Table 1

List of significantly up or downregulated P. aeruginosa genes that are discussed in this report

Affymetrix ORF #

Probe ID

a20 minutes

a60 minutes

Description

Symbol

Functional class


bFold change

P value

bFold change

P value


Group I: Upregulation (20 min) – Upregulation (60 min)

PA1964_at

PA1964

2.029

0.0112

2.381

0.0112

probable ATP-binding component of ABC transporter

Transport of small molecules

PA2760_at

PA2760

2.152

0.0416

2.94

0.0416

probable outer membrane protein precursor

Transport of small molecules

PA4687_hitA_at

PA4687

2.219

0.00808

2.069

0.00808

ferric iron-binding periplasmic protein HitA

hitA

Transport of small molecules

PA2743_infC_at

PA2743

2.044

0.000327

2.634

0.000327

translation initiation factor IF-3

infC

Translation, post-translational modification, degradation

PA2619_infA_at

PA2619

2.14

0.000526

3.644

0.000526

translation initiation factor

infA

Translation, post-translational modification, degradation

PA4266_fusA1_at

PA4266

2.18

0.012

3.88

0.012

elongation factor G

fusA1

Translation, post-translational modification, degradation

PA3655_tsf_at

PA3655

2.197

0.017

5.495

0.017

elongation factor Ts

tsf

Translation, post-translational modification, degradation

PA4665_prfA_at

PA4665

2.426

0.00398

2.774

0.00398

peptide chain release factor 1

prfA

Translation, post-translational modification, degradation

PA4273_rplA_at

PA4273

2.725

0.0349

6.018

0.0349

50S ribosomal protein L1

rplA

Translation, post-translational modification, degradation

PA3656_rpsB_at

PA3656

2.543

0.00953

7.267

0.00953

30S ribosomal protein S2

rpsB

Translation, post-translational modification, degradation

PA4744_infB_at

PA4744

2.783

0.0134

3.826

0.0134

translation initiation factor IF-2

infB

Translation, post-translational modification, degradation

PA4934_rpsR_at

PA4934

2.894

0.000276

6.619

0.000276

30S ribosomal protein S18

rpsR

Translation, post-translational modification, degradation

PA4255_rpmC_at

PA4255

2.927

0.00331

6.655

0.00331

50S ribosomal protein L29

rpmC

Translation, post-translational modification, degradation

PA4528_pilD_at

PA4528

2.144

0.014

2.65

0.014

type 4 prepilin peptidase PilD

pilD

Motility & Attachment

PA0408_pilG_at

PA0408

2.294

0.0144

4.026

0.0144

twitching motility protein PilG

pilG

Chemotaxis

PA5041_pilP_at

PA5041

2.169

0.00817

2.232

0.00817

type 4 fimbrial biogenesis protein PilP

pilP

Motility & Attachment

PA0410_pilI_at

PA0024

2.188

0.0484

2.267

0.0484

twitching motility protein PilI

pilI

Motility & Attachment

PA5042_pilO_at

PA5042

2.26

0.000345

2.056

0.000345

type 4 fimbrial biogenesis protein PilO

pilO

Motility & Attachment

PA4527_pilC_at

PA4527

2.27

0.00205

2.678

0.00205

still frameshift type 4 fimbrial biogenesis protein PilC

pilC

Motility & Attachment

PA5043_pilN_at

PA5043

2.34

0.000628

2.914

0.000628

type 4 fimbrial biogenesis protein PilN

