8,5509 0,00310019 2,08179398 4,861,39 FTL_1968 Ribonuclease G 1.8003 0,0043569 2,28108698 nd FTL_1365 Hypothetical protein 10.001 0,00444144 2,55844422 nd FTL_0203 VWA domain-containing protein 67,725 0,00496868 2,28589582 6,560,64 FTL_1724 Outer membrane protein assembly factor BamB 188,45 0,0050169...”
H16_A0909 Ribonuclease G and E from Ralstonia eutropha H16
H16_A0909 ribonuclease G from Cupriavidus necator H16
40% identity, 40% coverage
BT1500 Ribonuclease G from Bacteroides thetaiotaomicron VPI-5482
35% identity, 42% coverage
cce_0277 ribonuclease E from Cyanothece sp. ATCC 51142
39% identity, 35% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...UCYN_00380 UCYN_03680 UCYN_00750 * UCYN_00320 UCYN_07880 UCYN_00190 UCYN_09960 UCYN_04860 UCYN_03170 Cyanothece sp. BH68, ATCC 51142 cce_0277 cce_3135 cce_1800 * cce_0295 cce_5063 cce_5061 cce_0113 cce_3346 cce_3157 cce_1653 cce_0623 cce_3461 Gloeobacter violaceus PCC 7421 gvip208 gvip371 glr4180 * glr1019 gll1616 gll1448 gvip129 glr4144 gll3149 Microcystis aeruginosa NIES-843 MAE_15200...”
RNE_NOSS1 / Q8YP69 Ribonuclease E; AnaRne; RNase E; EC 3.1.26.12 from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (see paper)
alr4331 ribonuclease E from Nostoc sp. PCC 7120
40% identity, 35% coverage
- function: Endoribonuclease that plays a central role in rRNA and tRNA processing and mRNA decay. Has been shown to act on 9S rRNA (the precursor of 5S rRNA).
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits.)
subunit: May form homodimers or higher order multimers. Interacts with polynucleotide phosphorylase (PNPase, pnp) via the C4 Arg-rich motif (residues 670-678) (PubMed:24563514). A homotetramer formed by a dimer of dimers (By similarity). - "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria
Zhang, mLife 2022 - “...RNase E/G Cleaving ssRNA, participating in bulk RNA degradation rne ; rng / slr1129 (rne) alr4331 (rne) RNase Y Cleaving ssRNA, participating in bulk RNA degradation / rny / / RNase III Cleaving dsRNAs, participating rRNA maturation and bulk RNA degradation rnc rnc slr1646 ; slr0346...”
PA4477 cytoplasmic axial filament protein from Pseudomonas aeruginosa PAO1
NP_253167 cytoplasmic axial filament protein from Pseudomonas aeruginosa PAO1
PA14_58100 cytoplasmic axial filament protein from Pseudomonas aeruginosa UCBPP-PA14
39% identity, 40% coverage
BPSL1158 ribonuclease G from Burkholderia pseudomallei K96243
BURPS305_2639 TerL protein from Burkholderia pseudomallei 305
38% identity, 42% coverage
- The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons
Hickey, Frontiers in microbiology 2012 - “...305 46 BURPS305_2640 BURPS305_2639 Burkholderia sp. CCGE1001 45 BC1001_1032 BC1001_1033 Burkholderia pseudomallei K96243 45 BPSL1157 BPSL1158 Burkholderia thailandensis TXDOH 45 BthaT_010100019559 BthaT_010100019564 Burkholderia sp. 383 44 Bcep18194_A5642 NA Comamonas sp. NCIMB 9872 43 orf3 orf4 Achromobacter piechaudii ATCC 43553 43 HMPREF0004_2444 HMPREF0004_2445 Achromobacter sp. SY8 43...”
- The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons
Hickey, Frontiers in microbiology 2012 - “...sp. CCGE1002 52 BC1002_6580 NA Herminiimonas arsenicoxydans 47 HEAR0550 HEAR0551 Burkholderia pseudomallei 305 46 BURPS305_2640 BURPS305_2639 Burkholderia sp. CCGE1001 45 BC1001_1032 BC1001_1033 Burkholderia pseudomallei K96243 45 BPSL1157 BPSL1158 Burkholderia thailandensis TXDOH 45 BthaT_010100019559 BthaT_010100019564 Burkholderia sp. 383 44 Bcep18194_A5642 NA Comamonas sp. NCIMB 9872 43 orf3...”
PP0937 cytoplasmic axial filament protein from Pseudomonas putida KT2440
38% identity, 43% coverage
BthaT_010100019564 ribonuclease, Rne/Rng family protein from Burkholderia thailandensis TXDOH
39% identity, 42% coverage
- The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons
Hickey, Frontiers in microbiology 2012 - “...CCGE1001 45 BC1001_1032 BC1001_1033 Burkholderia pseudomallei K96243 45 BPSL1157 BPSL1158 Burkholderia thailandensis TXDOH 45 BthaT_010100019559 BthaT_010100019564 Burkholderia sp. 383 44 Bcep18194_A5642 NA Comamonas sp. NCIMB 9872 43 orf3 orf4 Achromobacter piechaudii ATCC 43553 43 HMPREF0004_2444 HMPREF0004_2445 Achromobacter sp. SY8 43 KYC_17542 KYC_17547 Achromobacter xylosoxidans A8 40...”
