From: Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes
Gene | Bnumber | TU(s) | TFs | Effect of Crl | Evidence | Reference(s) | GO Terms |
---|---|---|---|---|---|---|---|
aat | b0885 | aat | + | GEA and IMP | [11] | protein catabolic process, ubiquitin-dependent protein catabolic process via the N-end rule pathway | |
accB | b3255 | accBC | AccB (−), FadR(+) | + | GEA and IMP | [11] | lipid metabolic process, fatty acid metabolic process, fatty acid biosynthetic process |
accC | b3256 | accBC | AccB (−), FadR(+) | + | GEA and IMP | [11] | lipid metabolic process, fatty acid metabolic process, fatty acid biosynthetic process, metabolic process, negative regulation of fatty acid biosynthetic process, malonyl-CoA biosynthetic process |
acnB | b0118 | acnB | CRP(+) ArcA(−), Cra(−), Fis (−) | – | IMP | [13] | regulation of translation, propionate catabolic process, 2-methylcitrate cycle, glyoxylate cycle, tricarboxylic acid cycle metabolic process |
ada | b2213 | ada- alkB | Ada(+/−) | + | GEA | [13] | DNA dealkylation involved in DNA repair, regulation of transcription, cellular response to DNA damage stimulus, metabolic process, methylation, DNA demethylation |
allR | b0506 | allR | + | MSI | [10] | regulation of transcription, cellular response to DNA damage stimulus, negative regulation of transcription | |
bfr | b3336 | bfd -bfr | + | MSI, IMP | iron ion transport, cellular iron ion homeostasis, intracellular sequestering of iron ion, oxidation-reduction process | ||
bglG | b3723 | bglG bglG FB | CRP (+), Fis (−), H-NS (−), LeuO (+), RcsB-BglJ (+), StpA (−) | – | MSI, IMP | [16] | regulation of transcription, positive regulation of transcription |
bioB | b0775 | bioB FCD | BirA (−) | – | IMP | [13] | biotin biosynthetic process |
cbpA | b1000 | cbpA M | Fis (−) | + | GEA | [13] | protein folding |
crl | b0240 | crl | Fur (−) | – | MSI, IMP | [12] | regulation of transcription, DNA-templated, cellular protein complex assembly, positive regulation of transcription |
csgA | b1042 | csgBAC | CpxR (−), CsgD (+), FliZ (−) | + | APPH, MSI, IMP, GEA, IMP | cell adhesion, single-species biofilm formation, amyloid fibril formation | |
csgB | b1041 | csgBAC | CpxR(−), CsgD(+), FliZ(−) | + | APPH, MSI, IMP, GEA, IMP | cell adhesion, single-species biofilm formation, amyloid fibril formation | |
csgC | b1043 | csgBAC | CpxR (−), CsgD (+), FliZ (−) | + | MSI | [10] | |
csgD | b1040 | csgD EFG | BasR (+), Cra (+), CRP (+), CsgD (+), IHF (+), MlrA (+), OmpR (+), RcdA (+), CpxR(−), FliZ (−), RcsAB (−), RstA (−) | + | IMP | [13] | regulation of single-species biofilm formation |
cstA | b0598 | cstA | CRP (+) | + | GEA, IMP | [11] | cellular response to starvation |
cysP | b2425 | cysP UWAM | CysB (+), H-NS (−) | + | MSI | [10] | sulfur compound metabolic process, transport, sulfate transport, sulfate transmembrane transport |
djlC (ybeV) | b0649 | ybeU -djlC | + | MSI | [10] | positive regulation of ATPase activity | |
dps | b0812 | dps | Fis(−), H-NS(−),IHF(+), MntR(−), OxyR(+) | + | GEA, IMP | [11] | cellular iron ion homeostasis, response to stress, chromosome condensation, response to starvation, oxidation-reduction process |
fbaB | b2097 | fbaB | Cra(−) | + | GEA, IMP | [11] | glycolytic process, transcription |
flgM | b1071 | flgMN, flg A M N | CsgD(−) | – | GEA, IMP | [13] | regulation of transcription, bacterial-type flagellum organization, negative regulation of proteolysis, negative regulation of transcription |
fliA | b1922 | fliA Z -tcyJ | H-NS(+), MatA(−), SutR(−), NsrR(−), CsgD(−), FlhDC(+) | – | IMP | [13] | transcription initiation from bacterial-type RNAP promoter, sporulation resulting in formation of a cellular spore |
fur | b0683 | fur fldA-uof -fur uof -fur | CRP(+), Fur(−) | + | MSI, IMP | [12] | regulation of transcription, negative regulation of transcription |
gadA | b3517 | gadA X | AdiY(+), ArcA(+), CRP(−), FNR(−), Fis(−), GadE-RcsB(+), GadW(+−), GadX(+), H-NS(−), RcsB(−), TorR(−) | + | MSI | [10] | glutamate metabolic process, carboxylic acid metabolic process, intracellular pH elevation |
