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Table 1 Genes of the SOS regulon

From: Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

Label Gene Product Product Type Role BioProcess Ratio +/- MMC
Known SOS regulon genes
VC0082 rmuC DNA recombination protein rmuC cp : cell process 2.1.3 : DNA recombination; 5.8 : SOS response ; 8.1 : DNA replication, recombination, and repair ; 19.7
VC0092 lexA LexA repressor r : regulator 2.1.4 : DNA repair ; 2.2.2 : Transcription related ; 3.1.2.3 : Repressor ; 3.3.2 : Regulon (a network of operons encoding related functions) ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 9 : Transcription ; 12.1 : DNA interactions ; 15.10 : Adaptations to atypical conditions ; 25.5
VC0190 uvrD DNA helicase II e : enzyme 2.1.1 : DNA replication ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 9.1
VC0196 recQ ATP-dependent DNA helicase recQ e : enzyme 2.1.1 : DNA replication ; 2.1.3 : DNA recombination ; 2.1.4 : DNA repair; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8 : DNA metabolism ; 2.4
VC0394 uvrA UvrABC system protein A e : enzyme 2.1.4 : DNA repair ; 5.6.1 : Radiation ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 9.9
VC0397 ssb, exrB, lexC Single-stranded DNA-binding protein cp : cell process 2.1.3 : DNA recombination ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 3.8
VC0543 recA Protein recA e : enzyme 2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 2.3.6 : Turnover, degradation ; 3.1.3.4 : Proteases, cleavage of compounds ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 11.4 : Degradation of proteins, peptides, and glycopeptides ; 12.3 : Protein interactions ; 15.10 : Adaptations to atypical conditions ; 16.4
VC0544 recX Regulatory protein recX r : regulator Modulates recA activity; 5.8 : SOS response ; 15.10 : Adaptations to atypical conditions ; 11.4
VC0852 recN, radB DNA repair protein recN cp : cell process 2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 47.0
VC1191 unfA putative Superfamily II DNA and RNA helicase pe : putative enzyme ; 5.8 : SOS response ;   32.7
VC1368 unfB conserved hypothetical protein o : ORF of unknown function ; 5.8 : SOS response ;   16.0
VC1453 rstB1 RstB phage-related integrase e : enzyme 8.1.4 : Integration, recombination ; 5.8 : SOS response ; 17.2 : Prophage functions ; 25.7
VC1454 rstA1 RstA phage-related replication protein h : extrachromosomal origin 8.1.2 : Replication; 5.8 : SOS response ;; 17.2 : Prophage functions ; 33.8
VC1455 rstR1 Cryptic phage CTXphi transcriptional repressor rstR r : regulator 3.1.2.3 : Repressor ; 7.1 : Cytoplasm ; 8.1.3 : Regulation ; 5.8 : SOS response ; 12 : Regulatory functions ; 17.2 : Prophage functions ; 0.3
VC1462 rstB2 RstB phage-related integrase e : enzyme 8.1.4 : Integration, recombination; 5.8 : SOS response ; 17.2 : Prophage functions ; 28.2
VC1463 rstA2 RstA phage-related replication protein h : extrachromosomal origin 8.1.2 : Replication; 5.8 : SOS response ; 17.2 : Prophage functions ; 33.7
VC1464 rstR2 Cryptic phage CTXphi transcriptional repressor rstR r : regulator 3.1.2.3 : Repressor ; 7.1 : Cytoplasm ; 8.1.3 : Regulation; 5.8 : SOS response ; 12 : Regulatory functions ; 17.2 : Prophage functions ; 0.3
VC1845 ruvB Holliday junction ATP-dependent DNA helicase ruvB e : enzyme 2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 4.1
VC1846 ruvA Holliday junction ATP-dependent DNA helicase ruvA e : enzyme 2.1.3 : DNA recombination ; 2.1.4 : DNA repair ; 5.8 : SOS response ; 7.1 : Cytoplasm ; 8.1 : DNA replication, recombination, and repair ; 15.10 : Adaptations to atypical conditions ; 4.7
