PaperBLAST
PaperBLAST Hits for PP_4894 (86 a.a., MSKGHSLQDP...)
Show query sequence
>PP_4894
MSKGHSLQDPYLNTLRKEKVPVSIYLVNGIKLQGSIESFDQFVVLLKNTVSQMVYKHAIS
TVVPARPVRLPSPTDSEHGDSEPGNA
Running BLASTp...
Found 101 similar proteins in the literature:
PP4894 host factor-I protein from Pseudomonas putida KT2440
100% identity, 100% coverage
Pchl3084_0554 RNA chaperone Hfq from Pseudomonas chlororaphis subsp. aureofaciens 30-84
88% identity, 100% coverage
PFLU0520 Hfq protein (host factor-I protein) from Pseudomonas fluorescens SBW25
85% identity, 100% coverage
PA4944 RNA-binding protein Hfq from Pseudomonas aeruginosa PAO1
NP_253631 RNA-binding protein Hfq from Pseudomonas aeruginosa PAO1
85% identity, 100% coverage
- The Pseudomonas aeruginosa RpoH (σ32) Regulon and Its Role in Essential Cellular Functions, Starvation Survival, and Antibiotic Tolerance
Williamson, International journal of molecular sciences 2023 - “...PA3011 topA Topoisomerase 5.4 6.7 10 4 +++ PA3272 ATP-dependent helicase 17.7 8.5 10 5 PA4944 hfq RNA binding 2.1 3.4 10 3 PA4969 cpdA 3,5-cyclic-AMP phosphodiesterase 8.6 3.7 10 4 +++ PA4970 Conserved hypothetical protein 7.0 1.4 10 3 PA4971 aspP NTP pyrophosphohydrolase 11.9 6.1...”
- Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Shen, Microorganisms 2021 - “...phzB 1 1.95 PA4212 phzC Phenazine biosynthesis protein PhzC 1.16 PA4815 Integral membrane protein 1.78 PA4944 hfq RNA-binding protein Hfq 1.06...”
- From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment
Camus, Microbial genomics 2021 - “...PA4793 PA4793 Hypothetical protein 23 31 PA4837 PA4837 Probable outer-membrane protein precursor 28 31 Hfq PA4944 Hfq 19 29 PstS PA5369 Phosphate ABC transporter, periplasmic phosphate-binding protein 25 26 NA NA TonB-dependent receptor 24 25 Icd PA2623 Isocitrate dehydrogenase 21 30 RpsB PA3656 30S ribosomal protein...”
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...0.6 0.005 PA4853 fis Putative Fis-like DNA-binding protein 0.9 0.000 PA4941 hflC Protease 0.5 0.004 PA4944 hfq Motilities and Quorum sensing 0.6 0.001 PA4945 miaA Delta 2-isopentenylpyrophosphate 1.0 0.000 PA4960 serB Probable phosphoserine phosphatase 0.6 0.003 PA4961 Uncharacterized protein 0.5 0.005 PA4963 Uncharacterized protein 0.6 0.001...”
- Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
Yung, NPJ biofilms and microbiomes 2019 - “...39.2% 2.0 HutI PA5092 Imidazolonepropionase 3 11.2% 1.8 Pgl PA3182 6-phosphogluconolactonase 9 52.1% 1.5 Hfq PA4944 RNA-binding protein in P. aeruginosa 16 51.3% 1.5 Biofilm LldD PA4771 L-lactate dehydrogenase 12 39.60% 5.3 FolE2 PA5539 GTP cyclohydrolase 6 36.20% 2.9 PvdA PA2386 L-ornithine N(5)-monooxygenase 4 12.40% 2.1...”
- OprD Repression upon Metal Treatment Requires the RNA Chaperone Hfq in Pseudomonas aeruginosa
Ducret, Genes 2016 - “...GCC GGATCC TCAATGATGATGATGAT GATGAGCGTTGCCCGGCTCGG 249 Hfq insertion verification 314 TGCCGTATACTGTCGCTCAG PA4945 1390/3534 * 315 ATTGAACAGGGTCGATTTGC PA4944 * Without and with aadA insertion cassette . Figure A1 Hfq expression is not affected by the presence of Zn. Transcription of hsp70 , hfq and czcR genes in the...”
- Interconnection of post-transcriptional regulation: The RNA-binding protein Hfq is a novel target of the Lon protease in Pseudomonas aeruginosa
Fernández, Scientific reports 2016 - “...Probable fumarase Energy metabolism 2.6 PA4385 groEL GroEL protein Chaperone & heat shock proteins 2.7 PA4944 hfq Hfq Transcription, RNA processing degradation 2.3 PA5078 Conserved hypothetical protein Hypothetical 2.6 PA5429 aspA Aspartate ammonia-lyase Amino acid biosynthesis 4.4 a Functional class taken from www.pseudomonas.com 44 . b...”
- A method for in vivo identification of bacterial small RNA-binding proteins
Osborne, MicrobiologyOpen 2014 - “...n =5) prrF1,2 ( n =8) WTFe ( n =8) prrF1,2 ( n =9) Hfq (PA4944) 11** 5 1 3 1 PvdL (PA2424) 5* 0 0 3 1 LysR-type transcriptional regulator (PA1128) 3 0 0 2 0 Shikimate biosynthesis (PA1750) 3 0 0 2 1 Putative...”
- More
- Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa.
Malecka, Nucleic acids research 2021 - GeneRIF: Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa.
- Hfq and sRNA 179 Inhibit Expression of the Pseudomonas aeruginosa cAMP-Vfr and Type III Secretion Regulons.
Janssen, mBio 2020 - GeneRIF: Hfq and sRNA 179 Inhibit Expression of the Pseudomonas aeruginosa cAMP-Vfr and Type III Secretion Regulons.
- Architectural principles for Hfq/Crc-mediated regulation of gene expression.
Pei, eLife 2019 - GeneRIF: We describe high-resolution cryo-EM structures of the assembly of Hfq and Crc bound to the translation initiation site of a target mRNA. The core of the assembly is formed through interactions of two cognate RNAs, two Hfq hexamers and a Crc pair.
- Loss of RNA Chaperone Hfq Unveils a Toxic Pathway in Pseudomonas aeruginosa.
Hill, Journal of bacteriology 2019 - GeneRIF: Results have found that Hfq is critical for the growth of P. aeruginosa strain PAO1. The reduced growth observed in hfq mutants was due, at least in part, to the activities of genes whose expression is positively regulated by MexT.
- Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.
Sonnleitner, Nucleic acids research 2018 - GeneRIF: It has been shown that Crc and Hfq form an assembly in the presence of RNAs containing A-rich motifs, and that Crc interacts with both, Hfq and RNA. Through these interactions, Crc enhances the stability of Hfq/Crc/RNA complexes, which can explain its facilitating role in Hfq-mediated translational repression.
- Pervasive Targeting of Nascent Transcripts by Hfq.
Kambara, Cell reports 2018 - GeneRIF: findings indicate that Hfq binds many transcripts co-transcriptionally in P. aeruginosa, often in concert with Crc, and uncover direct regulatory targets of these proteins.
- The Pseudomonas aeruginosa CrcZ RNA interferes with Hfq-mediated riboregulation.
Sonnleitner, PloS one 2017 - GeneRIF: The studies further revealed that the Hfq-titrating RNA CrcZ can interfere with PrrF1-2/Hfq-mediated regulation of antR during the translation process.
- Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression.
Sonnleitner, PLoS genetics 2014 - GeneRIF: the RNA chaperone Hfq was identified as the principle post-transcriptional regulator of Carbon Catabolite repression in PAO1.
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HELO_3364 RNA chaperone Hfq from Halomonas elongata DSM 2581
80% identity, 94% coverage
- Contribution of mechanosensitive channels to osmoadaptation and ectoine excretion in Halomonas elongata
Vandrich, Extremophiles : life under extreme conditions 2020 - “...thereof). One domain (IPR010920, LSM domain superfamily) retrieved the same set plus, in addition, Hfq (HELO_3364). This is the expected behavior according to the InterPro domain annotation. The other 7 domains (IPR036019, IPR001185, IPR019823, IPR037673, IPR016688, IPR030192, IPR031334) did not retrieve entries from H.elongata . From...”
3m4gF / Q9HUM0 H57a hfq from pseudomonas aeruginosa (see paper)
93% identity, 83% coverage
PMI3365 protein Hfq (host factor-I protein) from Proteus mirabilis HI4320
73% identity, 90% coverage
HFQ_SALTY / P0A1R0 RNA-binding protein Hfq from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
NP_463222 host factor I for bacteriophage Q beta replication from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM4361 host factor I for bacteriophage Q beta replication, a growth-related protein from Salmonella typhimurium LT2
NP_458797 host factor-I protein(HF-I) from Salmonella enterica subsp. enterica serovar Typhi str. CT18
STM14_5242 RNA chaperone Hfq from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
73% identity, 84% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs (By similarity). Plays a central regulatory role in the microbial response to space flight conditions. Is essential for virulence and is required for efficient invasion of non-phagocytic cells (PubMed:17163975).
subunit: Homohexamer.
disruption phenotype: Drastically decreases survival in host macrophages (PubMed:19229334). Cells display drastically reduced virulence in vitro and in vivo (PubMed:17163975, PubMed:19229334). Mice infected with the deletion mutant show no signs of illness during the course of the experiment (PubMed:17163975, PubMed:19229334). - Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
Holmqvist, The EMBO journal 2016 - GeneRIF: The study reveals 3'-located Rho-independent terminators as a universal motif involved in Hfq-RNA interactions.
- Hfq and ArcA are involved in the stationary phase-dependent activation of Salmonella pathogenicity island 1 (SPI1) under shaking culture conditions.
Lim, Journal of microbiology and biotechnology 2013 (PubMed)- GeneRIF: Taken together, these results suggest that Hfq and ArcA regulate the hilD promoter, causing an accumulation of HilD, which can trigger a stationary phase-dependent activation of SPI1 genes under shaking culture conditions.
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...UniProt-IDs are: -Proteobacteria: SALTY, Salmonella typhimurium (P0A1R0); ECOLI Escherichia coli (P0A6X3); YERPE, Yersinia pestis (A4TRN9); HAEIN, Hemophilus...”
- Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition
Sauer, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...St Hfq constructs (St Hfq, GAM1-E102; UniProt ID code P0A1R0) were expressed as NusA fusions from a pETM60 vector in E. coli BL21(DE3) GOLD cells. NusA-Hfq was...”
- Structural basis for RNA 3'-end recognition by Hfq
Sauer, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...Hfq, GAM1 -E102 and St Hfq72, GAM1 -S72 ; UniProt ID P0A1R0) were expressed as NusA fusions from a pETM60 vector in E. coli BL21 (DE3) GOLD cells. NusA-Hfq was...”
- RNA type III secretion signals that require Hfq
Niemann, Journal of bacteriology 2013 - “...RNA-binding proteinsa LT2 locus Gene Mass (kDa) STM4361 STM2928 hfq truD 11.13 39.33 Protein description RNA-binding protein tRNA pseudouridine synthase No....”
- Virulence gene profiling and pathogenicity characterization of non-typhoidal Salmonella accounted for invasive disease in humans
Suez, PloS one 2013 - “...STM4241 + + + + + + + + + + + + + hfq STM4361 + + + + + + + ND + + + ND ND igeR STM0410 + + + + + + + + + relA STM2956 + + + +...”
- Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
Harvey, Infection and immunity 2011 - “...0.02 0.04 0.05 0.03 0.05 0.013 0.0062 General function STM4361 STM1751 hfq hns Host factor I DNA-binding protein HLP-II 10.08 8.73 0.0005 0.0033 Cell motility...”
- Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
Crabbé, Applied and environmental microbiology 2011 - “...PA5128 STM3425 STM3436 STM3438 STM3439 STM3448 STM3345 STM4391 STM4361 STM3701 rplF rpsS rplW rplD rpsL rplM rpsF hfq secB Gene function Acyl carrier protein...”
- A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis
Chowdhury, Journal of proteome research 2009 - “...observed from its interacting partner PhoQ (STM1230). C Mass spectrum of one peptide from Hfq (STM4361). Figure 8 Global proteomics study used to demonstrate a functional role of PhoP (STM1231) with Hfq using AMT (accurate mass and time) tag analysis from 3 biological replicate samples. A)...”
- “...ribosomal subunit protein S10 (rpsJ) STM3983 1 3-hydroxyacyl-coA dehydrogenase (EC 1.1.1.35) of 4-enzyme FadB (fadB) STM4361 1 host factor I for bacteriophage Q beta (hfq) We gratefully acknowledge the contributions of Therese RW. Clauss, Brianne O. Petritis, Karl K. Weitz, Nicola Toli, Samuel O. Purvine, Penny...”
- Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium
Yoon, PLoS pathogens 2009 - “...family) [99] STM3501/2 envZ / ompR two-component regulatory system responding to osmolarity and pH [100] STM4361 hfq host factor I for bacteriophage Q beta replication, a growth-related protein [33] The 14 regulators identified were diverse and included alternative sigma factors ( rpoS and rpoE ), two-component...”
- Gene set analyses for interpreting microarray experiments on prokaryotic organisms
Tintle, BMC bioinformatics 2008 - “...procedure was performed on (A), wild type [WT] cells; (B), cells of an hfq - (STM4361) knockout mutant; and (C), cells of an smpB - (STM2688) knockout mutant. Eight total comparisons are considered in this paper: LBlog ( hfq vs . WT; smpB vs . WT),...”
