PaperBLAST
PaperBLAST Hits for DDA3937_RS16230 (61 a.a., MLILTRRVGE...)
Show query sequence
>DDA3937_RS16230
MLILTRRVGETLMIGDEVTVTVLGVKGNQVRIGVNAPKEVSVHREEIYQRIQAEKSQPTS
Y
Running BLASTp...
Found 77 similar proteins in the literature:
Dd586_3183 carbon storage regulator, CsrA from Dickeya dadantii Ech586
ECA3366 carbon storage regulator from Erwinia carotovora subsp. atroseptica SCRI1043
Dd703_0999 carbon storage regulator, CsrA from Dickeya dadantii Ech703
Dda3937_03151, ECA3366, W5S_1009 carbon storage regulator CsrA from Pectobacterium atrosepticum SCRI1043
100% identity, 100% coverage
- Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle
Li, BMC genomics 2018 - “...network Rsm systempost-transcriptional gene regulation rsmA BCS7_16095 29 9 15 3 10 6 8 4 Dd586_3183 Dda3937_03151 Dd703_0999 rsmB c 29 9 15 3 10 6 8 4 1 1 0 rsmC BCS7_03480 29 9 15 3 10 6 7 4 Dd586_0685 Dda3937_02456 Dd703_3258 ExpI-ExpR Quorum-Sensing...”
- Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum
Liu, PLoS pathogens 2008 - “...ECA3254 ( glnB ), YP051343; ECA3281 ( rseC ), YP051370; ECA3282 ( rseB ), YP051371; ECA3366 ( rsmA ), YP051455; ECA3368 ( recX ), YP051457; ECA3420 , YP051511; ECA3421-3426 , YP051512-051517; ECA3427 , YP051518; ECA3428 ( hcp ), YP051519; ECA3430 , YP051520; ECA3432 ( vasK ),...”
- Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle
Li, BMC genomics 2018 - “...systempost-transcriptional gene regulation rsmA BCS7_16095 29 9 15 3 10 6 8 4 Dd586_3183 Dda3937_03151 Dd703_0999 rsmB c 29 9 15 3 10 6 8 4 1 1 0 rsmC BCS7_03480 29 9 15 3 10 6 7 4 Dd586_0685 Dda3937_02456 Dd703_3258 ExpI-ExpR Quorum-Sensing system expI/expR...”
- Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle
Li, BMC genomics 2018 - “...Rsm systempost-transcriptional gene regulation rsmA BCS7_16095 29 9 15 3 10 6 8 4 Dd586_3183 Dda3937_03151 Dd703_0999 rsmB c 29 9 15 3 10 6 8 4 1 1 0 rsmC BCS7_03480 29 9 15 3 10 6 7 4 Dd586_0685 Dda3937_02456 Dd703_3258 ExpI-ExpR Quorum-Sensing system...”
- The global response regulator ExpA controls virulence gene expression through RsmA-mediated and RsmA-independent pathways in Pectobacterium wasabiae SCC3193
Broberg, Applied and environmental microbiology 2014 - “...rsmA/wt W5S_0060 W5S_0593 W5S_0599 W5S_0965 W5S_1006 W5S_1009 W5S_1021 W5S_2118 W5S_2139 W5S_2142 W5S_2539 W5S_2933 W5S_3266 W5S_3268 W5S_4193 W5S_4205 W5S_4748...”
- Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193
Nykyri, PLoS pathogens 2012 - “...the Rcs phosphorelay system (RcsC; W5S_3208, RcsD; W5S_3206, RcsB; W5S_3207); a few global regulators (RsmA; W5S_1009, KdgR; W5S_2118, ExpM; W5S_2224, Hor; W5S_2637); and a regulatory RNA (rsmB; 36450193644673) [7] [9] , [17] , [27] , [30] , [32] , [33] , [47] [50] . All the...”
CSRA_YERE8 / A1JK11 Translational regulator CsrA; Carbon storage regulator; Post-transcriptional regulator RsmA from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) (see paper)
YPO3304 carbon storage regulator from Yersinia pestis CO92
YPK_3372 carbon storage regulator, CsrA from Yersinia pseudotuberculosis YPIII
98% identity, 100% coverage
- function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (PubMed:16359708). - Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen
Chain, Journal of bacteriology 2006 - “...acids, such as the 61-amino-acid carbon storage regulator crsA (YPO3304). The final set of proteins found to be absent in at least one genome was manually...”
- Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach
Liu, Molecular & cellular proteomics : MCP 2010 - “...13 8 11 8 9 8 11 13 A1JHR2 A1JN60 A1JQX1a A1JS10 A1JS26 A1JK11 A1JS31 A1JIS8 65 57 32 93 92 31 31 31 131 131 131 131 NME NME NME NME AIJQX1 is not a complete...”
- RovM and CsrA Negatively Regulate Urease Expression in <i>Yersinia pseudotuberculosis</i>
Dai, Frontiers in microbiology 2018 - “...mutagenesis was performed by overlap PCR to substitute the arginine residue at position 44 of Ypk_3372 (CsrA) into an alanine residue [CsrA(R44A)]. Briefly, two rounds of PCR were used to amplify the DNA of mutant CsrA(R44A). Primer pairs csrAexF BamH I/csrA-R44A M1R and csrA-R44A M2F/csrAexR Sal...”
- Loss of CNFY toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency
Heine, PLoS pathogens 2018 - “...KEGG accession for qRT-PCR tested transcripts: sopB (pYV0031), wrbA (YPK_2363), hdeB (YPK_1140), cnfY (YPK_2615), csrA (YPK_3372), rovA (YPK_1876), crp (YPK_0248), yscF (pYV0082), yopJ (pYV_0098), yopE (pYV0025), yopH (pYV0094), yopD (pYV0054), ypkA (pYV0001), frdA (YPK_3813), rfaH (YPK_3937), arcA (YPK_3606), napA (YPK_1387), if-3 (YPK_1821) Statistical analysis Graph Pad...”
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...defense Crp STM3466 Crp YPK_0248 100 99 Transcription Colonization, invasion, host defense CsrA STM2826 CsrA YPK_3372 100 95 Translation Colonization, invasion, host defense Dam STM3484 dam YPK_0228 96 70 Translation Invasion DnaK STM0012 DnaK YPK_3594 100 92 Protein stability Colonization EnvZ STM3501 EnvZ YPK_0173 97 88...”
CSRA_PECCC / P0DKY7 Translational regulator CsrA; Carbon storage regulator; Repressor RsmA from Pectobacterium carotovorum subsp. carotovorum (Erwinia carotovora subsp. carotovora) (see paper)
98% identity, 100% coverage
- function: Controls extracellular enzymes, N-(3-oxohexanoyl)-L- homoserine lactone, and pathogenicity. Repressor of virulence factors.
function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core.
ZfiA / b2696 carbon storage regulator from Escherichia coli K-12 substr. MG1655 (see 33 papers)
CSRA_ECOLI / P69913 Carbon storage regulator; Translational dual regulator CsrA from Escherichia coli (strain K12) (see 21 papers)
CSRA_SALTY / P69917 Translational regulator CsrA; Carbon storage regulator from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
B5XVB9 Translational regulator CsrA from Klebsiella pneumoniae (strain 342)
ECs_3553, NP_311580 pleiotropic regulatory protein for carbon source metabolism from Escherichia coli O157:H7 str. Sakai
NP_417176 carbon storage regulator from Escherichia coli str. K-12 substr. MG1655
NP_461747 carbon storage regulator from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
UTI89_C3057 carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties from Escherichia coli UTI89
STM2826 carbon storage regulator from Salmonella typhimurium LT2
NP_417176, b2696 carbon storage regulator from Escherichia coli str. K-12 substr. MG1655
ECP_2656 carbon storage regulator CsrA from Escherichia coli 536
Ent638_3171 carbon storage regulator from Enterobacter sp. 638
STM14_3412 carbon storage regulator CsrA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
97% identity, 100% coverage
- function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability, initially identified for its effects on central carbon metabolism (PubMed:8393005). Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems (PubMed:21488981, PubMed:28924029). Binds to the 5'-UTR of mRNA to repress or activate translation; 2 binding sites on the homodimer can bridge 2 sites within target RNA (By similarity). Exerts reciprocal effects on enzymes of gluconeogenesis and glycogen biosynthesis versus those of glycolysis (PubMed:16923806, PubMed:7493933). Negatively effects glycogen biosynthesis, gluconeogenesis, alters cell size and surface properties (PubMed:7493933, PubMed:7751274, PubMed:8393005). Activates regulates expression of glycolysis genes (PubMed:7493933). Represses biofilm formation (PubMed:11741870). Regulates glycogen synthesis under both aerobic and anaerobic conditions; overexpression strongly inhibits glycogen accumulation (PubMed:8393005). Binds to 4 sites in its own promoter, including the Shine-Dalgarno sequence, repressing its own translation; mutating the binding-sites decreases repression (PubMed:21696456). Indirectly activates transcription from 1 of its 5 promoters, which is responsible for increased expression during stationary phase (PubMed:21696456). Binds to at least 720 transcripts in strain K12 / CF7789, many of which are also part of the stringent response, including relA, spoT and dksA; slightly represses RelA and slightly activates DskA translation (PubMed:21488981). Binds to and represses the ECF sigma factor rpoE promoter (PubMed:28924029). Accelerates the degradation of glgC gene transcripts; overexpression further decreases glgC transcripts (PubMed:7751274). Binds 2 sites in the glgC mRNA leader, 1 of which overlaps the Shine-Dalgarno sequence, preventing ribosome-binding and thus destabilizing the mRNA (PubMed:12067347). Acts to inhibit interaction between the CcdB (also known as LetD) protein and the A subunit of DNA gyrase (PubMed:8604133). Required to activate motility and flagellum biosynthesis through the post-transcriptional activation of flhDC expression by binding to and stabilizing the flhDC message (PubMed:11298291). Represses translation of iraD mRNA via translational coupling to an upstream open reading frame (PubMed:28851853). Binds to mRNA and reduces levels of probable diguanylate cyclases dgcT and dgcZ (PubMed:18713317).
function: Binds to and is sequestered by non-coding small RNAs (sRNA) CsrB and CsrC which antagonize the activity of CsrA (PubMed:12694612, PubMed:9211896). The consensus RNA-binding site is CAGGA(U/A/C)G which is located in probable hairpin loops (PubMed:9211896). There are 18 sites in CsrB, which cooperatively binds about 18 copies of CsrA (PubMed:12694612, PubMed:9211896). CsrC has 9 sites, and cooperatively binds multiple copies of CsrA (PubMed:12694612). Indirectly activates expression of CsrB and CsrC, both dependently and independently of the BarA-UvrY two-component system (PubMed:12193630, PubMed:12694612). ppGpp activates transcription of CsrA-antagonistic small RNAs CsrB and CsrC, which down-regulates CsrA's action on translation during the stringent response (PubMed:21488981).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (PubMed:15866937).
disruption phenotype: Essential, it cannot be deleted when cells grow on LB but cells will grow with pyruvate as the sole carbon source; if glycogen synthesis is impaired then cells become viable (PubMed:19103924). Most deletion experiments use an allele which has a kanamycin-resistance cassette inserted after amino acid 50, which retains about 10% residual activity (PubMed:19103924, PubMed:8393005). Increased levels of glgC transcripts during both exponential and stationary phases (PubMed:7751274). Decreased levels of enzymes involved in glycolysis (PubMed:7493933). Increased biofilm formation (PubMed:11741870). Decreased expression of it antagonistic small RNAs CsrB and CsrC (PubMed:12694612). Allows basal levels of poly-GlcNAc synthesis and biofilm formation; this disrupted strain serves as a model system for biofilm formation (PubMed:19460094). Increased expression of RelA, about 1.5-fold increase in (p)ppGpp levels (PubMed:21488981). Increased levels of ECF sigma factor E (rpoE) (PubMed:28924029). - function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core.
disruption phenotype: Decreases expression of genes encoding virulence proteins (PubMed:19229334). Decreases virulence in mouse (PubMed:19229334). - Rcs phosphorelay affects the sensitivity of Escherichia coli to plantaricin BM-1 by regulating biofilm formation
Bian, Frontiers in microbiology 2022 - “...ArcA P09323 N-acetylglucosamine-specific EIICBA component 0.638 0.001929 NagE P04128 Type-1 fimbrial protein 0.3523 0.037 FimA P69913 Carbon storage regulator 0.3423 0.3935 CsrA P0AEV1 Regulator of RpoS 1.253 0.001616 RssB P45578 S-ribosylhomocysteine lyase 1.283 0.000602 LuxS P00490 Maltodextrin phosphorylase 0.6347 0.0004 MalP P0ACJ8 cAMP-activated global transcriptional regulator...”