Tery_0483 ribonuclease, Rne/Rng family from Trichodesmium erythraeum IMS101
40% identity, 35% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...slr1984 sll1043 Thermosynechococcus elongatus BP-1 tlr0597 Tlr0428 * tlr1220 tlr1873 tlr0652 tll2193 Trichodesmium erythraeum IMS101 Tery_0483 Tery_2839 Tery_2144 Tery_1105 Tery_2312 * Tery_0589 Tery_3730 Tery_1511 Tery_1541 Tery_2502 Tery_4663 * Mini-III Table 2 Summary of strains used in this study Strain Resistance Marker Enzyme Class Segregated Growth Defect...”
ABUW_0719 ribonuclease G from Acinetobacter baumannii
38% identity, 40% coverage
- Copy Number of an Integron-Encoded Antibiotic Resistance Locus Regulates a Virulence and Opacity Switch in Acinetobacter baumannii AB5075
Anderson, mBio 2020 - “...changes in band intensity ABUW_0456 NA Increased switching c ND ABUW_0466 NA Increased switching ND ABUW_0719 cafA Switching not increased No change ABUW_1032 rnc Inconsistent switching phenotype No change ABUW_1369 rnz Increased switching ND ABUW_2146 NA Increased switching ND ABUW_2751 rnhB Increased switching ND ABUW_2826 rnt...”
- “...synthesis of the 300-nt sRNA. (A) T26 insertions in rnr ( ABUW_0444 ), cafA ( ABUW_0719 ), rne ( ABUW_3478 ), and ABUW_5006 were moved into a VIR-O variant and electroporated with paadB or an empty vector control. Northern blotting was performed for all samples alongside...”
AM1_1705 ribonuclease E from Acaryochloris marina MBIC11017
38% identity, 39% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...Genome Enzyme Class RNase E/G RNase III RNase J1/J2 RNase II/R PNPase Acaryochloris marina MBIC11017 AM1_1705 AM1_1717 AM1_5197 * AM1_3444 AM1_4216 AM1_E0095 AM1_D0003 AM1_E0127 AM1_B0417 AM1_4810 AM1_A0095 AM1_5920 AM1_4121 Anabaena sp. PCC 7120 alr4331 all4107 alr0280 alr1158 * all3678 all4450 alr1240 all0136 all4396 Arthrospira platensis NIES-39...”
KPN_03655 RNase G from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
37% identity, 40% coverage
tlr0597 ribonuclease E from Thermosynechococcus elongatus BP-1
38% identity, 39% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...PCC 6803 slr1129 slr1646 slr0346 slr0954 * slr0551 sll1910 sll1290 slr1984 sll1043 Thermosynechococcus elongatus BP-1 tlr0597 Tlr0428 * tlr1220 tlr1873 tlr0652 tll2193 Trichodesmium erythraeum IMS101 Tery_0483 Tery_2839 Tery_2144 Tery_1105 Tery_2312 * Tery_0589 Tery_3730 Tery_1511 Tery_1541 Tery_2502 Tery_4663 * Mini-III Table 2 Summary of strains used in...”
VC0419 cytoplasmic axial filament protein from Vibrio cholerae O1 biovar eltor str. N16961
38% identity, 40% coverage
Cthe_0158 ribonuclease G from Clostridium thermocellum ATCC 27405
37% identity, 45% coverage
- Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum
Linville, PloS one 2013 - “...(Cthe_2376) and three mutations affecting genes related to transcription (Cthe_2724), translation (Cthe_2727) and RNA degradation (Cthe_0158). The mutations in Cthe_2376, Cthe_2724 and Cthe_2727 are all non-synonymous SNPS and Cthe_0158 has a deletion near the 3 end. The gyrB gene (Cthe_2376) encodes an ATP-dependent DNA gyrase enzyme...”
- “...possible that these mutations contribute to the enhanced hydrolysate tolerance of the PM. RNase G (Cthe_0158) endoribonuclease is required for the normal decay of several transcripts including mRNA from two genes in the glycolysis pathway, enolase (eno) and acetaldehyde dehydrogenase ( adhE ) [ 54 ]....”
- Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
Roberts, BMC systems biology 2010 - “...isoleucyl-tRNA synthetase A4N847 0 2.7.7.39 CDP-glycerol pyrophosphorylase Cthe_1276 pantetheine-phosphate adenylyltransferase A1SHB9 3.00E-07 2.7.8.8 phosphatidylserine synthase Cthe_0158 Ribonuclease A9JBA9 1.00E-68 4.1.1.65 phosphatidylserine decarboxylase Cthe_0505 formate acetyltransferase A4NBN7 0 1.3.99.1 succinate dehydrogenase Cthe_2355 L-aspartate oxidase Q97W79 1.00E-94 1.3.1.6 NADH-fumarate reductase Cthe_2355 L-aspartate oxidase B0VG44 5.00E-98 1.3.5.1 succinate dehydrogenase...”