pilN

Motility & Attachment

PA5044_pilM_at

PA5044

2.893

0.00702

3.12

0.00702

type 4 fimbrial biogenesis protein PilM

pilM

Motility & Attachment

PA4688_hitB_at

PA4688

2.282

0.0261

2.513

0.0261

iron (III)-transport system permease HitB

hitB

Membrane proteins

PA4747_secG_at

PA4747

2.294

0.00628

3.795

0.00628

secretion protein SecG

secG

Membrane proteins

PA4243_secY_at

PA4243

2.914

9.26E-05

6.799

9.26E-05

secretion protein SecY

secY

Membrane proteins

PA4276_secE_at

PA4276

2.274

2.07E-05

4.198

2.07E-05

secretion protein SecE

secE

Protein secretion/export apparatus

PA2968_fabD_at

PA2968

2.137

0.0131

3.506

0.0131

malonyl-CoA-[acyl-carrier-protein] transacylase

fabD

Fatty acid and phospholipid metabolism

PA1609_fabB_at

PA1609

2.373

0.0147

2.855

0.0147

beta-ketoacyl-ACP synthase I

fabB

Fatty acid and phospholipid metabolism

PA2967_fabG_at

PA2967

2.387

0.00109

3.416

0.00109

3-oxoacyl-[acyl-carrier-protein] reductase

fabG

Fatty acid and phospholipid metabolism

PA1610_fabA_at

PA1610

2.864

0.00295

4.071

0.00295

beta-hydroxydecanoyl-ACP dehydrase

fabA

Fatty acid and phospholipid metabolism

PA3645_fabZ_at

PA3645

2.854

2.25E-05

4.671

2.25E-05

(3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase

fabZ

Cell wall/LPS/capsule

PA5556_atpA_at

PA5556

2.202

0.00136

3.907

0.00136

ATP synthase alpha chain

atpA

Energy metabolism

PA5491_at

PA5491

2.354

0.0049

2.854

0.0049

probable cytochrome

Energy metabolism

PA5561_atpI_at

PA5561

2.558

0.0015

2.542

0.0015

ATP synthase protein I

atpI

Energy metabolism

PA3818_at

PA4263

2.746

0.00537

5.447

0.00537

extragenic suppressor protein SuhB

SuhB

Adaptation, protection

PA4743_rbfA_at

PA4743

2.824

0.0177

4.063

0.0177

ribosome-binding factor A

rbfA

Adaptation, protection

PA5117_typA_at

PA5117

3.136

0.000343

5.723

0.000343

regulatory protein TypA

TypA

Adaptation, protection

Group II: Upregulation (20 min) – No change (60 min)

PA0524_norB_at

PA0524

3.869

0.0456

nitric-oxide reductase subunit B

norB

Energy metabolism

PA3479_rhlA_at

PA3479

2.376

0.0364

rhamnosyltransferase chain A

rhlA

Secreted Factors (toxins, enzymes, alginate)

PA0177_at

PA0177

2.683

0.00294

probable purine-binding chemotaxis protein

Adaptation, protection

Group III: Downregulation (20 min) – No change (60 min)

PA2193_hcnA_at

PA2193

-2.268

0.0324

hydrogen cyanide synthase HcnA

hcnA

Central intermediary metabolism

PA2194_hcnB_at

PA2194

-2.762

0.018

hydrogen cyanide synthase HcnB

hcnB

Central intermediary metabolism

PA2195_hcnC_at

PA2195

-2.183

0.0437

hydrogen cyanide synthase HcnC

hcnC

Central intermediary metabolism

PA4385_groEL_at

PA4385

-2.16

0.00513

GroEL protein

groEL

Chaperones & heat shock proteins

PA4542_clpB_at

PA4542

-2.77

0.00253

ClpB protein

clpB

Translation, post-translational modification, degradation

Group IV: No change(20 min) – Upregulation(60 min)

