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Table 3 Genes expressed more highly in untreated P. aeruginosa drip-flow reactor biofilms (n = 6) than in several comparator transcriptomes.

From: Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis

  

DFB*

Comp.*

  

Gene ID

Name

Rank

Rank

Note

Description

PA0038

 

185

1734

 

hypothetical protein

PA0105-0107

coxBA

174

3225

O2

cytochrome c oxidase

PA0200

 

145

3494

 

hypothetical protein

PA0284

 

77

712

 

hypothetical protein

PA0409

pilH

56

539

 

Type IV pili biogenesis

PA0515-0519

nirFCMS

207

2547

O2

nitrite reduction

PA0523-0524

norCB

177

3770

O2

nitric oxide reductase

PA0586-0588

 

123

1848

O2

conserved hypothetical and serine protein kinase

PA0713

 

103

3107

O2

conserved hypothetical protein

PA717-0726

 

185

3323

 

hypothetical proteins of bacteriophage Pf1

PA0763

mucA

30

296

 

anti-sigma factor

PA1041

 

47

1850

 

probable outer membrane protein precursor

PA1174

napA

270

2433

O2

periplasmic nitrate reductase

PA1178

oprH

5

831

 

outer membrane protein H1 precursor

PA1190

 

105

3558

 

conserved hypothetical protein

PA1414

 

14

756

 

hypothetical protein

PA1431

rsaL

45

1835

O2

regulatory protein

PA1555-1556

 

64

1312

O2

cytochrome c oxidase

PA1592

 

4

67

 

hypothetical protein

PA1673

 

152

2346

O2

hypothetical protein

PA1746

 

173

2016

O2

hypothetical protein

PA1982-1983

exaAB

315

5317

 

alcohol dehydrogenase, cytochrome c550

PA2274

 

378

3473

 

putative monooxygenase

PA2381

 

64

1279

O2

conserved hypothetical protein

PA2485

 

161

2704

 

hypothetical protein

PA2501

 

133

1858

 

hypothetical protein

PA2622

cspD

19

591

 

stationary phase replication inhibitor

PA2754

 

140

1797

 

conserved hypothetical protein

PA2780-2781

 

205

2983

 

hypothetical proteins

PA2807-2808

ptrA

47

3378

Cu

hypothetical and two-component repressor

PA2862

lipA

176

2785

 

lactonizing lipase precursor

PA2883

 

121

2207

 

hypothetical protein

PA2937

 

53

3144

 

hypothetical protein

PA3040

 

40

553

 

conserved hypothetical protein

PA3049

rmf

11

1575

O2

ribosome modulation factor

PA3126

ibpA

134

1382

 

heat-shock protein IbpA

PA3181

 

226

2020

 

2-keto-3-deoxy-6-phosphogluconate aldolase

PA3186-3190

oprB

68

1936

 

glucose uptake

PA3205

 

16

1033

 

hypothetical protein

PA3235

 

101

2118

 

conserved hypothetical protein

PA3309

 

33

1076

O2

universal stress protein

PA3369-3371

 

196

3302

 

hypothetical proteins

PA3412

 

163

3772

Cu

probable transcriptional regulator

PA3415

 

225

2682

 

probable dihydrolipoamide acetyltransferase

PA3416-3417

 

259

2723

 

pyruvate dehydrogenase

PA3418

ldh

52

2352

 

leucine dehydrogenase

PA3515-3519

 

92

2804

Cu

hypothetical proteins and probable lyases

PA3523

 

128

3765

Cu

probable RND efflux membrane fusion protein

PA3552

pmrH

269

2400

 

lipopolysaccharide modification

PA3572

 

107

1616

 

hypothetical protein

PA3577

 

253

3216

 

hypothetical protein

PA3690-3691

 

57

1482

Cu

probable metal-transporting P-type ATPase

PA3792

leuA

38

603

 

2-isopropylmalate synthase

PA3819

 

44

508

 

conserved hypothetical protein

PA3920

 

79

2577

Cu

probable metal transporting P-type ATPase

PA3973

 

292

2829

 

probable transcriptional regulator

PA4352

 

114

1316

O2

conserved hypothetical protein

PA4550-4551

fimUpilV

167

2088

 

type 4 fimbrial biogenesis proteins

PA4577

 

124

2292

 

hypothetical protein

PA4607-4611

 

136

2173

 

hypothetical proteins

PA4739

 

143

1345

O2

conserved hypothetical protein

PA4773,4776

pmrB

166

2538

 

hypothetical and two-component sensor

PA4781-82

 

202

2538

 

probable two-component response regulator

PA5100

hutU

258

2660

O2

urocanase

PA5212

 

29

881

 

hypothetical protein

PA5427

adhA

112

2664

O2

alcohol dehydrogenase

PA5446

 

7

866

 

hypothetical protein

PA5460

 

118

3962

 

hypothetical protein

PA5475

 

294

2787

O2

hypothetical protein

  1. *Average Rank in drip flow biofilms (DFB) and three comparator microarray data sets (Comp. Rank) named in the Materials and Methods.