Family Search for PF02130 (YbeY)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF02130 hits 65 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
BC4300 hypothetical Metal-Binding Protein from Bacillus cereus ATCC 14579
Aligns to 12:152 / 156 (90.4%), covers 98.4% of PF02130, 173.8 bits
BSU25320 putative metalloprotease from Bacillus subtilis subsp. subtilis str. 168
Aligns to 12:152 / 157 (89.8%), covers 96.9% of PF02130, 167.5 bits
- Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
Engelen, BMC genomics 2012 - “...homolog) 2 BSU24790 yqgX yqgX ycbL putative metal-binding hydrolase BSU24890 folN yqgN ygfA 5-formyltetrahydrofolate cyclo-ligase BSU25320 yqfG yqfG ybeY putative metal-dependent hydrolase BSU25620 yqeL yqeL ybeB putative ribosomal maturation protein 2 BSU27370 yrrL yrrL yceG conserved hypothetical protein BSU27390 yrrK yrrK yqgF putative Holliday junction resolvase...”
SAUSA300_1530 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAOUHSC_01672 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
Aligns to 12:150 / 155 (89.7%), covers 96.1% of PF02130, 165.6 bits
- Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation
Lipońska, mBio 2021 - “...milliliter of kanamycin was used for recombinant selection. The ybeY ::Erm allele ( ybeY locus, SAUSA300_1530) was constructed with the same strategy, except that primer pairs P1247/P1238 and P1239/P1240 and a 1.3-kb erythromycin resistance marker (from pBTE) were used. The RNase transposon mutant alleles ( TableS1...”
- Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...protein SAUSA300_2197 RplP 0.45 Protein synthesis SAUSA300_1443 RluB 0.45 Protein synthesis SAUSA300_1159 NusA 0.45 Transcription SAUSA300_1530 YbeY 0.44 Conserved hypothetical protein SAUSA300_0820 SufS 0.44 Biosynthesis of cofactors, prosthetic groups, and carriers SAUSA300_1937 0.44 Mobile and extrachromosomal element functions SAUSA300_1049 MurI 0.43 Cell envelope SAUSA300_1679 AcsA 0.43...”
- Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
Chaudhuri, BMC genomics 2009 - “...b) Agarose gel showing sample results. M size markers, lane 1 SAOUHSC_00862 (non-essential), lane 2 SAOUHSC_01672 (essential). Each band represents a PCR product of a different size, corresponding to a transposon insertion in a different position. The white boxes represent the product size range expected for...”
lmo1465 similar to unknown proteins from Listeria monocytogenes EGD-e
Aligns to 13:157 / 161 (90.1%), covers 95.3% of PF02130, 157.7 bits
7y7oA / P67136 Crystal structure of metallo-endoribonuclease ybey from staphylococcus aureus (see paper)
Aligns to 12:136 / 147 (85.0%), covers 96.1% of PF02130, 155.9 bits
HMPREF0389_00692 rRNA maturation RNase YbeY from Filifactor alocis ATCC 35896
Aligns to 12:156 / 162 (89.5%), covers 94.6% of PF02130, 150.5 bits
- Filifactor alocis--a new emerging periodontal pathogen
Aruni, Microbes and infection 2015 - “...protease family protein (BFO_0185) Pseudo (BFO_1506) [CAAX amino terminal protease family protein] 8. Metalloprotease Metalloprotease (HMPREF0389_00692) Membrane-associated zinc metalloprotease (PGTDC60_1498) Transmembrane AAA- metalloprotease FtsH (PGTDC60_0044) Zinc metalloprotease (PGN_1582) Membrane-associated zinc metalloprotease (PG0383) Transmembrane AAA- metalloprotease FtsH (PGN_0043) Metalloprotease (TDE1242) Membrane-associated zinc metalloprotease (TDE2341) (TDE2337) aminopeptidase [Peptidase_M29;...”
- Proteome variation among Filifactor alocis strains
Aruni, Proteomics 2012 - “...zinc metalloprotease FtsH HMPREF0389_01001 Caax amino protease family protein HMPREF0389_00677 Caax amino protease HMPREF0389_00590 Metalloprotease HMPREF0389_00692 Glycoprotease family protein HMPREF0389_01443 Xaa pro dipeptidase HMPREF0389_01538 O-sialoglycoprotein endopeptidase HMPREF0389_01445 Serine protease HtrA HMPREF0389_01460 ATP-dependent Clp protease HMPREF0389_01648 Carboxy-processing protease HMPREF0389_00522 Oligoendopeptidase F HMPREF0389_00926 HMPREF0389_00527 Table 6 Proteome profiling...”
Csac_1839 protein of unknown function UPF0054 from Caldicellulosiruptor saccharolyticus DSM 8903
Aligns to 9:154 / 158 (92.4%), covers 96.1% of PF02130, 144.2 bits
- Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production
Chowdhary, PloS one 2015 - “...). Among the list of essential genes, 7 of them Csac_2571, Csac_1262, Csac_0970, Csac_1701, Csac_2220, Csac_1839 and Csac_2091, were found to be hypothetical and the re-annotation study predicted their function as O-antigen polymerase, histone family DNA-binding protein, uracil-DNA glycosylase, glycyl-tRNA synthase subunit, dCTP deaminase, metalloprotease ybeY...”
SSA_1613 hypothetical protein from Streptococcus sanguinis SK36
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 137.9 bits
SGO_RS03500 rRNA maturation RNase YbeY from Streptococcus gordonii str. Challis substr. CH1
Aligns to 11:160 / 165 (90.9%), covers 96.1% of PF02130, 137.1 bits
SP_0967 putative metalloprotease from Streptococcus pneumoniae TIGR4
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 136.4 bits
- A transcription factor contributes to pathogenesis and virulence in Streptococcus pneumoniae
Mahdi, PloS one 2013 - “...for genes that might be important to the disease process revealed 4 genes, SP_2089, SP_0569, SP_0967 and SP_0800, which showed high level of expression in both blood and brain. Two of these 4 genes are part of a highly connected network ( Figure 5 ) suggesting...”
- “...further analysis. 10.1371/journal.pone.0070862.g005 Figure 5 Interaction network data for connectivity of SP_0746 to SP_0800 and SP_0967 (highlighted in yellow). We then evaluated the contribution of selected genes preferentially up-regulated in various tissues to pathogenesis and virulence by targeted mutagenesis. Deletion replacement mutation of these genes (SP_0746,...”
spr0869 Conserved hypothetical protein from Streptococcus pneumoniae R6
SPD_0855 conserved hypothetical protein TIGR00043 from Streptococcus pneumoniae D39
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 136.1 bits
- The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
Vercruysse, PLoS pathogens 2014 - “...b0659 of E. coli MG1655, VC0960 of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322 under control of the constitutive tetracycline promoter. DNA manipulations were performed according to the methods...”
- The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
Yadav, PloS one 2015 - “...protein -1.8 (0.005) SPD_1729 conserved hypothetical protein -1.6 (0.002) SPD_1858 conserved hypothetical protein -1.5 (0.007) SPD_0855 conserved hypothetical protein -1.4 (0.05) SPD_1836 conserved hypothetical protein -1.4 (0.05) The functional annotation of the differentially regulated genes revealed that genes involved in galactose metabolism were exclusively up-regulated in...”