PA4272_rplJ_at

PA4272

5.918

0.00886

50S ribosomal protein L10

rplJ

Translation, post-translational modification, degradation

PA4271_rplL_at

PA4271

5.898

0.00319

50S ribosomal protein L17/L12

rplL

Translation, post-translational modification, degradation

PA2740_pheS_at

PA2740

3.323

0.000548

phenylalanyl-tRNA synthetase, alpha-subunit

pheS

Translation, post-translational modification, degradation

PA4240_rpsK_at

PA4240

3.283

0.0292

30S ribosomal protein S11

rpsK

Translation, post-translational modification, degradation

PA4267_rpsG_at

PA4267

3.104

0.0138

30S ribosomal protein S7

rpsG

Translation, post-translational modification, degradation

PA2739_pheT_at

PA2739

2.142

0.0375

phenylalanyl-tRNA synthetase, beta subunit

pheT

Translation, post-translational modification, degradation

PA3987_leuS_at

PA3987

2.632

0.0216

leucyl-tRNA synthetase

leuS

Amino acid biosynthesis and metabolism

PA0009_glyQ_at

PA0009

2.568

0.000361

glycyl-tRNA synthetase alpha chain

glyQ

Amino acid biosynthesis and metabolism

PA3525_argG_at

PA3525

2.45

0.0411

argininosuccinate synthase

argG

Amino acid biosynthesis and metabolism

PA3167_serC_at

PA3167

2.345

0.0396

3-phosphoserine aminotransferase

serC

Amino acid biosynthesis and metabolism

PA0904_lysC_at

PA0904

2.337

0.00528

aspartate kinase alpha and beta chain

lysC

Amino acid biosynthesis and metabolism

PA5263_argH_at

PA5263

2.29

0.00853

argininosuccinate lyase

argH

Amino acid biosynthesis and metabolism

PA4007_proA_at

PA4007

2.282

0.0231

gamma-glutamyl phosphate reductase

proA

Amino acid biosynthesis and metabolism

PA5277_lysA_at

PA5277

2.247

0.0334

diaminopimelate decarboxylase

lysA

Amino acid biosynthesis and metabolism

PA5143_hisB_at

PA5143

2.246

0.00461

imidazoleglycerol-phosphate dehydratase

hisB

Amino acid biosynthesis and metabolism

PA5039_aroK_at

PA5039

2.234

0.013

shikimate kinase

aroK

Amino acid biosynthesis and metabolism

PA0018_fmt_at

PA0018

2.222

0.0137

methionyl-tRNA formyltransferase

fmt

Amino acid biosynthesis and metabolism

PA5067_hisE_at

PA5067

2.212

0.00214

phosphoribosyl-ATP pyrophosphohydrolase

hisE

Amino acid biosynthesis and metabolism

PA3482_metG_at

PA3482

2.043

0.0312

methionyl-tRNA synthetase

metG

Amino acid biosynthesis and metabolism

PA5119_glnA_at

PA5119

2.038

0.0442

glutamine synthetase

glnA

Amino acid biosynthesis and metabolism

PA4439_trpS_at

PA4439

2.002

0.0155

tryptophanyl-tRNA synthetase

trpS

Amino acid biosynthesis and metabolism

PA0903_alaS_at

PA0903

2.099

0.0102

alanyl-tRNA synthetase

alaS

Transcription, RNA processing and degradation

PA4602_glyA3_at

PA4602

3.347

2.83E-05

serine hydroxymethyltransferase

glyA3

Amino acid biosynthesis and metabolism

PA0971_tolA_at

PA0971

2.249

0.000381

TolA protein

tolA

Transport of small molecules

PA5479_gltP_at

PA5479

2.413

0.00978

proton-glutamate symporter

gltP

Membrane proteins

PA3821_secD_at

PA3821

3.516

0.00324

secretion protein SecD

secD

Membrane proteins

PA3820_secF_at

PA3820

2.206

0.0411

secretion protein sec F Protein secretion

secF

Protein secretion/export apparatus

PA5070_tatC_at

PA5070

2.312

0.0209

transport protein TatC

tatC

Membrane proteins

PA0973_oprL_at

PA0973

2.281

0.00672

Peptidoglycan associated lipoprotein OprL precursor

oprL

Membrane proteins

PA0280_cysA_at

PA0280

2.018

0.0139

sulfate transport protein CysA

cysA

Transport of small molecules

PA5217_at

PA5217

2.141

0.00709

probable binding protein component of ABC iron transporter

Transport of small molecules

PA0295_at

PA0295

2.643

0.0147

probable periplasmic polyamine binding protein

Transport of small molecules

PA4461_at

PA4461

2.24

0.00116

probable ATP-binding component of ABC transporter

Transport of small molecules

PA5503_at

PA5503

2.229

0.000446

probable ATP-binding component of ABC transporter

Transport of small molecules

PA4450_murA_at

PA4450

2.855

0.00044