- Identification and monitoring of host cell proteins by mass spectrometry combined with high performance immunochemistry testing
Bomans, PloS one 2013 - “...Antigen 43 106.8 62 21 39 16 P0A862 Thiol peroxidase 17.8 60 76 53 76 P69913 Carbon storage regulator 6.9 56 33 <20 33 Total number of identified HCPs (score >20) 76 84 Database query was conducted by analyzing LC-MS/MS CID spectra using Proteome Discoverer V1.3...”
- Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
Yang, PloS one 2019 - “...21 Bifunctional protein GlmU glmU B5XZM7 Peptidoglycan biosynthesis CBO-treated 22 Carbon storage regulator homolog csrA B5XVB9 Protein biosynthesis CBO-treated 23 Cobalamin biosynthesis protein CobD cobD A6TDC6 Cobalamin biosynthesis CBO-treated 24 DNA ligase ligA A6TC47 Stress response CBO-treated 25 Ferrochelatase hemH B5Y0N2 Porphyrin biosynthesis CBO-treated 26 Hydroxyacylglutathione...”
- Dual role of CsrA in regulating the hemolytic activity of Escherichia coli O157:H7.
Sun, Virulence 2022 - GeneRIF: Dual role of CsrA in regulating the hemolytic activity of Escherichia coli O157:H7.
- Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
Tyagi, Toxins 2019 - “...YebG 2.3 1.8 ECs_3271 mntH manganese/divalent cation transporter 1.5 ECs_3476 grpE molecular chaperone GrpE 1.8 ECs_3553 csrA carbon storage regulator 2.4 1.4 ECs_3556 recA DNA recombination/repair protein RecA 1.7 1.6 ECs_3595 rpoS RNA polymerase sigma factor RpoS 3.2 1.9 ECs_3887 yghA NAD(P)-dependent oxidoreductase 1.9 1.7 ECs_4050...”
- Two Polyketides Intertwined in Complex Regulation: Posttranscriptional CsrA-Mediated Control of Colibactin and Yersiniabactin Synthesis in Escherichia coli.
Rehm, mBio 2021 - GeneRIF: Two Polyketides Intertwined in Complex Regulation: Posttranscriptional CsrA-Mediated Control of Colibactin and Yersiniabactin Synthesis in Escherichia coli.
- CsrA-Mediated Translational Activation of ymdA Expression in Escherichia coli.
Renda, mBio 2020 - GeneRIF: CsrA-Mediated Translational Activation of ymdA Expression in Escherichia coli.
- Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.
Berndt, Scientific reports 2019 - GeneRIF: findings expand the scope of pathways affected by the csrA regulon and emphasize its importance as a global regulator.
- Regulation of Iron Storage by CsrA Supports Exponential Growth of Escherichia coli.
Pourciau, mBio 2019 - GeneRIF: CsrA was found to regulate cellular iron levels and support growth by repressing the expression of FtnB and Bfr.
- An RNA-dependent mechanism for transient expression of bacterial translocation filaments.
Wang, Nucleic acids research 2018 - GeneRIF: Based on expression studies with site-directed mutants, an OFF-ON-OFF toggle model is proposed that results in transient translation of SepL and EspA filament assembly. Under this model, the nascent mRNA is translationally off, before being activated by CsrA, and then repressed by Hfq and Spot42.
- The pyrophosphohydrolase RppH is involved in the control of RsmA/CsrA expression in Azotobacter vinelandii and Escherichia coli.
Bedoya-Pérez, Microbiological research 2018 (PubMed)- GeneRIF: The authors propose that in both Azotobacter vinelandii and Escherichia coli, RppH activity plays a role in the expression of the translational regulator protein RsmA/CsrA.
- Translational Repression of the RpoS Antiadapter IraD by CsrA Is Mediated via Translational Coupling to a Short Upstream Open Reading Frame.
Park, mBio 2017 - GeneRIF: findings show that CsrA employs a novel regulatory mechanism to repress translation of iraD; CsrA binds to four sites in the iraD leader transcript but does not directly occlude ribosome binding to the iraD SD sequence; instead, CsrA represses translation of a short open reading frame encoded upstream of iraD, causing repression of iraD translation
- CsrA maximizes expression of the AcrAB multidrug resistance transporter.
Ricci, Nucleic acids research 2017 - GeneRIF: Data show that CsrA binds directly to the 5' end of the transcript encoding AcrAB.
- More
- Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
Holmqvist, The EMBO journal 2016 - GeneRIF: CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs.
- The role of ClpP, RpoS and CsrA in growth and filament formation of Salmonella enterica serovar Typhimurium at low temperature.
Knudsen, BMC microbiology 2014 - GeneRIF: Although a csrA mutant also accumulated high level of RpoS, growth impairment caused by lack of csrA was not related to RpoS levels in a similar way.
- ClpP deletion causes attenuation of Salmonella Typhimurium virulence through mis-regulation of RpoS and indirect control of CsrA and the SPI genes.
Knudsen, Microbiology (Reading, England) 2013 (PubMed)- GeneRIF: study suggests that ClpP affects SPI1 expression and thereby virulence indirectly through its regulation of both RpoS and CsrA
- Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD.
Martínez, Molecular microbiology 2011 - GeneRIF: CsrA negatively regulates hilD expression.
- CsrA and CsrB are required for the post-transcriptional control of the virulence-associated effector protein AvrA of Salmonella enterica.
Kerrinnes, International journal of medical microbiology : IJMM 2009 (PubMed)- GeneRIF: The expression of avrA is suggested to be regulated in a post-transcriptional manner by critical and effective concentrations of CsrA (see-saw regulation), which is achieved through the sequestering activity of CsrB.
- Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
García, Microbial genomics 2021 - “...L1 Ribosomal assembly/translation (J) 4.36 UTI89_C4165 rfaF 1 ADP-heptose-LPS heptosyltransferase 2 LPS biosynthesis (M) 4.32 UTI89_C3057 csrA Carbon storage regulator Regulation translation/transcription/ carbohydrate metabolism/biofilm (J) 4.24 UTI89_C4292 atpE Membrane-bound ATP synthase F0 sector subunit c ATP synthesis (C) 4.01 UTI89_C4290 UTI89_C4290 Hypothetical protein (NI) 3.94 UTI89_C3488...”
- Regulatory principles governing Salmonella and Yersinia virulence
Erhardt, Frontiers in microbiology 2015 - “...TCS Host defense Crp STM3466 Crp YPK_0248 100 99 Transcription Colonization, invasion, host defense CsrA STM2826 CsrA YPK_3372 100 95 Translation Colonization, invasion, host defense Dam STM3484 dam YPK_0228 96 70 Translation Invasion DnaK STM0012 DnaK YPK_3594 100 92 Protein stability Colonization EnvZ STM3501 EnvZ YPK_0173...”
- Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium
Yoon, PLoS pathogens 2009 - “...RNA polymerase, response to periplasmic stress [27] STM2688 smpB small protein B; tmRNA-binding protein [97] STM2826 csrA carbon storage regulator [30] STM2924 rpoS sigma S factor of RNA polymerase, major sigma factor during stationary phase [98] STM3466 crp catabolite activator protein (CAP), cyclic AMP receptor protein...”
- In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
Marchal, Genome biology 2004 - “...with STM1630 (putative inner membrane protein) 0.758303 CTTAAGAAATATTTAAT / / 1000 Some Salmonella only csrA STM2826 ; S. typhimurium carbon storage regulator 0.756990 CTTAGGTTTAACAGAAT m + 1111 All nine genomes dinP/yafK STM0313 ; Ortholog of E. coli damage-inducible protein P; putative tRNA synthetase (AAC73335.1); Blast hit...”
- The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora
Ancona, Scientific reports 2016 - “.... ( A ) Alignment of deduced amino acids of CsrA (accession # CBJ47311 and NP_417176) from E. amylovora and Escherichia coli ; and RsmA (accession #AAG04294) from Pseudomonas aeruginosa PAO1, and schematic map of the secondary structure of CsrA based on Schubert et al ....”
- 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 - “...of membrane-bound ATP synthase. gi|90111550 b3162 deaD CsdA 70.5 65.8 22 ATP-dependent RNA helicase. gi|16130603 b2696 csrA CsrA 6.9 57.03 38 Regulatory protein for carbon source metabolism. gi|16131818 b3988 rpoC RNAP ' 155.1 51.13 19 RNA polymerase; ' subunit. gi|145698340 b4049 dusA DusA 36.8 42.73 16...”
- Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
Ge, Journal of biosciences 2011 - “...3306283 1.3 deaD b3162 18 1798352 1798881 1.28 infC b1718 19 2816064 2816665 1.28 argZ b2696 20 4423043 4423188 1.28 rpsF b4200 21 124240 124961 1.26 aceE bO115 22 656533 656726 1.26 cspE b0623 23 4205797 4205918 1.26 purH b4006 24 1755357 1755502 1.25 lpp b1677...”
- Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli
Popella, Nucleic acids research 2022 - “...-4 to+5 > 10 GACATCTCAG -5 to+5 > 10 GACATCTCAGA -6 to+5 > 10 csrA ECP_2656 1259.7 KFFKFFKFFK - - - AGCATTCTT -4 to+5 > 10 AGCATTCTTT -5 to+5 > 10 AGCATTCTTTG -6 to+5 10 rpsH ECP_3394 5288.6 KFFKFFKFFK CTCATCTG -3 to+5 5 CTCATCTGT -4 to+5...”
- Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp. 638
Taghavi, PloS one 2015 - “...This is also consistent with the observed 12-fold decrease on sucrose in csrA expression levels (Ent638_3171), whose mRNA-binding protein CsrA [ 18 ] acts as an activator of the flhCD mRNA, which encodes the master regulator of motility and chemotaxis genes [ 19 ]. Enterobacter sp....”
- Monitoring Biofilm Formation and Microbial Interactions that May Occur During a Salmonella Contamination Incident across the Network of a Water Bottling Plant
Karampoula, Microorganisms 2019 - “...the present study, DNA fragments containing the promoter and coding regions of the genes csrA (STM14_3412), csgB (STM14_1309), sspH2 (STM14_2769), and fliD (STM14_2380) were PCR-amplified from the chromosomal DNA of the Salmonella enterica serovar Typhimurium 14028S using the corresponding primer pairs listed in Table 1 ....”
WP_004155916 carbon storage regulator CsrA from Erwinia amylovora ACW56400
97% identity, 100% coverage
CSRA_PROMI / Q93MI1 Translational regulator CsrA; Carbon storage regulator from Proteus mirabilis (see paper)
PMI0377 carbon storage regulator from Proteus mirabilis HI4320
95% identity, 97% coverage
- function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
function: Expression from a low-copy number plasmid has no effect on swimming, but blocks swarming and virulence factor expression as measured by cell lengthening and hemolysin, protease, urease and flagellin production (PubMed:12488561). Expression destabilizes hemolysin mRNA (PubMed:12488561). Complements an E.coli disruption mutant (PubMed:12488561).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core. - Proteus mirabilis and Urinary Tract Infections
Schaffer, Microbiology spectrum 2015 - “...of several inputs to flhDC regulation ( 99 ). RsmA/CsrA Overexpression of another gene, rsmA (PMI0377, r epressor of s econdary m etabolites, also called csrA ) results in repression of swarming motility and differentiation ( 100 ). The predicted protein is 96% identical to CsrA,...”
