Table 2

Partial list of genes induced and repressed more than 2-fold after 24 h in (i) K-12 yceP biofilms upon addition of 600 μM indole in LB glu medium (experiment performed in duplicate, and one standard deviation is shown), (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium.

Gene

b #

Fold change upon indole addition

Fold change upon trpE deletion

Fold change upon tnaA deletion

Description

Protein Size, aa

Transcription

sdiA

b1916

2.9 ± 0.8

1.0*

1.2

AHL transcriptional activator (LuxR/TraR family)

240

ygaV

b2667

2.2 ± 0.2

1.1*

-1.1*

hypothetical protein

99

soxS

b4062

2.3 ± 0.3

-2.8

-1.2

regulation of superoxide response regulon

107

cspA

b3556

1.8 ± 0.4

-4.6

-1.2*

cold shock protein 7.4, transcriptional activator of hns

70

mtlR

b3601

1.3* ± 0.4

-2.6

-1.4*

MtlR transcriptional repressor

195

yjcT

b4084

-1.1* ± 0.1

1.5*

-3.5

D-allose kinase

309

rhoL

b3782

2.2 ± 0.1

-1.1*

1.1*

rho operon leader peptide

33

Cell motility and secretion

hha

b0460

4.9 ± 0.0

-1.4

-1.4

haemolysin expression modulating protein

72

ybaJ

b0461

5.2 ± 0.8

-1.1*

1.0*

conserved hypothetical protein

124

mqsR

b3022

2.8 ± 0.7

1.1*

1.4

master regulator of chemotaxis via AI-2; interacts with QseB

98

sfmA

b0530

-1.3* ± 0.1

1.0*

-2.3

putative fimbrial-like protein

191

sfmC

b0531

-1.1* ± 0.1

-1.1*

-2.3

putative chaperone

230

sfmH

b0533

-1.2* ± 0.1

1.1*

-2.0

fimbrial assembly protein

325

flgA

b1072

1.1* ± 0.1

1.2*

-2.1

flagellar biosynthesis; assembly of basal-body periplasmic P ring

219

yehA

b2108

1.1* ± 0.0

-1.1*

-2.1

hypothetical protein

344

yhcA

b3215

1.1* ± 0.0

-1.7

-2.0

putative chaperone

224

yfcP

b2333

1.1* ± 0.1

1.3*

-2.0

putative fimbrial-like protein

179

Colanic acid synthesis genes

ypdI

b2376

-1.2* ± 0.2

1.3*

-2.5

YpdI colanic acid synthesis lipoprotein

91

Acid resistance

gadE

b3512

-4.3 ± 1.4

-1.6

1.1*

activator of acid resistance genes and putative LuxR transcriptional activator

175

gadA

b3517

-4.0 ± 1.3

-2.3

1.2*

glutamate decarboxylase A, isozyme, PLP-dependent

466

gadB

b1493

-2.8 ± 0.7

-2.6

1.2*

glutamate decarboxylase isozyme

466

gadC

b1492

-3.7 ± 0.0

-1.6

1.2*

acid sensitivity protein, putative transporter, encoding a γ-aminobutyrate antiporter