- Hfq regulates the expression of the thermostable direct hemolysin gene in Vibrio parahaemolyticus
Nakano, BMC microbiology 2008 - “...); O157, E. coli serotype O157:H7 (accession no. NP_313175 ); St, S. typhi (accession no. NP_458797 ). Previous studies showed that defects in the hfq gene decreased the growth rates of E. coli and P. aeruginosa , but not of S. typhimurium and V. cholerae [...”
- Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis
Jayeola, Frontiers in microbiology 2020 - “...) 1.17 NC 1.42 NC 1.65 STM14_2873 ( lrhA ) 1.03 NC 1.25 1.29 1.28 STM14_5242 ( hfq ) 2.25 NC NC 1.36 2.42 Stringent response STM14_4991 ( rpoC ) 1.29 NC 1.32 NC NC STM14_4506 ( rpoZ ) NC 1.19 1.08 NC 1.72 STM14_3564 (...”
- Global Screening of Salmonella enterica Serovar Typhimurium Genes for Desiccation Survival
Mandal, Frontiers in microbiology 2017 - “...S 1 [2.64] {8} STM14_4907 ( yiiQ ) hypothetical protein STM14_4907 S 1 [0.77] {3} STM14_5242 ( hfq ) s RNA-binding protein Hfq T 1 [0.57] {6} STM14_0870 ( tolB ) s , o translocation protein TolB U 1 [3.35] {15} STM14_1703 ( ssaH ) s...”
SO_0603 host factor-I protein from Shewanella oneidensis MR-1
75% identity, 88% coverage
Hfq / b4172 RNA-binding protein Hfq from Escherichia coli K-12 substr. MG1655 (see 56 papers)
HFQ_ECOLI / P0A6X3 RNA-binding protein Hfq; HF-1; Host factor-I protein; HF-I from Escherichia coli (strain K12) (see 8 papers)
b4172 RNA-binding protein Hfq from Escherichia coli str. K-12 substr. MG1655
B7MSJ0 RNA-binding protein Hfq from Escherichia coli O81 (strain ED1a)
NP_313175 RNA-binding protein Hfq from Escherichia coli O157:H7 str. Sakai
NP_418593 RNA-binding protein Hfq from Escherichia coli str. K-12 substr. MG1655
NP_710037 RNA-binding protein Hfq from Shigella flexneri 2a str. 301
Z5779 host factor I for bacteriophage Q beta replication, a growth-related protein from Escherichia coli O157:H7 EDL933
NP_313175 host factor I for bacteriophage Q beta replication from Escherichia coli O157:H7 str. Sakai
SF5M90T_4236 RNA chaperone Hfq from Shigella flexneri 5a str. M90T
87% identity, 67% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32 (PubMed:17158661). Binds with high specificity to tRNAs (PubMed:18230766). Binds sRNA antitoxin RalA (PubMed:24748661). In vitro, stimulates synthesis of long tails by poly(A) polymerase I (PubMed:10677490). Required for RNA phage Qbeta replication (PubMed:805130). Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation (PubMed:19909729).
subunit: Homohexamer (PubMed:12853626). Interacts with H-NS (PubMed:11222598).
disruption phenotype: Deletion of hfq seems to lead to a significant translational fidelity problem. Deletion increases persister cell formation (PubMed:19909729). Deletion abolishes the antitoxin activity of sRNA antitoxin RalA, preventing it from neutralizing toxin RalR (PubMed:24748661). - 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 - “...Description gi|16128878 b0911 rpsA S1 61.1 299.83 125 30S r-protein S1; translation initiation factor. gi|16131994 b4172 hfq Hfq 11.2 296.6 362 RNA chaperone; host factor for phage Q replication. gi|49176156 b1831 proQ ProQ 25.9 238.23 128 RNA chaperone; regulator of ProP expression. gi|145698316 b3164 pnp PNPase...”
- Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
Kim, PLoS genetics 2012 - “...(KPN_04570), existed between conserved miaA and hflX in the genome. E. coli K-12 MG1655 hfq (b4172) and K. pneumoniae MGH78578 hfq (KPN_04570) had one TSS detected upstream of hfq and in the coding region of miaA , with the genomic position of 4,397,824 and 5,000,510, respectively...”
- Remaining flexible in old alliances: functional plasticity in constrained mutualisms
Wernegreen, DNA and cell biology 2009 - “...WGLp186 BU567 BUsg547 Bbp512 Regulator of FtsH protease hfq b4172 Bpen082 - WGLp184 - - - RNA-binding protein that affects many cellular processes hha b0460 - -...”
- Genome-wide expression profiling in Escherichia coli K-12
Richmond, Nucleic acids research 1999 - “...D-serine and glycine b4141 yjeH 9.8 5.1 Putative transport b4172 *hfq 9.3 4.5 Host factor I for bacteriophage Q replication b0492 ybbN 9.1 9.9 Putative...”
- Peptidylarginine Deiminase Inhibitors Reduce Bacterial Membrane Vesicle Release and Sensitize Bacteria to Antibiotic Treatment
Kosgodage, Frontiers in cellular and infection microbiology 2019 - “...0.05) a B7MQF2 Trigger factor tig 81193 192.72 B7NKH1 UPF0227 protein YcfP ycfP 11941 166.86 B7MSJ0 RNA-binding protein Hfq hfq 256917 132.47 Q1R638 50S ribosomal protein L17 rplQ 126430 128.85 Q1R602 50S ribosomal protein L3 rplC 69461 254.77 Q1R619 50S ribosomal protein L24 rplX 6484.4 75.48...”
- RNA-binding protein Hfq downregulates locus of enterocyte effacement-encoded regulators independent of small regulatory RNA in enterohemorrhagic Escherichia coli.
Sudo, Molecular microbiology 2022 (PubMed)- GeneRIF: RNA-binding protein Hfq downregulates locus of enterocyte effacement-encoded regulators independent of small regulatory RNA in enterohemorrhagic Escherichia coli.
- Lactobacillus casei suppresses hfq gene expression in Escherichia coli O157:H7.
Mahdavi, British journal of biomedical science 2019 (PubMed)- GeneRIF: The results showed that, hfq was down-regulated in E. coli O157:H7 by L. casei.
- Structure of an Escherichia coli Hfq:RNA complex at 0.97 Å resolution.
Schulz, Acta crystallographica. Section F, Structural biology communications 2014 - GeneRIF: The crystal structure of Escherichia coli Hfq was identified along with its binding site for Hfq-RNA interaction.
- The association between Hfq and RNase E in long-term nitrogen-starved Escherichia coli.
McQuail, Molecular microbiology 2022 (PubMed)- GeneRIF: The association between Hfq and RNase E in long-term nitrogen-starved Escherichia coli.
- Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq.
Kavita, Nucleic acids research 2022 - GeneRIF: Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq.
- Synthesis of the NarP response regulator of nitrate respiration in Escherichia coli is regulated at multiple levels by Hfq and small RNAs.
Brosse, Nucleic acids research 2022 - GeneRIF: Synthesis of the NarP response regulator of nitrate respiration in Escherichia coli is regulated at multiple levels by Hfq and small RNAs.
- Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein.
Wang, RNA (New York, N.Y.) 2021 - GeneRIF: Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein.
- RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment.
Basu, Nature communications 2021 - GeneRIF: RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment.
- Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites.
Orans, Nucleic acids research 2020 - GeneRIF: Structure studies of an Escherichia coli Hfq Core and DNA complex reveals multifunctional binding sites.
- Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer.
Azam, Molecular microbiology 2020 - GeneRIF: Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer.
- Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.
Iosub, eLife 2020 - GeneRIF: Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.
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- hfq regulates acid tolerance and virulence by responding to acid stress in Shigella flexneri.
Yang, Research in microbiology (PubMed)- GeneRIF: evidence that Hfq regulates genes related to acid resistance for survival under acid stress and controls virulence through positive regulation of Type III secretion systems; propose hfq is a key factor in adaptation to host acid stress during infection, regulating acid stress tolerance and virulence in response to acid stress in S. flexneri
- Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data
Appasamy, 2023 - ncRPI-LGAT: Prediction of ncRNA-protein interactions with line graph attention network framework.
Han, Computational and structural biotechnology journal 2023 - Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
Amemiya, Transcription 2021 (no snippet) - Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...Aae Aquifex aeolicus (O66512), Lin Leptospira interrogans (Q8F5Z7), Kve Koribacter versatilis (Q1IIF9), Eco Escherichia coli (P0A6X3), Tma Thermotoga maritima (Q9WYZ6), Tfu Thermobifida fusca (Q47P13), Sco Streptomyces coelicolor (Q9RJ64, Q9RJ65), Mtb Mycobacterium tuberculosis (P9WIM1, P9WIL9), Msm Mycobacterium smegmatis (I7G3U5, A0QZ41), Krh Kocuria rhizophila (B2GIN6), Cgl Corynebacterium glutamicum...”
- An attenuated Shigella mutant lacking the RNA-binding protein Hfq provides cross-protection against Shigella strains of broad serotype
Mitobe, PLoS neglected tropical diseases 2017 - “..., 13 ]. 10.1371/journal.pntd.0005728.t001 Table 1 List of accession numbers. UniProtKB-ID GenBank Accession number Hfq P0A6X3 (HFQ_ECOLI) BAA00644.1 D00743.1 RpoE P0AGB6 (RPOE_ECOLI) AAC75626.1 U37089.1 RpoS P13445 (RPOS_ECOLI) AAC75783.1 D13548.1 IpaB P18011 (IPAB_SHIFL) AAA26522.1 J04117.1 IpaC P18012 (IPAB_SHIFL) AAA26523.1 J04117.1 IpaD P18013 (IPAB_SHIFL) AAA26524.1 J04117.1 IpaA P18010...”
- A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12
Strader, Journal of proteome research 2013 - “...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 Protein translocase subunit secA P0A6Z3 HtpG 4 11...”
- “...Elongation factor P 5 17 26 ** P21499 RNaseR 22 67 41.2 31 145 50.5 P0A6X3 Hfq-1 7 25 54 5 20 44 P0A805 Ribosome Recycling Factor 6 21 47 5 12 35.7 P0A8A8 Ribosome maturation factor rimP 6 40 33 6 80 35.3 ** Protein...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...Salmonella typhimurium (P0A1R0); ECOLI Escherichia coli (P0A6X3); YERPE, Yersinia pestis (A4TRN9); HAEIN, Hemophilus influenza, (P44437); LEGPA Legionella...”
- A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12
Strader, Molecular & cellular proteomics : MCP 2011 - “...P76116 P33355 P0AF93 P0CE47 P0A6P1 P0A6M8 P0A6N4 P0A6N8 P0A6X3 P21499 P0A805 P0A8A8 a Interacting proteins RimO ycaO yncE yehs yjgf Elongation factor Elongation...”
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- Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
Pieper, PloS one 2011 - “...>280 E APEX AV 280-80 APEX AV 80-10 Functional roles F C1 RNA-binding protein Hfq Z5779 hfq 11166 CY, Ho-6 1.95E-02 25095 9957 2079 mRNA degradosome component C1 putative acetoin dehydrogenase UcpA Z3691 ucpA 27831 CY 2.73E-03 4843 5038 1953 (oxidoreductive) sulfate metabolism C1 short chain...”
- Hfq regulates the expression of the thermostable direct hemolysin gene in Vibrio parahaemolyticus
Nakano, BMC microbiology 2008 - “...); Vc, V. cholerae (accession no. NP_230001 ); Ec, E. coli serotype O157:H7 (accession no. NP_313175 ). Arrows indicate the direction of transcription. The numbers of amino acids (aa) that comprise the proteins are indicated. (B) Sequence alignment of Hfq from various pathogens. Dashes indicate amino...”
- “...); Pa, P. aeruginosa (accession no. NP_233631 ); O157, E. coli serotype O157:H7 (accession no. NP_313175 ); St, S. typhi (accession no. NP_458797 ). Previous studies showed that defects in the hfq gene decreased the growth rates of E. coli and P. aeruginosa , but not...”
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...protein 1.69 -1.24 SF5M90T_2275 yfbB putative enzyme 1.62 -1.90 -1.85 SF5M90T_3225 yrdA putative transferase 1.51 SF5M90T_4236 hfq RNA-binding protein 1.45 -2.10 SF5M90T_3315 gph phosphoglycolate phosphatase 1.25 SF5M90T_2192 yeiR putative GTPases 1.03 SF5M90T_1919 yedE putative transport system permease protein 1.03 -1.83 -1.96 SF5M90T_3295 yhfC putative transport 0.97...”
CsakCS931_RS18715, WP_004385293 RNA chaperone Hfq from Cronobacter sakazakii
87% identity, 67% coverage
- Microbiological survey and genomic analysis of Cronobacter sakazakii strains isolated from US households and retail foods
Samadpour, Applied and environmental microbiology 2024 - “...( Cpa ), CsakCS931_RS08525 ( EfeO ), CsakCS931_RS09290 ( Fha ), CsakCS931_RS17840 ( FkpA ), CsakCS931_RS18715 ( Hfq ), CsakCS931_RS18895 ( HlyIII ), AFK66_RS20815 ( IbeB ), CsakCS931_RS21050 ( IucA ), CsakCS931_RS14245 ( NanR ), CsakCS931_RS15355 ( SodA ), and CsakCS931_RS03030 ( WcaD ). In all...”