BAB1_2156 Protein of unknown function UPF0054 from Brucella melitensis biovar Abortus 2308
Aligns to 8:142 / 158 (85.4%), covers 96.1% of PF02130, 135.1 bits
- Brucella and Its Hidden Flagellar System
Coloma-Rivero, Microorganisms 2021 - “...62 ] flgJ B. abortus Decreases biofilms, virulence and infection capacity. [ 69 ] ybeY (BAB1_2156) B. abortus Multiple dysregulations of expression of bacterial proteins, including proteins and flagellar regulators. [ 77 ] fliF , flhA , motB, flgE B. melitensis Dysfunction is the first step...”
- Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus
Budnick, Journal of bacteriology 2018 - “...cellular morphology of Brucella abortus. Brucella abortus 1_2156 (bab1_2156; also known as bab_rs26200) is located on chromosome I of Brucella melitensis biovar...”
- “...the results outlined in this report, here we refer to bab1_2156 as ybeY. An isogenic deletion of ybeY in B. abortus 2308 resulted in impaired growth in vitro...”
BruAb1_2129 conserved hypothetical protein TIGR00043 from Brucella abortus biovar 1 str. 9-941
Aligns to 21:155 / 171 (78.9%), covers 96.1% of PF02130, 134.8 bits
WP_010970840 rRNA maturation RNase YbeY from Agrobacterium fabrum
Atu0358 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 16:156 / 168 (83.9%), covers 95.3% of PF02130, 134.6 bits
- The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens.
Möller, Journal of bacteriology 2019 - GeneRIF: The RNase YbeY is vital for ribosome maturation, stress resistance, and virulence in Agrobacterium tumefaciens.
- The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens
Möller, Journal of bacteriology 2019 - “...Here, we classify the A. tumefaciens YbeY ortholog Atu0358 as another chromosomally encoded virulence factor with a major impact on Agrobacterium physiology and...”
- “...is a RNase involved in rRNA processing. RESULTS Atu0358 is the A. tumefaciens YbeY homologue. The fundamental influence of riboregulation on the fitness and...”
- A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
Davies, Journal of bacteriology 2008 - “...names are as follows: Agrobacterium tumefaciens, Atu0358; S. meliloti, SMc01113; Brucella abortus, BruAb1_2129; Rhizobium etli, RHE_CH00374; Rhizobium...”
T303_04255 rRNA maturation RNase YbeY from Streptococcus thermophilus ASCC 1275
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 134.3 bits
1xm5A / P0A898 Crystal structure of metal-dependent hydrolase ybey from e. Coli, pfam upf0054 (see paper)
Aligns to 15:144 / 152 (85.5%), covers 93.8% of PF02130, 133.9 bits
- Ligand: nickel (ii) ion (1xm5A)
YbeY / b0659 endoribonuclease YbeY from Escherichia coli K-12 substr. MG1655 (see 19 papers)
YBEY_ECOLI / P0A898 Endoribonuclease YbeY; EC 3.1.-.- from Escherichia coli (strain K12) (see 6 papers)
ybeY / MB|P0A898 putative metalloprotease ybeY from Escherichia coli K12 (see paper)
b0659 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
NP_415192 endoribonuclease YbeY from Escherichia coli str. K-12 substr. MG1655
UTI89_C0657 hypothetical protein from Escherichia coli UTI89
Aligns to 15:144 / 155 (83.9%), covers 93.8% of PF02130, 133.8 bits
- function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'- and 3'- ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.
cofactor: Zn(2+) (Binds 1 zinc ion.)
disruption phenotype: Mutants show defects in 16S rRNA maturation, ribosome activity, translational fidelity, and ribosome assembly. They have severe growth defect at high temperatures, essentially no thermotolerance at lethal temperatures. They also show a decrease in polysomes and a large increase in both free 50S and free 30S ribosomal subunits relative to 70S ribosomes. - The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
Vercruysse, PLoS pathogens 2014 - “...various organisms were constructed by PCR amplification of each ybeY homolog from chromosomal DNA (i.e. b0659 of E. coli MG1655, VC0960 of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322...”
- “...purification of YbeY and RNase R To construct the overexpression plasmid, ybeY of E. coli (b0659) and V. cholerae (VC0960) was cloned into pET28a under control of a T7 promoter with an N-terminal His-MBP-TEV(site)-tag. Purification of YbeY without RNase I contamination was accomplished by expression in...”
- Genome-wide expression profiling in Escherichia coli K-12
Richmond, Nucleic acids research 1999 - “...NarQ) b1593 b1593 5.7 -1.4 ORF, hypothetical protein b0659 ybeY 5.6 5.8 ORF, hypothetical protein b0281 intF 5.5 2.8 Putative phage integrase b1274 *topA...”
- Elevated Levels of Era GTPase Improve Growth, 16S rRNA Processing, and 70S Ribosome Assembly of Escherichia coli Lacking Highly Conserved Multifunctional YbeY Endoribonuclease.
Ghosal, Journal of bacteriology 2018 - GeneRIF: YbeY binds to Era and is involved in the 3'-end processing of 16S rRNA
- C21orf57 is a human homologue of bacterial YbeY proteins.
Ghosal, Biochemical and biophysical research communications 2017 - GeneRIF: This observation suggests that the function of HuYbeY in human cells is likely regulated through specific interactions with partner proteins similarly to the way YbeY is regulated in bacteria.
- Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli.
Vercruysse, mBio 2016 - GeneRIF: This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era).
- The Escherichia coli translation-associated heat shock protein YbeY is involved in rRNA transcription antitermination.
Grinwald, PloS one 2013 - GeneRIF: evidence which tie YbeY to the transcription antitermination process
- The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit.
Rasouly, Journal of bacteriology 2010 - GeneRIF: Data show that the in vitro activity of the translation machinery of ybeY deletion mutants is significantly lower than that of the wild type.
- Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing.
Davies, Molecular microbiology 2010 - GeneRIF: Deletion of ybeY strongly affects the maturation of rRNA, and causes striking defects in ribosome function including decreased ribosome activity, reduced translational fidelity and altered translation initiation factor binding.
- YbeY, a heat shock protein involved in translation in Escherichia coli.
Rasouly, Journal of bacteriology 2009 - GeneRIF: The authors provide evidence that YbeY, a conserved heat shock protein with unknown function, is involved in the translation process.
- The ybeY protein from Escherichia coli is a metalloprotein.
Zhan, Acta crystallographica. Section F, Structural biology and crystallization communications 2005 - GeneRIF: ybeY protein from Escherichia coli is a metalloprotein
- Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
García, Microbial genomics 2021 - “...a ATP synthesis (C) 2.78 UTI89_C4285 atpD ATP synthase subunit beta ATP synthesis (F) 2.73 UTI89_C0657 ybeY Endoribonuclease YbeY rRNA processing/ribosome biogenesis (J) 2.71 UTI89_C2852 iscS Cysteine desulfurase IscS Iron-sulphur cluster biosynthesis (E) 2.65 UTI89_C3221 recB RecBCD enzyme subunit RecB DNA repair (L) 2.62 UTI89_C0728 UTI89_C0728...”
VC0960 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 13:143 / 154 (85.1%), covers 93.0% of PF02130, 132.6 bits
RPA0446 Protein of unknown function UPF0054 from Rhodopseudomonas palustris CGA009
Aligns to 42:177 / 190 (71.6%), covers 96.1% of PF02130, 132.2 bits
- Molecular Basis of Bacterial Longevity
Pechter, mBio 2017 - “...recovery of colony-forming units (CFU). Three out of the five strains that we tested, the RPA0446 , RPA2580 , and RPA2698 deletion mutants, showed compromised longevities after growth arrest due to either carbon starvation or nitrogen starvation ( Fig.4A ; see Fig.S2 in the supplemental material)....”
