Table 2 Selected genes significantly up-regulated in water

Chemotaxis/motility

 Flagellar assembly protein

lpg1790

fliO

5.35

 Flagellar basal body rod protein

lpg1221

flgG

2.38

3.01

 Flagellar biosynthesis sigma factor

lpg1782

fliA

3.34

1.53

 Flagellar biosynthetic protein

lpg1788

fliQ

2.75

 Flagellar biosynthetic regulator

lpg1784

flhF

3.46

 Flagellar hook protein

lpg1219

flgE

4.17

3.79

 Flagellar L-ring protein

lpg1222

flgH

2.13

 Flagellar motor protein

lpg2318

motA

1.63

 Flagellar motor protein

lpg1780

motB

2.72

 Flagellar motor protein

lpg1781

motC

4.02

 Flagellar motor switch protein

lpg1792

fliM

3.48

1.44

 Flagellar P-ring protein

lpg1223

flgI

2.99

 Flagellin

lpg1340

fliC

1.22

1.71

Detoxification/adaptation

 Alkylhydroperoxidase

Lpg2349

ahpD

2.63

2.25

 Alkylhydroperoxide reductase

lpg2350

ahpC

1.74

1.64

 Alkylhydrogen peroxide reductase

lpg2965

ahpC

1.62

1.85

 Heat shock protein

lpg2024

dnaJ

1.56

1.96

 Heat shock protein

lpg2817

yrfI

1.62

2.77

 Aminoglycoside 6-adenylyltransferase

lpg2151

1.80

3.01

2.11

 Spectinomycin phosphotransferase

lpg1492

1.74

1.73

 Stress-induced protein

lpg2011

3.81

5.97

 Superoxide dismutase

lpg2348

sodC

2.45

2.88

 Universal stress protein A

lpg0935

1.59

Icm/dot effector

 Coiled-coil-containing protein

lpg1488

legC5

1.75

1.05

 F-box protein

lpg2144

legAU13

1.07

1.74

2.11

 Hypothetical

lpg0096

ceg4

2.69

2.16

 Hypothetical

lpg2591

ceg33

3.35

4.83

 Hypothetical

lpg1290

lem8

1.59

2.48

2.20

 Hypothetical

lpg1496

lem10

1.51

2.79

3.28

 Protein SdhA

lpg0376

sdhA

1.31

1.60

 Protein SidA

lpg0621

sidA

2.47

 Sid related protein-like

lpg2157

sdeA

2.33

1.60

 UBOX-containing protein

lpg2830

legU2

1.35

2.34

 UVB-resistance protein

lpg1976

legG1

1.66

1.65

Lipid metabolism

 3-hydroxybutyrate dehydrogenase

lpg2316

bdhA

2.40

1.31

Other functions

 6S RNA

3.65

3.55

 RsmY

2.57

 RsmZ

1.58

1.80

 Response regulator TutC

lpg2146

2.39

1.10

 Sensor histidine kinase

lpg0230

pleD

2.95

2.27

 Sensor protein LuxN

lpg2734

1.23

1.89

 Sensory box protein, GGDEF/EAL domain

lpg0029

rre41

1.33

1.07

 Sensory box protein, GGDEF/EAL domain

lpg1025

yegE

1.37

4.85

2.16

 Serine/threonine-protein kinase

lpg0208

pkn5

1.25

 Sigma 54 modulation protein YhbH

lpg1206

3.95

4.04

 Signal transduction protein

lpg0156

3.11

5.19

 Enhanced entry protein EnhA

lpg1336

enhA

1.10

2.06

 Enhanced entry protein EnhA

lpg1386

1.28

1.31

 Enhanced entry protein EnhA

lpg2641

enhA

2.57

3.75

 Enhanced entry protein EnhA

lpg0910

enhA

1.72

3.18

 Enhanced entry protein EnhB

lpg2640

enhB

2.40

 Enhanced entry protein EnhC

lpg1172

2.58

5.87

 Enhanced entry protein EnhC

lpg1356

2.70

2.88

 RtxA

lpg0645

1.57

3.04

Transcription

 DNA binding protein

lpg2441

1.79

 RNA polymerase sigma-54 factor

lpg0477

1.44

 Transcription repair coupling factor

lpg0954

mfd

2.04

2.14

 Transcriptional regulator

lpg0586

1.24

3.75

4.48

 Transcriptional regulator, ArsR family

lpg2723

3.63

1.18

 Transcriptional regulator, AsnC family

lpg1486

2.33

 Transcriptional regulator, DeoR family

lpg2167

1.76

 Transcriptional regulator, LuxR family

lpg2524

1.52

1.73

 Transcriptional regulator, LysR family

lpg2138

3.58

4.21

 Transcriptional regulator, MarR family

lpg2140

1.80

1.90

Transport and binding

 IcmC (DotE)

lpg0453

icmC

1.27

−1.11

 IcmC homolog (DotV)

lpg0472

2.06

2.69

 IcmD (DotP)

lpg0454

icmD

1.25

1.77

 IcmO (DotL)

lpg0446

icmO

2.07

−1.50

 IcmP (DotM)

lpg0445

icmP

2.15

3.54

 IcmT

lpg0441

icmT

1.39

1.79

−1.09

 IcmV

lpg2687

icmV

1.00

−1.89

 Erythromycin resistance protein/ABC transporter

lpg1616

uup

1.86

1.61

 Multidrug resistance protein/efflux pump

lpg0257

2.67

3.09

 Multidrug resistance protein/efflux pump

lpg0429

oprM

1.12

1.65

 Multidrug resistance protein/efflux pump

lpg2189

ygjT

1.76

2.28

−1.85

Viral functions/phage/transposases

 Prophage regulatory protein

lpg2563

1.22

 Transposase

lpg2120

2.01

 Transposase

lpg2363

1.65