BCAL2395 ribonuclease G from Burkholderia cenocepacia J2315
38% identity, 42% coverage
AdhR / b3247 RNase G (EC 3.1.26.12) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
rng / P0A9J0 RNase G (EC 3.1.26.12) from Escherichia coli (strain K12) (see 51 papers)
RNG_ECOLI / P0A9J0 Ribonuclease G; RNase G; Cytoplasmic axial filament protein; CafA protein; EC 3.1.26.- from Escherichia coli (strain K12) (see 16 papers)
P0A9J0 ribonuclease III (EC 3.1.26.3) from Escherichia coli K-12 (see paper)
rng / SP|P0A9J1 ribonuclease G; EC 3.1.26.- from Shigella flexneri (see 5 papers)
b3247 bundles of cytoplasmic filaments from Escherichia coli str. K-12 substr. MG1655
NP_417713 RNase G from Escherichia coli str. K-12 substr. MG1655
37% identity, 40% coverage
- function: An endonuclease that acts in the processing of the 5'-end of precursors of 16S rRNA, generates a precursor with 3 extra nucleotides at its 5'-end (which is matured by Rnm) (PubMed:10329633, PubMed:10362534, PubMed:10722715, PubMed:20176963, PubMed:24489121, PubMed:26694614, PubMed:32343306). It prefers 5'-monophosphorylated over 5'-OH or 5'-triphosphorylated substrates and cleaves single- stranded sites rich in A and U residues; contributes to RNA turnover (PubMed:10722715, PubMed:10762247, PubMed:11380618, PubMed:12450135, PubMed:18078441, PubMed:21717341). 5'-monophosphate-assisted cleavage requires at least 2 and preferably 3 or more unpaired 5'-terminal nucleotides for cleavage. The optimal spacing between the 5' end and the scissile phosphate appears to be 6 nucleotides. Any sequence of unpaired nucleotides at the 5'-end is tolerated (PubMed:26694614). Processes the 5'-end precursors of 23S rRNA (PubMed:21717341). Participates in processing of tRNA(Pro) (proK and proM) (PubMed:27288443). Also involved in metabolism of some mRNAs (PubMed:11380618, PubMed:12450135, PubMed:18078441). Cells overproducing this protein form chains of cell with cytoplasmic axial filaments (PubMed:8300545). Could be involved in chromosome segregation and cell division. It may be one of the components of the cytoplasmic axial filaments bundles, or merely regulate the formation of this structure (Probable).
function: Confers adaptive resistance to aminoglycoside antibiotics through modulation of 16S rRNA processing.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homodimer, in equilibrium with possible higher multimers.
disruption phenotype: Slow processing of the 17S rRNA precursor to 16S rRNA, with significant accumulation of a 16.3S rRNA precursor with 66 extra nucleotides at its 5' end (PubMed:10329633, PubMed:10362534, PubMed:20176963, PubMed:32343306). Ribosomes with the precursor 16S rRNA show decreased translational fidelity and an increased sensitivity to aminoglycoside antibiotics neomycin and paromomycin (PubMed:20176963). In contrast another group, using independently generated rng deletions in 2 different strains, showed decreased sensitivity to aminoglycoside antibiotics kanamycin, neomycin, paromomycin and streptomycin (PubMed:24489121). A double rne-rng mutated strain no longer processes the 17S rRNA precursor (PubMed:10329633, PubMed:10362534). Significant accumulation of AdhE and enolase, greatly increased stability of adhE and eno mRNA (PubMed:11380618, PubMed:12450135). Accumulation of a 23S rRNA precursor (PubMed:21717341). - Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate
van, Nucleic acids research 2016 - “...16 tRNA-dihydrouridine synthase A. gi|16128424 b0439 lon Lon 87.4 41.2 17 DNA-binding ATP-dependent protease. gi|90111563 b3247 rng RNaseG 55.3 12.93 7 (Endo) ribonuclease G. gi|162135892 b0143 pcnB PAP I 53.8 12.4 9 Poly(A) polymerase. gi|49176463 b4411 encB EncB 4.8 12.4 3 Entericidin B; translationally repressed by...”
- RNase G controls tpiA mRNA abundance in response to oxygen availability in Escherichia coli.
Lee, Journal of microbiology (Seoul, Korea) 2019 (PubMed)- GeneRIF: RNase G cleaves the 5' untranslated region of triosephosphate isomerase A (tpiA) mRNA, leading to destabilization of the mRNA in E. coli.
- Single amino acid changes in the predicted RNase H domain of Escherichia coli RNase G lead to complementation of RNase E deletion mutants.
Chung, RNA (New York, N.Y.) 2010 - GeneRIF: 2 distinct spontaneously derived single amino acid substitutions within the predicted RNase H domain of RNase G, generating the rng-219 and rng-248 alleles, result in complementation of the growth defect associated with various RNase E mutants.
- Sensing of 5' monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo.