- Hfq plays important roles in virulence and stress adaptation in Cronobacter sakazakii ATCC 29544.
Kim, Infection and immunity 2015 - GeneRIF: Together, these data strongly suggest that hfq plays important roles in the virulence of Cronobacter sakazakii by participating in the regulation of multiple genes.
KPN_04570 RNA-binding protein Hfq from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
70% identity, 84% coverage
XF0089 host factor-I protein from Xylella fastidiosa 9a5c
XF_RS00365 RNA chaperone Hfq from Xylella fastidiosa 32
86% identity, 76% coverage
VF_2323, WP_011262725 RNA chaperone Hfq from Aliivibrio fischeri ES114
VF_2323 RNA-binding protein Hfq from Vibrio fischeri ES114
75% identity, 91% coverage
WP_011036893 RNA chaperone Hfq from Xanthomonas campestris JX
84% identity, 76% coverage
VAS14_18834 RNA chaperone Hfq from Photobacterium angustum S14
VAS14_18834 RNA-binding protein Hfq from Vibrio angustum S14
73% identity, 94% coverage
- Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14
Matallana-Surget, PloS one 2012 - “...initiation factor IF-2 1.45 1.38 17 1.27 1.31 15 1.35 1.56 26 1.23 1.46 13 VAS14_18834 RNA-binding protein Hfq 1.46 1.69 2 3.08 0.00 1 1.54 0.00 1 3.45 0.00 1 VAS14_00891 putative glutaredoxin 1 1.47 1.04 2 1.32 1.08 2 0.94 0.00 1 1.41 1.31...”
- “...double-stranded DNA and RNA and function as transcriptional activators [43] . The RNA chaperone Hfq (VAS14_18834, Table 1 ) presented a higher abundance under UVB treatment. This protein is known to bind small regulatory non-coding RNA (sRNAs) and facilitate post-transcriptional gene regulation by helping these sRNA...”
WP_005915027 RNA chaperone Hfq from Xanthomonas euroxanthea
XCV1768 Host factor-I protein from Xanthomonas campestris pv. vesicatoria str. 85-10
84% identity, 76% coverage
GM298_16695 RNA chaperone Hfq from Enterobacter sp. HSTU-ASh6
69% identity, 83% coverage
NT01EI_RS01835 RNA chaperone Hfq from Edwardsiella ictaluri 93-146
87% identity, 67% coverage
- The RNA chaperone Hfq has a multifaceted role in Edwardsiella ictaluri
Akgul, Frontiers in cellular and infection microbiology 2024 - “...from CLC Bio. 2.3 In-frame deletion of the hfq gene The nucleotide sequence otpf hfq (NT01EI_RS01835) was retrieved from the E. ictaluri strain 93-146 genome (GenBank accession: CP001600) ( Williams etal., 2012 ), and the process of hfq mutant construction was illustrated in Figure1 . For...”
LMH90_010755 RNA chaperone Hfq from Enterobacter hormaechei
87% identity, 66% coverage
APL_1961 RNA-binding protein Hfq from Actinobacillus pleuropneumoniae L20
WP_005599741 RNA chaperone Hfq from Actinobacillus pleuropneumoniae serovar 1 str. 4074
87% identity, 74% coverage
PANA_RS17940 RNA chaperone Hfq from Pantoea ananatis LMG 20103
87% identity, 65% coverage
Smlt1736 putative phage-related protein (host factor-I protein) from Stenotrophomonas maltophilia K279a
WP_004152891 RNA chaperone Hfq from Stenotrophomonas maltophilia K279a
84% identity, 77% coverage
K3G22_16320 RNA chaperone Hfq from Shewanella putrefaciens
75% identity, 88% coverage
NP_760222 RNA-binding protein Hfq from Vibrio vulnificus CMCP6
75% identity, 97% coverage
PD0066 host factor-I protein from Xylella fastidiosa Temecula1
84% identity, 76% coverage
JHW33_RS18790, WP_013573763 RNA chaperone Hfq from Rahnella aceris
87% identity, 67% coverage
HFQ_VIBCH / Q9KV11 RNA-binding protein Hfq from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see paper)
NP_230001, VC0347 host factor-I, putative from Vibrio cholerae O1 biovar eltor str. N16961
85% identity, 78% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs (By similarity). Essential for virulence in the suckling mouse model of cholera pathogenesis.
disruption phenotype: A hfq deletion mutant cannot colonize the murine small intestine despite retaining the ability to produce the colonization factor TCP. Deletion of hfq does not impair production of the sigma factor RpoS. Expression and activity of the sigma factor sigma-E are dramatically increased in the hfq mutant. - Switching fatty acid metabolism by an RNA-controlled feed forward loop
Huber, Proceedings of the National Academy of Sciences of the United States of America 2020 - “...we added the 3XFLAG epitope to the C terminus of the chromosomal hfq locus ( vc0347 ) and tested protein production at various stages of growth. Hfq was produced under all tested conditions ( SI Appendix , Fig. S1 A ), allowing us to employ a...”
- Vibrio cholerae Combines Individual and Collective Sensing to Trigger Biofilm Dispersal
Singh, Current biology : CB 2017 - “...for each condition. Relative mRNA levels were measured using the CT method with hfq (gene VC0347) as an internal control [ 47 ]. WT V.cholerae (strain KDV428) was used as a control reference. We determined that the HapR-10aa-sfGFP fusion did not significantly change the transcriptional profile...”
- A Genome-Wide Screen Reveals that the Vibrio cholerae Phosphoenolpyruvate Phosphotransferase System Modulates Virulence Gene Expression
Wang, Infection and immunity 2015 - “...VC0826 tcpP 1.0 1010 VC0827 tcpH 1.0 1010 VC0984 VC1021 VC0347 VC2529 toxR luxO hfq rpoN 0.00006 1.0 1010 0.00073 1.0 1010 VC0034 tcpG, dsbA 0.00025 VC0965 ptsI...”
- Mining regulatory 5'UTRs from cDNA deep sequencing datasets
Livny, Nucleic acids research 2010 - “...protein Regulation of transcription, DNA-dependent 57 VC1901 Sodium/proton antiporter Sodium ion transport, hydrogen transport 58 VC0347 RNA-binding protein Hfq Targeting of mRNA for destruction, involved in RNA interference 59 VC0038 Hypothetical protein 60 VC0381 Hypothetical protein 61 VC1576 Hypothetical protein 62 VC1613 Hypothetical protein 63 VC1891...”
- Hfq regulates the expression of the thermostable direct hemolysin gene in Vibrio parahaemolyticus
Nakano, BMC microbiology 2008 - “...regions. Vp, V. parahaemolyticus strain RIMD2210633 (accession no. BA000032 ); Vc, V. cholerae (accession no. NP_230001 ); Ec, E. coli serotype O157:H7 (accession no. NP_313175 ). Arrows indicate the direction of transcription. The numbers of amino acids (aa) that comprise the proteins are indicated. (B) Sequence...”
- “...GenBank. Vp, V. parahaemolyticus strain RIMD2210633 (accession no. BA000032 ); Vc, V. cholerae (accession no. NP_230001 ); Vv, V. vulnificus (accession no. NP_760222 ); Pa, P. aeruginosa (accession no. NP_233631 ); O157, E. coli serotype O157:H7 (accession no. NP_313175 ); St, S. typhi (accession no. NP_458797...”
- Positive regulation of fur gene expression via direct interaction of fur in a pathogenic bacterium, Vibrio vulnificus
Lee, Journal of bacteriology 2007 - “...acid sequence of the Hfq protein from V. cholerae (NP_230001) revealed an ORF composed of 86 amino acid residues, which shows 94% and 87% amino acid identities...”
WP_012886271 RNA chaperone Hfq from Dickeya parazeae
87% identity, 69% coverage
SGGMMB4_00878 RNA chaperone Hfq from Sodalis glossinidius str. 'morsitans'
87% identity, 67% coverage
HFQ_PECCC / Q9ZI76 RNA-binding protein Hfq; Bacteriocin gene regulator from Pectobacterium carotovorum subsp. carotovorum (Erwinia carotovora subsp. carotovora) (see paper)
75% identity, 80% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs (By similarity). Involved in the regulation of the bacteriocin carotovoricin.
subunit: Homohexamer.
YPK_3799 RNA chaperone Hfq from Yersinia pseudotuberculosis YPIII
80% identity, 75% coverage
- Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud, mSystems 2020 - “...24,38,32,54,28 YPK_3718 YPK_3717 47, 49, 50, 107 IrGS41 4186557 5.2 3.9 3.1 AAGGGGCAATCTTTGCAA 8.94 38,54,24 YPK_3799 YPK_3798 134, 194 IrGS42 4216234 11.9 9.6 7.5 TTGGTATAGGTTTTGCAG + 10.1 32,54 YPK_3826 YPK_3827, YPK_3828 167 IrGS43 4341322 3.8 NA NA ATGGCACAGTTACTGCAG + 7.68 NA YPK_3934 NA NA IrGS44 4441905...”
- “...YPK_3743 E NA 15, 22, 123 IrGAs22 4186557 5.2 3.9 3.1 CAGGAACGGATCTTGCAA + 9.38 NA YPK_3799 NA IrGAs23 4288435 11.2 13.7 10.2 CTGGCTCAATTAATGCAT 10.3 24,28,54 YPK_3887 NA 102, 178 IrGAs24 4309656 5.1 5.0 3.4 CTGGTGTAAATATTGCAC + 9.89 NA YPK_3909 NA IrGAs25 4371420 11.5 7.9 5.2 GCGGCGCATTTTTTGCAT...”
HI0411 host factor-I protein (hfq) from Haemophilus influenzae Rd KW20
85% identity, 75% coverage
VP2817 putative host factor-I from Vibrio parahaemolyticus RIMD 2210633
M892_12140 RNA chaperone Hfq from Vibrio campbellii ATCC BAA-1116
85% identity, 78% coverage
- Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival
Wagley, PLoS pathogens 2021 - “...VP1267 involved in cell wall membrane, VP0622, VP0589 (YajC) involved in intracellular trafficking and secretion, VP2817 (HfQ) assigned to translation category, VPA1499 (LldD), VP1161 and VP1053 involved in energy production and conversion, VP0240 involved in carbohydrate metabolism and VP0171 and VP0174 involved in inorganic ion transport...”
- The Vibrio parahaemolyticus small RNA RyhB promotes production of the siderophore vibrioferrin by stabilizing the polycistronic mRNA
Tanabe, Journal of bacteriology 2013 - “...on the sequence of the flanking region of hfq (VP2817), and E. coli DH5 was used as a host for the cloning of pET-21b()-hfq. E. coli...”
- “...mRNA. On the other hand, V. parahaemolyticus Hfq (VP2817) has been reported to negatively regulate the production of thermostable direct hemolysin (69) and to...”
- Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
Hazen, Applied and environmental microbiology 2009 - “...0 0 0 0 VP3074 VP2780 VP0098 Predicted protein VP2817 VP2331 VP2582 VP0160 VP1210 VP0261 VP1294 VP1283 VP0268 VPA1222 VP2986 VP2923 VP2766 VP2178 VP0262 VP0280...”
- “...50S ribosomal protein L17 VP0275 VP2529 VP0265 VP2335 VP2817 VP2331 VP0160 VP1210 VP0261 VPA0321 VPA0286 VP2627 VP2619 VP2029 VPA0577 VP2530 VP0646 VP0448...”
- Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
Wang, Frontiers in microbiology 2013 - “...auxiliary component 1.17E-06 1.86 0.49 3.80 Q M892_01320 Immunogenic protein 1.77E-05 1.63 0.41 3.98 R M892_12140 RNA-binding protein Hfq 1.46E-06 2.94 1.96 1.50 R M892_18180 Ecotin precursor 6.37E-05 1.51 0.99 1.53 R M892_26640 Hemolysin 6.13E-08 1.93 0.54 3.57 R M892_05800 Lipoprotein-related protein 6.13E-08 1.20 0.24 5.00...”
Q56928 RNA-binding protein Hfq from Yersinia enterocolitica
85% identity, 67% coverage
PmVP161_0914, WP_005716974 RNA chaperone Hfq from Pasteurella multocida
85% identity, 71% coverage
DYL72_09115 RNA chaperone Hfq from Vibrio anguillarum
84% identity, 77% coverage
A4TRN9 RNA-binding protein Hfq from Yersinia pestis (strain Pestoides F)
84% identity, 67% coverage
WP_001983665 RNA chaperone Hfq from Acinetobacter baumannii
84% identity, 40% coverage
ACICU_02310 uncharacterized host factor I protein from Acinetobacter baumannii ACICU
KZA74_07030, WM39_12950 RNA chaperone Hfq from Acinetobacter baumannii
84% identity, 41% coverage
Q6F9W2 RNA-binding protein Hfq from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
84% identity, 40% coverage
4v2sA / P0A6X3 Crystal structure of hfq in complex with the srna rydc (see paper)
88% identity, 76% coverage
BB3170 putative RNA-binding regulatory protein from Bordetella bronchiseptica RB50
BP2193 putative RNA-binding regulatory protein from Bordetella pertussis Tohama I
76% identity, 88% coverage
AK34_1317 RNA chaperone Hfq from Burkholderia dolosa AU0158
BCAL1879 Hfq protein from Burkholderia cenocepacia J2315
74% identity, 94% coverage
- An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity
Schaefers, PLoS pathogens 2017 - “...protein W precursor 11.4 AK34_3656 Peptidoglycan hydrolase VirB1 11.6 AK34_2361 Probable transmembrane protein 3.1 hfq (AK34_1317) RNA-binding protein 2.8 AK34_4984 FOG: GGDEF domain 2.4 AK34_1354 Dioxygenases related to 2-nitropropane dioxygenase 5.8 AK34_3566 Enoyl-CoA hydratase 13.6 AK34_3563 Acetyl-CoA synthetase 13.9 AK34_3562 Butyryl-CoA dehydrogenase 15.8 AK34_3722 4-carboxymuconolactone decarboxylase...”
- Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection
Pita, Applied microbiology and biotechnology 2023 - “...upregulated (Supplemental Table S6 ). Curiously, the genes that code for the Hfq chaperone ( BCAL1879 ) and the acyl carrier protein AcpP ( BCAL0995 and BCAL2875 ), previously described by our research group as essential for Bcc full virulence in C. elegans (Sousa et al....”
- Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence
Ferreira, Applied and environmental microbiology 2013 - “...2.1 1.7 1.6 1.6 1.5 1.6 Transcription BCAL0562 BCAL0787 BCAL1879 BCAL1538 BCAL3055 BCAL3151 BCAL3178 BCAM0742 1.2 1.3 1.3 1.3 1.3 1.5 1.4 1.6 1.6 1.8 1.7 1.8...”
- The second RNA chaperone, Hfq2, is also required for survival under stress and full virulence of Burkholderia cenocepacia J2315
Ramos, Journal of bacteriology 2011 - “...performed a functional analysis of the 79-amino-acid protein Hfq (BCAL1879 in the genome sequence of B. cenocepacia J2315, Fig. 1A) from the clinical isolate B....”
bglu_1g14550 Small nuclear ribonucleoprotein (Sm protein) from Burkholderia glumae BGR1
83% identity, 80% coverage
- The Roles of Two hfq Genes in the Virulence and Stress Resistance of Burkholderia glumae
Kim, The plant pathology journal 2018 - “...The two copies of hfq genes present in B. glumae were located in chromosome 1, bglu_1g14550 ( hfq 1 gene) and bglu_1g19700 ( hfq 2 gene); the length of hfq 1 gene was 255 nt, compared with the 555 nt sequence length of the hfq 2...”
- “...hfq genes and a double defective mutant were generated. The defective hfq 1 gene ( bglu_1g14550 ) was verified by PCR, targeting the upstream sequence of the target gene, and an inner sequence of the pVIK112 vector. As a result, a clear band was observed in...”
LV28_24345 RNA chaperone Hfq from Pandoraea pnomenusa
83% identity, 80% coverage
- Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536(T) Isolated from a Cystic Fibrosis Patient
Lim, Frontiers in microbiology 2016 - “...argininosuccinate synthase (LV28_16050), endonuclease III (LV28_23310), 3-isopropylmalate dehydrogenase (LV28_23930), 3-isopropylmalate dehydrogenase (LV28_23930), RNA-binding protein Hfq (LV28_24345), chorismate synthase (LV28_04475), acetolactate synthase large and small subunit (LV28_04625 and LV28_04620), and chemotaxis protein CheY (LV28_14025). These identified virulence factors are well-characterized virulence determinants in the Burkholderia pseudomallei (close...”
Hsero_2948 RNA chaperone Hfq from Herbaspirillum seropedicae SmR1
75% identity, 88% coverage
Q8Y025 RNA-binding protein Hfq from Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)
75% identity, 87% coverage
lpg0009 host factor-I protein for bacteriophage Q beta replication from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Q5X982 RNA-binding protein Hfq from Legionella pneumophila (strain Paris)
lpp0009 hypothetical protein from Legionella pneumophila str. Paris
74% identity, 84% coverage
- The Hfq homolog in Legionella pneumophila demonstrates regulation by LetA and RpoS and interacts with the global regulator CsrA
McNealy, Journal of bacteriology 2005 - “...Hfq lies in open reading frame (ORF) lpg0009 of the Legionella Genome Project (http: //legionella.cu-genome.org/; last accessed November 2004). The Legionella...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...influenza, (P44437); LEGPA Legionella pneumophila (Q5X982). -Proteobacteria: NEIME, Neisseiriameningitides (B9VV05); RALSO, Ralstonia solanacearum (Q8Y025)....”
- A Unique cis-Encoded Small Noncoding RNA Is Regulating Legionella pneumophila Hfq Expression in a Life Cycle-Dependent Manner
Oliva, mBio 2017 - “...other bacterial species. In L.pneumophila , Hfq is an 85-amino-acid protein encoded by the gene lpp0009 . The hfq gene is organized in an operon with the putative GTP-binding protein HflX encoded by gene lpp0010 ( Fig.1A ). Although the L.pneumophila hfq gene shares the conserved...”
- “...three-step PCR. For the construction of the hfq deletion mutant strain, three overlapping fragments ( lpp0009 upstream region primers hfq -Mut_F and hfq- apra_R, antibiotic cassette-primers apra_F and apra_R, lpp0009 downstream region primers hfq- apra_F and hfq -Mut_R; Table2 ) were amplified independently and purified on...”
- The Flagellar Regulon of Legionella-A Review
Appelt, Frontiers in cellular and infection microbiology 2017 - “...0.262 lpp2635, flhB Similar to FlhB protein 0.295 lpp0010 Similar to GTP-binding protein HflX 0.296 lpp0009 Similar to host factor-1 protein 0.366 plpp0131 Similar to alanyl tRNA synthetase 0.370 lpp1742, prfB Highly similar to peptide chain release factor 2 0.371 lpp2386 Unknown 0.374 lpp1234, flgL Flagellar...”
- Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
Sahr, Molecular microbiology 2009 - “...factor) 0.58 - lpp2546 SdbB 0.58 0.38 lpp1231 FlgI 0.60 2.47 lpp1226 FlgD 0.61 3.66 lpp0009 Similar to host factor-1 protein Hfq 0.65 1.67 lpp2692 EnhC 0.68 - Table 3 Flagella gene expression of letA and rsmYZ mutants as compared to wild type L. pneumophila strain...”
FTT_0630 host factor I for bacteriophage Q beta replication from Francisella tularensis subsp. tularensis SCHU S4
73% identity, 64% coverage
- Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors
Spidlova, Microorganisms 2020 - “...41 ] FTT_0627 FTL_0895 FTN_1054 hupB global regulator, DNA non-specific binding protein [ 42 ] FTT_0630 FTL_0898 FTN_1051 hfq RNA-binding protein, necessary for stress response, negative regulator of pdp operon [ 43 , 44 , 45 ] FTT_0748 FTL_1364 FTN_0720 iclR important only for F. novicida...”
- Whole genome transcriptomics reveals global effects including up-regulation of Francisella pathogenicity island gene expression during active stringent response in the highly virulent Francisella tularensis subsp. tularensis SCHU S4
Murch, Microbiology (Reading, England) 2017 - “...highest and statistically significant expression levels observed in the dataset ( Fig. 10b ). Hfq (FTT_0630), Q5NH41, which binds RNAs facilitated by the stringent response protein RelA showed a 1.2-fold increase in expression, although this was not statistically significant ( Fig. 10c ). Stress response proteins...”
- The francisella tularensis proteome and its recognition by antibodies
Kilmury, Frontiers in microbiology 2010 - “...2D-Western blot Unknown Havlasova et al. ( 2002 ), Janovska et al. ( 2007a ) FTT_0630 Host factor I for bacteriophage Q beta replication hfq Mouse 2D-Western blot/proteome microarray Cytoplasmic Havlasova et al. ( 2005 ), Eyles et al. ( 2007 ) FTT_0682 Hypothetical protein Human,...”
FTA_RS04620 RNA chaperone Hfq from Francisella tularensis subsp. holarctica FTNF002-00
FTL_0898 host factor I for bacteriophage Q beta replication from Francisella tularensis subsp. holarctica
FTN_1051 host factor I for bacteriophage Q beta replication from Francisella tularensis subsp. novicida U112
73% identity, 64% coverage
- Functional characterization of Francisella tularensis subspecies holarctica genotypes during tick cell and macrophage infections using a proteogenomic approach
Schütz, Frontiers in cellular and infection microbiology 2024 - “...FTA_RS04605 hupB WP_003015647.1 global regulator, DNA non-specific binding protein 1.73 7.68E-39 -4.48 1.57E-251 -2.76 8.90E-265 FTA_RS04620 hfq WP_003015654.1 RNA-binding protein, necessary for stress response, negative regulator ofpdpoperon 2.35 4.97E-21 -4.71 1.36E-80 -2.36 0.00E+00 FTA_RS06925 iclR WP_003016591.1 important only forF. novicidavirulence in vivo 1.99 5.00E-20 -2.87 2.61E-40...”
- Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors
Spidlova, Microorganisms 2020 - “...] FTT_0627 FTL_0895 FTN_1054 hupB global regulator, DNA non-specific binding protein [ 42 ] FTT_0630 FTL_0898 FTN_1051 hfq RNA-binding protein, necessary for stress response, negative regulator of pdp operon [ 43 , 44 , 45 ] FTT_0748 FTL_1364 FTN_0720 iclR important only for F. novicida virulence...”
- Hfq, a novel pleiotropic regulator of virulence-associated genes in Francisella tularensis
Meibom, Infection and immunity 2009 - “...FTL_0195 FTL_0221 FTL_0317 FTL_0392 FTL_0421 FTL_0568 FTL_0570 FTL_0898 FTL_0899 FTL_1016 FTL_1394 Gene product F. TULARENSIS Hfq PROTEIN VOL. 77, 2009 1871...”
- “...program), but the change is less than twofold. coded by FTL_0898) was identified by in silico analysis of the LVS genome. It consists of 109 amino acids and is...”
- Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors
Spidlova, Microorganisms 2020 - “...FTT_0627 FTL_0895 FTN_1054 hupB global regulator, DNA non-specific binding protein [ 42 ] FTT_0630 FTL_0898 FTN_1051 hfq RNA-binding protein, necessary for stress response, negative regulator of pdp operon [ 43 , 44 , 45 ] FTT_0748 FTL_1364 FTN_0720 iclR important only for F. novicida virulence in...”
- “...29 ] FTT_1360c (FTN_1325) pdpD FPI, Pathogenicity determinant protein D [ 28 , 29 ] FTN_1051 hfq Host factor for bacteriophage Q RNA replication [ 29 ] FTN_0549 sspA Stringent starvation protein A [ 29 ] FTN_1054 hupB DNA-binding protein HU-beta [ 29 ]...”
- The RNA chaperone Hfq is important for growth and stress tolerance in Francisella novicida
Chambers, PloS one 2011 - “...an ermC ORF flanked by 1,170 bp upstream and 1,128 bp downstream of the hfq (FTN_1051) ORF was constructed via fusion of three separate PCR products [28] . Primers for the cassette contained overlapping sequences and are listed in Table 2 . The following PCR reaction...”
- “...unknown if the F. novicida homolog possessed the same characteristics. The F. novicida hfq gene (FTN_1051) is located on the negative strand at bps 11102711110600 of the genome. The gene encodes a 109 amino acid protein and is 99.39% identical to its F. tularensis LVS homolog...”
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...OstA 4 # tnfn1_pw060323p06q105 FTN_0810 ROK family protein 4 tnfn1_pw060419p01q139 FTN_0836 kinase-like protein 2 tnfn1_pw060418p04q134 FTN_1051 hfq host factor I for bacteriophage Q beta replication 2 tnfn1_pw060420p03q121 FTN_1064 PhoH family protein, putative ATPase 4 tnfn1_pw060328p05q177 FTN_1192 chitin-binding protein 6 tnfn1_pw060419p04q183 FTN_1240 BolA family protein 4 tnfn1_pw060418p02q190...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...OstA 4 # tnfn1_pw060323p06q105 FTN_0810 ROK family protein 4 tnfn1_pw060419p01q139 FTN_0836 kinase-like protein 2 tnfn1_pw060418p04q134 FTN_1051 hfq host factor I for bacteriophage Q beta replication 2 tnfn1_pw060420p03q121 FTN_1064 PhoH family protein, putative ATPase 4 tnfn1_pw060328p05q177 FTN_1192 chitin-binding protein 6 tnfn1_pw060419p04q183 FTN_1240 BolA family protein 4 tnfn1_pw060418p02q190...”
- MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress
Guina, Journal of bacteriology 2007 - “...Glutaredoxin 1 Peroxidase/catalase Gene regulation induced FTN_0488 FTN_0549 FTN_0085 FTN_1051 FTN_1465 FTN_0289 -- -- -- -- 1.9 -- 3.4 10.0 4.7 2.8 8.1 3.6 2.2...”