- “...) PMI3692 putative lipoprotein NR cr NR ( 56 ) Phenotypes observed by overexpression rsmA/csrA PMI0377 carbon storage regulator NR - - ( 100 ) mrpJ d PMI0271 fimbrial operon regulator - - aberr ( 162 , 203 ) wosA PMI0608 regulator of swarming motility ++...”
CSRA_SERMA / O85735 Translational regulator CsrA; Carbon storage regulator; Repressor of secondary metabolites from Serratia marcescens (see paper)
100% identity, 81% coverage
- function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
function: Involved in the process of swarming and quorum-sensing signal production; overexpression strongly inhibits swarming motility, pigment and N-acylhomoserine lactone (quorum-sensing signal) production but not swimming motility or swarmer cell differentiation (PubMed:11287746).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core.
disruption phenotype: Swarming motility initiates later than in wild- type; once initiatated the swarming velocity is normal (PubMed:11287746).
K3G22_13785 carbon storage regulator CsrA from Shewanella putrefaciens
93% identity, 92% coverage
SO3426, SO_3426 carbon storage regulator from Shewanella oneidensis MR-1
93% identity, 92% coverage
A0KPF9 Translational regulator CsrA from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
100% identity, 89% coverage
PST_1371 carbon storage regulator from Pseudomonas stutzeri A1501
87% identity, 100% coverage
EQU24_RS07950 carbon storage regulator CsrA from Methylotuvimicrobium buryatense
88% identity, 92% coverage
- A methanotrophic bacterium to enable methane removal for climate mitigation
He, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...consistent with downregulation (1.5 to 2.0 log 2 -fold) of the carbon storage regulator csrA (EQU24_RS07950), which has been shown to negatively mediate glycogen synthesis in Escherichia coli ( 35 ). It is not clear why the cells would increase carbon storage, but it may reflect...”
VP2546 carbon storage regulator from Vibrio parahaemolyticus RIMD 2210633
M892_13560 carbon storage regulator CsrA from Vibrio campbellii ATCC BAA-1116
95% identity, 88% coverage
- Environmental magnesium ion affects global gene expression, motility, biofilm formation and virulence of Vibrio parahaemolyticus
Li, Biofilm 2024 - “...transcriptional regulator EbgR VP2478 2.6976 7.25E-12 response regulator VP2516 opaR 2.9274 0.000122252 transcriptional regulator OpaR VP2546 csrA 2.2577 4.83E-08 carbon storage regulator CsrA VP2603 0.4863 3.34E-06 LysR family transcriptional regulator VP2752 oxyR 2.7041 5.88E-19 DNA-binding transcriptional regulator OxyR VP2777 2.1875 9.87E-08 transcriptional regulator VP2808 nsrR 2.8367...”
- “...Mg 2+ . The expression levels of opaR (VP2516), oxyR (VP2752), cadC (VP2893) and csrA (VP2546) were all upregulated more than 2-fold by Mg 2+ , suggesting that these regulators are likely be involved in adaptation to Mg 2+ stress. OpaR is a master global regulator...”
- L-arabinose affects the growth, biofilm formation, motility, c-di-GMP metabolism, and global gene expression of Vibrio parahaemolyticus
Zhang, Journal of bacteriology 2023 (secret) - Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
Hazen, Applied and environmental microbiology 2009 - “...protein 50S ribosomal protein L17 VP0082 VP0275 VP0186 VP2546 VP1210 VP0261 VPA1414 VP0273 VP2098 Transmembrane protein 50S ribosomal protein L30 50S ribosomal...”
- Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
Wang, Frontiers in microbiology 2013 - “...1.48 1.55 T M892_13405 Periplasmic negative regulator of sigma E 1.17E-05 1.51 0.88 1.72 T M892_13560 Carbon storage regulator 1.18E-04 1.75 1.05 1.67 T M892_20245 Universal stress protein A 1.03E-09 3.31 1.71 1.94 T M892_05075 Translocation protein TolB 3.03E-05 1.18 0.65 1.82 U M892_05460 ABC transporter,...”
VC0548 carbon storage regulator from Vibrio cholerae O1 biovar eltor str. N16961
95% identity, 88% coverage
TE101_05290 carbon storage regulator CsrA from Alteromonas macleodii
90% identity, 95% coverage
- Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise
Hou, The ISME journal 2018 - “...coli or RsmX-Z in pathogenic bacteria. Together with the carbon storage protein A (CsrA) homolog Te101_05290, these RNAs likely control the expression of numerous genes in responding to changes in the environment. Subject terms Water microbiology Microbial ecology Bacterial genetics Marine microbiology issue-copyright-statement International Society for...”
- “...they can sequester and antagonize the respective regulatory proteins. Notably, Alteromonas Te101 possesses a CsrA (TE101_05290) homolog, as shown by the 87% sequence identify with the E. coli homolog and the presence of likely autoregulatory A(N)GGA motifs in its ribosome binding region. We conclude that Aln1a-c,...”
CSRA_PSEAE / O69078 Translational regulator CsrA; Carbon storage regulator; Global translational regulatory protein RsmA from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 4 papers)
NP_249596 carbon storage regulator from Pseudomonas aeruginosa PAO1
PA14_52570 RsmA, regulator of secondary metabolites from Pseudomonas aeruginosa UCBPP-PA14
PA0905 RsmA, regulator of secondary metabolites from Pseudomonas aeruginosa PAO1
85% identity, 100% coverage
- function: A key translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Mediates global changes in gene expression, shifting from rapid growth to stress survival by linking envelope stress, the stringent response and the catabolite repression systems. Usually binds in the 5'-UTR; binding at or near the Shine-Dalgarno sequence prevents ribosome-binding, repressing translation, binding elsewhere in the 5'-UTR can activate translation and/or stabilize the mRNA. Its function is antagonized by small RNA(s).
function: Binds to mRNA to regulate gene activity at a post- transcriptional level (Probable). Represses expression of many toxic extracellular enzymes and compounds; decreases translation of lasI and rhlI (PubMed:11673439). Positively controls swarming motility and rhanolipid and lipase, possibly via expression of rhlA; activates transcription of the CsrA/RsmA antagonistic sRNA RsmZ (PubMed:15126453). Overexpression dramatically reduces extracellular protease, elastase (lasB) and staphyolytic (lasA) activities, decreases HCN production, decreases levels of autoinducers 3-oxo-C12-HSL (3-oxo- N-(tetrahydro-2-oxo-3-furanyl)-dodecanamide) and C4-HSL (N- butanoylhomoserine lactone), and abolishes production of cytotoxic internal lectin PA-IL (lecA) (PubMed:11673439). Control of hcn expression is post-transcriptional (PubMed:11673439). Replaces endogenous gene(s) in E.coli and P.fluorescens (PubMed:16359708).
function: Probably binds to and is sequestered by non-coding small RNA (sRNA) RsmZ; overexpression of rsmZ produces very similar phenotypes to deletion of rsmA, while rsmZ deletion has no phenotype (PubMed:15126453).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (PubMed:16104018).
disruption phenotype: Grows slightly more slowly; 30% reduction in staphylolytic activity, increased production of lectin PA-IL, blue- green pigment pyocyanine and HCN (PubMed:11673439). Increases levels of autoinducers 3-oxo-C12-HSL (3-oxo-N-(tetrahydro-2-oxo-3-furanyl)- dodecanamide) and C4-HSL (N-butanoylhomoserine lactone) in early log phase which becomes nearly wild-type (3-oxo-C12-HSL) or 2-fold greater (C4-HSL) by late log phase (PubMed:11673439). Loss of swarming mobility and rhamnolipid production, loss of sRNA RsmZ expression, decreased lipase, increases synthesis of pyocyanine and HCN (PubMed:15126453). Loss of swarming mobility, overproduction of pyocyanine, reduction in lipase biosynthesis (PubMed:16359708). - Two Homologues of the Global Regulator Csr/Rsm Redundantly Control Phaseolotoxin Biosynthesis and Virulence in the Plant Pathogen Pseudomonas amygdali pv. phaseolicola 1448A
Ramírez-Zapata, Microorganisms 2020 - “...from Pph 1448A shows a very high identity to RsmA from strain PAO1 (accession no. NP_249596; 80.7 % id.), but had no activity as repressor ( Figure 8 A), whereas RsmE is less similar (63.5% id.) but leads to a strong repression ( Figure 8 A)....”
- RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa.
Allsopp, Proceedings of the National Academy of Sciences of the United States of America 2017 - GeneRIF: RsmA and AmrZ have roles in orchestrating assembly of all three type VI secretion systems in Pseudomonas aeruginosa
- Pseudomonas aeruginosa AlgU Contributes to Posttranscriptional Activity by Increasing rsmA Expression in a mucA22 Strain.
Stacey, Journal of bacteriology 2016 - GeneRIF: AlgU controls rsmA transcription and is responsible for RsmA activity in mucA mutant strains.
- An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses in Pseudomonas aeruginosa.
Marden, Proceedings of the National Academy of Sciences of the United States of America 2013 - GeneRIF: Despite striking changes in topology, RsmF adopts a tertiary structure similar to other CsrA family members and binds a subset of RsmA mRNA targets, suggesting that RsmF activity is mediated through a conserved mechanism of RNA recognition.
- Effect of overexpressing rsmA from Pseudomonas aeruginosa on virulence of select phytotoxin-producing strains of P. syringae.
Kong, Phytopathology 2012 (PubMed)- GeneRIF: The rsmA gene is consistently important in the overarching phenotypes disease and endophtyic colonization but its role varies with pathovar in certain underpinning phenotypes in the phytotoxin-producing strains of P. syringae.
- [Differential expression of two phenazine-producing loci mediated by deficiency of the global regulator rsmA in Psedomonas aeruginosa PAO1].
Cui, Wei sheng wu xue bao = Acta microbiologica Sinica 2012 (PubMed)- GeneRIF: Overexpression of the rsmA gene results in dramatical decrease of pyocyanin production.
- Pseudomonas aeruginosa biofilm matrix polysaccharide Psl is regulated transcriptionally by RpoS and post-transcriptionally by RsmA.
Irie, Molecular microbiology 2010 - GeneRIF: RsmA represses polysaccharide psl translation.
- Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA.
Brencic, Molecular microbiology 2009 - GeneRIF: RsmA acts as a negative translational regulator.
- More
- BosR: A novel biofilm-specific regulator in Pseudomonas aeruginosa
Dostert, Frontiers in microbiology 2022 - “...regulator 2.6 PA14_49880 (yfiR) B Tripartite signaling repressor 52.0 PA14_50180 fleR Two-component response regulator 9.1 PA14_52570 rsmA Carbon storage regulator 319.8 PA14_59790 pvrR A Two-component response regulator 3.1 PA14_59800 pvrS A Two-component kinase 2.9 PA14_60260 pilR Two-component response regulator 17.6 PA14_62490 dksA Suppressor protein 17.3 PA14_64230...”
- Response of Pseudomonas aeruginosa to the Innate Immune System-Derived Oxidants Hypochlorous Acid and Hypothiocyanous Acid
Farrant, Journal of bacteriology 2020 - “...regulator of multidrug efflux 0.0370 0.0002 <0.0001 PA14_45950 rsaL PA1431 Regulatory protein 0.1666 0.0367 0.0385 PA14_52570 rsmA PA0905 Posttranscriptional global regulator 0.0340 0.0003 <0.0001 PA14_56620 pyeR (2) PA4354 ArsR family transcriptional regulator 0.0396 0.0010 0.0068 PA14_60860 nfxB PA4600 TetR family transcriptional regulator of multidrug efflux 0.0515...”
- Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells
Coleman, Antimicrobial agents and chemotherapy 2020 (secret) - 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 - “...10 3 + PA0764 mucB Negative regulator for alginate biosynthesis 2.9 1.9 10 3 + PA0905 rsmA CsrA carbon storage regulator 2.8 4.4 10 2 + PA0916 Ribosomal protein S12 methylthiotransferase 2.0 3.2 10 3 PA1211 / -hydrolase 2.1 1.3 10 2 PA1212 Major facilitator superfamily;...”
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...(3.11) PA2184 yciE 3.58 6.19 (0.56) 91.89 (17.63) PA0529 yiiM 2.46 10.40 (3.24) 1.94 (0.05) PA0905; rsmA csrA 2.38 3.58 (0.67) 1.96 (0.20) a Fold-change in relative abundance of P. aeruginosa transcripts as determined via RNA-seq or qRT-PCR, and of E. coli transcript as determined via...”
- Pf4 Phage Variant Infection Reduces Virulence-Associated Traits in Pseudomonas aeruginosa
Tortuel, Microbiology spectrum 2022 - “...12.50 PA4231 pchA Salicylate biosynthesis isochorismate synthase Fur, RsmA, PchR 10.53 Virulence/biofilm switch GAC pathway PA0905 rsmA RsmA AlgU, AlgR, RsmY, RsmZ 7.19 PA0928 gacS Sensor/response regulator hybrid 2.24 PA3345 hptB Histidine phosphotransfer protein HptB 3.81 PA3346 hsbR* HptB-dependent secretion and biofilm regulator HsbR 2.34 PA3347...”
- Transcriptome Analysis of Pseudomonas aeruginosa Biofilm Following the Exposure to Malaysian Stingless Bee Honey
Seder, Advances and applications in bioinformatics and chemistry : AABC 2021 - “...biofilm using RT-qPCR versus 2.4-fold repression in the microarray experiment ( Figure 3C ); for PA0905 ( RsmA ), 3.00-fold induction versus 2.1-fold induction; for PA4958 ( FimW ), 2.1-fold repression versus 1.4-fold repression; for PA3708 ( WspA ), 2.5-fold repression versus 1.93-fold repression, for PA3345...”
- Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital
Esposito, Frontiers in microbiology 2021 - “...BLASTn ( Alikhan et al., 2011 ) against the rmtD1 allele of the P. aeruginosa (PA0905 strain), recovered from a human patient (GenBank accession number. DQ914960). Genetic context analysis of bla SPM-1 and rmtD1 resistance genes of Pa151 were performed with BLASTn algorithm and manually curated...”
- “...in the environmental Pa151 strain, displayed 100% identity to the rmtD1 gene from P. aeruginosa PA0905 strain, recovered from a human patient in 2005, in Brazil ( Doi et al., 2007 ). The rmtD1 was subsequently identified in K. pneumoniae and other Enterobacterales in Latin America,...”
- Peptide 1018 inhibits swarming and influences Anr-regulated gene expression downstream of the stringent stress response in Pseudomonas aeruginosa
Wilkinson, PloS one 2021 - “...total in S5 Table ) PA4853 ( fis ) 1 D DNA-binding protein -1.8 -2.1 PA0905 ( rsmA ) 1 D RNA binding protein translational regulator 1.6 NC PA4725 ( cbrA ) 1 D two-component sensor -1.5 NC PA5261 ( algR ) 1 D alginate biosynthesis...”
- COVID-19 Vaccine and Death: Causality Algorithm According to the WHO Eligibility Diagnosis
Pomara, Diagnostics (Basel, Switzerland) 2021 - “...cod.PA0278, Leica Biosystems NewCastle Ltd., Newcastle upon Tyne NE12 8EW, UK), Anti-IgG (clone RWP49, cod. PA0905, Leica Biosystems NewCastle Ltd., Newcastle upon Tyne NE12 8EW, UK). We applied the proposed flowchart to these exemplificative cases related to a single COVID-19 vaccine, even though we recommend to...”
- Manipulating the type VI secretion system spike to shuttle passenger proteins
Wettstadt, PloS one 2020 - “...before vgrG1a (PA0091) STOP codon This study PAO1rsmA::pldA-bla TEM-1 PAO1 with deletion in rsmA ( PA0905 ) and an insertion of bla TEM-1 before pldA (PA3487) STOP codon [ 1 ] PAO1rsmAtssB2 PAO1 with deletion in rsmA ( PA0905 ) and tssB2 ( PA1657 ) This...”
- “...before vgrG4b (PA3486) STOP codon This study PAO1rsmA::vgrG4b-bla TEM-1 PAO1 with deletion in rsmA ( PA0905 ) and an insertion of bla TEM-1 before vgrG4b (PA3486) STOP codon This study E. coli DH5 F endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 80dlacZM15 ( lacZYA-argF)U169...”
- More
HMPREF0010_03075, WP_000906487 carbon storage regulator CsrA from Acinetobacter nosocomialis
91% identity, 67% coverage
7yr6E / O69078 Cryo-em structure of pseudomonas aeruginosa rsmz RNA in complex with two rsma protein dimers (see paper)
93% identity, 90% coverage
TERTU_2809 carbon storage regulator from Teredinibacter turnerae T7901
86% identity, 89% coverage
WP_016209832 carbon storage regulator CsrA from Piscirickettsia salmonis T-GIM
88% identity, 64% coverage
- Core non-coding RNAs of Piscirickettsia salmonis
Segovia, PloS one 2018 - “...protein by nine imperfect repeat sequences localized in the CsrC hairpins [ 59 ]. CsrA (WP_016209832) and CsrC ncRNA are also present in P . salmonis , reinforcing the predicted P . salmonis ncRNAs ( S2 Table ) and transcriptomics analyses ( S3 Table ). Additionally,...”
MARME_RS03780 carbon storage regulator CsrA from Marinomonas mediterranea MMB-1
84% identity, 92% coverage
Alvin_1102 carbon storage regulator, CsrA from Allochromatium vinosum DSM 180
86% identity, 78% coverage
ETAE_2858 carbon storage regulator from Edwardsiella tarda EIB202
98% identity, 80% coverage
lpg0781 global regulator (carbon storage regulator) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
77% identity, 73% coverage
- Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs-LvbR network, effector proteins and the flagellum
Hochstrasser, Environmental microbiology 2022 - “...as the upstream region of the corresponding genes with the following sizes: P csrA (515bp, lpg0781 ) and P 6SRNA (534bp, ssrS , between lpg0877 and lpg0876 ). The PCR products were cloned into SacI and XbaIdigested pCM009 (Schell et al ., 2016 ) using the...”
- Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing
Wee, Nature communications 2021 - “...the k- mers aligned to a region of the genome spanning between loci lpg0748 and lpg0781 representing an 18kb cluster of genes involved in LPS biosynthesis and modification (Fig. 2 ) 31 . A total of 22 genes in this cluster each had at least one...”
- “...lpg0766, lpg0767, lpg0768, lpg0769, lpg0771, lpg0772, lpg0773, lpg0774, lpg0775, lpg0777 (lag-1), lpg0778, lpg0779, lpg0780 and lpg0781 (Fig. 2 and Supplementary Table 1 ). Two additional conservative SEER analyses using more stringently subsampled datasets resulted in a smaller number of significantly enriched k- mers (205 and 61,...”
- csrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila
Abbott, Journal of bacteriology 2016 - “...material). Induced expression constructs. Wild-type (WT) csrA (lpg0781), csrT (lpg2094), and csrA-22 (lpg1003) with C-terminal His6 tags were amplified from...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...species: L. pneumophila contains five CsrA homologs (Lpg0781, Lpg1593, Lpg1003, Lpg1257, and Lpg2094), L. longbeachae contains four homologs (Llo2071, Llo2874,...”
- Small Regulatory RNA and Legionella pneumophila
Faucher, Frontiers in microbiology 2011 - “...(Suzuki et al., 2006 ). Legionella pneumophila contains four CsrA homologs, of which one ( lpg0781 ) was identified as able to complement a csrA deletion in E. coli (Fettes et al., 2001 ). The roles of the other CsrA homologs are currently unknown. In L....”
- The PmrA/PmrB two-component system of Legionella pneumophila is a global regulator required for intracellular replication within macrophages and protozoa
Al-Khodor, Infection and immunity 2009 - “...well as the RpoE sigma factor encoding genes (lpg0781 and lpg1577), was regulated in a PmrA/PmrB-dependent manner. The global regulator encoding gene csrA was...”
lpp0845 global regulator CsrA from Legionella pneumophila str. Paris
77% identity, 94% coverage
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “...mutant csrA - by inserting an apramycin-resistance cassette after the amino acid Tyr48 of the lpp0845 gene encoding the major CsrA in L . pneumophila Paris ( S1A Fig ). CsrA is essential for L . pneumophila , but such a truncated CsrA variant has a...”
- “...a double Flag-Tag at the C-terminal end or without Flag-Tag) full-length cDNAs encoding CsrA ( lpp0845 ) were amplified by PCR using primer CsrA-F tctagaATGTTGATTTTGACTCGGCGTATAG and CsrA-R ctgcagTTATACTGCTTGTTCCGAATCATC or CsrA-Flag-R ctgcagTTACTTATCGTCA TCGTCCTTGTAGTCCTTATCGTCATCGTCCTTGTAGTCTACTGCTTGTTCCGAATCATC, respectively, and cloned into pGEM-T easy vector (Promega). The fragment was verified by sequencing,...”
- Legionella pneumophila CsrA regulates a metabolic switch from amino acid to glycerolipid metabolism
Häuslein, Open biology 2017 - “...Paris was constructed by inserting an apramycin-resistance cassette after the amino acid Tyr48 of the lpp0845 gene encoding the major CsrA in L. pneumophila Paris [ 35 ]. 4.2. Oxygen consumption experiments Legionella pneumophila Paris wt and csrA mutant were grown to exponential phase (OD 600...”
- Specific real-time PCR for simultaneous detection and identification of Legionella pneumophila serogroup 1 in water and clinical samples
Mérault, Applied and environmental microbiology 2011 - “...the LPS gene cluster region between lpp0826 (rmlA) and lpp0845 (csrA homologue) in Sg6, -10, -12, -13, and -14 Primer designation Primer sequence 6 Csra-LpsLR1...”
- Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
Sahr, Molecular microbiology 2009 - “...and the chemiluminescence substrate of the manufacturer CsrA overexpression and purification Full-length cDNAs encoding CsrA (Lpp0845) were amplified by PCR using primer CsrA-for ATACCATGGTGATTTTGACTCGGCGTATAG and CsrA-rev CCCCCCGGGTACTGCTTGCGAATCAGATTC. Fragments were cloned in frame into the expression vector pIVEX2.3d (Roche Diagnostics), which adds a hexa-histidine tag to the...”
- “...- lpp0384 50S ribosomal protein L1 2.53 - lpp0383 50S ribosomal protein L11 1.98 - lpp0845 Global regulator CsrA 1.66 - Table 2 Selection of PE phase genes down-regulated in the letA and rsmYZ mutants Gene name Known or predicted product letA/wt rsmYZ/wt lpp0728 Similar to...”
PXO_00146 carbon storage regulator from Xanthomonas oryzae pv. oryzae PXO99A
E2J5T5 Translational regulator CsrA from Xanthomonas oryzae pv. oryzae
XAC1743 carbon storage regulator from Xanthomonas axonopodis pv. citri str. 306
XOO2938 carbon storage regulator from Xanthomonas oryzae pv. oryzae KACC10331
90% identity, 74% coverage
- The rsmA-like gene rsmA(Xoo) of Xanthomonas oryzae pv. oryzae regulates bacterial virulence and production of diffusible signal factor
Zhu, Molecular plant pathology 2011 - “...number NC_007705.1), XOO2938 (accession number NC_006834.1) and PXO_00146 (accession number NC_010717.1), all of which were annotated as csrA/rsmA (hereafter...”