Jourdan, Molecular microbiology 2008 (PubMed)- GeneRIF: Escherichia coli RNase G sensing a 5' monophosphate is required in vivo for the normal rapid decay of functional mRNAs.
- Cytoplasmic axial filaments in Escherichia coli cells: possible function in the mechanism of chromosome segregation and cell division.
Okada, Journal of bacteriology 1994 - GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...142 P0A8V6 FADR Transcription Cytoplasm 143 P0A959 ALAA Amino acid transport and metabolism Cytoplasm 144 P0A9J0 RNG Translation, ribosomal structure and biogenesis Cytoplasm 145 P0A9V1 LPTB General function prediction only Cytoplasm 146 P0AE08 AHPC Posttranslational modification, protein turnover, chaperones Cytoplasm 147 P0AEI1 MIAB Translation, ribosomal structure...”
- Affinity-based capture and identification of protein effectors of the growth regulator ppGpp
Wang, Nature chemical biology 2019 - “...ribosome biogenesis GTPase 3.27 P24203 YjiA putative metal-binding GTPase 3.26 P08192 FolC dihydrofolate synthase 3.25 P0A9J0 RnG ribonuclease G 2.99 P0A7E9 PyrH uridylate kinase 2.96 P37759 RfbB dTDP-glucose 4,6-dehydratase 2.92 P0AG24 SpoT bifunctional ppGpp synthase/hydrolase 2.87 P46853 YhhX uncharacterized oxidoreductase 2.78 P00350 Gnd 6-phosphogluconate dehydrogenase 2.76...”
- Exposure of E. coli to DNA-Methylating Agents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N-Acetylneuraminate Lyase NanA
Di, Frontiers in microbiology 2016 - “...OTHER 1.62 3317 0.0068 Probable deferrochelatase/peroxidase YfeX yfeX P76536 1.53 2041 0.0014 Ribonuclease G rng P0A9J0 1.53 2041 0.0014 Transcriptional regulatory protein TyrR tyrR P07604 1.38 3005 0.0041 Uncharacterized oxidoreductase YdgJ ydgJ P77376 1.32 3008 0.0066 Aminomethyltransferase gcvT P27248 1.32 3206 0.0033 Probable acrylyl-CoA reductase AcuI...”
- A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12
Strader, Journal of proteome research 2013 - “...I * 11 86 66 Ribonuclease I P30850 Exoribonuclease 2 11 29 21.1 Exoribonuclease 2 P0A9J0 RNase G 13 43 37 Ribonuclease G P0A6X3 Protein hfq * 6 35 64.7 Protein hfq P05055 PNP transferase * 15 58 29.8 Polyribonucleotide nucleotidyltransferase P10408 SecA 22 64 35.8...”
RNG_SALTS / A0A0H3NGK0 Ribonuclease G; RNase G; EC 3.1.26.- from Salmonella typhimurium (strain SL1344) (see 2 papers)
37% identity, 40% coverage
- function: Acts in the processing of the 5'-end of precursors of 16S rRNA. Confers adaptive resistance to aminoglycoside antibiotics through modulation of 16S rRNA processing (PubMed:24489121). An endoribonuclease, it prefers 5'-monophosphorylated substrates and cleaves single-stranded sites rich in A and U residues; also contributes to 23S rRNA processing, tRNA processing and mRNA turnover (By similarity). Involved in decay of speF mRNA, has a preference for adenine nucleotides (PubMed:30742606).
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Homodimer, and possible higher multimers.
disruption phenotype: No visible phenotype in rich media. Significant accumulation of a 16S rRNA precursor. Increased resistance to aminoglycoside antibiotics kanamycin and paramomycin (PubMed:24489121). Increased lifetime of speF mRNA.
RNE_SYNY3 / P72656 Ribonuclease E; RNase E; SynRne; Ribonuclease E/G; EC 3.1.26.12 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see 10 papers)
P72656 ribonuclease E (EC 3.1.26.12) from Synechocystis sp. PCC 6803 (see paper)
slr1129 ribonuclease E from Synechocystis sp. PCC 6803
38% identity, 36% coverage
- function: Endoribonuclease that plays a central role in rRNA processing and mRNA decay, and probably tRNA processing (PubMed:17661085, PubMed:25248550, PubMed:32209657, PubMed:9751718). Acts on 9S rRNA (the precursor of 5S rRNA) and RNAI, a molecule that controls the replication of ColE1 plasmid. Upon expression in E.coli does not purify with endogenous degradosome proteins (PubMed:9751718). Prefers 5'- monophosphorylated substrates over 5'-triphosphorylated substrates. Complements an rne temperature-sensitive mutation in E.coli, despite being considerably shorter and not able to interact with the E.coli degradosome (PubMed:10762247). Cleaves AU-rich sequences in vitro, tested with psbA2 mRNA. Complements both an rne temperature-sensitive mutation and an rng deletion in E.coli (PubMed:17661085). Acts in the degradation of psaL mRNA in the presence but not the absence of the sRNA PsrR1 (PubMed:25248550). Cleaves the rimO-crhR transcript, contributing to the very short half-life of rimO mRNA (PubMed:32209657).