OFAG_00111 RNA chaperone Hfq from Oxalobacter paraformigenes
68% identity, 87% coverage
OFBG_00195 RNA chaperone Hfq from Oxalobacter formigenes OXCC13
68% identity, 87% coverage
NGO0326 Hfq from Neisseria gonorrhoeae FA 1090
79% identity, 71% coverage
- Epitope determination of immunogenic proteins of Neisseria gonorrhoeae
Connor, PloS one 2017 - “...are split evenly between Fig 1 and Fig 2 . The former covers epitopes of NGO0326, NGO0564, NGO0592, NGO0777, NGO1429, and NGO1577, while the latter summarizes epitope mappings of NGO1656, NGO1852, NGO2094, NGO2095 polypeptides 1 and 2, NGO2095 polypeptide 4 as well as NGO0170, which was...”
- “...meningitidis antibody. 10.1371/journal.pone.0180962.g001 Fig 1 Epitope mapping (n = 9) of the polypeptides of A) NGO0326, B) NGO0564, C) NGO0592, D) NGO0777, E) NGO1429, F) NGO1577. The boxes embody 50% of the values, while the whiskers comprise 98% of the data. Outliers are marked with a...”
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...and full-length proteins. A 1.5% agarose gel: M Hyperladder I (bioline, Bio-33025-26), 1 NGO0170, 2 NGO0326, 3 NGO0451, 4 NGO0564 (+ control), 5 NGO0642, 6 NGO0777, 7 NGO0916, 8 NGO1043, 9 NGO1500 (- control), 10 NGO1634, 11 NGO1656, 12 NGO1657, 13 NGO1796, 14 NGO1852. B SDS-PAGE...”
- “...each of produced proteins: M Spectra Multicolor Low Range Protein Ladder (Thermo Scientific, 26628), 1 NGO0326, 2 NGO0777, 3 NGO1043, 4 NGO 1657, 5 NGO1852. C SDS-PAGE (10%) of 0.5 g each of produced proteins: M PageRuler Plus Prestained Protein Ladder (Thermo Scientific, 26619), 1 NGO0170,...”
- Transcript analysis of nrrF, a Fur repressed sRNA of Neisseria gonorrhoeae
Ducey, Microbial pathogenesis 2009 - “...oxidative stress and intermediary 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...”
NMB0748 host factor-I from Neisseria meningitidis MC58
NMV_1646 RNA chaperone Hfq from Neisseria meningitidis 8013
79% identity, 71% coverage
- The Hfq regulon of Neisseria meningitidis
Huis, FEBS open bio 2017 - “...permease Membrane components 2.2 3.5 NMB0607 secD Protein translocase subunit Protein transport/translocation 4.0 2.0 2.6 NMB0748 hfq Host factorI protein RNA chaperone 289.3 g 16.0 g NMB0763 cysK Cysteine synthase Amino acid metabolism 2.4 2.7 NMB0881 cysT f Sulfate transport system permease Membrane components 7.3 2.2...”
- Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display
Connor, PloS one 2016 - “...1 121 28.12 NMB0588 Cytoplasmic membrane No - NGO0326* RNA-binding protein Hfq 1 109 10.78 NMB0748 Cytoplasm No - NGO0451* replicative DNA helicase 1 76 52.18 NMB0885 Cytoplasm No - NGO0564* dihydrolipoamide acetyltransferase 1 310 54.69 NMB1342 Cytoplasm Yes [ 46 ] NGO0584 50S ribosomal protein...”
- Transcriptional profiling of Neisseria meningitidis interacting with human epithelial cells in a long-term in vitro colonization model
Hey, Infection and immunity 2013 - “...genes, three were identified as transcriptional regulators, hfq (NMB0748), phoP (also termed misR) (NMB0595), and lrp (NMB1650), all upregulated at later time...”
- Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival
Echenique-Rivera, PLoS pathogens 2011 - “...the different time points. For a more detailed analysis, see Table S1 . Hfq ( NMB0748 ), a RNA chaperone and key modulator of riboregulation in bacteria, was also up-regulated during incubation in blood. The up-regulation of Hfq in blood suggests that non-coding RNAs might also...”
- Role of Hfq in iron-dependent and -independent gene regulation in Neisseria meningitidis
Mellin, Microbiology (Reading, England) 2010 - “...Putative transport protein 1.98 2.70 1.55 1.63 Unclassified: NMB0024 pilS cassette 2.83 2.85 1.34 1.00 NMB0748 hfq Host factor for Q phage 289.26 837.89 1.10 1.63 NMB0763 cysK Cysteine synthase 2.72 2.65 1.66 1.15 NMB0993 Rubredoxin ETC protein 9.13 5.25 2.46 2.10 NMB1617 TehB Methyltransferase 2.98...”
- Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis
Pannekoek, FEMS microbiology letters 2009 - “...natural transformation of strain H44/76 with pHfq10 and selection for erythromycin resistance. Replacement of hfq (NMB0748) by the erythromycin cassette was confirmed by PCR with combinations of primers JP19-20, JP22, ABHfq1 and ABHfq4. Oligonucleotides are listed in Table 1 . Table 1 Oligonucleotides used in this...”
- The RNA chaperone Hfq is involved in stress response and virulence in Neisseria meningitidis and is a pleiotropic regulator of protein expression
Fantappiè, Infection and immunity 2009 - “...locus of N. meningitidis. In N. meingitidis, the hfq gene (NMB0748) is predicted to encode a protein that is similar to host factor I protein or Hfq. The...”
- The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
Heidrich, Nucleic acids research 2017 - “...Poorly characterized NMV_0522 395 3.0 COG0457 R Poorly characterized NMV_1106 ( nrdA ) 377 1.9 NMV_1646 ( hfq ) 345 3.2 NMV_0309 343 2.0 COG1611 R Poorly characterized NMV_1440 ( sucA ) 309 3.0 NMV_1803 ( rpsO ) 305 1.4 NMV_1593 246 3.6 COG1469 S Poorly...”
Pnuc_1286 RNA chaperone Hfq from Polynucleobacter sp. QLW-P1DMWA-1
79% identity, 78% coverage
CC1745 host factor-I protein from Caulobacter crescentus CB15
CCNA_01819 RNA-binding protein, Hfq family from Caulobacter crescentus NA1000
YP_002517192 RNA-binding protein, Hfq family from Caulobacter vibrioides NA1000
56% identity, 84% coverage
- Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus
da, BMC microbiology 2016 - “...function. Interestingly, among these genes, seven were predicted to be essential (CC0653, CC0035, CC0260, CC1247, CC1745, CC2912 were downregulated and CC3655 was upregulated) [ 34 ]. Table 1 Genes differentially expressed in the spdR mutant relative to the wild type strain Gene a Fold change b...”
- “...subunit ribosomal protein S10/NusE CC1363 0.456 Membrane-bound proton translocating pyrophosphatase CC1387 0.344 Cold-shock protein CspD CC1745 0.291 RNA-binding protein Hfq CC1746 0.312 GTP-binding protein HflX CC1991 0.470 Preprotein translocase subunit SecD CC2912 0.350 Quinolinate synthetase CC3164 0.389 Cro/CI family transcriptional regulator CC3205 0.456 Transcription antitermination protein...”
- Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus
Vogt, mBio 2024 - “...(2.1-fold upregulation), encoding hflX , the second gene in the hfq-hflX operon [the hfq ( CCNA_01819 ) mRNA increased 1.98-fold in our experiment, and was excluded by our cutoff criteria]. The large set of repressed genes included transcripts encoding TBDRs ( CCNA_02895 , CCNA_03263 , CCNA_01042...”
- Crosstalk between the tricarboxylic acid cycle and peptidoglycan synthesis in Caulobacter crescentus through the homeostatic control of α-ketoglutarate
Irnov, PLoS genetics 2017 - “...and cell morphology A recent genome-wide Tn-Seq study in C . crescentus annotated hfq ( CCNA_01819 ) as essential for viability in PYE medium at 30C [ 26 ], which is a common laboratory growth condition for C . crescentus . When we attempted to generate...”
- Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation.
Santiago-Frangos, Proceedings of the National Academy of Sciences of the United States of America 2019 - GeneRIF: Solved crystal structure of Caulobacter crescentus RNA-binding protein Hfq family (Hfq) and investigated its structural role in RNA binding and annealing regulation.
HFQ_AZOC5 / Q43971 RNA-binding protein Hfq from Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / LMG 6465 / NBRC 14845 / NCIMB 13405 / ORS 571) (see paper)
AZC_3080 protein hfq from Azorhizobium caulinodans ORS 571
55% identity, 85% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs (By similarity). Seems to be involved in the regulation of NifA.
subunit: Homohexamer. - The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
Lee, BMC genomics 2008 - “...ntr B /ntr Y Signal transduction histidine kinase AZC_2924 rpo F RNA polymerase 54 factor AZC_3080 nfr A Translation regulator of nif A AZC_3083 ntr X Transcriptional regulator AZC_3084 ntr Y Signal transduction histidine kinase AZC_3086 ntr C Transcriptional regulator AZC_3087 ntr B Signal transduction histidine...”
- “...regulator [ 39 ] and at the translational level by the nrf A gene product (AZC_3080) [ 40 ]. FixK also activates transcription of the cyt NOQP operon (AZC_4523-AZC_4526), encoding the high-affinity terminal oxidase cytochrome cbb3 that is induced under microaerobiosis [ 41 , 42 ]....”
Q8TCX0 Delta 2-isopentenyl pyrophosphate transferase-like protein (Fragment) from Homo sapiens
83% identity, 56% coverage
RSP_2843 Host factor I protein from Rhodobacter sphaeroides 2.4.1
56% identity, 83% coverage
- Role of the Irr protein in the regulation of iron metabolism in Rhodobacter sphaeroides
Peuser, PloS one 2012 - “...0.58 0.68 1.90 1.59 DnaK suppressor protein RSP_2693 (0.42) 0.67 2.45 1.62 Superoxide dismutase (Fe-Mn) RSP_2843 hfq 0.50 0.81 1.77 1.22 RNA-binding protein Hfq RSP_4203 0.39 1.03 2.31 1.05 putative glutaredoxin family protein/Thio-disulfide isomerase Oxidative phosphorylation RSP_01000104 nuo (0.44) 0.56 0.831.15 1.21 1.86 0.901.05 Putative NADH...”
- “...universal stress protein (RSP_0697), chaperones like grpE , groES , groEL and hfq (RSP_1219, RSP_2310-11, RSP_2843), the superoxide dismutase encoding gene RSP_2693, and glutaredoxin and thioredoxin encoding genes. In contrast to other genes of iron storage, mbfA showed a different expression pattern, that it shares with...”
- Effects of the cryptochrome CryB from Rhodobacter sphaeroides on global gene expression in the dark or blue light or in the presence of singlet oxygen
Frühwirth, PloS one 2012 - “...rnd (0.94) 0.40 ( 0.60 ) Ribonuclease D RSP_2131 rne 1.07 0.60 0.71 Ribonuclease E RSP_2843 hfq 1.20 0.59 0.57 RNA-binding protein Hfq Others RSP_0030 1.05 0.39 0.62 PAS sensor GGDEF/EAL domain RSP_0905 sitB 1.20 0.75 2.10 ABC Mn+2/Fe+2 transporter, ATPase subunit RSP_2877 coxL 1.11 0.71...”
WP_003496145 RNA chaperone Hfq from Agrobacterium tumefaciens
Atu1450 putative RNA-binding protein Hfq from Agrobacterium tumefaciens str. C58 (Cereon)
49% identity, 90% coverage
ZZ6_0899 RNA chaperone Hfq from Zymomonas mobilis subsp. mobilis ATCC 29191
53% identity, 46% coverage
- pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis
So, BMC microbiology 2014 - “...The acyl-carrier protein ( acpP , ZZ6_0066); chaperone protein DnaJ (ZZ6_0618), RNA chaperone protein Hfq (ZZ6_0899), DNA polymerase III chi subunit ( holC , ZZ6_0042) and 2-dehydro-3-deoxyphosphooctonate aldolase protein ( kdsA , ZZ6_1604) genes were PCR amplified from Z. mobilis ATCC 29191. The genes were respectively...”
- “...2-dehydro-3-deoxyphosphooctonate aldolase (KdsA, ZZ6_1604; 292 aa), chaperone protein DnaJ (ZZ6_0618; 375 aa), RNA chaperone Hfq (ZZ6_0899; 161 aa) and DNA polymerase III chi subunit (HolC, ZZ6_0042; 148 aa). These proteins were previously included in a large scale analysis of protein-protein binding interactions in E. coli [...”
RL2284 putative host factor protein from Rhizobium leguminosarum bv. viciae 3841
51% identity, 79% coverage
- Factors governing attachment of Rhizobium leguminosarum to legume roots at acid, neutral, and alkaline pHs
Parsons, mSystems 2024 - “...family protein, member of the VOC superfamily pH 7.0 Required in attachment and rhizosphere only RL2284 hfq RNA-binding protein Hfq. Global post-transcriptional regulator pH 6.5 & 7.0 RL4065 a , d Hypothetical cytoplasmic protein with no conserved domains pH 6.5, 7.0, and 7.5 Required in attachment...”
- “...rhizosphere and/or colonization of pea roots (at 5 dpi). The global post-transcriptional RNA-binding protein Hfq (RL2284) is required for bacterial survival in the rhizosphere as well for attachment, but at no other stages of nodule formation, including root colonization ( Table 3 ). In S. meliloti...”