- Novel Virulence Factors Deciphering Klebsiella pneumoniae KpC4 Infect Maize as a Crossing-Kingdom Pathogen: An Emerging Environmental Threat
Huang, International journal of molecular sciences 2022 - “...E. amylovora D4I307 Fire blight Pear/apple KpC4_0520 rsmAXoo 82.14 RNA-binding protein Xanthomonas oryzae pv. Oryzae E2J5T5 Bacterial leaf blight Rice KpC4_2459 iutA 75.93 Siderophore-mediated iron acquisition Pantoea stewartii H3RJF2 Stewart wilt of sweet corn Maize ijms-23-16005-t003_Table 3 Table 3 Annotation of open reading frames (ORFs) of...”
- The post-transcriptional regulator rsmA/csrA activates T3SS by stabilizing the 5' UTR of hrpG, the master regulator of hrp/hrc genes, in Xanthomonas
Andrade, PLoS pathogens 2014 - “...in the activation of the pathogenicity and HR of XCC The rsmA gene of XCC (XAC1743, GenBank accession number NP_642074) consists of 213 bp nucleotides and encodes a protein comprising 70 amino acids [46] . RsmA of XCC displays 74% identity with E. coli K12 CsrA...”
- “...phase. Wt= X. citri subsp. citri strain 306, rsm A =mutant with a deletion of XAC1743 ( rsmA ) harboring the empty plasmid pUFR047, pUFRrsmA=complementation of rsmA with rsmA cloned in pUFR047, hrpG= hprG mutant [9] , pUFRhrpG=complementation of hrpG with hrpG cloned into pUFR047, and...”
- The rsmA-like gene rsmA(Xoo) of Xanthomonas oryzae pv. oryzae regulates bacterial virulence and production of diffusible signal factor
Zhu, Molecular plant pathology 2011 - “...was identical to XOO_2790 (accession number NC_007705.1), XOO2938 (accession number NC_006834.1) and PXO_00146 (accession number NC_010717.1), all of which were...”
DP16_RS13530 carbon storage regulator CsrA from Stenotrophomonas maltophilia
88% identity, 78% coverage
- Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature
Patil, Microbial genomics 2021 - “...DP16_RS05720 Sulphate transporter 2.53105 0.0011 0.0036 DP16_RS21940 YebC/PmpR family DNA-binding transcriptional regulator 2.50375 0.00005 0.00022 DP16_RS13530 Carbon storage regulator CsrA csrA 2.46402 0.00005 0.00022 DP16_RS00255 Large-conductance mechanosensitive channel protein MscL mscL 2.45568 0.00005 0.00022 DP16_RS11010 Translation initiation factor IF-1 infA 2.43986 0.00005 0.00022 DP16_RS07410 NAD(P)H-dependent oxidoreductase...”
PD0095 carbon storage regulator from Xylella fastidiosa Temecula1
XF0125 carbon storage regulator from Xylella fastidiosa 9a5c
87% identity, 73% coverage
CSRA2_PSEPH / P69920 Translational regulator CsrA2; Carbon storage regulator 2; Regulator of secondary metabolites RsmA from Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CFBP 6595 / CHA0) (see 6 papers)
Pchl3084_4387, WP_002554426 carbon storage regulator CsrA from Pseudomonas chlororaphis
PSPTO1844, PSPTO_1844 carbon storage regulator from Pseudomonas syringae pv. tomato str. DC3000
YP_236624 Carbon storage regulator from Pseudomonas syringae pv. syringae B728a
76% identity, 98% coverage
- function: A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:10570200, PubMed:11807065, PubMed:15601712, PubMed:23635605). Represses expression of hcnA; alterations in the ribosome-binding site relieve the repression (PubMed:10570200). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequence in loops to which the CsrA proteins bind (PubMed:11807065, PubMed:14622422, PubMed:16286659). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation; each sRNA can bind more than one protein (PubMed:14622422, PubMed:16286659). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Deletion of rsmY or rsmZ alone has no detectable phenotype, but a double sRNA deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and protects cucumber plants from fungal infection less well than wild-type (PubMed:14622422). The triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core, while the alpha-helices form wings that extend away from the core.
disruption phenotype: Increased expression of aprA (usually repressed by this protein) (PubMed:10570200). Partially suppresses a gacA deletion mutant (PubMed:10570200, PubMed:11807065). Double csrA1-csrA2 deletion mutants fully suppress the requirement for GacA/GacS in control of its regulon (PubMed:15601712). Decreased expression and stability of RsmY and RsmZ sRNAs (PubMed:15601712). - Two Homologues of the Global Regulator Csr/Rsm Redundantly Control Phaseolotoxin Biosynthesis and Virulence in the Plant Pathogen Pseudomonas amygdali pv. phaseolicola 1448A
Ramírez-Zapata, Microorganisms 2020 - “...so only one is shown for each. Abbreviations (accession numbers): Pf0-1, P. fluorescens Pf0-1 (RsmA, WP_002554426; RsmE, WP_003179932); 1448A, P. amygdali pv. phaseolicola 1448A; B728a, P. syringae pv. syringae B728a; DC3000, P. syringae pv. tomato DC3000; accession numbers for 1448A, B728a and DC3000 proteins are indicated...”
- Roles of the Gac-Rsm pathway in the regulation of phenazine biosynthesis in Pseudomonas chlororaphis 30-84
Wang, MicrobiologyOpen 2013 - “...csaR Transcriptional activator 0.54 0.38 0.71 0.50 Pchl3084_0554 hfq RNA chaperone 1642.19 1408.2 0.84 0.28 Pchl3084_4387 rsmA Translational regulator 151.82 307.24 2.02 0.03 Pchl3084_2024 rsmE Translational regulator 292.7 204.83 0.70 0.06 Pchl3084_3970 rsmX ncRNA 1486.51 201.13 0.14 0.02 Pchl3084_5419 rsmY ncRNA 38112.4 329.2 0.01 0.02 Pchl3084_1190...”
- The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions
Liu, Frontiers in plant science 2021 - “...rsmX5 7.59 4.52 1.68 18.7 3.74 4.9 PSPTO_1629 rsmA1 2.49 / 2.32 1.9 / 1.57 PSPTO_1844 rsmA2 20 15.56 / 11.28 6.16 1.83 PSPTO_3943 rsmA4 / / / / / / PSPTO_5621 rsmA5 2.28 / 1.69 1.66 2.93 4.86 Differential expression in rsmA23 versus Pst DC3000,...”
- Homologues of the RNA binding protein RsmA in Pseudomonas syringae pv. tomato DC3000 exhibit distinct binding affinities with non-coding small RNAs and have distinct roles in virulence
Ge, Molecular plant pathology 2019 - “...resistance rsmA1(Pspto1629 ) Km r , rsmA1 ::Kan , DC3000 derivative This study rsmA2 ( Pspto1844) Km r , rsmA2 ::Kan , DC3000 derivative This study rsmA3(Pspto3566) Km r , rsmA3 ::Kan , DC3000 derivative This study rsmA4(Pspto3943) Km r , rsmA4 ::Kan , DC3000 derivative...”
- Homologues of the RNA binding protein RsmA in Pseudomonas syringae pv. tomato DC3000 exhibit distinct binding affinities with non-coding small RNAs and have distinct roles in virulence
Ge, Molecular plant pathology 2019 - “...RsmE: ABW16953; P. fluorescens A506 RsmE: AFJ58988; P. syringae pv. syringae B728a RsmA1: YP_236820; RsmA2: YP_236624; RsmA3: YP_236409; P. syringae pv. tomato DC3000 RsmA1: AAO55149; RsmA2: AAO55363; RsmA3: AAO57040; RsmA4: AAO57404; RsmA5: YP_003355050. Click here for additional data file. Fig. S2 Effect of RsmA1 of P....”
CBU_1050 carbon storage regulator from Coxiella burnetii RSA 493
73% identity, 79% coverage
- Quantitative Proteome Profiling of Coxiella burnetii Reveals Major Metabolic and Stress Differences Under Axenic and Cell Culture Cultivation
Dresler, Frontiers in microbiology 2019 - “...maturation factor RbfA as well as the ribosome-associated inhibitor A (RaiA, CBU_0020) are downregulated. CsrA2 (CBU_1050), a stress response regulator, is upregulated. In addition, caseinolytic proteases (Clp, chaperon), such as ClpA and ClpP-like proteins CBU_0353, CBU_1483, and CBU_1538, were upregulated for NMI in ACCM-D. Exponential phase...”
- “...to ACCM-2 ACCM-D to ACCM-2 Regulation CBU_0303 SpoT GTP pyrophosphokinase 3.59 1.46 NaN 1.59 0.65 CBU_1050 CsrA2 Translational regulator 0.10 0.13 1.53 2.89 3.72 CBU_1596 RpoD Sigma factor 0.60 0.63 0.97 1.01 1.06 CBU_1669 RpoS Sigma factor 0.62 0.36 0.75 659.15 382.27 CBU_1916 UspA2 Universal stress...”
- A CsrA-Binding, trans-Acting sRNA of Coxiella burnetii Is Necessary for Optimal Intracellular Growth and Vacuole Formation during Early Infection of Host Cells
Wachter, Journal of bacteriology 2019 (secret)
XaFJ1_GM001161 carbon storage regulator CsrA from Xanthomonas albilineans
81% identity, 80% coverage
HZ99_RS09580 carbon storage regulator CsrA from Pseudomonas fluorescens
76% identity, 98% coverage
PFLU4746 carbon storage regulator homolog from Pseudomonas fluorescens SBW25
GIB64_12670, GIB65_24765, PflSS101_4138 carbon storage regulator CsrA from Pseudomonas lactis
77% identity, 97% coverage
- Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25
Gallie, Molecular biology and evolution 2019 - “...tipped in favor of ribosomes by decreasing RsmA/E activity in two ways. First, rsmA1 ( pflu4746 ) and rsmE ( pflu4165 ) were individually deleted from 6B 4 , giving 6B 4 - rsmA1 and 6B 4 - rsmE ( supplementary text S2 , Supplementary Material...”
- Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase
Remigi, Molecular biology and evolution 2019 - “...their translation inhibition activity. Three CsrA/RsmA homologs are present in SBW25 and were named rsmA1 (PFLU4746), rsmA2 (PFLU4324) and rsmE (PFLU4165). The phenotypic effect of the Gac/Rsm pathway was investigated by creating deletion mutants for the response regulator gacA and the two CsrA/RsmA homologs rsmA1 and...”
- Genomic Analysis of Three Cheese-Borne Pseudomonas lactis with Biofilm and Spoilage-Associated Behavior
Quintieri, Microorganisms 2020 - “...ITEM 17299 Attachment Switching from planktonic to biofilm state csr A/ rsm A GIB65_24765 PROKKA_01891 GIB64_12670 c-di-GMP regulated gac S/ gac A GIB65_18615/ GIB65_01605 PROKKA_02681/ PROKKA_01410 GIB64_19800 GIB64_28045 lux Q GIB65_08270 PROKKA_00312 GIB64_13935 luxR GIB65_04815 PROKKA_03671 GIB64_14810 rhlR/rhlI GIB65_06785/ GIB65_06780 PROKKA_01310/ PROKKA_01311 GIB64_11890/ GIB64_11895 sag S...”