function: mRNA for psbA2, one of the core proteins in photosystem II, is degraded in the dark under control of a cis-acting AU-rich box in its 5'-UTR. RNase E cuts in this box, suggesting it is involved in this dark-induced mRNA instability.
function: CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Endogenous RNase E is required for correct processing of pre-crRNA for the CRISPR3 subtype III-B system in this genome (genes sll7080 to sll7095). This CRISPR3 system does not include a cas6 gene, which is the usual RNase involved in crRNA maturation.
catalytic activity: Endonucleolytic cleavage of single-stranded RNA in A- and U- rich regions.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
subunit: Fractionates in a 250-300 kDa region, which is too small to be the equivalent of an RNA degradosome, as occurs with E.coli RNase E (PubMed:12601000). Interacts with polynucleotide phosphorylase (PNPase, pnp), probably via the C4 Arg-rich motif (residues 665-673) (PubMed:24563514).
disruption phenotype: Essential, it cannot be deleted (PubMed:12601000, PubMed:17661085, PubMed:29403013). Knockdown experiments show decreased amounts of crRNA precursor processing (PubMed:29403013). - A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis
Mudd, Journal of experimental botany 2008 - “...P21513 ( E. coli ), BAD03665 ( Oryza sativa ), Q8KAA6 ( Chlorobium tepidum ), P72656 ( Synechocystis sp. PCC 6803). The Zn-link motif co-ordinates a zinc ion involved in quaternary structure ( Callaghan et al. , 2005 a ), S1 domains of A . thaliana...”
- Photosynthesis in Synechocystis sp. PCC 6803 is not optimally regulated under very high CO2
Carrasquer-Alvarez, Applied microbiology and biotechnology 2025 - “...polymerase group 2 sigma factor B 2.86 0.05 2.06 sll1504 Hypothetical protein 2.94 0.01 2.07 slr1129 rne Ribonuclease E 3.70 0.77 2.07 sll0005 Hypothetical protein 3.68 0.71 2.10 ssl3364 cp12 CP12 polypeptide 3.18 0.05 2.21 slr1660 Hypothetical protein 4.72 1.57 2.23 slr0195 Hypothetical protein 3.03 0.17...”
- Regulation of RNase E during the UV stress response in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803
Watanabe, mLife 2023 - “...21 . In the cyanobacterium Synechocystis 6803, complete genetic disruption of the rne gene (gene slr1129 ) failed to segregate into a homozygous mutant line 22 , 23 , and partial disruption of RNase E led to severe growth inhibition and affected the expression of a...”
- Regulation of pSYSA defense plasmid copy number in Synechocystis through RNase E and a highly transcribed asRNA
Kaltenbrunner, Frontiers in microbiology 2023 - “...performed as published ( Behler et al., 2018 ). In short, codon-optimized and TEV site-fused slr1129 from Synechocystis 6803 was expressed under control of an IPTG-inducible promoter on pQE70. Expression was induced with 1mM IPTG in E. coli M15 [pREP4] at an OD 600 of 0.7...”
- "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria
Zhang, mLife 2022 - “...7120 Endoribonucleases RNase E/G Cleaving ssRNA, participating in bulk RNA degradation rne ; rng / slr1129 (rne) alr4331 (rne) RNase Y Cleaving ssRNA, participating in bulk RNA degradation / rny / / RNase III Cleaving dsRNAs, participating rRNA maturation and bulk RNA degradation rnc rnc slr1646...”
- Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition
Hoffmann, Nucleic acids research 2021 - “...labelled by an asterisk. ( E ) The 5 UTR of the rne gene ( slr1129 ). ( F ) Representative northern blot analysis of PmgR1 ( n = 4). A longer exposure is shown to highlight low abundance processing products. ( G ) Representative northern...”
- RNA helicase-regulated processing of the Synechocystis rimO-crhR operon results in differential cistron expression and accumulation of two sRNAs
Rosana, The Journal of biological chemistry 2020 (secret) - Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cavaiuolo, Frontiers in microbiology 2020 - “...The RNase E and RNase J Enzymes of Synechocystis 6803 A single gene product ( slr1129 , WP_010871286.1) with homology to E. coli ( Ec ) RNase E and RNase G is present in Synechocystis ( Sy ) ( Figure 1A and Supplementary Figure S1A )....”
- Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria
Kopf, Scientific reports 2015 - “...6714; sequence of Ncr0700 is 91% identical in a 195 nt long overlap TU87 Ncr0020 slr1129 TU2357 D082_20640 Kopf et al., 2014 19 ribonuclease E; conserved arrangement TU3332 Ncr1575 slr0040 TU1031 D082_08870 Kopf et al., 2014 19 , this paper, Figure 2B cmpA ; conserved arrangement...”