UDP-N-acetylglucosamine 1-carboxyvinyltransferase

murA

Cell wall/LPS/capsule

PA3644_lpxA_at

PA3644

2.83

0.00038

UDP-N-acetylglucosamine acyltransferase

lpxA

Cell wall/LPS/capsule

PA5276_lppL_i_at

PA5276

2.786

0.0149

Lipopeptide LppL precursor

lppL

Cell wall/LPS/capsule

PA3643_lpxB_at

PA3643

2.561

0.0247

lipid A-disaccharide synthase

lpxB

Cell wall/LPS/capsule

PA5012_waaF_at

PA5012

2.092

0.00978

heptosyltransferase II

waaF

Cell wall/LPS/capsule

PA3337_rfaD_at

PA3337

3.397

0.0498

ADP-L-glycero-D-mannoheptose 6-epimerase

rfaD

Cell wall/LPS/capsule

PA5129_grx_at

PA5129

3.855

0.0334

glutaredoxin

grx

Energy metabolism

PA5555_atpG_at

PA5555

3.527

0.0287

ATP synthase gamma chain

atpG

Energy metabolism

PA5554_atpD_at

PA5554

3.011

0.00384

ATP synthase beta chain

atpD

Energy metabolism

PA3621_fdxA_at

PA3621

3.01

0.0042

ferredoxin I

fdxA

Energy metabolism

PA5559_atpE_at

PA5559

2.734

0.0205

atp synthase C chain

atpE

Energy metabolism

PA5560_atpB_at

PA5560

2.433

0.0148

ATP synthase A chain

atpB

Energy metabolism

PA2995_nqrE_at

PA2995

2.216

0.00617

Na+-translocating NADH:quinone oxidoreductase subunit Nqr5

nqrE

Energy metabolism

PA5553_atpC_at

PA5553

2.175

0.00502

ATP synthase epsilon chain

atpC

Energy metabolism

PA0362_fdx1_at

PA0362

2.125

0.000346

ferredoxin [4Fe-4S]

fdx1

Energy metabolism

PA3527_pyrC_at

PA3527

2.218

0.0211

dihydroorotase

pyrC

Nucleotide biosynthesis and metabolism

PA5331_pyrE_at

PA5331

2.156

0.0166

orotate phosphoribosyltransferase

pyrE

Nucleotide biosynthesis and metabolism

PA3654_pyrH_at

PA3654

2.434

0.0212

uridylate kinase

pyrH

Nucleotide biosynthesis and metabolism

PA3763_purL_at

PA3763

2.279

0.00792

phosphoribosylformylglycinamidine synthase

purL

Nucleotide biosynthesis and metabolism

Group V: No change(20 min) – Downregulation(60 min)

PA1174_napA_at

PA1174

-3.425

0.0251

periplasmic nitrate reductase protein NapA

napA

Energy metabolism

PA1175_napD_at

PA1175

-2.949

0.0134

NapD protein of periplasmic nitrate reductase

napD

Energy metabolism

PA1176_napF_at

PA1176

-2.949

0.024

ferredoxin protein NapF

napF

Energy metabolism

PA1173_napB_at

PA1173

-3.077

0.00344

cytochrome c-type protein NapB precursor

napB

Energy metabolism

PA2248_bkdA2_at

PA2248

-5.076

0.0072

2-oxoisovalerate dehydrogenase (beta subunit)

bkdA2

Amino acid biosynthesis and metabolism

PA2247_bkdA1_at

PA2247

-9.434

0.00376

2-oxoisovalerate dehydrogenase (alpha subunit)

bkdA1

Amino acid biosynthesis and metabolism

PA2250_lpdV_at

PA2250

-3.497

0.00576

lipoamide dehydrogenase-Val

lpdV

Amino acid biosynthesis and metabolism

Group VI: Downregulation (20 min) – Downregulation (60 min)

PA3049_rmf_at

PA3049

-6.25

0.000723

-25.907

0.000723

ribosome modulation factor

rmf

Translation, post-translational modification, degradation

PA3622_rpoS_at

PA3622

-2.653

0.00961

-2.967

0.00961

sigma factor RpoS

rpoS

Transcriptional regulators

PA4762_grpE_at

PA4762

-2.915

0.00501

-0.479

0.00501

heat shock protein GrpE

grpE

DNA replication, recombination, modification and repair

PA5054_hslU_at

PA5054

-3.226

0.000316

-0.428

0.000316

heat shock protein HslU

hslU

Chaperones & heat shock proteins

PA5053_hslV_at

PA5053

-2.597

0.00113

-0.352

0.00113

heat shock protein HslV

hslV

Chaperones & heat shock proteins

PA1596_htpG_at

PA1596

-2.695

0.00706

-0.434

0.00706

heat shock protein HtpG

htpG

Chaperones & heat shock proteins


Genes are categorized by their transcription patterns and related functions. The microarray results are the mean of four replicates of each gene.

aThe microarray results are the mean of four replicates of each gene.

bThe fold change is a positive number when the expression level in the experiment increased compared to the control and is a negative number when the expression level in the experiment decreased.

Nde et al. BMC Genomics 2008 9:473   doi:10.1186/1471-2164-9-473

Open Data