- “...ITEM 17298 ITEM 17299 Attachment Switching from planktonic to biofilm state csr A/ rsm A GIB65_24765 PROKKA_01891 GIB64_12670 c-di-GMP regulated gac S/ gac A GIB65_18615/ GIB65_01605 PROKKA_02681/ PROKKA_01410 GIB64_19800 GIB64_28045 lux Q GIB65_08270 PROKKA_00312 GIB64_13935 luxR GIB65_04815 PROKKA_03671 GIB64_14810 rhlR/rhlI GIB65_06785/ GIB65_06780 PROKKA_01310/ PROKKA_01311 GIB64_11890/ GIB64_11895...”
- The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis
Song, Microbial biotechnology 2015 - “...involving the two sRNAs RsmY (PflSS101_4962) and RsmZ (PflSS101_1168), and the two repressor proteins RsmA (PflSS101_4138) and RsmE (PflSS101_3491), in lipopeptide biosynthesis and predicted the potential target genes of the Rsm repressor proteins. Strain SS101 was originally isolated from the rhizosphere of wheat (de Souza etal...”
- “...massetolide biosynthesis. In silico analysis of the SS101 genome led to the identification of rsmA (PflSS101_4138), rsmE (PflSS101_3491) and csrA (PflSS101_3653). Phylogenetic analyses showed that they clustered closely with their homologues in other P.fluorescens strains and Pseudomonas species at both DNA and protein levels ( Fig.S1...”
PFLU4165 carbon storage regulator from Pseudomonas fluorescens SBW25
71% identity, 78% coverage
2mf0A / P0DPC3 Structural basis of the non-coding RNA rsmz acting as protein sponge: conformer l of rsmz(1-72)/rsme(dimer) 1to3 complex (see paper)
71% identity, 95% coverage
PFLU_4165, PflSS101_3491 carbon storage regulator CsrA from Pseudomonas lactis
71% identity, 91% coverage
CSRA1_PSEPH / P0DPC3 Translational regulator CsrA1; Carbon storage regulator 1; Regulator of secondary metabolites RsmE from Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CFBP 6595 / CHA0) (see 6 papers)
Pchl3084_2024 carbon storage regulator CsrA from Pseudomonas chlororaphis subsp. aureofaciens 30-84
71% identity, 91% coverage
- function: A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability (PubMed:17704818, PubMed:23635605). Post-transcriptionally represses the expression of genes controlled by GacA/GacS (PubMed:15601712, PubMed:23635605). Binds the 5' UTR of mRNA; the mRNA binds to the outside edge to each monomer and each dimer could bind the same mRNA twice (PubMed:17704818). Recognizes a (A/U)CANGGANG(U/A) consensus, binds to GGA (part of the Shine-Dalgarno sequence) in the 5' UTR loop, which prevents ribosome binding (PubMed:17704818, PubMed:23635605, PubMed:24561806). Overexpression represses target protein expression; mutating nucleotides in the 5' UTR abolishes repression in vivo (PubMed:17704818, PubMed:23635605). Binds specifically to small RNAs (sRNA) RsmX, RsmZ and RsmY; these sRNAs fold into secondary structures with multiple GGA sequences in loops to which the CsrA proteins bind (PubMed:15601712, PubMed:16286659, PubMed:24828038). Binding to RsmX, RsmY or RsmZ titrates the protein so that it can no longer bind mRNA and repress translation (PubMed:15601712, PubMed:24828038). RsmZ can bind up to 5 CsrA1 (rsmE) dimers; they bind cooperatively to GGA sequences in RsmZ in a defined order (PubMed:24561806, PubMed:24828038). Required for optimal expression and stability of sRNAs RsmX, RsmY and RsmZ (PubMed:15601712, PubMed:16286659). Four CsrA1 dimers maximally protect RsmZ from RNase activity (PubMed:24828038). Deletion of rsmX, rsmY or rsmZ alone has no detectable phenotype, but a double rsmY-rsmZ deletion has a marked decrease in production of secondary metabolites HCN, exoprotease AprA, antifungal agent 2,4-diacetylphloroglucinol and swarming motility, and protects cucumber plants from fungal infection less well than wild- type; the triple sRNA deletion has even stronger loss of these phenotypes (PubMed:16286659).
subunit: Homodimer (PubMed:17704818, PubMed:23635605, PubMed:24561806, PubMed:24828038). The beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (PubMed:17704818, PubMed:24561806, PubMed:24828038).
disruption phenotype: Increased expression of genes controlled by GacA/GacS (aprA, hcnA, phlA), partially suppresses a gacS deletion mutant (PubMed:15601712). Double csrA1-csrA2 deletion mutants fully suppress the requirement for GacA/GacS in control of its regulon (PubMed:15601712). Decreased expression and stability of RsmY and RsmZ sRNAs (PubMed:15601712). - Roles of the Gac-Rsm pathway in the regulation of phenazine biosynthesis in Pseudomonas chlororaphis 30-84
Wang, MicrobiologyOpen 2013 - “...hfq RNA chaperone 1642.19 1408.2 0.84 0.28 Pchl3084_4387 rsmA Translational regulator 151.82 307.24 2.02 0.03 Pchl3084_2024 rsmE Translational regulator 292.7 204.83 0.70 0.06 Pchl3084_3970 rsmX ncRNA 1486.51 201.13 0.14 0.02 Pchl3084_5419 rsmY ncRNA 38112.4 329.2 0.01 0.02 Pchl3084_1190 rsmZ ncRNA 1679.64 261.26 0.16 0.05 Figure 2...”
E2P69_RS21330 carbon storage regulator CsrA from Xanthomonas perforans
71% identity, 97% coverage
WP_003179932 carbon storage regulator CsrA from Pseudomonas sp. PSB1
71% identity, 91% coverage
Q91_0863 carbon storage regulator CsrA from Cycloclasticus sp. P1
75% identity, 92% coverage
PPUTLS46_020631, RPPX_02245 carbon storage regulator CsrA from Pseudomonas putida S12
PP_4472 carbon storage regulator CsrA from Pseudomonas putida KT2440
75% identity, 97% coverage
- Adaptive Laboratory Evolution Restores Solvent Tolerance in Plasmid-Cured Pseudomonas putida S12: a Molecular Analysis
Kusumawardhani, Applied and environmental microbiology 2021 - “...(iii) Biofilm formation. In ALE-derived strains, we observed a constitutive upregulation of the rsmA locus (RPPX_02245). Upregulation of the rsmA locus may be caused by the mutations found in the gacS or gacA locus and is known to promote a motile lifestyle in Pseudomonas ( 21...”
- Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids
Fu, PloS one 2015 - “...the PhaC1 protein, putatively through a Gac/Rsm regulatory cascade [ 35 ]. Two CsrA homologs (PPUTLS46_020631 and PPUTLS46_015344) were detected in the transcriptome, but not in the proteome, of P . putida LS46, suggesting these regulators were likely expressed at low levels, and with no significant...”
- The Pseudomonas putida CsrA/RsmA homologues negatively affect c-di-GMP pools and biofilm formation through the GGDEF/EAL response regulator CfcR
Huertas-Rosales, Environmental microbiology 2017 - “...., 2016 rsmE Null PP_3832 derivative of KT2440 HuertasRosales et al ., 2016 rsmA Null PP_4472 derivative of KT2440 HuertasRosales et al ., 2016 rsmIE Double null PP_1746/PP_3832 derivative of KT2440 HuertasRosales et al ., 2016 rsmEA Double null PP_3832/PP_4472 derivative of KT2440 HuertasRosales et al...”
- Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida
Huertas-Rosales, Applied and environmental microbiology 2016 - “...in PP_3832 (rsmE) Null mutant derivative of KT2440 in PP_4472 (rsmA) Null mutant derivative of KT2440 in PP_1746 and PP_3832 Null mutant derivative of KT2440 in...”
- “...PP_4472 Null mutant derivative of KT2440 in PP_1746 and PP_4472 Null mutant derivative of KT2440 in PP_1746, PP_3832 and PP_4472 23 39 This study This study...”
PSPTO_3566 carbon storage regulator from Pseudomonas syringae pv. tomato str. DC3000
YP_236409 Carbon storage regulator from Pseudomonas syringae pv. syringae B728a
78% identity, 87% coverage
PP3832, PP_3832 carbon storage regulator from Pseudomonas putida KT2440
62% identity, 94% coverage
- Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
Huertas-Rosales, Frontiers in molecular biosciences 2021 - “...CfcR phosphorylation and activation PP_3765 turB H-NS family protein (MvaT homolog) Repressor of gene expression PP_3832 rsmE Post-transcriptional regulatory protein RsmE PP_4099 uvrY Two-componenent system response regulator Operon with uvrC (nucleotide excision repair) Non-coding RNAs PP_mr05 rsmY Non-coding RNA PP_mr44 Non-coding RNA PP_mr52 Non-coding RNA DNA...”
- The Pseudomonas putida CsrA/RsmA homologues negatively affect c-di-GMP pools and biofilm formation through the GGDEF/EAL response regulator CfcR
Huertas-Rosales, Environmental microbiology 2017 - “...., 2011 rsmI Null PP_1476 derivative of KT2440 HuertasRosales et al ., 2016 rsmE Null PP_3832 derivative of KT2440 HuertasRosales et al ., 2016 rsmA Null PP_4472 derivative of KT2440 HuertasRosales et al ., 2016 rsmIE Double null PP_1746/PP_3832 derivative of KT2440 HuertasRosales et al .,...”
- Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida
Huertas-Rosales, Applied and environmental microbiology 2016 - “...in PP_1746 (rsmI) Null mutant derivative of KT2440 in PP_3832 (rsmE) Null mutant derivative of KT2440 in PP_4472 (rsmA) Null mutant derivative of KT2440 in...”
- “...PP_1746 and PP_3832 Null mutant derivative of KT2440 in PP_3832 and PP_4472 Null mutant derivative of KT2440 in PP_1746 and PP_4472 Null mutant derivative of...”
- ATP-dependent RecG helicase is required for the transcriptional regulator OxyR function in Pseudomonas species
Yeom, The Journal of biological chemistry 2012 - “...lsfA, and PP3639, the metabolism-related genes aceA and PP3832, a transporter gene cysP, and a regulatory gene rpoX. Of the identified oxidative stress-related...”
F382_01930 carbon storage regulator CsrA from Mannheimia haemolytica D153
68% identity, 87% coverage
TERTU_2436 carbon storage regulator from Teredinibacter turnerae T7901
76% identity, 84% coverage
MARME_RS09140 carbon storage regulator CsrA from Marinomonas mediterranea MMB-1
64% identity, 90% coverage
lpg2094 carbon storage regulator RsmA from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
PtVFX2014_07430 carbon storage regulator CsrA from Legionella pneumophila
65% identity, 71% coverage
- csrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila
Abbott, Journal of bacteriology 2016 - “...expression constructs. Wild-type (WT) csrA (lpg0781), csrT (lpg2094), and csrA-22 (lpg1003) with C-terminal His6 tags were amplified from Lp02 genomic DNA...”
- “...ICE-ox of L. pneumophila Philadelphia-1 carries the csrA paralog lpg2094, which we name here csrT (csrA paralog for ICE transfer) (4). To test the effect of...”
- Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires' disease: a unique mosaic genetic backbone
Borges, Scientific reports 2016 - “.../ PtVFX2014_07340 ) 32 60 . The prpA-lvrABC gene cluster includes a csrA paralog ( lpg2094 / PtVFX2014_07430 ) encoding a RNA-binding protein that belongs to a superfamily of global regulators that are widely distributed among bacterial species. In L. pneumophila , CsrA-like proteins have been...”