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SYNPCC7002_A0788 ribonuclease E from Synechococcus sp. PCC 7002
39% identity, 36% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...PCC 7942 Synpcc7942_0878 Synpcc7942_1645 Synpcc7942_2120 * Synpcc7942_1846 Synpcc7942_1911 Synpcc7942_1124 Synpcc7942_1546 Synpcc7942_2440 Synechococcus sp. PCC 7002 SYNPCC7002_A0788 SYNPCC7002_A0061 SYNPCC7002_A2542 SYNPCC7002_A0384 * SYNPCC7002_A1273 SYNPCC7002_A1543 SYNPCC7002_A0574 SYNPCC7002_A1066 Synechocystis sp. PCC 6803 slr1129 slr1646 slr0346 slr0954 * slr0551 sll1910 sll1290 slr1984 sll1043 Thermosynechococcus elongatus BP-1 tlr0597 Tlr0428 * tlr1220 tlr1873...”
VV1_1453 Ribonuclease G and E from Vibrio vulnificus CMCP6
37% identity, 40% coverage
D082_20640 Rne/Rng family ribonuclease from Synechocystis sp. PCC 6714
36% identity, 36% coverage
ASUC_RS04730 ribonuclease G from Actinobacillus succinogenes 130Z
37% identity, 43% coverage
- Mutation breeding of high-stress resistant strains for succinic acid production from corn straw
Wu, Applied microbiology and biotechnology 2024 - “...isomerase SNV 951,040 A C Exonic ASUC_RS004615 -ketoacyl-ACP synthase I SNV 97,821 G A Exonic ASUC_RS04730 Ribonuclease G SNV 1,667,663 A G Exonic ASUC_RS07820 N-acetylglucosamine kinase InDel 1,029,930 T - Exonic ASUC_RS11105 LexA-regulated protein InDel 1,148,006 A - Upstream ASUC_RS05460 Porin OmpA InDel 1,971,944 T -...”
Q8KAA6 Ribonuclease G from Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
37% identity, 35% coverage
PMM1501 S1 RNA binding domain:Ribonuclease E and G from Prochlorococcus marinus sp. MED4
38% identity, 35% coverage
- A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage
Stazic, Genetics 2016 - “...RNA Clean and Concentrator-5 Kit. Using oligonucleotides RPA PMM1501 59-UTR/CDS probe forward (fwd) and RPA PMM1501 59-UTR/CDS probe reverse (rev) (Table S1), a...”
- “...the N terminus was amplified by PCR using oligonucleotides PMM1501 short 2147 C9K12 fwd and PMM1501_C9K12 rev (Table S1). The resulting fragment was cloned into...”
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...NIES-843 MAE_15200 MAE_31570 MAE_60800 MAE_28410 * MAE_62670 MAE_23880 MAE_46880 MAE_53390 Prochlorococcus marinus pastoris CCMP 1986 PMM1501 PMM1603 PMM0949 * PMM1652 PMM0868 PMM0847 PMM1191 Synechococcus elongatus PCC 7942 Synpcc7942_0878 Synpcc7942_1645 Synpcc7942_2120 * Synpcc7942_1846 Synpcc7942_1911 Synpcc7942_1124 Synpcc7942_1546 Synpcc7942_2440 Synechococcus sp. PCC 7002 SYNPCC7002_A0788 SYNPCC7002_A0061 SYNPCC7002_A2542 SYNPCC7002_A0384 * SYNPCC7002_A1273...”
- Antisense RNA protects mRNA from RNase E degradation by RNA-RNA duplex formation during phage infection
Stazic, Nucleic acids research 2011 - “...during phage infection. MATERIALS AND METHODS Construction of rne expression plasmid pQE70PMM1501 Oligonucleotides used for PMM1501 cloning were PMM1501_C_K12 fw and PMM1501_C_K12 rev. Lowercase letters indicate PaeI or BamHI site ( Supplementary Table S1 ). Both oligonucleotides were optimized for E. coli codon usage (Kazusa Codon...”
- “...Usage Database) without impairing the PMM1501 wild-type amino acid composition. The resulting coding sequence of PMM1501 was cloned in pQE70 (QIAGEN, Germany). Overexpression and purification of recombinant RNase E from Prochlorococcus MED4 Escherichia coli TOP10 F served as the host strain for construction and propagation of...”
NGO0113 putative ribonucleases G / cytoplasmic axial filament protein from Neisseria gonorrhoeae FA 1090
37% identity, 40% coverage
NMA0672 hypothetical protein NMA0672 from Neisseria meningitidis Z2491
37% identity, 40% coverage
NGFG_00252 ribonuclease G from Neisseria gonorrhoeae MS11
37% identity, 40% coverage
Synpcc7942_0878 ribonuclease, Rne/Rng family from Synechococcus elongatus PCC 7942
37% identity, 35% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...pastoris CCMP 1986 PMM1501 PMM1603 PMM0949 * PMM1652 PMM0868 PMM0847 PMM1191 Synechococcus elongatus PCC 7942 Synpcc7942_0878 Synpcc7942_1645 Synpcc7942_2120 * Synpcc7942_1846 Synpcc7942_1911 Synpcc7942_1124 Synpcc7942_1546 Synpcc7942_2440 Synechococcus sp. PCC 7002 SYNPCC7002_A0788 SYNPCC7002_A0061 SYNPCC7002_A2542 SYNPCC7002_A0384 * SYNPCC7002_A1273 SYNPCC7002_A1543 SYNPCC7002_A0574 SYNPCC7002_A1066 Synechocystis sp. PCC 6803 slr1129 slr1646 slr0346 slr0954 *...”