511

gadX

b3516

-2.0 ± 0.4

-1.2

-1.2

activator of gadA and gadBC

274

hdeA

b3510

-4.8 ± 0.2

-2.3

1.0*

periplasmic chaperone of acid-denatured protein

110

hdeB

b3509

-3.9 ± 0.6

-2.3

1.2*

10K-L protein, periplasmic protein related to acid resistance protein

112

hdeD

b3511

-3.0 ± 0.5

-1.6

-1.5

protein involved in acid resistance

190

Phage-related genes

cspI

b1552

1.8 ± 0.7

1.0*

-3.7

Qin prophage; cold shock-like protein

70

ypjF

b2646

1.4* ± 0.2

1.2*

-12.1

CP4-57 prophage

109

ymfI

b1143

1.1* ± 0.1

1.1*

-5.7

E14 prophage

113

ydaY

b1366

1.0* ± 0.0

1.0*

-4.6

Rac prophage

119

ydfP

b1553

-1.2* ± 0.2

1.2*

-2.6

Qin prophage

165

ydfE

b1577

1.0* ± 0.1

1.3*

-2.5

Qin prophage

255

yeeV

b2005

-1.5* ± 0.5

1.1*

-2.5

CP4-44 prophage

124

stfE

b1157

1.4* ± 0.4

-1.1*

-2.3

E14 prophage; putative tail fiber protein

166

b1364

b1364

1.2* ± 0.1

1.1*

-2.3

Rac prophage

93

yfjW

b2642

1.4* ± 0.4

-1.1*

-2.1

CP4-57 prophage

567

yeeU

b2004

1.0* ± 0.0

-1.1*

-2.0

CP4-44 prophage; putative structural protein

122

yfjT

b2637

-1.4* ± 0.6

1.1*

-2.0

CP4-57 prophage

155

ynaE

b1375

1.8 ± 0.6

-1.9

-2.0

Rac prophage

88

Amino acid transport and metabolism

tnaA

b3708

1.7 ± 0.0

-1.3*

-14.9

tryptophan deaminase, PLP-dependent

476

tnaC

b3707

1.5 ± 1.1

1.1*

32.0

tryptophanase leader peptide

24

mtr

b3161

-1.1* ± 0.1

-1.3

-5.7

Mtr tryptophan ArAAP transporter

414

aroP

b0112

1.0* ± 0.0

-1.2*

-5.3

AroP phenylalanine/tyrosine/tryptophan APC transporter

457

proC

b0386

-1.2 ± 0.0

1.0*

-3.0

pyrroline-5-carboxylate-reductase

269

Carbohydrate transport and metabolism

melB

b4120

1.2* ± 0.1

1.1*

-7.5

melibiose permease II

469

eno

b2779

-1.9 ± 0.2

-1.2*

1.1*

Enolase

432

yegB

b2077

-1.2* ± 0.2

1.1*

-3.2

multidrug transport protein (MFS family)

prpB

b0331

-2.4 ± 0.6

-1.1*

1.0*

putative carboxyphosphonoenolpyruvate mutase

296

Other metabolism

htrL

b3618

2.2 ± 0.1

1.1*

-1.2*

involved in lipopolysaccharide biosynthesis

290

pyrG

b2780

-2.2 ± 0.2

1.0*

1.0*

CTP synthetase

545

pheL

b2598

-1.2 ± 0.1

-4.9

2.3

chorismate mutase-P-prephenate dehydratase leader peptide

15

yodA

b1973

1.5 ± 0.4

1.0*

-7.5

cadmium-induced metal binding protein

216

chaA

b1216

-1.4* ± 0.4

1.2*

-7.0

sodium-calcium/proton antiporter

366

nhaA

b0019

-1.2* ± 0.0

-1.4

-3.2

Na+/H antiporter, pH dependent

388

ybdS

b0612

-1.3* ± 0.3

-1.2*

-3.2

citrate carrier

487

Energy production and conversion

rsxA

b1627

1.1* ± 0.0

-1.1*

-14.9

integral membrane protein of SoxR-reducing complex

193

ynbA

b1408

1.1* ± 0.0

1.4*

-4.6

putative diacylglycerol cholinephosphotransferase

203

Posttranslational modification, protein turnover, chaperones

htpX

b1829

2.8 ± 1.1

-1.1*

1.1*

heat shock protein, integral membrane protein

293

Translation

ksgA

b0051

-1.9 ± 0.6

-1.3*

-3.0

S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase

273

infA

b0884

1.0* ± 0.1

-1.3*

-3.0

protein chain initiation factor IF-1

72

Defense mechanisms

soda

b3908

1.2* ± 0.3

-3.2

1.1*

superoxide dismutase, manganese

206

Poorly-characterized genes

ycfR

b1112

2.7 ± 0.8

1.0*

-1.4

hypothetical protein

85

ylaD

b0459

2.3 ± 0.3

1.0*

-2.8*

maltose O-acetyltransferase

183

yebE

b1846

2.4 ± 0.1

1.1*

-2.1

hypothetical protein

219

yncJ

b1436

2.7 ± 0.5

-1.1*

-1.2

hypothetical protein

76

yejG

b2181

2.4 ± 0.4

-1.5

-1.2*

hypothetical protein

114

ybjM

b0848

-1.3* ± 0.3

-1.4

-8.6

hypothetical protein

125

b0309

b0309

-1.5* ± 0.6

-1.4

-4.6

hypothetical protein

70

ypjB

b2649

1.1* ± 0.0

1.2*

-3.7

hypothetical protein

263

apaG

b0050

-2.2 ± 0.9

-1.3

-3.7

hypothetical protein

125

ydiY

b1722

-1.1* ± 0.1

1.2*

-3.5

hypothetical protein

252

ymfA

b1122

-1.1* ± 0.1

1.0*

-3.5

hypothetical protein

156

yeiU

b2174

1.2* ± 0.1

-1.2*

-3.0

hypothetical protein

249

yahO

b0329

-1.8 ± 0.4

1.3

1.3

hypothetical protein

91

psiF

b0384

-1.9 ± 0.3

-1.1*

-1.3

induced by phosphate starvation; pho regulon member, requiring phoRB system

112

ycdF

b1005

-2.0 ± 0.1

1.1*

-1.2

hypothetical protein

76

yciG

b1259

-2.1 ± 0.1

1.2*

1.6

hypothetical protein

78

ycgZ

b1164

-2.9 ± 0.6

1.3

1.7

hypothetical protein

78

ymgC

b1167

-2.1 ± 0.3

1.2*

1.5

hypothetical protein

82

ymgA

b1165

-2.4 ± 1.3

1.1

1.7

hypothetical protein

90

ymgB

b1166

-5.2 ± 1.3

1.2

1.5

hypothetical protein, putative acid-resistance protein

88

Full data available using GEO accession number 4562. Asterisk indicates p value greater than 0.05 (data are less reliable but included for completeness). Negative values indicate repressed genes. b # indicates the Blattner number for each gene. Boldface indicates most significant fold changes.

Lee et al. BMC Microbiology 2007 7:42   doi:10.1186/1471-2180-7-42