- csrR, a Paralog and Direct Target of CsrA, Promotes Legionella pneumophila Resilience in Water
Abbott, mBio 2015 - “...Technologies) and SuperSignal West Pico chemiluminescent substrate (Thermo Scientific). A His-tagged derivative of CsrA paralog Lpg2094 was the positive control. SUPPLEMENTAL MATERIAL TableS1 Legionella strains surveyed for csrA -like genes, with NCBI taxonomy identification numbers indicated. TaxID, taxonomy identification number. The superscript a indicates previously published...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...CsrA homologs (Lpg0781, Lpg1593, Lpg1003, Lpg1257, and Lpg2094), L. longbeachae contains four homologs (Llo2071, Llo2874, Llo1850, and Llo1813), L. drancourtii...”
- Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires' disease: a unique mosaic genetic backbone
Borges, Scientific reports 2016 - “...comprising homologs of the T4SS ( tra/trb genes), a prpA-lvrABC gene cluster ( PtVFX2014_07415 - PtVFX2014_07430 ), several membrane transporters, and multiple other potential virulence factors 58 . For instance, it harbors a homolog of an efflux pump YdhE/NorM belonging to the multidrug and toxin extrusion...”
- “...) 32 60 . The prpA-lvrABC gene cluster includes a csrA paralog ( lpg2094 / PtVFX2014_07430 ) encoding a RNA-binding protein that belongs to a superfamily of global regulators that are widely distributed among bacterial species. In L. pneumophila , CsrA-like proteins have been implicated in...”
HD1430 carbon storage regulator CrsA from Haemophilus ducreyi 35000HP
66% identity, 85% coverage
PSPTO_1629 carbon storage regulator from Pseudomonas syringae pv. tomato str. DC3000
56% identity, 91% coverage
Bpet1351 carbon storage regulator from Bordetella petrii DSM 12804
67% identity, 80% coverage
- Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas
Sobrero, Frontiers in molecular biosciences 2020 - “...fibrosis (Le Coustumier et al., 2011 ). In B. petrii , we found an annotation (Bpet1351) of 62 amino acids sharing 67% identity with the CsrA counterpart of P. aeruginosa strain PAO1 (RsmA). The genomic context of Bpet1351 did not reveal evidences of mobile genetic elements....”
- “...other -proteobacteria, we did not detect a homolog of FliW in B. petrii . Thus, Bpet1351 is a chromosomally encoded CsrA homolog with a potential role of interaction with RNAs in B. petrii . The second -proteobacterial csrA allele is X994_313 in chromosome 1 of Burkholderia...”
YP_236820 Carbon storage regulator from Pseudomonas syringae pv. syringae B728a
60% identity, 89% coverage
X994_313 carbon storage regulator CsrA from Burkholderia pseudomallei
69% identity, 70% coverage
- Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas
Sobrero, Frontiers in molecular biosciences 2020 - “...role of interaction with RNAs in B. petrii . The second -proteobacterial csrA allele is X994_313 in chromosome 1 of Burkholderia pseudomallei strain TSV202, which encodes a 79 amino acid polypeptide with a predicted secondary structure consisting in a 1 2 3 4 1 2 topology....”
- “...representatives of -proteobacteria or Bacillus ( Supplementary Table 1 ); however, the protein encoded by X994_313 is 46% identical to P. aeruginosa RsmA (including a clear conservation of the residues involved in protein-RNA interaction) but it is only 25% identical to the CsrA homolog of the...”
pOZ176_186 carbon storage regulator CsrA from Pseudomonas aeruginosa PA96
65% identity, 90% coverage
CBU_0024 carbon storage regulator from Coxiella burnetii RSA 493
63% identity, 84% coverage
CSRA_GEOTN / A4ISU9 Translational regulator CsrA from Geobacillus thermodenitrificans (strain NG80-2) (see paper)
51% identity, 72% coverage
- function: A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Usually binds in the 5'- UTR at or near the Shine-Dalgarno sequence preventing ribosome-binding, thus repressing translation. Its main target seems to be the major flagellin gene, while its function is anatagonized by FliW.
subunit: Homodimer; the beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core. Each of the alpha-helical wings interacts with an FliW monomer, yielding a FliW-CsrA(2)-FliW complex.
LIMLP_17575 carbon storage regulator CsrA from Leptospira interrogans serovar Manilae
49% identity, 70% coverage
LEPBI_I3210 carbon storage regulator-like protein from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
49% identity, 75% coverage
Dde_3150 carbon storage regulator from Desulfovibrio desulfuricans G20
49% identity, 73% coverage
GSU3041 carbon storage regulator from Geobacter sulfurreducens PCA
46% identity, 77% coverage
- Global transcriptional analysis of Geobacter sulfurreducens gsu1771 mutant biofilm grown on two different support structures
Jaramillo-Rodríguez, PloS one 2023 - “...1 protein -2.137 0.46 gsu1024 ppcD Energy metabolism and electron transport cytochrome c -3.095 0.3 gsu3041 csrA Regulatory functions and transcription RNA-binding protein CsrA -3.696 0.43 gsu3356 - Signal transduction diguanylate cyclase, HAMP domain-containing -2.074 0.74 Expression of c -type cytochromes and PilA Given their critical...”
- “...mRNA translation [ 63 ]. In our RNA-seq analyses, we identified a CsrA homolog ( gsu3041 ) that was downregulated in the gsu1771 biofilm. In E . coli and related bacteria, CsrA plays a key role in controlling physiological processes such as carbon metabolism, virulence, motility,...”
- Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens
Leang, BMC genomics 2009 - “...flhB ) flagellar biosynthetic protein FlhB -1.11 Flagella biogenesis GSU3040 hypothetical protein N. D. 86 GSU3041 carbon storage regulator -1.04 GSU3042 ( flgL ) flagellar hook-associated protein FlgL -1.05 GSU3043 ( flgK ) flagellar hook-associated protein FlgK -1.05 GSU3044 hypothetical protein -1.21 GSU3045 ( flgM )...”
DVU0521 carbon storage regulator from Desulfovibrio vulgaris Hildenborough
52% identity, 69% coverage
CSRA_BACSU / P33911 Translational regulator CsrA from Bacillus subtilis (strain 168) (see 4 papers)
NP_391417 carbon storage regulator from Bacillus subtilis subsp. subtilis str. 168
42% identity, 81% coverage
- function: A translational regulator that binds mRNA to regulate translation initiation and/or mRNA stability. Usually binds in the 5'- UTR at or near the Shine-Dalgarno sequence preventing ribosome-binding, thus repressing translation. Represses expression of flagellin (hag) in a post-transcriptional fashion. Specifically binds to 2 sites in the 5'-UTR of hag mRNA in a cooperative fashion; the second site overlaps the Shine-Dalgarno sequence and prevents 30S ribosomal subunit binding (PubMed:17555441). Mutation of either binding site abolishes CsrA regulation of hag expression (PubMed:17555441, PubMed:21895793). Repression is greater in the 1A96 than 168 genetic background and higher in minimal than rich medium (PubMed:17555441). Translation repression is antagonized by FliW (PubMed:21895793). Partner switching by flagellin between FliW and CsrA provides a flagellar assembly checkpoint to tightly control the timing of flagellin synthesis. Flagellin binds to assembly factor FliW, freeing CsrA to repress translation of the flagellin mRNA. When the flagellar hook is assembled flagellin is secreted, depleting intracellular flagellin, which frees FliW to interact with CsrA and inhibits CsrA binding to mRNA. This derepresses flagellin translation and provides protein for flagellar assembly. Once the flagellar filament is completed cytoplasmic flagellin levels rise and CsrA translation repression of flagellin reinitiates (PubMed:21895793, PubMed:27516547). Overexpression leads to a dramatic reduction in motility, a significant reduction in flagellin synthesis and reduced flagella assembly (PubMed:21895793).
subunit: Homodimer (PubMed:17555441). The beta-strands of each monomer intercalate to form a hydrophobic core while the alpha-helices form wings that extend away from the core (By similarity). Two molecules of FliW interact with 1 homodimer (PubMed:21895793, PubMed:27516547). mRNA and FliW bind to different sites on CsrA (PubMed:27516547).
disruption phenotype: Increased expression of flagellin (hag), 30% decrease in motility halo (PubMed:17555441). Suppresses the motility loss and flagellar assembly defect of an fliW deletion (PubMed:21895793). Suppresses the phenotypes associated with deletion of the intracellular flagella chaperone fliS (PubMed:23144244). - FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism.
Mukherjee, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: Data show that FliW does not bind to the same residues of carbon storage regulator A (CsrA) required for RNA binding.
- Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein.
Altegoer, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein FliW has been reported.
- CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding.
Yakhnin, Molecular microbiology 2007 (PubMed)- GeneRIF: represses flagellin protein (hag) translation initiation by blocking ribosome binding.
Cbei_4295 carbon storage regulator, CsrA from Clostridium beijerincki NCIMB 8052
45% identity, 81% coverage
- Effects of supplementary butyrate on butanol production and the metabolic switch in Clostridium beijerinckii NCIMB 8052: genome-wide transcriptional analysis with RNA-Seq
Wang, Biotechnology for biofuels 2013 - “...of the expression for PTS transporter genes as discussed above. The expression level of csrA (Cbei_4295, encoding carbon storage regulator) was much lower than that of the other granulose formation genes (Figure 4 C). Discussion With 40mM sodium butyrate supplemented into the ABE fermentation with Clostridium...”
- Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation
Zhang, Biotechnology for biofuels 2013 - “...Cbei_4274 and Cbei_4289, and MotA/TolQ/ExbB proton channel Cbei_4273), carbon storage regulation (carbon storage regulator CsrA Cbei_4295), nitrogen assimilation (glutamine synthetase Cbei_0444), and cell cycle progression and development (signal transduction histidine kinase regulating citrate/malate metabolism Cbei_4175, multi-sensor signal transduction histidine kinase Cbei_4430, and histidine kinase internal region...”
- Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq
Wang, BMC genomics 2012 - “...catalytic region of alpha amylase (Cbei_4906) were organized in another adjacent operon [ 19 ]. Cbei_4295 was annotated as the csrA gene. The five putative granulose formation genes (Cbei_4905-4909) in C. beijerinckii 8052 were grouped into cluster C6 based on their expression profiles (Figure 5 )....”
- “...levels over the stationary phase (point C-E) (Figure 4C ). Notwithstanding, the expression of csrA (Cbei_4295) was only detectable at A, C and F, which was much lower than those of the other granulose formation genes (Figure 4C ). It is not yet clear whether the...”
PFLU4324 carbon storage regulator from Pseudomonas fluorescens SBW25
52% identity, 78% coverage
TP0657 carbon storage regulator (csrA) from Treponema pallidum subsp. pallidum str. Nichols
43% identity, 74% coverage
CA_C2209 carbon storage regulator CsrA from Clostridium acetobutylicum ATCC 824
CAC2209 Carbon storage regulator, csrA from Clostridium acetobutylicum ATCC 824
38% identity, 79% coverage
- Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain
Tan, Molecular bioSystems 2015 (PubMed)- “...acetobutylicum by insertionally inactivating the encoding gene, CA_C2209 using the ClosTron. Disruption of csrA obviously decreases the growth of the organism...”
- “...investigated the global effects of CsrA (encoded by CA_C2209) in C. acetobutylicum by RNA-seq. This study represented the first attempt to investigate the...”
- Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq
Wang, BMC genomics 2012 - “...]. In addition, glgP encodes a granulose phosphorylase (CAC1664, functions to depolymerize granulose), and csrA (CAC2209) encodes a putative carbon storage regulator, which was reported to repress the expression of both glgA and glgP in Escherichia coli [ 5 , 75 ]. In C. beijerinckii 8052,...”
- Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum
Alsaker, Journal of bacteriology 2005 - “...depolymerize granulose and a putative carbon storage regulator (CAC2209, csrA), which in E. coli represses the expression of both glycogen biosynthesis (glgA)...”
