Table 1.
Genes regulated by Crl in Escherichia coli
| 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] |
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