- Factors governing attachment ofRhizobium leguminosarumto legume roots
Parsons, 2022 - Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)
SMc01048 RNA-binding protein Hfq from Sinorhizobium meliloti 1021
51% identity, 79% coverage
GDI_2262 RNA chaperone Hfq from Gluconacetobacter diazotrophicus PA1 5
Q8RMG6 RNA-binding protein Hfq from Gluconacetobacter diazotrophicus
54% identity, 74% coverage
- Transcriptomic Response of the Diazotrophic Bacteria Gluconacetobacter diazotrophicus Strain PAL5 to Iron Limitation and Characterization of the fur Regulatory Network
Soares, International journal of molecular sciences 2022 - “...Genes involved in regulation, clustering Fe-S and BNF were differentially expressed. The ntrX (GDI_2263), nrfA (GDI_2262), HesB and fxdB genes (GDI_2370) were all downregulated, as were the nifH (GDI_0436) and nifK (GDI_0438) genes. Seven transposase genes belonging to five different families (IS5/IS1182, IS21, IS110, and IS256)...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...-Proteobacteria: GLUDI, Gluconacetobacter diazotrophicus (Q8RMG6); Acidobacteria: ACIBL, Acidobacteria bacterium (Q1IIF9). Spirochaetales: LEPIN, Leptospira...”
ZMO0347 RNA-binding protein Hfq from Zymomonas mobilis subsp. mobilis ZM4
57% identity, 41% coverage
- Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering
Asefi, Microbial cell factories 2024 - “...the physiological aspect of Z mobilis . In addition, there were two genes, ZMO1107 and ZMO0347, whose expression significantly decreased in Z. mobilis under ethanol stress [ 21 ]. Analysis and homologous study on these two genes revealed that they have approximately 50% and 70% identity...”
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Shabbir, Microbial cell factories 2023 - “...involvement in ethanol production by the mean of their expression level. For example, hfq ( ZMO0347 ) encoding RNA chaperone, and nhaA ( ZMO0119 ) encoding sodium proton antiporter protein are used for enhancing the ability of Z. mobilis ( AcR ) to produce sodium acetate...”
- Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis
Tang, Frontiers in bioengineering and biotechnology 2022 - “...Woodson, 2008 ; Frohlich and Gottesman, 2018 ). Hfq in Z. mobilis , encoded by ZMO0347 , was also discovered to contribute to multiple stress responses such as lignocellulosic hydrolysate inhibitor tolerance ( Yang et al., 2010 ). Overexpression of hfq enabled the recombinant Z. mobilis...”
- Impact of hfq and sigE on the tolerance of Zymomonas mobilis ZM4 to furfural and acetic acid stresses
Nouri, PloS one 2020 - “...Korea). All primers are listed in S1 Table . To overexpress sigE (ZMO1404) and hfq (ZMO0347) genes in Z . mobilis ZM4, recombinant plasmids pBBR1MCS-2/sigE and pBBR1MCS-2/hfq were constructed in E . coli DH5. For this purpose, we used 250 bp upstream and 200 bp downstream...”
- Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Han, Frontiers in bioengineering and biotechnology 2020 - “...in an indirect way. Our previous study identified that the UTR region of hfq gene (ZMO0347) is sensitive to ethanol stress and act as a post-transcriptional regulator to increase sensitivity of Hfq protein under lower-level ethanol stress ( Cho et al., 2017 ). In this study,...”
- Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis
Shen, Microbial cell factories 2019 - “...genotype, whereas the presence of 1.5kb PCR fragment indicate the recombinant genotype. For deletion of ZMO0347 , 2.8kb PCR fragment generated by primer pair 0347check-F/R represents the wild-type genotype, whereas the presence of 2.1kb PCR fragment indicates the recombinant genotype. For mCherry insertion, 1.5kb PCR fragment...”
- “...system, and the deficient of ZMO0028 improved transformation efficiency of Z. mobilis [ 44 ]. ZMO0347 encodes the RNA chaperone Hfq involving in tolerance against multiple hydrolysate inhibitors such as acetate, vanillin, furfural, and HMF in Z. mobilis [ 45 47 ]. Since both genes are...”
- Phenotypic and genomic analysis of Zymomonas mobilis ZM4 mutants with enhanced ethanol tolerance
Carreón-Rodríguez, Biotechnology reports (Amsterdam, Netherlands) 2019 - “...processes and metabolism. Also, it has been shown that the 5 untranslated regions of genes ZMO0347 and ZMO1142, encoding the RNA binding protein Hfq and a thioredoxin reductase, down-regulate downstream gene expression under ethanol stress [ 18 ]. It has been also shown that some regulatory...”
- Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4
Chang, Biotechnology for biofuels 2018 - “...22 ]. The overexpression of sodium-proton antiporter gene nhaA (ZMO0119) and RNA chaperone gene hfq (ZMO0347) improved mutant strain ZM4 (AcR) ability to grow under a relatively high concentration of sodium acetate [ 18 20 ], and the overexpression of reductase genes ZMO1116, ZMO1696, and ZMO1885...”
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HFQ_BRUA2 / Q2YPW9 RNA-binding protein Hfq from Brucella abortus (strain 2308) (see paper)
BAB1_1134 Host factor Hfq from Brucella melitensis biovar Abortus 2308
BMEI0872 NFRA PROTEIN from Brucella melitensis 16M
BOV_1070 RNA-binding protein Hfq from Brucella ovis ATCC 25840
51% identity, 79% coverage
- function: RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs (By similarity). Contributes to long-term survival under nutrient deprivation, to stationary phase-dependent hydrogen peroxide and acid stress resistance and is required for prolonged survival in the intracellular environment of the host macrophage. Therefore, contributes not only to a generalized stress response in stationary phase but also to pathogenesis in mice, allowing the brucellae to adapt to the harsh conditions encountered within macrophages.
disruption phenotype: Cells show increased sensitivity to hydrogen peroxide and decreased survival at pH 4.0 during stationary phase growth. It is less able to withstand prolonged starvation. It fails to replicate in cultured murine macrophages and is completely cleared from spleens and livers of infected mice 10 weeks after infection. - The RNA chaperone Hfq independently coordinates expression of the VirB type IV secretion system and the LuxR-type regulator BabR in Brucella abortus 2308
Caswell, Journal of bacteriology 2012 - “...of a B. abortus hfq mutant. The hfq gene (BAB1_1134) in B. abortus 2308 was mutated using a nonpolar, unmarked gene excision approach. The hfq gene, along...”
- “...a similar fashion; however, the hfq coding region (BAB1_1134) was amplified with primers rHfq-For and rHfq-Rev (Table 1). The amplified DNA fragment was...”
- Comparative Transcriptome Analysis of Artificially Induced Rough-Mutant Brucella Strain RM57 and Its Parent Strain Brucella melitensis M1981
Peng, Frontiers in veterinary science 2019 - “...hypothetical membrane spanning protein BMEII1116 7.73 5.60 LuxR family transcriptional regulator, quorum-sensing system regulator VjbR BMEI0872 4.71 2.27 host factor-I protein, Hfq BMEII0704 6.02 8.00 Bacterioferritin (cytochrome b1) BMEI0569 6.58 7.00 manganese transport protein MntH BMEII0906 7.36 6.50 acid stress chaperone HdeA BMEII0581 9.36 4.68 Cu/Zn...”
- “...mutant strain relative to the parent line. Particularly, BMEII1116 (encoding quorum-sensing system regulator VjbR) and BMEI0872 (encoding Hfq protein) were both significantly down-regulated in RM57 relative to M1981. A similar profile was observed in the qRT-PCR result ( Table 1 ). In addition, expression of four...”
- Impact of Hfq on global gene expression and intracellular survival in Brucella melitensis
Cui, PloS one 2013 - “...and Discussion Construction and Growth Characteristics of the B. melitensis hfq Mutant The hfq gene (BMEI0872) is located in clockwise orientation at bps 900419900655 in the genome of B. melitensis 16 M chromosome I and it is flanked by the hflX gene, encoding the gtp-binding protein,...”
- Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
He, Frontiers in cellular and infection microbiology 2012 - “...BMEII1037 Mice 14979322 165 cobW BMEII0308 Macrophages 12438693 166 glt1 BMEII0039 Mice 14979322 167 hfq BMEI0872 Macrophage, mice 12730323 168 mosC BMEI0267 Mice 14979322 169 rbsC BMEII0701 Mice, macrophages, HeLa 14979322 170 tldD BMEI1468 Mice 14979322 S: FUNCTION UNKNOWN** 171 BMEI1809 BMEI1809 Mice, macrophages, HeLa 14979322...”
- Cross-regulation in a three-component cell envelope stress signaling system of <i>Brucella</i>
Chen, mBio 2023 - “...sulfur cluster insertion protein ErpA ( BOV_0886 ) , and the RNA chaperone Hfq ( BOV_1070 ) are essential in B. ovis but not in B. abortus ( 35 ). TCS mutants sensitive (and resistant) to cell envelope disruptors in vitro We next generated a set...”
LIC12245 host factor-1 from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Q8F5Z7 RNA-binding protein Hfq from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
LA_1517 host factor I related protein from Leptospira interrogans serovar lai str. 56601
42% identity, 98% coverage
- Leptospira interrogans serovar copenhageni harbors two lexA genes involved in SOS response
Fonseca, PloS one 2013 - “...0.21 LIC10016 maf Cell division Inhibitor 1.15 0.89 LIC10837 sulA Cell division Inhibitor 0.71 0.06 LIC12245 hfq Host factor-1 (RNA degradation) 0.47 0.17 LIC12017 clpB ATP-dependent protease 0.34 0.08 LIC10222 dnaE DNA polymerase III subunit alpha 0.69 0.13 LIC12109 dnaB Replicative DNA helicase 0.61 0.19 LIC11339...”
- Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira
Kavela, Microbiology spectrum 2023 - “..., LA_1743 7.03 5.32 Q8F5I8 Signal transduction histidine kinase baeS , LA_1693 2.54 1.55 + Q8F5Z7 RNA-binding protein Hfq hfq , LA_1517 4.04 3.54 + Q8F6Q0 Chemotaxis protein CheA (EC 2.7.13.3) cheA , LA_1251 7.65 5.36 Q8F7C7 NifU_N domain-containing protein LA_1019 3.42 2.26 + Q8F7E1 Putative...”
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...the sequences refer to the alignment position numbers. Aae Aquifex aeolicus (O66512), Lin Leptospira interrogans (Q8F5Z7), Kve Koribacter versatilis (Q1IIF9), Eco Escherichia coli (P0A6X3), Tma Thermotoga maritima (Q9WYZ6), Tfu Thermobifida fusca (Q47P13), Sco Streptomyces coelicolor (Q9RJ64, Q9RJ65), Mtb Mycobacterium tuberculosis (P9WIM1, P9WIL9), Msm Mycobacterium smegmatis (I7G3U5,...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...(Q1IIF9). Spirochaetales: LEPIN, Leptospira interogans (Q8F5Z7). Aquafecales: AQUAE Aquifex aeolicus, (O66512). Thermotogales: THEMA, Thermotoga maritime...”
- Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira
Kavela, Microbiology spectrum 2023 - “...transduction histidine kinase baeS , LA_1693 2.54 1.55 + Q8F5Z7 RNA-binding protein Hfq hfq , LA_1517 4.04 3.54 + Q8F6Q0 Chemotaxis protein CheA (EC 2.7.13.3) cheA , LA_1251 7.65 5.36 Q8F7C7 NifU_N domain-containing protein LA_1019 3.42 2.26 + Q8F7E1 Putative lipoprotein LA_1004 2.81 1.71 + +...”
BJP26_08430 RNA chaperone Hfq from Sphingomonas melonis TY
51% identity, 46% coverage
CAC1834 Host factor I protein Hfq from Clostridium acetobutylicum ATCC 824
CA_C1834 RNA chaperone Hfq from Clostridium acetobutylicum ATCC 824
46% identity, 85% coverage
- The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
Venkataramanan, BMC genomics 2013 - “...is well conserved among many prokaryotes. A structural CBLAST of the annotated C. acetobutylicum Hfq (CAC1834) with the two Hfq crystal structures, one from E. coli [ 58 ] (3GIB_B) and the other from S. aureus [ 54 ] (1KQ1_H), showed conservation in the sequence and...”
- “...under both butanol and butyrate stress (Additional file 5 : Figure S2). The Hfq gene (CAC1834) was found to be mildly differentially expressed (upregulated) only under butanol stress. Identification of the putative Hfq binding module on 65 sRNAs may prove useful for deconvoluting the stress-responsive regulatory...”
- Small RNAs in the genus Clostridium
Chen, mBio 2011 - “...not have evidence that sCAC610 works with the putative RNA chaperone Hfq protein (coded by CAC1834) in C.acetobutylicum . However, we observed that sCAC610 displays a consistent location and distance to its downstream putative ABC transporter gene in all the genomes in which it was identified....”
- Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins
Liu, Biotechnology for biofuels 2018 - “...Elongation Factor Tu (Ef-Tu) 10 CA_C2990 396 7307 23 2 6.2 Cold shock protein 11 CA_C1834 448 9203 19 4 5.9 Host factor I protein Hfq 12 CA_C3125 299 7908 7 3 5.4 Ribosomal protein L29 13 CA_C2712 571 28,400 28 10 4.9 Crotonase 14 CA_C1807...”