gadB | b1493 | gadBC | AdiY(+),CRP(−), Fis(−), FliZ(−), GadE(+), GadW(+−), GadX(+), RcsB(+) | + | MSI, GEA | glutamate metabolic process, carboxylic acid metabolic process, intracellular pH elevation | |
gadC | b1492 | gadBC | AdiY(+), CRP(−), Fis(−), FliZ(−), GadE(+), GadW(+−), GadX(+), RcsB(+) | + | MSI | [10] | amino acid transmembrane transport, transport, amino acid transport, intracellular pH elevation |
gadE | b3512 | gadE- mdtEF gadE | ArcA(+), CRP(−), EvgA(+), FliZ(−), GadE(+), GadW(+), GadX(+), H-NS(−), PhoP(+), YdeO(+) | + | MSI | [10] | regulation of transcription |
gadW | b3515 | gadW | GadW (+), GadX (−), H-NS(−), PhoP (+), SdiA (+), YdeO (+) | + | MSI | [10] | regulation of transcription, cellular response to DNA damage stimulus |
glgS | b3049 | glgS | CRP(+) | + | GEA | [13] | glycogen biosynthetic process, positive regulation of cellular carbohydrate metabolic process, negative regulation of single-species biofilm formation on inanimate substrate, negative regulation of bacterial-type flagellum-dependent cell motility |
glnH | b0811 | glnH PQ | IHF(+), NtrC(+/−) | + | GEA, IMP | [11] | transport, amino acid transport |
gltA | b0720 | gltA | ArcA(−), CRP(+), IHF(+) | + | GEA, IMP | [11] | tricarboxylic acid cycle, metabolic process, cellular carbohydrate metabolic process |
grxB | b1064 | grxB | + | GEA, IMP | [11] | cell redox homeostasis, oxidation-reduction process | |
hdeA | b3510 | hdeAB- yhiD | FliZ(−), GadE(+), GadW(+/−), GadX(+/−), H-NS(−), Lrp(−), MarA(−), PhoP(+), RcsB(+), TorR(+) | + | MSI, GEA | cellular response to stress, cellular response to acidic pH | |
hdeB | b3509 | hdeAB- yhiD | FliZ(−), GadE(+), GadW(+/−), GadX(+/−), H-NS(−), Lrp(−), MarA(−), PhoP(+), RcsB(+), TorR(+) | + | MSI | [10] | response to pH change, cellular response to stress |
hdeD | b3511 | hdeD | GadE(+), GadX(+), H-NS(−), PhoP(+),RcsB(+) | + | MSI | [10] | response to pH change |
hdhA | b1619 | hdhA | + | GEA, IMP | [11] | lipid metabolic process, metabolic process, steroid metabolic process, lipid catabolic process, bile acid, catabolic process, protein homotetramerization, oxidation-reduction process | |
iadA | b4328 | yjiH G-iadA | + | MSI | [10] | proteolysis | |
luxS (ygaG) | b2687 | luxS | + | MSI, GEA, IMP | cell-cell signaling involved in quorum sensing, L-methionine biosynthetic process from S-adenosylmethionine, quorum sensing | ||
malE | b4034 | malE FG | CRP(+), CreB(−), Fis(+), MalT(+) | + | GEA, IMP | [11] | cellular response to DNA damage stimulus, carbohydrate transport, maltose transport, detection of maltose stimulus, maltodextrin transport, cell chemotaxis |
msrB | b1778 | msrB | – | IMP | [13] | protein repair, response to oxidative stress | |
narU | b1469 | narU | + | MSI | [10] | nitrate transport, nitrite transport, nitrate assimilation | |
ompF | b0929 | ompF | CRP(+), CpxR(−), EnvY(+), Fur(+), IHF(+/−), OmpR(+/−), PhoB(+), RstA(−) | – | GEA, IMP | [41] | transport, ion transport, ion transport, drug transmembrane transport, bacteriocin transport |
ompT | b0565 | ompT envY -ompT | PhoP(+) | – | IMP | [13] | proteolysis |
ompX | b1482 | ompX | FNR(−) | + | GEA, IMP | [11] | |
osmC | b4376 | osmC | H-NS(−), Lrp(+/−) | + | GEA, IMP | [11] | hyperosmotic response, response to oxidative stress, response to hydroperoxide, oxidation-reduction process |
osmY | b1388 | osmY | CRP(−), Fis(−), FliZ(−), IHF(−), Lrp(−) | + | GEA, IMP | [11] | response to osmotic stress |
paaA | b1389 | paaAB C D E F G H IJ K | CRP(+), IHF(+), PaaX(−) | + | MSI | [10] | phenylacetate catabolic process, oxidation-reduction process |
paaB | b1391 | paaAB C D E F G H IJ K | CRP (+), IHF (+), PaaX (−) | + | MSI | [10] | phenylacetate catabolic process |
paaD | b1393 | paaAB C D E F G H IJ K | CRP (+), IHF (+), PaaX (−) | + | MSI | [10] | phenylacetate catabolic process |
paaF | b1395 | paaAB C D E F G H IJ K | CRP (+), IHF (+), PaaX (−) | + | MSI | [10] | lipid metabolic process, fatty acid metabolic process, phenylacetate catabolic process |
