Table 2 Top 100 most RpoS-dependent genes in stationary phase.

abgABT*

24/41/26

Aminoacyl aminohydrolase family proteins/transporter

AbgR

aceBA

164/422

Glyoxylate cycle

IclR FruR IHF CRP ArcA

acs-yjcH-actP

541/357/163

Acetyl-CoA synthetase/Unknown/Acetate permease

Fis IHF CRP

aidB

79

Isovaleryl CoA dehydrogenase

RpoS Ada Lrp

puuCB

576/214

Putrescine degradation II

astCADBE

3492/1270/2402/512/388

Arginine degradation

RpoS RpoN ArgR NtrC

blc

568

Outer membrane lipoprotein

RpoS

csiD-ygaF-gabD*

357/67/44

Carbon starvation-induced gene/L-2-hydroxyglutarate oxidase/succinate semialdehyde dehydrogenase

RpoS CRP HNS CsiR Lrp

csiE

792

Stationary phase inducible protein

RpoS CRP HNS

cstA

46

Peptide transporter

CRP

ddpXA

39/31

D-ala-D-ala dipeptidase/transporter

RpoN NtrC

dppABDF*

74/64/148/122

Dipeptide ABC transporter

FNR IHF PhoB

ecnB

67

Entericidin B

RpoS

espI

78

Virulence protein

fadBA

26/125

Fatty acid β-oxidation I

Fis ArcA FadR

fadE

74

Fatty acid β-oxidation I

FadR ArcA

fadH

64

2,4-dienoyl-CoA reductase

fadI*

77

Fatty acid β-oxidation I

FadR ArcA

fucAO

32/123

Fucose catabolic process

FucR CRP

gadAXW

66/46/2

Glutamate dependent acid resistance

RpoS Fis FNR GadEXW CRP H-NS TorR

galS

140

GalS transcriptional dual regulator

GalS GalR CRP

garD

41

Galactarate dehydratase

CdaR

garPLR*

40/56/21

Degradation of D-glucarate and D-galactarate

H-NS FNR CadR

hcaR

46

Transcriptional activator of hca cluster

HcaR ArcA

katE

416

Catalase HPII

RpoS Fis

lsrABF*

46/118/124

Putative ABC transporter

RpoS CRP LsrR

lsrR

46

LsrR transcriptional repressor

CRP LsrR

malKLM

40/5/6

Maltose transport

RpoS MalT CRP

msyB*

40

Acidic protein

RpoS

osmY

27

Osmotically inducible protein

RpoS IHF CRP Fis

otsBA

211/220

Trehalose biosynthesis I

RpoS

phnB

56

Unknown

potFGH*

52/18/4

Putrescine ABC transporter

RpoN NtrC

poxB

787

Pyruvate oxidase

prpR

416

DNA-binding transcriptional activator

PrpR RpoN CRP

psiF

73

Phosphate starvation-induced protein

puuA

393

Putrescine degradation II

sufABCDS*

124/88/71/43/25

Fe-S cluster assembly

OxyR IHF IscR Fur RpoS

talA

67

Transaldolase A

RpoS

tam

86

Trans-aconitate methyltransferase

RpoS

tdcBCD

41/5/5

Threonine degradation I

tktB

168

Transketolase II

RpoS

tnaLAB

443/189/750

Tryptophan catabolism

RpoS CRP TorR

treF

45

Cytoplasmic trehalase

ugpBAECQ

161/129/46/184/4

Glycerol-3-P ABC transporter

PhoB CRP

xylFGHR

265/7/10/5

Xylose ABC transporter

RpoS Fis CRP XylR

yahO

241

Unknown

RpoS

ybaST

19/70

Glutaminase/ABC transporter

GadX RpoS

ybgS

82

Unknown

RpoS

ybhPO

251/7

Predicted DNase/cardiolipin synthase

RpoS

ycaC

653

Predicted hydrolase

BaeR Fnr RpoS

ycaP

66

Unknown

ycgB

478

Unknown

RpoS

yciGFE

205/405/38

Unknown

RpoS HNS

ydbC

100

Predicted oxidoreductase

ydcST*

125/22

Putative ABC transporter

RpoS

yeaGH

771/458

Protein kinase/Unknown

RpoS RpoN NtrC

yeaT

106

Unknown

yeaX

48

Predicted oxidoreductase

yebV

72

Unknown

yedI

60

Unknown

yedK

43

Unknown

yedK

43

Unknown

yegP

185

Unknown

RpoS

yegS

112

Lipid kinase

yehZYX*

787/95/60

ABC transporter

RpoS RpoH

yeiCN

64/31

Unknown

yfcG

187

Glutathione S-transferase

ygaM

155

Stress-induced protein

RpoS

ygdI

90

Unknown

ygeV

55

Putative transcriptional regulator

yghA

326

Unknown

yhbO

231

Stress response protein

RpoS

yhcO

214

Unknown

RpoS

yhfG-fic

133/111

Unknown/Stationary phase protein

RpoS

yhjD

41

Unknown

yhjY

55

Putative lipase

yiaG

449

Predicted transcriptional regulator

RpoS

yjfN

43

Unknown

yjgB

55

Putative oxidoreductase

yjjM

70

Predicted transcriptional regulator

ykgC

127

Predicted oxidoreductase

yncB

57

Predicted oxidoreductase

yniA

63

Unknown

yodD

290

Unknown

yphA

135

Inner membrane protein

ytfQRT-yjfF

879/76/36/34

Putative ABC transporter

Z0608

55

Putative outer membrane protein

Z1504

93

Unknown

Z1629

117

Unknown

Z1923

64

Prophage CP-933X protein

Z1924

137

Prophage CP-933X protein

Z2296

57

Unknown

Z2297

254

Unknown

Z2298

55

Unknown

Z3624

64

D-fructokinase

Z3625

139

Sucrose hydrolase

Z4874

60

Unknown

Z5000

48

Putative regulatory protein

Z5352

125

Unknown