VC2043 topB DNA topoisomerase 3 e : enzyme 2.1.1 : DNA replication ; 2.2.2 : Transcription related ; 3.1.1.1 : DNA bending, supercoiling, inversion ; 7.1 : Cytoplasm; 5.8 : SOS response ; 8.1 : DNA replication, recombination, and repair ; 9 : Transcription ; 12 : Regulatory functions ; 4.8
VC2287 dinB DNA polymerase IV e : enzyme 2.1.1 : DNA replication; 5.8 : SOS response ; 8.1 : DNA replication, recombination, and repair ; 19.4
VC2326 yebG dsDNA-binding SOS-regulon protein pcp : putative cell process ; 5.8 : SOS response ;   4.0
VC2711 recG, spoV, radC ATP-dependent DNA helicase recG e : enzyme 2.1.1 : DNA replication; 5.8 : SOS response ; 8 : DNA metabolism ; 4.1
VCA0291 intIA Site-specific recombinase IntIA e : enzyme 2.1.3 : DNA recombination ; 7.1 : Cytoplasm ; 8.1.4 : Integration, recombination; 5.8 : SOS response ; 8.1 : DNA replication, recombination, and repair ; 14.4
VCA0952 vpsT, csgD LuxR family transcriptional regulator VpsT r : regulator 3 : Regulation ; 3.1.2 : Transcriptional level ; 5.12 : Biofilm production ; 5.8 : SOS response ; 12 : Regulatory functions ; 12.1 : DNA interactions ; 14 : Cell envelope ; 14.1 : Surface structures ; 14.3 : Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides ; 2.8
New SOS regulon genes
VC0083 ubiE Ubiquinone/menaquinone biosynthesis methyltransferase UbiE e : enzyme 1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ; 4.5 : Menaquinone and ubiquinone ; 9.0
VC0084 ubiJ Ubiquinone biosynthesis protein UbiJ e : enzyme 1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ; 4.5 : Menaquinone and ubiquinone ; 5.2
VC0085 ubiB ubiquinone biosynthesis protein UbiB e : enzyme 1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ; 5 : Inner membrane protein 4.5 : Menaquinone and ubiquinone ; 3.7
VC0086 tatA Sec-independent protein translocase TatA t : transporter 4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ; 7 : Transport and binding proteins ; 3.2
VC0087 tatB Sec-independent protein translocase protein TatB t : transporter 4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ; 7 : Transport and binding proteins ; 4.0
VC0088 tatC Sec-independent protein translocase protein TatC t : transporter 4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family ; 4.S.160 : protein ; 5 : Inner membrane protein 7 : Transport and binding proteins ; 5.5
VC0091   putative O-Methyltransferase involved in polyketide biosynthesis pe : putative enzyme 5.6.4 : Drug resistance/sensitivity ; 15.8 : Toxin production and resistance ; 13.7
VC0851 smpA small protein A lp : lipoprotein    12.7
VC1190   putative phosphoribosylaminoimidazole-succinocarboxamide synthase PurC pe : putative enzyme 1.5.2.1 : Purine biosynthesis ; 2 : Cytoplasmic 2.3 : Purine ribonucleotide biosynthesis ; 16.8
VC1369   putative ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic component pt : putative transporter 4.3.A.1.p : periplasmic binding component; 9 : Periplasmic 7 : Transport and binding proteins ; 2.4
VC1370   putative Signal transduction histidine kinase domain, Methyl-accepting chemotaxis domain and GGDEF family protein pr : putative regulator 3 : Regulation ; 5 : Inner membrane protein 12 : Regulatory functions ; 2.3
VC1461 cep Colonization factor f : factor 5.13 : Virulence associated ; 5 : Inner membrane protein 15.9 : Pathogenesis ; 52.4
  1. The different categories correspond to those of MAGE annotation platform