- “...thiolsulfide oxidoreductase ( 40 ), did not have a longevity phenotype ( Fig.S2 ). The RPA0446 and RPA2580 mutants had wild-type growth rates on acetate when either ammonium or nitrogen gas was supplied as a nitrogen source. The RPA2698 strain had a slightly lower growth rate...”
YP_003431738 putative metalloprotease from Hydrogenobacter thermophilus TK-6
Aligns to 16:147 / 147 (89.8%), covers 93.8% of PF02130, 131.4 bits
- Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species
Oshima, International journal of evolutionary biology 2012 - “...S9 YP_003432379 ribosomal protein L18 YP_003432892 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_003432936 ATP-dependent protease YP_003433556 UDP-N-acetylglucosamine pyrophosphorylase YP_003431738 putative metalloprotease YP_003431749 diaminopimelate decarboxylase YP_003431809 dihydrodipicolinate reductase YP_003431998 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_003432481 ribosomal protein S20 YP_003432953 queuine tRNA-ribosyltransferase YP_003431834 ATP-dependent protease La YP_003431839 tRNA delta(2)-isopentenylpyrophosphate transferase YP_003431873 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase...”
YBEY_HAEIN / P71335 Endoribonuclease YbeY; EC 3.1.-.- from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
HI0004 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 14:144 / 154 (85.1%), covers 91.5% of PF02130, 130.8 bits
- function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
cofactor: Zn(2+) (Binds 1 zinc ion.) - Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus
Lee, Journal of microbiology and biotechnology 2023 - “...YbeY from E. coli (PDB code: 1XM5); TM1509 from Thermotoga maritima (PDB code: 1TVI); and HI0004 from Haemophilus influenzae (PDB code: 1XAX). Furthermore, a comparison of Sa YbeY with E. coli YbeY and A. aeolicus YbeY, whose crystal structures were identified, showed that the three proteins...”
- NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog
Yeh, Protein science : a publication of the Protein Society 2005 - “...HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog DEOK CHEON YEH, LISA M. PARSONS, JAMES F. PARSONS, FANG...”
- “...of the 154-residue conserved hypothetical protein HI0004 has been determined using multidimensional heteronuclear NMR spectroscopy. HI0004 has sequence...”
- NMR assignment of the hypothetical protein HI0004 from Haemophilus influenzae--a putative essential gene product
Cheon, Journal of biomolecular NMR 2004 - A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
Akerley, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...Vch Bbu Tpa N E N N N N E N HI0004 HI0175 HI0303 HI0338 HI0466 HI0570 HI0767 HI1086 HI1282 HI1608 HI1654 HI1731 N N E N E UPF0054 Predicted transmembrane...”
- “...in viability for several conserved genes (homologs of HI0004, HI0767, HI1282, HI1608, and HI1654) that have been examined in B. subtilis (ref. 4;...”
- Diacylglycerol kinase is involved in regulation of expression of the lantibiotic mutacin II of Streptococcus mutans
Chen, Journal of bacteriology 1998 - “...E. coli (U82598), Haemophilus influenzae (HI0004), Mycobacterium leprae (B1937_F1_21), Mycoplasma genitalium (MG388, U02265), Mycoplasma pneumoniae (AE000027),...”
ZMO_RS00305 rRNA maturation RNase YbeY from Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
ZMO0074 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
Aligns to 13:158 / 176 (83.0%), covers 96.9% of PF02130, 129.6 bits
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Shabbir, Microbial cell factories 2023 - “...1 : Tables S7, S10). Proteins and genes associated with translation, ribosomal structure, and biogenesis ZMO_RS00305 (ybeY) and ZMO_RS04930 (tsaE) were up-regulated only in ZM532 (Additional file 1 : Tables S7, S10). However, several proteins such as ZMO_RS07450 (tilS), ZMO_RS03355, ZMO_RS00625 (trmB), and ZMO_RS06475 were down-regulated...”
- “...were up-regulated exclusively in ZM532. Proteins associated with translation, ribosomal structure, and biogenesis, such as ZMO_RS00305 (ybeY) and ZMO_RS04930 (tsaE) were up-regulated only in ZM532. However, several proteins such as ZMO_RS07450 (tilS), ZMO_RS03355, ZMO_RS00625 (trmB), and ZMO_RS06475 were down-regulated under the stress conditions (Additional file 1...”
- Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
Yan, Applied and environmental microbiology 2019 - “...gene, ZMO1399; and two hypothetical 174 protein genes, ZMO0074 and ZMO1821. The two downregulated genes were oxidoreductase 175 encoding gene ZMO1116 and...”
- “...374 ZMO0833, ZMO1303, ZMO1984, ZMO1949, ZMO1696, ZMO1576, ZMO1399, ZMO0074, 375 ZMO1821, ZMO1116 and ZMO1335) for overexpression. The pHW20a plasmid we used was...”
- Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
Yi, Biotechnology for biofuels 2015 - “...2.84 2.01 Metabolism of other amino acids ZMO1309 Leucyl aminopeptidase 2.33 2.03 Genetic/environmental/cellular process/organismal systems ZMO0074 Hypothetical protein 5.02 3.61 Genetic/environmental/cellular process/organismal systems ZMO0143 c ATP - binding cassette superfamily 2.11 2.00 Genetic/environmental/cellular process/organismal systems ZMO0282 RND family efflux transporter subunit MFP 6.05 7.14 2.55 Genetic/environmental/cellular...”
- “...up-regulated over twofold change under at least two phenolic aldehyde inhibitors. ZMO0020 , ZMO0021 , ZMO0074 , ZMO0268 , ZMO0270 , ZMO0384 , ZMO0388 , ZMO0391 , ZMO0440 , ZMO0486 , ZMO1334 , ZMO1346 , ZMO1386 , ZMO1602 , ZMO1821 , ZMO1880 , ZZM4_0133 , and...”
MAB_1669 rRNA maturation RNase YbeY from Mycobacteroides abscessus ATCC 19977
MAB_1669 hypothetical protein from Mycobacterium abscessus ATCC 19977
Aligns to 11:148 / 170 (81.2%), covers 89.1% of PF02130, 129.1 bits
NGR_c00430 hypothetical protein from Rhizobium sp. NGR234
Aligns to 17:156 / 173 (80.9%), covers 81.4% of PF02130, 128.2 bits
RL0393 hypothetical protein from Rhizobium leguminosarum bv. viciae 3841
Aligns to 17:156 / 171 (81.9%), covers 80.6% of PF02130, 126.9 bits
Rv2367c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 15:153 / 182 (76.4%), covers 90.7% of PF02130, 125.6 bits
- Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions
Perrone, Scientific reports 2017 - “...GGG TCGCCACCATCA GGG Rv0896 gltA2 23 GGG ATGACCCGCCTGCCC GGGG T GGGG TCTCT GG CACCAT GGG Rv2367c 34 GGG TC GGGG CTGAATC GGG C GG CTC GG C GGG Rv0166 fadD5 36 GGG TC GGG CC GGG ATTGCC GGGG ACTTGCC GGGG GCTT GG C GGGGG Rv1704c cycA...”
- A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
Bhagavat, Scientific reports 2017 - “...14 FAH Rv3536c Probable hydratase 15 Thioesterase/thiol ester dehydrase-isomerase Rv1532c Conserved hypothetical protein 16 Zincin-like Rv2367c Conserved hypothetical protein 17 MFS general substrate transporter Rv3331 Probable sugar-transport integral membrane protein SugI 18 Rhomboid-like Rv1337 Probable integral membrane protein 19 MetI-like Rv0929 Phosphate-transport integral membrane ABC transporter...”