ACIAD0830 ribonuclease G, endoribonuclease G (cytoplasmic axial filament protein ) from Acinetobacter sp. ADP1
35% identity, 40% coverage
gvip208 ribonuclease E from Gloeobacter violaceus PCC 7421
39% identity, 39% coverage
- Genetic and genomic analysis of RNases in model cyanobacteria
Cameron, Photosynthesis research 2015 - “...cce_1800 * cce_0295 cce_5063 cce_5061 cce_0113 cce_3346 cce_3157 cce_1653 cce_0623 cce_3461 Gloeobacter violaceus PCC 7421 gvip208 gvip371 glr4180 * glr1019 gll1616 gll1448 gvip129 glr4144 gll3149 Microcystis aeruginosa NIES-843 MAE_15200 MAE_31570 MAE_60800 MAE_28410 * MAE_62670 MAE_23880 MAE_46880 MAE_53390 Prochlorococcus marinus pastoris CCMP 1986 PMM1501 PMM1603 PMM0949 *...”
PGN_1391 putative ribonuclease E from Porphyromonas gingivalis ATCC 33277
31% identity, 45% coverage
PG1256 ribonuclease, Rne/Rng family from Porphyromonas gingivalis W83
32% identity, 41% coverage
NP_850987 RNAse E/G-like protein from Arabidopsis thaliana
AT2G04270 RNEE/G (RNASE E/G-LIKE); endoribonuclease from Arabidopsis thaliana
35% identity, 37% coverage
- Arabidopsis CSP41 proteins form multimeric complexes that bind and stabilize distinct plastid transcripts.
Qi, Journal of experimental botany 2012 - GeneRIF: Arabidopsis CSP41 proteins form multimeric complexes that bind and stabilize distinct plastid transcripts.
- Knockout of the plastid RNase E leads to defective RNA processing and chloroplast ribosome deficiency.
Walter, The Plant journal : for cell and molecular biology 2010 (PubMed)- GeneRIF: RNase E mutants have multiple defects in chloroplast RNA metabolism, but RNase E is not essential for survival.
- The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme
Schein, RNA (New York, N.Y.) 2008 - GeneRIF: RNase E participates in the initial endonucleolytic cleavage of the polyadenylation-stimulated RNA degradation process in the chloroplast, perhaps in collaboration with the two other chloroplast endonucleases, RNase J and CSP41.
- “...Escherichia coli, P21513; Arabidopsis thaliana, NP_850987; rice (Oryza sativa), NP_001061542; tomato (Lycopersicon esculentum) (this work); Streptomyces,...”
- A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis.
Mudd, Journal of experimental botany 2008 - GeneRIF: Loss of At2g04270 function resulted in the arrest of chloroplast development, loss of autotrophic growth, and reduced plastid ribosomal, psbA and rbcL RNA levels.
- Development of a Target Enrichment Probe Set for Conifer (REMcon)
Khan, Biology 2024 - “...472 95 MA_24252 AT4G24090 600 96 MA_19954 AT2G02590 414 97 MA_11407 AT3G47860 312 98 MA_10909 AT2G04270 318 99 MA_6888 AT3G24080 2286 100 MA_4586 AT2G22650 303 biology-13-00361-t002_Table 2 Table 2 Recovery of targeted gene regions, including potentially paralogous loci, across conifer families and four non-conifer gymnosperms. Locus...”
- Proteomics, phylogenetics, and coexpression analyses indicate novel interactions in the plastid CLP chaperone-protease system
Rei, The Journal of biological chemistry 2022 - “...17.1 0.01060 AT1G02150.1 pentatricopeptide repeat (PPR) protein (6 or 7 repeats). Coexpresses with RNAse E/G At2g04270 DNARNA 3 123 26 97 3.7 0.01700 AT5G67030.1 zeaxanthin epoxidase (ZEP) metabolism 3 62 13 49 3.2 0.04950 AT5G64840.1 ABC transporter family protein (ATGCN5) metabolism 3 49 2 47 15.6...”
- Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model
Lindquist, PloS one 2014 - “...signalling, thylakoid membrane organization (is a ascorbate peroxidase) 22.8 5.0 4.9 Yes (MS/MS) Yes AtRNEE/G At2g04270, Chloroplast mRNA processing, chloroplast organisation, thylakoid membrane organization (is a ribonuclease) 11.2 4.3 0.4 Yes (MS/MS) Yes AtsAPX At4g08390, Oxidation-reduction processes (is a ascorbate peroxidase) 17.0 5.3 2.2 Yes (MS/MS...”