PP1746, PP_1746 carbon storage regulator, putative from Pseudomonas putida KT2440
49% identity, 90% coverage
CD630_02340, CDIF630erm_00356, WP_003425267 carbon storage regulator CsrA from Clostridioides difficile CD37
CD0234 carbon storage regulator from Clostridium difficile 630
37% identity, 86% coverage
- Clostridioides difficile Flagella
Marvaud, International journal of molecular sciences 2024 - “...hook-associated protein F1 CD630_02320 flgL Flagellar hook-associated protein F1 CD630_02330 fliW Flagellar assembly factor F1 CD630_02340 csrA Carbon storage regulator homolog F1 CD630_02350 fliS1 Flagellar protein F1 CD630_02360 fliS2 Flagellar protein F1 CD630_02370 fliD Flagellar hook-associated protein F1 CD630_02380 Conserved hypothetical protein F1 CD630_02390 fliC Flagellin...”
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...-2.21 0.22 -3.88 -0.46 CD630_02330 CDIF630erm_00355 fliW Flagellar assembly factor FliW -2.66 -0.81 -3.16 0.15 CD630_02340 CDIF630erm_00356 crsA Carbon storage regulator CsrA -1.87 0.09 -2.57 -0.46 CD630_02350 CDIF630erm_00357 fliS1 Flagellar protein FliS1 -1.33 1.91 -3.04 1.89 CD630_02360 CDIF630erm_00358 fliS2 Flagellar protein FliS2 -1.03 0.15 -2.30 0.20...”
- “...0.22 -3.88 -0.46 CD630_02330 CDIF630erm_00355 fliW Flagellar assembly factor FliW -2.66 -0.81 -3.16 0.15 CD630_02340 CDIF630erm_00356 crsA Carbon storage regulator CsrA -1.87 0.09 -2.57 -0.46 CD630_02350 CDIF630erm_00357 fliS1 Flagellar protein FliS1 -1.33 1.91 -3.04 1.89 CD630_02360 CDIF630erm_00358 fliS2 Flagellar protein FliS2 -1.03 0.15 -2.30 0.20 CD630_02370...”
- Carbon storage regulator CsrA plays important roles in multiple virulence-associated processes of Clostridium difficile.
Gu, Microbial pathogenesis 2018 (PubMed)- GeneRIF: Overexpression of csrA in C. difficile 630Deltaerm resulted in flagella defect and poor motility. Overexpression of csrA in C. difficile 630Deltaerm increased the toxin production. csrA overexpression enhanced the adherence ability to Caco-2cells and solvent production of C. difficile 630Deltaerm.
- The flagellin FliC of Clostridium difficile is responsible for pleiotropic gene regulation during in vivo infection
Barketi-Klai, PloS one 2014 - “...protein FlgK (or HAP1) 0.40 CDR0234 CD630_02330 * fliW Flagella assembly factor FliW 2.03 CDR0235 CD630_02340 * csrA Carbon storage regulator homolog CsrA 4.36 CDR0236 CD630_02350 * fliS1 Flagellar protein FliS 3.99 CDR0237 CD630_02360 * fliS2 Flagellar protein FliS2 2.17 CDR0238 CD630_02370 * fliD Flagellar cap...”
- Biofilm regulation in Clostridioides difficile: Novel systems linked to hypervirulence
Taggart, PLoS pathogens 2021 - “...CD3510 Putative membrane protein 9.78 CD3511 Putative type IV pilus secretion protein 9.25 Flagellum biogenesis CD0234 csrA Carbon storage regulator homolog CsrA 1.35 CD0254 flgD Basal-body rod modification protein FlgD 1.24 CD0255 flgE Flagellar hook protein FlbE (distal rod protein) 1.29 CD0255A flbD Flagellar protein FlbD...”
ArtHe_17680 carbon storage regulator CsrA from Arthrobacter sp. Helios
40% identity, 74% coverage
PflSS101_3653 carbon storage regulator CsrA from Pseudomonas lactis
44% identity, 88% coverage
PPUTLS46_015344 carbon storage regulator CsrA from Pseudomonas putida LS46
47% identity, 90% coverage
PSLF89_RS34715 carbon storage regulator from Piscirickettsia salmonis LF-89 = ATCC VR-1361
44% identity, 82% coverage
- Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas
Sobrero, Frontiers in molecular biosciences 2020 - “...riboregulatory functions (Agaras et al., 2013 ). The second case is a csrA -like sequence (PSLF89_RS34715) also found in a cryptic plasmid from the fish pathogen Piscirickettsia salmonis (Ortiz-Severin et al., 2019 ). P. salmonis is a -proteobacterium related to the intracellularly adapted species of Coxiella,...”
- Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors
Ortiz-Severín, Pathogens (Basel, Switzerland) 2019 - “...them corresponded to transcriptional regulators identified in pPSLF89-1, a CsrA family protein carbon storage regulator (PSLF89_RS34715), responsible for bacterial metabolic shifts and stationary-stage phenotypes including virulence in other pathogens such as L. pneumophila [ 42 ], and a Crp/Fnr family transcriptional regulator (PSLF89_RS34760), which responds to...”
plpp0016 hypothetical protein from Legionella pneumophila str. Paris
50% identity, 59% coverage
PSPTO_3943 carbon storage regulator, putative from Pseudomonas syringae pv. tomato str. DC3000
45% identity, 73% coverage
TDE2355 carbon storage regulator from Treponema denticola ATCC 35405
52% identity, 72% coverage
BB0184 carbon storage regulator (csrA) from Borrelia burgdorferi B31
33% identity, 70% coverage
- Lyme Disease Pathogenesis
Coburn, Current issues in molecular biology 2021 - “...gene(s) a Gene location(s) Findings / evidence in vitro Findings/evidence in vivo Regulation CsrA ( bb0184 ) chr Carbon storage regulator A controls expression of a number of infection-relevant genes (Kama et al., 2011; Arnold et al., 2018 ). A mutant lacking csrA is non-infectious in...”
- Analysis of a flagellar filament cap mutant reveals that HtrA serine protease degrades unfolded flagellin protein in the periplasm of Borrelia burgdorferi
Zhang, Molecular microbiology 2019 - “...in B. burgdorferi ( Sal et al ., 2008 ). Thirdly, we previously demonstrated that BB0184 (CsrA Bb ), a homolog of B. subtilis CsrA, specifically represses FlaB synthesis by inhibiting the translation initiation of flaB mRNA ( Sze et al. , 2011 ). We recently...”
- “...aadA1 , a streptomycin resistance gene. A kanamycin resistance mutant of csrA Bb (gene locus, bb0184 ) was generated in our previous reports ( Sze et al. , 2013 ). To construct a double mutant of fliD Bb -csrA Bb , a new streptomycin resistance csrA...”
- The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation
Drecktrah, PLoS pathogens 2015 - “...suggesting transcript levels of this gene respond positively and negatively to nutrient levels. csrA ( bb0184 ), which encodes the carbon storage regulator, is induced under conditions mimicking mammalian infection [ 76 ] and was upregulated during recovery. Additionally, two genes encoding proteins in the master...”
- “..., Esteve-Gassent MD , Maruskova M , Seshu J ( 2009 ) Overexpression of CsrA (BB0184) alters the morphology and antigen profiles of Borrelia burgdorferi . Infect Immun 77 : 5149 5162 . 10.1128/IAI.00673-09 19737901 77 Zhang J-R , Hardham JM , Barbour AG , Norris...”
- CsrA (BB0184) is not involved in activation of the RpoN-RpoS regulatory pathway in Borrelia burgdorferi
Ouyang, Infection and immunity 2014 - “...(BB0184) Is Not Involved in Activation of the RpoN-RpoS Regulatory Pathway in Borrelia burgdorferi Zhiming Ouyang, Jianli Zhou, Michael V. Norgard Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA...”
- “...Hfq (40, 41); and a putative RNA-binding protein, BB0184 (42-47). The B. burgdorferi protein designated BB0184 was originally annotated as a homologue of carbon...”
- Borrelia host adaptation Regulator (BadR) regulates rpoS to modulate host adaptation and virulence factors in Borrelia burgdorferi
Miller, Molecular microbiology 2013 - “...479 499 21801026 Sanjuan E Esteve-Gassent MD Maruskova M Seshu J 2009 Overexpression of CsrA (BB0184) alters the morphology and antigen profiles of Borrelia burgdorferi Infect Immun 77 5149 5162 19737901 Schiefner A Gerber K Seitz S Welte W Diederichs K Boos W 2005 The crystal...”
- “...and virulence Mol Microbiol 77 128 142 20444101 Sze CW Li C 2011 Inactivation of bb0184 , which encodes carbon storage regulator A, represses the infectivity of Borrelia burgdorferi Infect Immun 79 1270 1279 21173314 Sze CW Morado DR Liu J Charon NW Xu H Li...”
- Contributions of environmental signals and conserved residues to the functions of carbon storage regulator A of Borrelia burgdorferi
Karna, Infection and immunity 2013 - “...regulates itself. Since the ORF upstream of CsrABb (bb0184) is FliW (bb0183), we hypothesized that the levels of FliW could affect the functions of...”
- “...26. Sze CW, Li C. 2011. Inactivation of bb0184, which encodes carbon storage regulator A, represses the infectivity of Borrelia burgdorferi. Infect. Immun....”
- Comparative molecular analyses of Borrelia burgdorferi sensu stricto strains B31 and N40D10/E9 and determination of their pathogenicity
Chan, BMC microbiology 2012 - “...( A ). Using the primers in Additional Table 1 , complete genes bb0153 , bb0184 ( csrA ), bb0219, bb0268, bb0383 ( bmpA ), bb0647 ( bosR ), bba25 ( dbpB ), bba68 ( cspA ), bbd14, bbd18, bbe22 ( pncA ), bbg02, bbh06 (...”
- “...Infect Immun 2008 76 3 1239 1246 10.1128/IAI.00897-07 18195034 Sze CW Li C Inactivation of bb0184, which encodes carbon storage regulator A, represses the infectivity of Borrelia burgdorferi Infect Immun 2011 79 3 1270 1279 10.1128/IAI.00871-10 21173314 Brissette CA Verma A Bowman A Cooley AE Stevenson...”
- Borrelia burgdorferi requires the alternative sigma factor RpoS for dissemination within the vector during tick-to-mammal transmission
Dunham-Ems, PLoS pathogens 2012 - “...) and dsrA ( bb0577 ) as well as the carbon storage regulator csrA ( bb0184 ) [12] . Based upon microarray analysis of mammalian host-adapted spirochetes [13] , it was proposed that RpoS functions as a gatekeeper for controlling the upregulation of mammalian host-phase genes...”
- More
BH0184 carbon storage regulator from Borrelia hermsii DAH
33% identity, 69% coverage
lpg1257 LvrC from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
36% identity, 88% coverage
- Legionella pneumophila p45 element influences host cell entry and sensitivity to sodium
Christensen, PloS one 2019 - “...of these is encoded on p45, lvrC [ 29 , 39 ]. The lvrC ( lpg1257 ) gene maintains 39% identity with csrA ( lpg1593 ) [ 29 ], is located within the lvh/lvr region, and is believed to be involved in regulation of Lvh [...”
- csrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila
Abbott, Journal of bacteriology 2016 - “...not of csrA-22 or another ICE-associated csrA paralog, lpg1257 of ICE-Trb-1, both of whose protein sequences are less similar to canonical CsrA. Likewise, B....”
- “...L. pneumophila strain Lp02 (core csrA, ICE-ox csrT, and lpg1257) but not two others (core csrR and csrA-22 [22]) (see Table S2 in the supplemental material;...”
- Two Fis regulators directly repress the expression of numerous effector-encoding genes in Legionella pneumophila
Zusman, Journal of bacteriology 2014 - “...contains five CsrA homologs (Lpg0781, Lpg1593, Lpg1003, Lpg1257, and Lpg2094), L. longbeachae contains four homologs (Llo2071, Llo2874, Llo1850, and Llo1813),...”
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