- Identifying co-targets to fight drug resistance based on a random walk model
Chen, BMC systems biology 2012 - “...] atpB 0.46 In Vitro essential ATP synthase A chain [ 55 , 67 ] Rv2367c 0.28 Not Essential hypothetical protein Rv3355c 0.01 Not Essential conserved hypothetical protein Rv2199c 0.55 Not Essential conserved membrane protein Rv3310 1.38 Not Essential acid phosphatase [ 68 ] nadC 0.59...”
- The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
Fu, BMC microbiology 2007 - “...Rv3885C MMPL7 Rv2475C LTP1 Rv0236C NUOJ NUOB NUON MMPL9 Rv2752C Rv0177 Rv0176 HEMB PRCA Rv2553C Rv2367C RPLT GID CMK Rv3122 EMBB Rv1303 Rv1907C Rv2792C) Energy production and respiration 3 (FTSZ WAG31 Rv0902C HEMK NARL Rv2147C Rv3267 Rv1477 LPPW SIGC Rv2864C RECA Rv2826C Rv1697 LEUC LEUD Rv3909...”
- “...Rv1711 Rv3672c Rv2554c Rv3856c Rv3212 Rv1043c Rv0525 Rv1339 Rv2956 Rv2759c Rv2879c Rv1780 Rv2475c Rv2752c Rv0177 Rv2367c) (Rv1632c Rv2808 Rv3122 Rv1907c) Zone-3 (Information Pathways) (Rv2147c Rv3267 Rv1697 Rv3909 Rv2574 Rv3376 Rv2125 Rv1546 Rv1099c Rv2908c Rv1073 Rv0636 Rv0637 Rv0277c) (Rv2826c Rv2360c Rv2827c Rv3647c Rv0299 Rv2822c Rv0057) Zone-4 (Cell...”
VT47_20845 rRNA maturation RNase YbeY from Pseudomonas syringae pv. syringae
Aligns to 10:141 / 166 (79.5%), covers 93.8% of PF02130, 125.5 bits
SMc01113 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
Aligns to 17:156 / 168 (83.3%), covers 96.1% of PF02130, 125.1 bits
- Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing
Babu, Nucleic acids research 2020 - “...any ybeY mutant was described in an earlier study, which showed that the ybeY gene (SMc01113) is critically required for Sinorhizobium meliloti symbiosis with alfalfa ( Medicago sativa ) plants ( 2 ). In addition to being symbiotically defective, loss of YbeY also rendered the S....”
- Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria
Robledo, Microorganisms 2020 - “...growth and overall symbiotic performance on alfalfa roots [ 134 ]. The gene annotated as SMc01113 in the chromosome of the S. meliloti reference strain Rm1021 is almost ubiquitous in bacteria and has been included in the proposed minimal prokaryotic genome [ 135 ]. It encodes...”
- OxyR-Dependent Transcription Response of Sinorhizobium meliloti to Oxidative Stress
Lehman, Journal of bacteriology 2018 - “...Antioxidants and regulators katA cpo oxyR glgA1 SMc03924 SMc01113 ABC ABC ABC ABC transporter transporter transporter transporter 0.5 mM oxyR mutant 0.65 1.09...”
- “...secreted peroxidase (SMc01944) and a gene of unknown function (SMc01113) whose expression has been previously shown to be induced by H2O2 (48, 49). Role of...”
- Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation
Saramago, Nucleic acids research 2017 - “...S. meliloti mutants and derivative strains Sm YbeY is encoded by the gene annotated as SMc01113 in the genome of the reference Rm1021 strain ( 31 ). S. meliloti Sm ybeY and Sm ybeY FLAG derivatives were both generated in the ExpR + Sm2011 derivative strain...”
- “...To create an in-frame deletion of ybeY , 938-bp and 921-bp DNA fragments flanking the SMc01113 ORF were PCR amplified from genomic DNA with primer pairs YbeY_F1/YbeY_iR and YbeY_iF/YbeY_R1. Primers YbeY_iR and YbeY_iF carry Hind III sites at their 5-ends. The resulting PCR products were thus...”
- RNA-binding proteins involved in post-transcriptional regulation in bacteria
Van, Frontiers in microbiology 2015 - “...models assigned a probable RNA-binding site for YbeY. Phenotypically, there are striking similarities between an smc01113 mutant, the ybeY ortholog in S. meliloti , and an hfq mutant ( Pandey et al., 2011 ). Mutated YbeY indeed causes an increased sensitivity to various stresses, similarly to...”
- Riboregulation in plant-associated α-proteobacteria
Becker, RNA biology 2014 - “...may be related to riboregulation is the S. meliloti SMc01113 protein, a homolog to E. coli YbeY. This protein is broadly conserved in bacteria and comprises an...”
- “...proteins involved in RNA silencing.68 Phenotypes of a SMc01113 mutant are pleiotropic and resemble those of hfq mutants.68 In E. coli, YbeY modulates...”
- Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria
Pandey, BMC genomics 2014 - “...in this process. We have recently reported evidence that the highly conserved bacterial protein YbeY (SMc01113 in Sinorhizobium meliloti ) may play a major, previously unrecognized role in bacterial sRNA regulation [ 16 ]. ybeY , which is one of the 206 genes that comprise the...”
- “...YbeY cavity. Second, we noted striking parallels between the phenotypes of S. meliloti hfq and smc01113 ( ybeY ) mutants, an observation that suggested there might be an underlying mechanistic connection. To test this hypothesis, we carried out a limited study in S. meliloti in which...”
- Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti
Torres-Quesada, RNA biology 2014 - “...is the widely conserved Argonaute-like protein YbeY (SMc01113), whose loss-of-function has been shown to produce phenotypes and to compromise trans-sRNA...”
- More
YPO2618 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 15:144 / 157 (82.8%), covers 93.0% of PF02130, 123.6 bits
BL0861 hypothetical protein from Bifidobacterium longum NCC2705
Aligns to 8:145 / 182 (75.8%), covers 85.3% of PF02130, 123.3 bits
YPTB1111 hypothetical protein from Yersinia pseudotuberculosis IP 32953
Aligns to 15:144 / 157 (82.8%), covers 93.0% of PF02130, 122.8 bits
Q98BK1 Endoribonuclease YbeY from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
mlr5536 hypothetical protein from Mesorhizobium loti MAFF303099
Aligns to 26:159 / 166 (80.7%), covers 94.6% of PF02130, 122.7 bits
- Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency.
Suyal, Scientific reports 2019 - “...B7K5E6), MurC (UDP-N-acetylmuramateL-alanine ligase, B2JHF9), MloA (Protein MloA, Q8RN11), LipB (Octanoyltransferase, Q89JM6), YbeY (Endoribonuclease YbeY, Q98BK1), ProB, atpA, AtpH, ThrB, TufA, GpmA (2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, B2JC95), AskA (Acetate kinase, B8HVB6), ThyA (Thymidylate synthase, Q0SEI1), RpsF (30S ribosomal protein S6), Tkt, AccC (Biotin carboxylase, Q06862), PanD (Aspartate...”
- A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
Davies, Journal of bacteriology 2008 - “...RL0393; Bradyrhizobium japonicum, b110793; Mesorhizobium loti, mlr5536; and "Aquifex aeolicus," Aq1354. Downloaded from http://jb.asm.org/ on February 12, 2017...”