- The nucleoid as a site of rRNA processing and ribosome assembly
Bohne, Frontiers in plant science 2014 - “...al., 1998 ; Guo et al., 2013 RNase E Endonuclease Processing of 23S-4.5S precursor GRMZM2G328309_P01 AT2G04270 Stoppel et al., 2012 RNase J 5 to 3 exonuclease and endonuclease 5 end maturation of 16S and 23S rRNA precursors GRMZM2G103315_P01 AT5G63420 Bollenbach et al., 2005 ; Sharwood et...”
- Analysis of miRNAs and their targets during adventitious shoot organogenesis of Acacia crassicarpa
Liu, PloS one 2014 - “...protein 76 AT5G35407 1 MIR396B; miRNA AT2G36400 3 growth-regulating factor 3 AT3G01910 3 sulfite oxidase AT2G04270 3 RNAse E/G-like AT3G52910 3 growth-regulating factor 4 AT5G16690 3 origin recognition complex subunit 3 MIR397 AT5G18420 3 unknown protein AT2G29130 2 laccase 2 AT4G05105 2 MIR397A; miRNA MIR398 AT5G14550...”
- RHON1 is a novel ribonucleic acid-binding protein that supports RNase E function in the Arabidopsis chloroplast
Stoppel, Nucleic acids research 2012 - “...RNA isolation, denaturing gel electrophoresis and autoradiography. The Arabidopsis nuclear genome encodes one RNE protein (At2g04270), which has been characterized in several recent studies, supporting its endonucleolytic function within the chloroplast stroma ( 17 , 20 ). It was proposed that the rne mutation causes mainly...”
- “...of genes located in between revealed a mutation ( rne-2 ) in the RNE gene At2g04270 with a single G-to-A transition of the last nucleotide of the seventh intron ( Supplementary Figure S1B ). Sequencing of RT-PCR products uncovered an alternative splice site 18 nucleotides farther...”
- Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome
Hotto, G3 (Bethesda, Md.) 2011 - “...insertions in the genes At3g03710 ( pnp1-1 ; SALK_013306), At5g02250 ( rnr1-3 ; SALK_090294), and At2g04270 ( rne1-1 ; SALK_093546) and have been previously characterized ( Alonso et al. 2003 ; Bollenbach et al. 2005 ; Mudd et al. 2008 ; Marchive et al. 2009 )....”
- A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis
Mudd, Journal of experimental botany 2008 - “...of plant RNase E/G-like proteins are not known. Arabidopsis thaliana contains a single nuclear gene (At2g04270) encoding a product with the conserved catalytic domain of RNase E/G-like proteins. At2g04270 and the adjacent At2g04280 gene form converging transcription units with a 40 base overlap at their 3...”
- “...in cotyledons, rosette and cauline leaves. T-DNA insertions in exon 6 or intron 11 of At2g04270 result in loss of the 125 kDa band or truncation to a 110 kDa band. Loss of At2g04270 function resulted in the arrest of chloroplast development, loss of autotrophic growth,...”
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RNE_ARATH / F4IV66 Ribonuclease E/G-like protein, chloroplastic; RNase E/G-like protein; RNase E; EC 3.1.26.- from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
35% identity, 37% coverage
- function: Involved in intercistronic processing of primary transcripts from chloroplast operons. The endonucleolytic activity of the enzyme depends on the number of phosphates at the 5' end, is inhibited by structured RNA, and preferentially cleaves A/U-rich sequences.
cofactor: Mg(2+) (Binds 1 Mg(2+) ion per subunit.)
cofactor: Zn(2+) (Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between subunits.)
subunit: Part of a chloroplastic degradosome-like complex. Interacts with RHON1 (PubMed:18441049, PubMed:22735703). A homotetramer formed by a dimer of dimers (By similarity).
disruption phenotype: Reduced photosynthetic activity and retarded growth. Increased number and decreased size of chloroplasts. Loss of autotrophic growth. Pale cotyledons when grown on sucrose-complemented medium.
rne / CAB76425.1 endoribonuclease E, partial from Arabidopsis thaliana (see paper)
37% identity, 34% coverage
B739_0313 ribonuclease E/G from Riemerella anatipestifer RA-CH-1
30% identity, 46% coverage
TM1606 cytoplasmic axial filament protein, putative from Thermotoga maritima MSB8
36% identity, 35% coverage
P51211 Ribonuclease E/G-like protein from Porphyra purpurea
33% identity, 34% coverage
CAC1256 Ribonucleases G/E family protein from Clostridium acetobutylicum ATCC 824
27% identity, 39% coverage
lmo1543 similar to ribonuclease G from Listeria monocytogenes EGD-e
28% identity, 40% coverage
Rru_A2767 ribonuclease G (RNase G) from Rhodospirillum rubrum ATCC 11170
31% identity, 36% coverage
RSP_0624 ribonuclease E/G from Cereibacter sphaeroides 2.4.1
RSP_0624 hypothetical protein from Rhodobacter sphaeroides 2.4.1
29% identity, 30% coverage
thalar_00580 ribonuclease E/G from Litoreibacter arenae DSM 19593
27% identity, 28% coverage
CC2341 hypothetical protein from Caulobacter crescentus CB15
34% identity, 11% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 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