paaH | b1398 | paaAB C D E F G H IJ K | CRP(+), IHF(+), PaaX(−) | + | MSI | [10] | fatty acid metabolic process, phenylacetate catabolic process, oxidation-reduction process |
paaK | b3916 | paaAB C D E F G H IJ K | CRP(+), IHF(+), PaaX(−) | + | MSI | [10] | metabolic process, phenylacetate catabolic process |
pfkA | b0871 | pfkA | Cra(−) | + | GEA, IMP | [11] | fructose 6-phosphate metabolic process, glycolytic process |
poxB | b4226 | poxB, poxB-l taE-ybjT | Cra(+), MarA(+), SoxS (+) | + | GEA, IMP | [11] | pyruvate metabolic process, oxidation-reduction process |
ppa | b0384 | ppa | + | GEA, IMP | [11] | phosphate-containing compound metabolic process | |
psiF | b1676 | phoA -psiF | PhoB(+) | + | MSI | [10] | |
pykF | b1235 | pykF | Cra(−) | + | GEA, IMP | [11] | glycolytic process, metabolic process, response to heat, phosphorylation |
rssB | b0721 | rssB | + | IMP | [10] | protein destabilization, positive regulation of proteolysis, regulation of nucleic acid-templated transcription (phosphorelay signal transduction system) | |
sdhC | b4719 | sdhC DAB -sucA BC D | CRP(+), Fur(+), ArcA(+/−), Fnr(−) | – | IMP | [13] | aerobic respiration. Cytochrome complex assembly, tricarboxylic acid cycle, oxidation-reduction process |
sdsN | b1646 | sdsN | + | GEA | [42] | small RNA | |
sodC | b4059 | sodC | + | GEA | [13] | superoxide metabolic process, removal of superoxide radicals, oxidation-reduction process | |
ssb | b0726 | ssb | ArcA(−), LexA(−) | + | GEA, IMP | [11] | recombinational repair, DNA replication, cellular response to DNA damage stimulus, SOS response |
sucA | b0729 | sucA B sucA BC D | ArcA(+/−), FNR(−), IHF(−) | + | GEA, IMP | [11] | glycolytic process, tricarboxylic acid cycle, metabolic process, oxidation-reduction process |
sucD | b2464 | sucA B sucA BC D | ArcA(+/−),FNR(−),IHF(−) | + | GEA, IMP | [11] | tricarboxylic acid cycle, metabolic process, protein autophosphorylation |
talA | b1886 | talA- tktB | CreB(+) | + | GEA, IMP | [11] | carbohydrate metabolic process, pentose-phosphate shunt |
tar | b1920 | tar- tap-cheRBYZ | Fnr(+) | – | IMP | [13] | chemotaxis, signal transduction |
tcyJ (fliY) | b3116 | tcyJ fliA Z -tcyJ | H-NS(+), MatA(−), SutR(−), NsrR(−), CsgD(−), FlhDC(+) | – | IMP | [13] | L-cystine transport |
tdcC | b3708 | tdc AB C DEFG , tdc B C DEFG | CRP(+), FNR(+), IHF(+), TdcA(+), TdcR (+) | + | MSI | [10] | L-serine transport, threonine transport, proton transport, serine transport |
tnaA | b3453 | tna C A B | CRP(+), TorR (+) | + | GEA, IMP | [11] | cellular amino acid metabolic process, aromatic amino acid family metabolic process |
ugpB | b3495 | ugpB AECQ | CRP(+), PhoB(+/−) | + | GEA, IMP | [11] | glycerophosphodiester transport, transport, glycerol-3-phosphate transport |
uspA | b0607 | uspA | FadR(−), IHF(+) | + | GEA, IMP | [11] | response to stress |
uspG (ybdQ) | b1004 | uspG | + | GEA, IMP | [11] | response to stress, protein adenylylation, protein autophosphorylation, nucleotide phosphorylation, regulation of cell motility | |
wrbA | b0453 | wrbA- yccJ | CsgD(+) | + | MSI, GEA, IMP | response to oxidative stress, negative regulation of transcription | |
ybaY | b0753 | ybaY | + | MSI | [10] | ||
ybgS | b0897 | ybgS | + | MSI | [10] | ||
ycaC | b1674 | ycaC | BaeR(+), Fnr(−) | + | MSI, GEA, IMP | metabolic process | |
ydhY | b1784 | ydhY VWXUT | FNR (+), NarL (−), NarP (−) | + | MSI | [10] | oxidation-reduction process |
yeaH | b2013 | yea G H | NtrC (+) | + | MSI | [10] | |
yeeE | b2665 | yeeE D | + | MSI | [10] | ||
ygaU | b3535 | ygaU | CpxR (+) | + | GEA, IMP | [11] | |
yhjR | b3555 | yhjR | + | MSI | [10] | bacterial cellulose biosynthetic process | |
yiaG | b4045 | yiaG | + | MSI | [10] | regulation of transcription | |
yjbJ | b4329 | yjbJ | FliZ (−) | + | MSI | [10] | |
yjiG | b1044 | yjiH G-iadA | + | MSI | [10] | ||
ymdA | b1138 | ymdA | + | MSI | [10] | ||
ymfE | b0885 | ymfED | + | MSI | [10] |