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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