PA14_12310 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
Q02SF0 Endoribonuclease YbeY from Pseudomonas aeruginosa (strain UCBPP-PA14)
PA3982 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 14:142 / 160 (80.6%), covers 94.6% of PF02130, 122.4 bits
- The world of ribonucleases from pseudomonads: a short trip through the main features and singularities
Apura, Microbial biotechnology 2021 - “...the role of the enzyme on the regulation of virulence determinants in P. aeruginosa (PA3982 (PA14_12310 in the PA14 genome)). This endoribonuclease demonstrated a critical role in the virulence of P. aeruginosa at different levels. In this pathogen, YbeY controls bacterial resistance to oxidative stresses through...”
- Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa
Xia, mBio 2020 - “...essential for the 16S rRNA maturation and ribosome assembly. In P. aeruginosa , gene PA3982 (PA14_12310 in the PA14 genome) encodes an YbeY homolog. To examine the function of YbeY in P. aeruginosa , we constructed a ybeY mutant in wild-type PA14. Deletion of the ybeY...”
- Protein Interaction Networks of Catalytically Active and Catalytically Inactive PqsE in Pseudomonas aeruginosa
Taylor, mBio 2022 - “...Gene Displayed gene name WT/ rhlR strain log 2 abundance ratio P54292 rhlR rhlR 9.965784285 Q02SF0 ybeY ybeY 2.956800118 Q02LM8 kynB kynB 1.616357697 Q02DL4 thrB thrB 1.365692537 Q02FF4 ureA ureA 1.264836648 Q9I3F5 acnA acnA 1.002888279 Q02V73 glyS glyS 1.008682243 Q59638 aceF aceF 1.067938829 B7UZY2 cysD cysD...”
- The world of ribonucleases from pseudomonads: a short trip through the main features and singularities
Apura, Microbial biotechnology 2021 - “...on the role of the enzyme on the regulation of virulence determinants in P. aeruginosa (PA3982 (PA14_12310 in the PA14 genome)). This endoribonuclease demonstrated a critical role in the virulence of P. aeruginosa at different levels. In this pathogen, YbeY controls bacterial resistance to oxidative stresses...”
- Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa
Xia, mBio 2020 - “...is essential for the 16S rRNA maturation and ribosome assembly. In P. aeruginosa , gene PA3982 (PA14_12310 in the PA14 genome) encodes an YbeY homolog. To examine the function of YbeY in P. aeruginosa , we constructed a ybeY mutant in wild-type PA14. Deletion of the...”
- “...the Creative Commons Attribution 4.0 International license . To confirm that the P. aeruginosa ybeY (PA3982) gene is a true ortholog of the ybeY gene in E. coli , we complemented the PA14 ybeY mutant with an E. coli ybeY gene, which restored the bacterial growth...”
DIP1717 Conserved hypothetical protein from Corynebacterium diphtheriae NCTC 13129
Aligns to 11:150 / 196 (71.4%), covers 90.7% of PF02130, 120.9 bits
- Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
Wittchen, BMC genomics 2018 - “...Cell wall, membrane, envelop biogenesis DIP1720 - DIP1713 8 not detected dnaJ2 , DIP1719, DIP1718, DIP1717, DIP1716, DIP1715, era , recO . Replication, recombination and repair; Cell wall, membrane, envelop biogenesis; Coenzyme metabolism; Inorganic ion transport and metabolism; Function unknown; Signal transduction mechanisms; Post-translational modification, protein...”
PD1781 conserved hypothetical protein from Xylella fastidiosa Temecula1
Aligns to 19:151 / 161 (82.6%), covers 91.5% of PF02130, 118.3 bits
E2P69_RS09245 rRNA maturation RNase YbeY from Xanthomonas perforans
Aligns to 22:151 / 161 (80.7%), covers 91.5% of PF02130, 117.8 bits
CBU_0567 conserved hypothetical protein TIGR00043 from Coxiella burnetii RSA 493
Aligns to 13:144 / 152 (86.8%), covers 93.0% of PF02130, 117.6 bits
Q9K0P7 Endoribonuclease YbeY from Neisseria meningitidis serogroup B (strain MC58)
Aligns to 28:160 / 169 (78.7%), covers 84.5% of PF02130, 117.3 bits
CJM1cam_0120 rRNA maturation RNase YbeY from Campylobacter jejuni
Aligns to 4:122 / 134 (88.8%), covers 79.8% of PF02130, 116.2 bits
Cj0121 hypothetical protein Cj0121 from Campylobacter jejuni subsp. jejuni NCTC 11168
CJSA_0112 rRNA maturation RNase YbeY from Campylobacter jejuni subsp. jejuni IA3902
Aligns to 4:122 / 135 (88.1%), covers 79.8% of PF02130, 116.2 bits
- Posttranscriptional Regulation in Response to Different Environmental Stresses in Campylobacter jejuni
Li, Microbiology spectrum 2022 - “...for comparison. It was noteworthy that the following RNases were also found in module II: Cj0121, rnc , rnhA , Cj1710c. All except Cj0121 displayed differential upregulation in the three conditions of interest (highlighted in bold text in Fig.6e ). All four RNases in module II...”
- “...weak/moderate negative coexpression against tlp1 to 4 (0.35 to 0.527) (Fig.S23). All these indicated that Cj0121, rnc , rnhA , Cj1710c, and rnhB were the most likely candidates that degraded tlp1 to 4 transcripts without digesting CjSA21. DISCUSSION This study presents one of the most comprehensive...”
- RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist
Svensson, eLife 2021 - “...RNase HI (Cj1636c); rnhB RNase HII (Cj0010c); rppH RNA 5' pyrophosphohydrolase (Cj0581); ybeY endoribonuclease YbeY (Cj0121). ( B ) RNase III affects PtmG expression via CJnc190 processing. Related to main Figure 3B . PtmG-3FLAG protein and transcript were measured in WT, 180/190, and C-190(Proc) strains (...”
- Structure and genotypic plasticity of the Campylobacter fetus sap locus
Tu, Molecular microbiology 2003 - “...26% respectively. The Cf0020 product shares 59% identity with Cj0121, the function of which is unknown, and the Cf0013 and Cf0019 predicted products have no...”
- RNAseq Reveals Complex Response of Campylobacter jejuni to Ovine Bile and In vivo Gallbladder Environment
Kreuder, Frontiers in microbiology 2017 - “...lipoprotein 1.8 2.3 obgE GTPase ObgE 1.5 3.4 CJSA_0111 Putative recombination protein RecO 5.4 5.6 CJSA_0112 Putative metalloprotease 3.1 1.9 thrB Homoserine kinase 2.2 2.0 CJSA_0149 Cytochrome c family protein 1.5 1.6 CJSA_0150 Putative 6-pyruvoyl tetrahydropterin synthase 1.8 1.9 CJSA_0228 Hypothetical protein 1.6 1.7 CJSA_0233 Sulfatase...”
YBEY_THEMA / Q9X1J7 Endoribonuclease YbeY; EC 3.1.-.- from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TM1509 conserved hypothetical protein from Thermotoga maritima MSB8
Aligns to 9:133 / 150 (83.3%), covers 93.8% of PF02130, 116.0 bits
- function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
cofactor: Zn(2+) (Binds 1 zinc ion.) - Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus
Lee, Journal of microbiology and biotechnology 2023 - “...code: 1OZ9), which presents a similar protein fold; YbeY from E. coli (PDB code: 1XM5); TM1509 from Thermotoga maritima (PDB code: 1TVI); and HI0004 from Haemophilus influenzae (PDB code: 1XAX). Furthermore, a comparison of Sa YbeY with E. coli YbeY and A. aeolicus YbeY, whose crystal...”
- NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure
Penhoat, Journal of structural and functional genomics 2005 (PubMed)- “...NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure Catherine Herve du Penhoat1,6, Zhaohui Li2,6,...”
- “...matrix metalloproteinase, structural genomics, Thermotoga maritima, TM1509, UPF0054, zinc-binding protein Abstract The 150-residue protein TM1509 is encoded in...”
SPOA0008 rRNA maturation RNase YbeY from Ruegeria pomeroyi DSS-3
Aligns to 14:156 / 165 (86.7%), covers 91.5% of PF02130, 115.8 bits
H375_7840 rRNA maturation RNase YbeY from Rickettsia prowazekii str. Breinl
Aligns to 14:161 / 167 (88.6%), covers 93.8% of PF02130, 112.9 bits
RP741 unknown from Rickettsia prowazekii str. Madrid E
Aligns to 27:174 / 180 (82.2%), covers 93.8% of PF02130, 112.7 bits
- Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect
Kondo, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...detected: ftsZ, sdhB, pgpA, g3pdh, czcR, an ORF homologous to RP741 in the genome of R. prowazekii, and an ORF homologous to BMEI0172 in the genome of Brucella...”
- “...was an unidentified ORF located between BMEI0172 and RP741. In the upstream region of ftsZ, where Kondo et al. non-LTR retrotransposon-like sequence was...”
RSP_3598 rRNA maturation RNase YbeY from Cereibacter sphaeroides 2.4.1
RSP_3598 Protein of unknown function UPF0054 from Rhodobacter sphaeroides 2.4.1
Aligns to 14:161 / 167 (88.6%), covers 92.2% of PF02130, 110.5 bits
- Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
Spanka, International journal of molecular sciences 2021 - “...mL 1 kanamycin. The same procedure was also applied to delete the gene ybeY ( RSP_3598 ) in the Rhodobacter sphaeroides 2.4.1 wild type strain. For the up and down fragment amplification the primer pairs KO_3598_ybeY_up_f/KO_3598_ybeY_up_r and KO_3598_ybeY_dw_f /KO_3598_ybeY_dw_r were used. Plasmid construction was carried out...”
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...RSP_2638, RSP_2640, RSP_2641, RSP_2739, RSP_2763, RSP_2764, RSP_2816, RSP_2952, RSP_2953, RSP_3067, RSP_3068, RSP_3378, RSP_3426, RSP_3552, RSP_3597, RSP_3598, RSP_3634, RSP_3809, RSP_3810, RSP_4244, RSP_4245, RSP_4248, RSP_4305 RpoHII regulon (99 genes) Energy metabolism Biosynthesis and degradation of polysaccharides RSP_0482 Electron transport RSP_0108, RSP_0109, RSP_0110, RSP_0112, RSP_0474, RSP_2785, RSP_3212, RSP_3305, RSP_3537...”
BB0060 conserved hypothetical protein from Borrelia burgdorferi B31
Aligns to 11:151 / 155 (91.0%), covers 95.3% of PF02130, 108.5 bits
- Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi
Petroni, Nature communications 2023 - “...Z (tRNA 3 endonuclease; bb0755 ), RNase M5 (5S maturation nuclease; bb0626 ), YbeY ( bb0060 ) and exoribonuclease orthologs of Oligoribonuclease ( bb0619 ) and PNPase ( bb0805 ) 38 , 85 , 87 . Processed RNA ends often result in/depend on RNA secondary structures...”
- Gene Regulation and Transcriptomics
Samuels, Current issues in molecular biology 2021 - “...ribonucleases, which includes the endoribonucleases RNase III (BB0705), RNase P (BB0441), RNase Z (BB0755), YbeY (BB0060), RNase Y (BB0504), RNase M5 (BB0626), and RNase HII (BB0046) and the exoribonuclease PNPase (BB0805) ( Fraser et al., 1997 ; Archambault et al., 2013 ; Anacker et al., 2018...”
- Transcript decay mediated by RNase III in Borrelia burgdorferi
Snow, Biochemical and biophysical research communications 2020 - “...RNase Z (BB0755), RNase M5 (BB0626), PNPase (BB0805), RNase HII (BB0046), RNase P (BB0441), YbeY (BB0060) and Oligoribonuclease (BB0619) [ 13 ]. Of these, only two loci, bb0626 and bb0046 , were disrupted by signature-tagged transposons in the construction of a STM library [ 14 ],...”
YBEY_ARATH / Q8L5Z4 Endoribonuclease YBEY, chloroplastic; EC 3.1.-.- from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_850072 haloacid dehalogenase-like hydrolase family protein from Arabidopsis thaliana
AT2G25870 haloacid dehalogenase-like hydrolase family protein from Arabidopsis thaliana
Aligns to 144:271 / 584 (21.9%), covers 79.8% of PF02130, 108.1 bits
- function: Endoribonuclease required for chloroplast ribosomal RNA (rRNA) processing and essential for normal growth and development. May be involved in maturation of both the 5' and 3' ends of 16S, 23S, and 4.5S rRNAs. Cleaves chloroplast rRNAs, mRNAs and tRNAs in vitro.
cofactor: Zn(2+) (Binds 1 zinc ion.)
disruption phenotype: Seedling lethality. - The conserved endoribonuclease YbeY is required for chloroplast ribosomal RNA processing in Arabidopsis.
Liu, Plant physiology 2015 - GeneRIF: AtYbeY is a chloroplast-localized endoribonuclease that is required for chloroplast rRNA processing and thus for normal growth and development.[YbeY]
- A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites
Guggisberg, Nature communications 2014 - “...sequences: E. coli YidA, EOU46719; M. tuberculosis Rv3813c, NP_218330; C. reinhardtii FER_156463, ADF43173; A. thaliana At2g25870, ABO38782. Figure 4 PfHAD1 fosmidomycin-resistance alleles result in loss of phosphatase activity Displayed are the means standard error of the mean (SEM) of enzyme activity from at least three independent...”
- Mining the soluble chloroplast proteome by affinity chromatography
Bayer, Proteomics 2011 - “...AT2G17340 Pantothenate kinase-related O + AT2G21350 RNA binding C + AT2G23390 Acyl-CoA N-acyltransferase M + AT2G25870 Haloacid dehalogenase-like family protein M + AT2G31890 b) ATRAP; putative RNA binding domain C + AT2G44760 Unknown protein C + AT3G02900 a) Unknown protein C + AT3G04650 FAD-dependent oxidoreductase C...”
- “...C O O + AT2G17240 CUP2 Chloroplast unknown protein 1 C C C C + AT2G25870 HAC Haloacid dehalogenase-like family protein M C O M + AT2G35800 SUC Substrate carrier family protein O O O O + AT3G04650 ORE FAD-dependent oxidoreductase C C C C +...”
- Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development
Tsuchiya, BMC plant biology 2010 - “...EDM2 -induced" catalytic activity (MF) 2.60e-06 AT5G39080, AT3G63510, AAE14, PSD2, AT1G22430, SAL1, ATALN, AT5G09300, AT4G31390, AT2G25870, SRS, FC2, AT2G47880, AtCXE17, CSLA11, PKp3, UGT80B1, MCM4, ADC1, AT5G61480, AT2G26870 AT4G33920, CYP78A8, B120, XCP1, ATPREP2, CYP79B2, AT2G04845, AT5G24670, PAL4, CINV2, AT5G38710 set 10 "only EDM2 -suppressed" response to biotic...”
