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Table 1 Genes regulated by Crl in Escherichia coli

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 [40]MSI, [11]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 [8] APPH, MSI, IMP, [9] GEA, IMP cell adhesion, single-species biofilm formation, amyloid fibril formation
csgB b1041 csgBAC CpxR(−), CsgD(+), FliZ(−) + APPH, MSI, IMP, GEA, IMP [8] APPH, MSI, IMP, [9] 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 [40]MSI, [13]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 [40]MSI, [13]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 [10]MSI, [11] 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 [13]MSI, [11] 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 [10]MSI, [11] 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]  
  1. Genes regulated by Crl, Bnumbers, TUs to which they belong (in bold are possible candidates regulated by Crl, since they are controlled by Crl and σS, but they did not have a change of expression in the data we evaluated), TFs regulating the TU, the effect of Crl, evidences, references, and associated GO terms. Experimental evidence types supporting regulation by Crl: APPH Assay of protein purified to homogeneity, GEA Gene expression analysis, transcriptional fusions (lacZ), MSI Mapping of signal intensities, such as RNA-seq or microarray analysis; IMP Inferred from mutant phenotype (such as a mutation of a TF that has a visible cell phenotype and it is inferred that the regulator might be regulating the genes responsible for the phenotype). Growth conditions were 30 °C, as the stationary phase was induced for all experiments. All experiments were done with E. coli K-12 or derivative strains. This information, including regulatory interactions can be accessed at RegulonDB (http://regulondb.ccg.unam.mx/) by consulting the Crl regulon