PPE_RS12655 RNA chaperone Hfq from Paenibacillus polymyxa E681
43% identity, 88% coverage
O66512 RNA-binding protein Hfq from Aquifex aeolicus (strain VF5)
57% identity, 70% coverage
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...percent identity. Numbers above the sequences refer to the alignment position numbers. Aae Aquifex aeolicus (O66512), Lin Leptospira interrogans (Q8F5Z7), Kve Koribacter versatilis (Q1IIF9), Eco Escherichia coli (P0A6X3), Tma Thermotoga maritima (Q9WYZ6), Tfu Thermobifida fusca (Q47P13), Sco Streptomyces coelicolor (Q9RJ64, Q9RJ65), Mtb Mycobacterium tuberculosis (P9WIM1, P9WIL9),...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...(Q8F5Z7). Aquafecales: AQUAE Aquifex aeolicus, (O66512). Thermotogales: THEMA, Thermotoga maritime (Q9WYZ6). Fermicutes: BACSU, Bacillus subtilis (O31796);...”
5szeA / O66512 Crystal structure of aquifex aeolicus hfq-RNA complex at 1.5a (see paper)
57% identity, 70% coverage
C1A50_RS13605, PPSC2_RS42680 RNA chaperone Hfq from Paenibacillus polymyxa SC2
45% identity, 81% coverage
- Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism
Luo, Frontiers in microbiology 2018 - “...phosphotransferase F 99.46 95.39 kinB C1A50_RS19570 PPSC2_RS48955 PPE_RS18645 Two-component sensor histidine kinase 96.95 89.75 hfq C1A50_RS13605 PPSC2_RS42680 PPE_RS12655 RNA chaperone Hfq 97.53 93.09 To date, no studies have been reported on the biofilm formation pathway in P. polymyxa . We explored the possible pathways responsible for...”
- “...F 99.46 95.39 kinB C1A50_RS19570 PPSC2_RS48955 PPE_RS18645 Two-component sensor histidine kinase 96.95 89.75 hfq C1A50_RS13605 PPSC2_RS42680 PPE_RS12655 RNA chaperone Hfq 97.53 93.09 To date, no studies have been reported on the biofilm formation pathway in P. polymyxa . We explored the possible pathways responsible for biofilm...”
Q1IIF9 RNA-binding protein Hfq from Koribacter versatilis (strain Ellin345)
48% identity, 83% coverage
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...the alignment position numbers. Aae Aquifex aeolicus (O66512), Lin Leptospira interrogans (Q8F5Z7), Kve Koribacter versatilis (Q1IIF9), Eco Escherichia coli (P0A6X3), Tma Thermotoga maritima (Q9WYZ6), Tfu Thermobifida fusca (Q47P13), Sco Streptomyces coelicolor (Q9RJ64, Q9RJ65), Mtb Mycobacterium tuberculosis (P9WIM1, P9WIL9), Msm Mycobacterium smegmatis (I7G3U5, A0QZ41), Krh Kocuria rhizophila...”
STH1746 host factor-1 protein from Symbiobacterium thermophilum IAM 14863
55% identity, 70% coverage
DMR38_10895 RNA chaperone Hfq from Clostridium sp. AWRP
44% identity, 90% coverage
CD630_19740 RNA chaperone Hfq from Clostridioides difficile 630
CD1974 HfQ protein from Clostridium difficile 630
45% identity, 76% coverage
- Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
Boudry, RNA biology 2021 - “...family 20.15 3.82847 CD630_19100 ( eutV ) + Two-component response regulator, Ethanolamine specific 10.55 4.55715 CD630_19740 ( hfq ) - Hfq RNA chaperone 105.1 5.05609 CD630_22991 - Putative phage protein TA 75.25 6.03728 CD630_23050 ( pilW ) + Type IV pilus protein 70.28 4.96316 CD630_24830 +...”
- Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
Boudry, RNA biology 2021 - “...the hfq 5UTR mRNA [ 68 ]. Accordingly, we observed a significant 105-fold enrichment of CD1974 hfq mRNA in the 3xFLAG Hfq-immunoprecipitated sample as compared to the control with a MACS peak covering almost the entire gene being found (Supplementary Figure S5G). Intriguingly, a faint transcript...”
- Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile
Boudry, Journal of bacteriology 2014 - “...of FLAG tag sequence (3FLAG) in translational fusion with CD1974 sequence. This DNA fragment was cloned into the StuI and BamHI sites of the pRPF185 vector...”
- “...Strain construction using a knockdown system. We identified the CD1974 gene as encoding a C. difficile orthologue of the Hfq protein (30% amino acid sequence...”
- Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function
Caillet, RNA (New York, N.Y.) 2014 - “...the pathogenic clostridium Clostridium difficile ( Soutourina et al. 2013 ). Moreover, a gene ( CD1974 ), homologous to hfq , has been shown to be transcribed in this bacterium (I Verstraete, O Soutourina, pers. comm.). The C. difficile Hfq (Cd-Hfq) protein exhibits 46% identity (31...”
C3P4Y3 RNA-binding protein Hfq from Bacillus anthracis (strain A0248)
BC3713 Hfq protein from Bacillus cereus ATCC 14579
GBAA3842 host factor-I protein from Bacillus anthracis str. 'Ames Ancestor'
BAS3559 host factor-I protein from Bacillus anthracis str. Sterne
BMB171_RS18400 RNA chaperone Hfq from Bacillus thuringiensis BMB171
49% identity, 79% coverage
- Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
Mao, Microorganisms 2024 - “...Thioredoxin 1 GIS011 Transcriptional regulation A9VQG4 rex 1 Swiss-Prot A9VT66 codY 1 B7IXH3 nusB 1 C3P4Y3 hfq 1 C3PAG9 nrdR 1 WP_000421293.1 codY 1 GIS004 DNA protection A0R883 recF 1 Swiss-Prot A0RH75 lexA 1 A9VHS5 recO 1 C1ER74 noc 1 C3LFM1 uvsE 1 C3P9M9 disA 1...”
- SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
Yeak, BMC microbiology 2023 - “...BC4847 BC4847 D-alanyl-D-alanine carboxypeptidase 0.6 MS 165 BC1659 BC1659 hypothetical protein 0.6 0.6 S 166 BC3713 YmaH Hfq protein 0.6 0.6 R 167 BC4961 YutE hypothetical Cytosolic Protein 0.6 S 168 BC4856 MenF Isochorismate synthase 0.6 HQ 169 BC3372 YqeC 6-phosphogluconate dehydrogenase 0.6 0.6 G 170...”
- Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis
Passalacqua, PloS one 2012 - “.... One gene of note, however, was the inclusion of the RNA binding protein Hfq (GBAA3842) as being in the>900 category only for the EtOH sample (raw scores ranged from 76350 for non-EtOH samples), strongly suggesting a role for this protein in this specific type of...”
- Genetic evidence for the involvement of the S-layer protein gene sap and the sporulation genes spo0A, spo0B, and spo0F in Phage AP50c infection of Bacillus anthracis
Plaut, Journal of bacteriology 2014 - “...7702 csaB 7702 BAS0566 7702 sap 7702 eag 7702 BAS1792 7702 BAS3559 7702 spo0A 7702 spo0F JB220 spo0B P. C. Hanna lab T. M. Koehler lab This study This study...”
- “...Create BAS0842 mutant Create BAS1792 mutant Create BAS3559 mutant Create BAS4076 mutant Create BAS5185 mutant Confirm BAS0566 mutant Confirm BAS0841 mutant...”
- The RNA Chaperone Protein Hfq Regulates the Characteristic Sporulation and Insecticidal Activity of Bacillus thuringiensis
Yu, Frontiers in microbiology 2022 - “...starting strain of this study, Bt BMB171, has three copies of hfq gene: BMB171_RS08230 and BMB171_RS18400 are located on the chromosome, while BMB171_RS27540 is located on the only large plasmid pBMB171 ( He et al., 2010 ). We then defined them as hfq 1, hfq 2,...”
LMRG_00745 hfq protein from Listeria monocytogenes 10403S
lmo1295 similar to host factor-1 protein from Listeria monocytogenes EGD-e
51% identity, 78% coverage
- Mutant and Recombinant Phages Selected from In Vitro Coevolution Conditions Overcome Phage-Resistant Listeria monocytogenes
Peters, Applied and environmental microbiology 2020 (secret) - Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB
Liu, Frontiers in microbiology 2017 - “...Two DE fragments identified between the promoters 6 LMRG_00672 LMRG_00671 A , B No 7 LMRG_00745 A , B No Host factor-I protein 8 LMRG_00884 LMRG_00885 B , A No 9 LMRG_00906 LMRG_00910, LMRG_00909, LMRG_00908, LMRG_00907 A , H , B No RpoD ( A )...”
- PrfA-like transcription factor gene lmo0753 contributes to L-rhamnose utilization in Listeria monocytogenes strains associated with human food-borne infections
Salazar, Applied and environmental microbiology 2013 - “...LMRG_02001 LMRG_00293 LMRG_00221 LMRG_00365 LMRG_00010 LMRG_00745 LMRG_02602 LMRG_01030 LMRG_01444 LMRG_01763 LMRG_01236 LMRG_00278 LMRG_01602 LMRG_00472...”
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Oliver, BMC genomics 2009 - “...low temperature requirement C protein, also similar to B. subtilis YutG protein 2.8 50.03 18.94 LMRG_00745 lmo1295( hfq ) similar to host factor-1 protein 4.83 49.77 11.19 LMRG_01948 lmo2748 similar to B. subtilis stress protein YdaG 207.5 49.37 0 LMRG_00583 lmo1140 unknown 11.93 47.84 4.28 LMRG_02036...”
- Acid shock of Listeria monocytogenes at low environmental temperatures induces prfA, epithelial cell invasion, and lethality towards Caenorhabditis elegans
Neuhaus, BMC genomics 2013 - “...[ 30 ] 25C 1* 1* 1.7 2.3 1.5 37C 1.9 2.1 2.4 2.5 1* lmo1295 hfq RNA-binding protein Contributes to virulence [ 31 ] 25C 1* 2.1 3.4 2.8 0.6 37C 1* 3.7 2.8 1.7 1* lmo1377 lisR TCS response regulator Contributes to virulence [...”
- “...demonstrated by the induction of B -influenced genes (lmo0433, lmo0434, lmo0596, lmo0669, lmo0783, lmo0880, lmo0913, lmo1295, lmo2067, lmo2085, lmo2434, lmo2713; Tables 1 and 2 ), B seems to be activated after acid shock. Furthermore, we observed down regulation of several genes belonging to the rsb -operon...”
- Transcriptomic and phenotypic analyses identify coregulated, overlapping regulons among PrfA, CtsR, HrcA, and the alternative sigma factors sigmaB, sigmaC, sigmaH, and sigmaL in Listeria monocytogenes
Chaturongakul, Applied and environmental microbiology 2011 - “...new primers and probes for sigH, sigC, hfq (lmo1295), hrcA, and cggR (lmo2460) for these experiments. qRT-PCR was performed as described in reference 36...”
- Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
Oliver, Applied and environmental microbiology 2010 - “...lmo0937 lmo0953 lmo0956 lmo0957 lmo0994 lmo1140 lmo1241 lmo1295 lmo1375 lmo1425 lmo1428 lmo1433 lmo1602 lmo1605 lmo1606 lmo1694 lmo1799 lmo2085 lmo2130 lmo2191...”
- Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype
Zemansky, Journal of bacteriology 2009 - “...lmo2460, lmo2461 lmo2758 lmo2770 lmo0202, lmo1255, lmo1295, lmo1953 lmo2016 lmo2020 Gene namea Annotationa Similar to PTS system, beta-glucoside-specific...”
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Oliver, BMC genomics 2009 - “...temperature requirement C protein, also similar to B. subtilis YutG protein 2.8 50.03 18.94 LMRG_00745 lmo1295( hfq ) similar to host factor-1 protein 4.83 49.77 11.19 LMRG_01948 lmo2748 similar to B. subtilis stress protein YdaG 207.5 49.37 0 LMRG_00583 lmo1140 unknown 11.93 47.84 4.28 LMRG_02036 lmo0937...”
- Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e sigmaB regulon
Hain, BMC microbiology 2008 - “...2 [ 40 ]. We also observed and confirmed that the expression of Hfq ( lmo1295 ) to be dependent on B in L. monocytogenes [ 41 ]. The homolog protein in E. coli interacts with many regulatory sRNAs increasing e.g. the stability of the sRNA...”
- The RNA-binding protein Hfq of Listeria monocytogenes: role in stress tolerance and virulence
Christiansen, Journal of bacteriology 2004 - “...the L. monocytogenes EGD-e genome sequence revealed that the lmo1295 gene is predicted to encode a protein similar to host factor 1 protein, also known as Hfq...”
- “...that could not be amplified by RT-PCR. protein encoded by lmo1295 (designated hfq) consists of 77 amino acids and is 62% similar and 46% identical to the E....”