- Identification, cloning and characterization of sis7 and sis10 sugar-insensitive mutants of Arabidopsis
Huang, BMC plant biology 2008 - “...AT1G71870 1830 4621 0.40 0.016 glutathione S-transferase AT2G30860 36776 92522 0.40 0.002 hydrolase family protein AT2G25870 981 2438 0.40 0.000 endo-beta-1,4-glucanase AT1G64390 2208 5381 0.41 0.011 heat shock protein 100, putative AT5G15450 1817 4398 0.41 0.026 eIF-2 family protein AT1G76810 748 1809 0.41 0.035 auxin transport...”
- “...brassinosteroids 0.66 0.99 AT2G17033 pentatricopeptide repeat-containing protein 0.61 0.71 AT2G19640 SET domain-containing protein 0.51 0.93 AT2G25870 hydrolase family protein 0.63 1.14 AT2G30860 glutathione S-transferase 0.70 0.91 AT2G30870 early dehydration-induced gene ERD13 0.91 1.08 AT2G31400 pentatricopeptide repeat-containing protein 0.53 0.73 AT2G31660 importin beta-2 subunit family protein 0.76...”
WQ49_RS25680 rRNA maturation RNase YbeY from Burkholderia cenocepacia
BCAL0909 hypothetical protein from Burkholderia cenocepacia J2315
Aligns to 123:251 / 258 (50.0%), covers 94.6% of PF02130, 103.8 bits
HP1160 conserved hypothetical protein from Helicobacter pylori 26695
Aligns to 6:128 / 140 (87.9%), covers 76.7% of PF02130, 103.7 bits
- High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
Loh, Infection and immunity 2018 - “...HP1484 HP1459 HP1426 HP1288 HP1240 HP1193 HP1162 HP1160 HP1546 HP1116 HP0385 HP1412 jhp0955 jhp0954 HP0441 jhp0936 HP0996 jhp1408 HP0008 HP0903 HP0681...”
- Helicobacter Pylori's plasticity zones are novel transposable elements
Kersulyte, PloS one 2009 - “...Shi32, in jhp0244 (methyltransferase of type II restriction modification system); strain Shi417, between hp1159 and hp1160 ; strain G27, between HPP12_1009 and the tRNA gene HPP12_t21 . Type 1b TnPZ insertion site: strain P12 in gene HPAG1_0439 (encodes type I restriction-modification R protein (hsdR)). Type 2...”
- “...group (one strain) the TnPZs were located at other sites (type 1, between hp1159 and hp1160 ; type 2, in hp1402 ); this strain lacked the above-mentioned 0.5 kb deletion in or near orfQ and the orfG ::IS Hp608 insertion. The genome sequence of German strain...”
TTHA1045 hypothetical protein from Thermus thermophilus HB8
Aligns to 12:139 / 139 (92.1%), covers 86.8% of PF02130, 102.6 bits
- The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
Ohyama, BMC genomics 2014 - “...[ 21 ] (21%) -CASP family protein TTHA0252 YP_143518.1 mRNA? Exo [ 6 ] YbeY TTHA1045 YP_144311.1 rRNA precursor? Endo [ 16 ] (29%) (21%) PhoH-like protein TTHA1046 YP_144312.1 ? ?? [ 22 ]** (50%) (47%) L-PSP TTHA0137 YP_143403.1 ? Endo [ 23 ] (50%) (37%)...”
- “...motif. Therefore, we predicted that TTHA1046 is a putative RNase. The E. coli ortholog of TTHA1045, YbeY, may be involved with rRNA maturation based on mutagenic studies and its strong genetic interactions with PNPase and RNase R [ 28 ]. Furthermore, there is tertiary structural similarity...”
TP0650 conserved hypothetical protein from Treponema pallidum subsp. pallidum str. Nichols
Aligns to 19:148 / 160 (81.2%), covers 82.2% of PF02130, 98.3 bits
BPSL0672 unkown domain/putative metalloprotease fusion protein from Burkholderia pseudomallei K96243
Aligns to 136:263 / 270 (47.4%), covers 92.2% of PF02130, 97.2 bits
- Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei
Mohd-Padil, Scientific reports 2017 - “...and BPNC10048R that was predicted to interact with two genes at its 3 site - bpsl0672 , a metalloprotease fusion protein (FC=0.76) and bpsl0671 , a hypothetical protein (FC=0.72) (Fig. 2C ). Three sRNA candidates, BPNC10196F_1129_SIPHT, BPNC10209R and BPNC10146R, are located between genes encoding ribosomal proteins....”
- “...BPNC10113R bpsl1725 up up up up Candidate_369_SIPHT bpss1184 up up nd na BPNC10048R bpsl0671 , bpsl0672 down down, down up nd, up BPNC10196F_1129_SIPHT bpsl3221 down down up down BPNC10209R bpsl3223 down down down down BPNC10146R bpsl2159 down down down down BPNC10037R bpsl0493 , bpsl0494 up up,...”
TWT283 unknown from Tropheryma whipplei str. Twist
Aligns to 14:145 / 171 (77.2%), covers 87.6% of PF02130, 96.6 bits
YBEY_HUMAN / P58557 Endoribonuclease YbeY; EC 3.1.-.- from Homo sapiens (Human) (see paper)
Aligns to 15:148 / 167 (80.2%), covers 80.6% of PF02130, 95.7 bits
- function: Single strand-specific metallo-endoribonuclease involved in rRNA maturation.
cofactor: Zn(2+) (Binds 1 zinc ion.)
PG0510 conserved hypothetical protein from Porphyromonas gingivalis W83
Aligns to 13:138 / 151 (83.4%), covers 89.9% of PF02130, 86.9 bits
CT422 possible metalloenzyme from Chlamydia trachomatis D/UW-3/CX
Aligns to 16:150 / 161 (83.9%), covers 88.4% of PF02130, 80.0 bits
- Autoprocessing and self-activation of the secreted protease CPAF in Chlamydia-infected cells
Chen, Microbial pathogenesis 2010 - “...GCGGCCGC .TTA.AAC.CCC.AGG.GAA.AGC.AAT-3(reverse); For cloning CT408, 5-CGC GGATCC .ATG.CCG.ACC.CGT.TCT.CTC-3(forward) and 5-TTTCCTTTT GCGGCCGC .TTA.AAA.GTA.TTT.TTT.ACT.TTC.TTT-3 (reverse); For cloning CT422, 5-CGC GGATCC .ATG.CTT.ATT.TTG.GAT.CGA.TCT.TCT-3 (forward) and 5-TTTCCTTTT GCGGCCGC .TTA.TAC.TGC.AGG.ACG.TAA.TAA-3 (reverse); For cloning CT431, 5-CGC GGATCC .ATG.CCT.GAA.GGG.GAA.ATG.ATG-3 (forward) and 5-TTTCCTTTT GCGGCCGC .CTA.CAA.GTC.GTT.AAA.AGA.GAA-3 (reverse); For cloning CT441, 5-CCG GAATTC .ATG.ATG.AGA.TTC.GCT.CGC.TTT-3(forward) and 5-TTTCCTTTT GCGGCCGC...”
- Profiling of human antibody responses to Chlamydia trachomatis urogenital tract infection using microplates arrayed with 156 chlamydial fusion proteins
Sharma, Infection and immunity 2006 - “...dnaK CT406, hypothetical CT407, dksA CT421, hypothetical CT422, metalloproteas CT425, hypothetical CT427, hypothetical CT431, clpP CT442, crpA CT446, euo CT449,...”