4nl3F / Q92C58 Crystal structure of listeria monocytogenes hfq in complex with u6 rna (see paper)
51% identity, 78% coverage
Q9WYZ6 RNA-binding protein Hfq from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
46% identity, 76% coverage
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...Lin Leptospira interrogans (Q8F5Z7), Kve Koribacter versatilis (Q1IIF9), Eco Escherichia coli (P0A6X3), Tma Thermotoga maritima (Q9WYZ6), Tfu Thermobifida fusca (Q47P13), Sco Streptomyces coelicolor (Q9RJ64, Q9RJ65), Mtb Mycobacterium tuberculosis (P9WIM1, P9WIL9), Msm Mycobacterium smegmatis (I7G3U5, A0QZ41), Krh Kocuria rhizophila (B2GIN6), Cgl Corynebacterium glutamicum (Q8NQE2, Q8NQE3). UniProt sequence...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...(O66512). Thermotogales: THEMA, Thermotoga maritime (Q9WYZ6). Fermicutes: BACSU, Bacillus subtilis (O31796); STAAM, Staphylococcus aureus (Q99UG9). accompanied...”
3hsbB / O31796 Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer (see paper)
45% identity, 77% coverage
Clocel_2035 RNA chaperone Hfq from Clostridium cellulovorans 743B
43% identity, 85% coverage
- Clostridium cellulovorans Proteomic Responses to Butanol Stress
Costa, Frontiers in microbiology 2021 - “...growth conditions. The most up-regulated protein in COG class J is the RNA chaperone Hfq (Clocel_2035, FC = 3.09). Hfq is a global modulator of the activity of small regulatory RNAs (sRNAs) ( Cho et al., 2014 ). sRNAs act as major posttranscriptional regulators of gene...”
- “...). These data seem to find confirmation in C. cellulovorans since the RNA chaperone Hfq (Clocel_2035) was among the most up-regulated protein under butanol-stress (FC = 3.09). Therefore, overexpression of Hfq is another interesting strategy that would be worth testing. Recently, overexpression of several sRNA regulators...”
O31796 RNA-binding protein Hfq from Bacillus subtilis (strain 168)
NP_389616 Hfq RNA chaperone from Bacillus subtilis subsp. subtilis str. 168
U712_09100 RNA chaperone Hfq from Bacillus subtilis PY79
45% identity, 76% coverage
- High Resolution Analysis of Proteome Dynamics during Bacillus subtilis Sporulation
Tu, International journal of molecular sciences 2021 - “...assigned regulons. Module UniProt ID Protein Function Product Brown P50727 Fer Electron transfer Ferredoxin Brown O31796 Hfq Unknown RNA chaperone Brown O07609 YhfK Unknown Unknown Brown P45872 PrfA Translation Peptide chain release factor 1 Brown P94521 YsdC Unknown Unknown Brown P54550 YqjM Reduction of double bonds...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...maritime (Q9WYZ6). Fermicutes: BACSU, Bacillus subtilis (O31796); STAAM, Staphylococcus aureus (Q99UG9). accompanied by decreased growth rates and...”
- Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis
Berry, Applied and environmental microbiology 2002 - “...in 88 aa) Similar to B. subtilis HfQ protein SW:HFQ_BACSU (O31796) (46.55 in 58 aa) and to E. coli Hfq protein SW:HFQ_ECOLI (P25521) (36.2 in 58 aa) Similar to...”
- “...matches Similar to B. subtilis Hfq protein SW:HFQ_BACSU (O31796) (45.45 in 55 aa) Similar to B. subtilis transition state regulatory protein AbrB or CpsX...”
- RNA-binding protein Hfq plays a vital role in cellulose decomposition throughout affecting cellulase gene expression.
Yang, Biotechnology letters 2021 (PubMed)- GeneRIF: RNA-binding protein Hfq plays a vital role in cellulose decomposition throughout affecting cellulase gene expression.
- Bacillus subtilis Hfq: A role in chemotaxis and motility.
Jagtap, Journal of biosciences 2016 (PubMed)- GeneRIF: We further demonstrate that Hfq positively regulates the expression of flagellum and chemotaxis genes (fla/che) that control chemotaxis and motility, thus assigning a new function for Hfq in B. subtilis.
- Impact of Hfq on the Bacillus subtilis transcriptome.
Hämmerle, PloS one 2014 - GeneRIF: Hfq confers a survival advantage on Bacillus subtilis; in the absence of Hfq, the levels of their convergently transcribed antitoxin/antisense RNAs were also reduced to a similar extend as the toxin mRNAs. Thus, Hfq seems to affect both the toxin and antitoxin transcripts in a positive manner.
- Transcriptional regulation and adaptation to a high-fiber environment in Bacillus subtilis HH2 isolated from feces of the giant panda
Zhou, PloS one 2015 - “...most non-essential genes were down-regulated to conserve energy. Interestingly, the expression of the Hfq protein (U712_09100), several sporulation kinases and genes of proteins involved in sporulation was decreased in the cellulose group. The Hfq protein is an RNA-binding protein associated with small regulatory RNAs (sRNAs) and...”
Q65JA8 RNA-binding protein Hfq from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)
43% identity, 80% coverage
Bphy_1711 RNA chaperone Hfq from Burkholderia phymatum STM815
Bphy_1711 RNA chaperone Hfq from Paraburkholderia phymatum STM815
48% identity, 49% coverage
BCAL1538 Hfq protein from Burkholderia cenocepacia J2315
55% identity, 29% coverage
- Surface-Exposed Protein Moieties of Burkholderia cenocepacia J2315 in Microaerophilic and Aerobic Conditions
Seixas, Vaccines 2024 - “...2.6. Production of Anti-Hfq2 and Anti-GroEL Polyclonal Antibodies Nucleotides 350 to 538 of the hfq2 (BCAL1538) gene and nucleotides 1192 to 1461 of the groEL (BCAL3146) gene were amplified from the B. cenocepacia J2315 genome with the primer pairs AMG1_Fw (GAATTCGCCGCGTGAAGGCTACGGTT) / AMG1_Rv (GTCGACTACTGGCCGTCCGGCACGAT) and AMG3_Fw...”
- “...(E) extracellular. Figure 3 Subcellular localization of B. cenocepacia J2315 BCAL3146 (GroEL), BCAL2645 (OmpA), and BCAL1538 (HFQ2). After bacterial growth in ASM medium under aerobic conditions, cells were harvested and divided into the following fractions: Cytoplasmic proteins (Lane 1), Outer Membrane proteins (Lane 2), and Extracellular...”
- Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence
Ferreira, Applied and environmental microbiology 2013 - “...1.7 1.6 1.6 1.5 1.6 Transcription BCAL0562 BCAL0787 BCAL1879 BCAL1538 BCAL3055 BCAL3151 BCAL3178 BCAM0742 1.2 1.3 1.3 1.3 1.3 1.5 1.4 1.6 1.6 1.8 1.7 1.8 1.6...”
- Burkholderia cepacia Complex: Emerging Multihost Pathogens Equipped with a Wide Range of Virulence Factors and Determinants
Sousa, International journal of microbiology 2011 - “...[ 64 ], as well the construction of an insertion mutant in B. cenocepacia J2315 BCAL1538 (C. G. Ramos, S. A. Sousa, J. H. Leito, unpublished results). A combination of one or more of the previous approaches has allowed the identification of several potential virulence factors,...”
- The second RNA chaperone, Hfq2, is also required for survival under stress and full virulence of Burkholderia cenocepacia J2315
Ramos, Journal of bacteriology 2011 - “...which was the focus of this work. The gene encoding Hfq2 (BCAL1538) is also located in chromosome I, about 370 kb from the gene for Hfq (Fig. 1B), and is...”
- “...regulator), BCAL1537 (putatively exported lipoprotein), BCAL1538 (Hfq2 chaperone), BCAL1539 (putative exported protein), BCAL1540 (transmembrane lipoprotein),...”
4y91F / Q9WYZ6 Crystal structure of a thermotoga maritima hfq homolog
46% identity, 79% coverage
bglu_1g19700 hypothetical protein from Burkholderia glumae BGR1
55% identity, 30% coverage
- The Roles of Two hfq Genes in the Virulence and Stress Resistance of Burkholderia glumae
Kim, The plant pathology journal 2018 - “...present in B. glumae were located in chromosome 1, bglu_1g14550 ( hfq 1 gene) and bglu_1g19700 ( hfq 2 gene); the length of hfq 1 gene was 255 nt, compared with the 555 nt sequence length of the hfq 2 gene ( Supplementary Fig. 1 )....”
- “...glumae BGR1 ( Fig. 1A ). The in-frame mutation of the hfq 2 gene ( bglu_1g19700 ) was verified through PCR, targeting the specific upstream and downstream sequences of the target genes. The results indicate that 445 bp, within the target gene were deleted from HFQ2...”
RBAM_017140 Hfq from Bacillus amyloliquefaciens FZB42
44% identity, 76% coverage
GSU1999 hfq protein from Geobacter sulfurreducens PCA
46% identity, 66% coverage
SERP0871 host factor-I protein, putative from Staphylococcus epidermidis RP62A
33% identity, 90% coverage
SAR1279 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
32% identity, 90% coverage
SAKG18_12120 RNA chaperone Hfq from Staphylococcus aureus
Q2FYZ1 RNA-binding protein Hfq from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SA1145 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SACOL1324 hfq protein, putative from Staphylococcus aureus subsp. aureus COL
YP_499813 host factor 1 protein from Staphylococcus aureus subsp. aureus NCTC 8325
35% identity, 71% coverage
- IS256-Mediated Overexpression of the WalKR Two-Component System Regulon Contributes to Reduced Vancomycin Susceptibility in a Staphylococcus aureus Clinical Isolate
Kuroda, Frontiers in microbiology 2019 - “...120.7 194.1 10.0 6.2 SAKG18_09620 qoxD Quinol oxidase subunit 4 463.8 112.1 91.2 4.1 5.1 SAKG18_12120 hfq RNA-binding protein Hfq 38.9 6.8 23.7 5.7 1.6 SAKG18_12180 hypothetical protein 51.1 8.0 24.0 6.4 2.1 SAKG18_12260 hypothetical protein 46.4 16.2 9.4 2.9 4.9 SAKG18_25270 ABC-2 family transporter protein...”
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC
Müller, Nature communications 2019 - “...of the Sm-fold. Secondary structure elements of Staphylococcus aureus (Sau) Hfq (beige; PDB 1KQ2; UniProt Q2FYZ1) and Arthrobacter aurescens (Aau) PafBC (blue) are shown below each alignment. Naturally fused PafBC proteins were separated into PafB and PafC parts before alignment (asterisks). Alignment is colored according to...”
- Induction of attachment-independent biofilm formation and repression of Hfq expression by low-fluid-shear culture of Staphylococcus aureus
Castro, Applied and environmental microbiology 2011 - “...as23R uspF uspR tdcFF tdcFR SArRNA01 SArRNA01 SA1145 SA1145 SA1234 SA1234 SA1869 SA1869 SA1984 SA1984 SA1532 SA1532 SA0455 SA0455 ACCGTGAGGTCAAGCAAATC...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...SA0309 SA0519 SA0520 SA0521 SA0641 SA0723 SA0743 SA0746 SA1145 SA1396 SA1452 SA1549 SA1559 SA1577 SA1617 SA1709 SA1941 SA1964 SA1984 SA2284 SA2285 SA2286 SA2287...”
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
Ben, Journal of bacteriology 2008 - “...SA2189 SA2469 SA1324 SA0328 SA1538 SA1525 SAR1898 SA1145 SACOL0350 SACOL0336 SA0909 SA1941 SA1193 SA0170 SAR0358 SA0355 Cytoplasm Conserved hypothetical...”
- Global regulation of gene expression by ArlRS, a two-component signal transduction regulatory system of Staphylococcus aureus
Liang, Journal of bacteriology 2005 - “...SA0126 SA0127 SA0899 SA0904 SA0956 SA0978 SA1090 SA1091 SA1145 SA1154 SA1266 SA1267 SA1268 SA1552 SA1577 SA1630 SA1637 SA1638 SA1752 SA1848 SA1882 SA1883 SA1991...”
- Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions
Efthimiou, Frontiers in microbiology 2019 - “...SACOL1522 gb | AAC441352 Cell surface elastin binding protein 3.19 0.0085 (B) Transcription regulators hfq SACOL1324 sp | P255211 HFQ_ECOLI Hfq protein (Host factor-! protein) (HF-I) (HF-1) 3.53 0.0024 sarA SACOL0672 gb | AAM74164.11 AF515775_2 Staphylococcal accessory regulator variant 3.39 0.0308 Biofilm formation scc SACOL1169 ref...”
- Hfq is a global regulator that controls the pathogenicity of Staphylococcus aureus
Liu, PloS one 2010 - “...some post-transcription regulation of Hfq protein. Recently Becher et al. reported that mRNA of hfq (SACOL1324) could be detected in COL by DNA microarray, but the Hfq protein was undetectable [29] . This result is consistent with our observation. The different expression profiles of Hfq in...”
- Hfq is a global regulator that controls the pathogenicity of Staphylococcus aureus.
Liu, PloS one 2010 - GeneRIF: Hfq is a global regulator and controls the pathogenicity.
1kq2H / A0A0H3JV59 Crystal structure of an hfq-RNA complex (see paper)
37% identity, 65% coverage
GBAA_RS29265 RNA chaperone Hfq from Bacillus anthracis str. 'Ames Ancestor'
43% identity, 64% coverage
BA1656 host factor-I protein from Bacillus anthracis str. Ames
39% identity, 67% 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