CTL0681 hypothetical protein from Chlamydia trachomatis 434/Bu
Aligns to 16:150 / 161 (83.9%), covers 88.4% of PF02130, 77.3 bits
TC0705 conserved hypothetical protein from Chlamydia muridarum Nigg
Aligns to 16:150 / 161 (83.9%), covers 90.7% of PF02130, 73.8 bits
CPn0509 predicted Metalloenzyme from Chlamydophila pneumoniae CWL029
Aligns to 17:149 / 158 (84.2%), covers 89.1% of PF02130, 72.4 bits
- Novel Chlamydia pneumoniae vaccine candidates confirmed by Th1-enhanced genetic immunization
Li, Vaccine 2010 - “...in Round 3: cutE , Cpn0420, ide , oppA_2 , ssb , glgX , Cpn0020, Cpn0509, fabD , rl1 , atoC , and Cpn0095 [ 14 ]. These 12 highest ranking ORFs were now cloned as full-length genes into genetic immunization plasmid CMVi-UB. Candidates ide and...”
- “..._a, ide _b, Cpn0095_a, oppA _2_a, glgX _b, Cpn0020_b) or full-length genes (Cpn0420, ssb , Cpn0509, fabD , atoC , rl1 ) with the plasmid-based vaccination with gene fragments ( ide _ab, Cpn0095_a) or full-length genes ( cutE , Cpn0420, oppA _2, ssb , Cpn0509, fabD...”
YBEY_MYCGE / P47628 Endoribonuclease YbeY; EC 3.1.-.- from Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37) (Mycoplasmoides genitalium) (see paper)
Aligns to 15:149 / 154 (87.7%), covers 86.8% of PF02130, 68.5 bits
- function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
cofactor: Zn(2+) (Binds 1 zinc ion.)
disruption phenotype: Probably essential, it was not disrupted in a global transposon mutagenesis study.
TGME49_003420 4'-phosphopantetheinyl transferase domain-containing protein from Toxoplasma gondii ME49
2 alignments in 620:819 / 1145 (16.9%), covering up to 42.6% of PF02130, 68.2 bits
PF3D7_0420200 holo-[acyl-carrier-protein] synthase, putative from Plasmodium falciparum 3D7
Aligns to 194:302 / 594 (18.4%), covers 54.3% of PF02130, 57.4 bits
- Genome-wide SNP analysis of Plasmodium falciparum shows differentiation at drug-resistance-associated loci among malaria transmission settings in southern Mali
Coulibaly, Frontiers in genetics 2022 - “...presented. Gene Protein description PopPairs Mean TjD PF3D7_0221000 Plasmodium exported protein, unknown function 21 3.99 PF3D7_0420200 Holo-[acyl-carrier-protein] synthase, putative (ACPS) 15 3.17 PF3D7_0422800 Serpentine receptor 12, putative (SR12) 10 3.42 PF3D7_0619600 Conserved Plasmodium protein, unknown function 1 3.07 PF3D7_0630600 Deubiquitinating enzyme MINDY, putative 10 3.20 PF3D7_0709000...”
- Critical role for isoprenoids in apicoplast biogenesis by malaria parasites
Okada, eLife 2022 - “...proteins include the key MEP pathway enzymes DXR (PF3D7_1467300) and IspD (PF3D7_0106900), holo ACP synthase (PF3D7_0420200), FabB/F (PF3D7_0626300), and the E1 subunit of pyruvate dehydrogenase (PF3D7_1446400). These observations suggest that protein N-termini in Plasmodium can have sequence properties compatible with apicoplast targeting that are broader and...”
- “...proteins include the key MEP pathway enzymes DXR (PF3D7_1467300) and IspD (PF3D7_0106900), holo ACP synthase (PF3D7_0420200), FabB/F (PF3D7_0626300), and the E1 subunit of pyruvate dehydrogenase (PF3D7_1446400). Thus, apicoplast import despite lack of identifiable signal peptide by SignalP is not unique to PPS but general to multiple...”
- Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression
Lasonder, Nucleic acids research 2016 - “...GO terms in the apicoplast including type II fatty acid synthesis with 4 repressed transcripts (PF3D7_0420200 (Holo-ACP synthase); PF3D7_0615100 (Fabl); PF3D7_1020800 (Dihydrolipoamide S-acetyltraferase) and PF3D7_1124500 (Pyruvate dehyrdogenase E1 subunit) in the pathway (Supplementary Figure S7). We previously found an important distinction for this pathway between rodent...”
- Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites
Samad, PLoS genetics 2015 - “...4 PF3D7_0412300 1.77 1.77 1.20 1.46 12 4 PF3D7_0418000 1.23 - 1.43 - 32 4 PF3D7_0420200 - - 2.72 1.84 14 4 PF3D7_0424900 1.88 - - - 11 4 PF3D7_0425000 1.61 1.06 - - 27 5 PF3D7_0503200 - - 1.11 - 11 5 PF3D7_0511300 - -...”
- Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity
Mobegi, Molecular biology and evolution 2014 - “...2.03 20 1.80 Plasmodium-exported protein PF3D7_0321200 PFC0935c 17 1.65 15 1.68 N -acetylglucosamine-1-phosphate transferase, putative PF3D7_0420200 PFD0980w 16 1.30 13 2.02 Holo-(acyl-carrier protein) synthase PF3D7_0508800 PFE0435c 5 1.10 4 1.07 Single-stranded DNA-binding protein (SSB) PF3D7_0601500 PFF0075c 6 1.05 5 1.64 Plasmodium-exported protein (PHISTb) PF3D7_0710200 PF07_0042 131...”
- Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans
Ramakrishnan, Progress in lipid research 2013 - “...HAD Hydroxyacyl ACP dehydratase Tb927.8.1440 LmjF07.0430 LmjF07.0440 PF3D7_1323000 TGME49_121570 EAR Enoyl ACP reductase Tb927.10.11930 LmjF.04.0290 PF3D7_0420200 TGME49_051930 PPTase Phosphopantetheinyl transferase Tb927.3.1840 LmjF.25.1770 PF3D7_0420200 TGME49_003420 FASI pathway FASI Fatty acid synthase type I - - - TGME49_094820 PPTase Phosphopantetheinyl transferase - - - TGME49_014440 Table 2 Comparison...”
XP_016883883 endoribonuclease YbeY isoform X7 from Homo sapiens
Aligns to 16:73 / 125 (46.4%), covers 29.5% of PF02130, 54.2 bits
PKNH_0513000 holo-[acyl-carrier-protein] synthase, putative from Plasmodium knowlesi strain H
Aligns to 214:326 / 628 (18.0%), covers 58.9% of PF02130, 51.6 bits
PVX_090105 holo-(acyl-carrier protein) synthase, putative from Plasmodium vivax
Aligns to 49:156 / 511 (21.1%), covers 55.0% of PF02130, 48.8 bits
- Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
Diez, PloS one 2017 - “...PVX_003795 serine-repeat antigen (SERA) 4 629831630120 5.205 PVX_003770 merozoite surface protein 5 5 1132736 10.20 PVX_090105 holo-[acyl-carrier-protein] synthase, putative (ACPS) 5 964771 3.624 PVX_089950 bifunctional dihydrofolate reductase-thymidylate synthase, DHFR-TS 6 199049199165 4.703 PVX_001850 hypothetical protein 6 605656608119 3.788 PVX_111260 hypothetical protein, conserved 6 635433635539 4.406 PVX_111220...”
Or search for genetic data about PF02130 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory