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Table 3 Most relevant genes differentially expressed under elevated pressure ( Pressure ) and under elevated pressure and DOT ( Pressure oxygen )

From: New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure

ID

Name

Gene

Pressure

Pressure oxygen

   

FC

Adj. P-val

FC

Adj. P-val

Transcription regulators

      

PP_2088

RNA polymerase sigma factor SigX

sigX

-1.88

1.9 E-03

-1.65

5.6 E-03

PP_5108

RNA polymerase sigma-32 factor

rpoH

+1.49*

3.6 E-03

+1.57

8.7 E-03

PP_1429

sigma E regulatory protein, MucB/RseB

algN

+1.64

1.5 E-03

+1.46*

1.3 E-02

PP_1863

transcriptional regulator LysR family

 

+2.77

3.1 E-03

  

PP_2475

transcriptional regulator TetR family

 

+1.59

7.8 E-03

+1.75

7.5 E-03

PP_3439

transcriptional regulator AraC family

 

-1.55

7.7 E-03

-1.59

5.4 E-03

PP_4508

transcriptional regulator AraC family

 

-1.45*

1.2 E-02

-1.55

3.6 E-03

Global regulatory proteins

PP_4265

transcriptional regulator Anr

anr

+1.61

1.2 E-02

-1.99

2.9 E-02

Signal sensing and transduction

PP_2258

sensory box protein

 

-1.51

1.6 E-02

-1.56

3.2 E-02

PP_2643

methyl-accepting chemotaxis transducer

 

-6.82

2.9 E-07

-15.45

8.5 E-08

PP_1761

sensory box protein/GGDEF family protein

 

-1.77

1.9 E-03

-1.71

2.8 E-03

PP_1762

conserved hypothetical protein

 

-1.45*

2.9 E-02

-1.54

9.3 E-03

PP_2097

sensory box protein

 

-1.49*

5.0 E-03

-1.52

2.0 E-02

PP_4405

sensory box protein

 

+2.04

8.0 E-03

+1.39*

8.9 E-02

PP_5324

response regulator

 

-1.53

4.3 E-03

-1.47*

9.2 E-03

PP_2356

phytochrome family protein (two-component sensor activity)

 

-1.73

4.6 E-03

-1.85

1.3 E-03

PP_4362

Hpt protein (two-component system)

 

-1.36*

7.4 E-02

-1.52

9.0 E-03

PP_4503

winged helix family two component transcriptional regulator

 

+1.56

2.3 E-03

+1.39*

8.9 E-02

PP_0997

sigma-54 dependent transcriptional regulator/sensory box protein

 

-1.46

2.0 E-02

-1.88

4.7 E-04

Stress response (Chaperones, DNA repair)

PP_4179

heat shock protein HtpG

htpG

+1.65

1.0 E-02

+1.92

2.0 E-02

PP_4728

heat shock protein GrpE

grpE

+1.33*

6.2 E-02

+1.72

7.2 E-03

PP_1360

co-chaperonin GroES

groES

+1.61

2.0 E-02

+1.77

8.2 E-02

PP_1361

chaperonin 60 kDa

groEL

+1.78

1.0 E-02

+2.19

6.0 E-03

PP_1522

cold shock protein CspA

cspA-1

-1.51

9.1 E-03

-1.75

3.3 E-03

PP_1092

endonuclease III

nth

-1.67

1.6 E-03

-1.58

3.7 E-03

PP_1624

group II intron-encoding maturase

 

-1.68

1.3 E-03

-1.73

1.2 E-03

PP_1630

RecX protein

recX

+1.54

1.5 E-03

+1.53

1.6 E-02

PP_0483

excinuclease ABC A subunit

uvrA

  

-1.67

6.1 E-03

PP_2295

antirestriction protein, putative

 

-1.44*

9.1 E-03

-1.51

5.4 E-03

PP_2326

universal stress protein family protein

 

-1.51

2.6 E-02

-1.51

1.3 E-02

Cell envelope

PP_0267

outer membrane ferric siderophore receptor putative

 

+1.54

1.2 E-02

+1.73

6.6 E-03

PP_0504

outer membrane protein OprG

oprG

+2.55

5.8 E-04

-3.39

3.1 E-04

PP_1185

outer membrane protein H1

oprH

+6.63

2.9 E-04

+4.76

1.1 E-04

PP_3293

conserved hypothetical protein (predicted ion channel)

 

-1.47*

4.5 E-03

-1.74

6.4 E-03

PP_4454

opine ABC transporter permease protein putative

 

+1.95

2.6 E-03

+1.36

4.6 E-02

PP_4465

porin putative

 

+2.33

1.9 E-03

+1.60

1.1 E-01

PP_2445

integral membrane protein TerC

 

-1.95

1.9 E-03

-2.25

1.3 E-03

PP_1150

membrane protein putative

   

-4.14

3.1 E-04

PP_4592

membrane protein putative

 

-1.74

3.1 E-03

-2.20

1.9 E-03

PP_0916

transporter LysE family

   

+1.83

1.6 E-03

PP_1068

amino acid ABC transporter ATP-binding protein

   

+1.80

1.3 E-03

PP_3023

amino acid efflux protein putative

   

+1.51

6.4 E-03

PP_5073

conserved hypothetical protein (periplasmic protein)

 

+5.70

1.9 E-03

+5.98

8.1 E-06

PP_4841

branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative

 

+1.95

8.5 E-03

  

PP_4842

branched-chain amino acid ABC transporter, permease protein, putative

 

+3.07

4.9 E-03

  

PP_5233

ammonium transporter

amtB

+1.87

8.0 E-03

  

PP_4867

extracellular ligand-binding receptor

 

+1.79

3.3 E-03

  

PP_1076

glycerol uptake facilitator protein

glpF

+2.23

3.0 E-03

+2.03

4.7 E-04

PP_2454

ribose ABC transporter

rbsB

+1.88

1.4 E-02

+3.81

5.4 E-05

PP_2119

ABC efflux tranporter/ATP-binding protein

 

-2.19

4.1 E-03

-2.10

1.2 E-03

PP_0508

conserved hypothetical protein (same operon as efflux ABC transporter ATP-binding prot.)

 

+2.55

8.8 E-03

+3.36

1.8 E-02

PP_5307

biopolymer transport protein ExbD

exbD

  

+2.30

1.8 E-03

PP_0906

multidrug efflux RND transporter putative

 

-2.11

1.4 E-04

-2.19

2.1 E-03

PP_0033

sugar transferase putative

 

-1.74

1.9 E-03

-2.20

9.6 E-03

PP_3422

lytic transglycosylase

ltg

-1.74

1.9 E-03

-1.97

9.9 E-04

PP_4897

N-acetylmuramoyl-L-alanine amidase

 

+1.67

3.6 E-03

  

PP_4384

flagellar basal body L-ring protein

 

-1.48*

5.6 E-03

  

Secretion systems

PP_0806

surface adhesion protein putative (same operon as type I secretion system)

 

-1.58

6.2 E-03

-1.39

5.2 E-02

PP_1055

type II secretion pathway protein GspN

gspN

+1.52

3.1 E-03

  

PP_3087

excinuclease ABC A subunit putative (type VI)

 

+1.64

3.1 E-03

+2.27

1.7 E-03

PP_3093

conserved hypothetical protein (type VI)

 

+1.65

6.1 E-03

+2.39

3.6 E-03

PP_3094

hypothetical protein (type VI)

 

+1.61

1.0 E-02

+2.60

3.5 E-05

PP_3095

chaperone-associated ATPase putative (type VI)

 

+1.60

2.0 E-02

+1.79

5.6 E-03

PP_3096

hypothetical protein (type VI)

 

+1.60

1.1 E-02

+1.97

2.4 E-02

PP_3098

conserved hypothetical protein (type VI)

   

+2.27

2.3 E-04

PP_3099

hypothetical protein (type VI)

 

+1.65

1.5 E-02

+2.00

1.1 E-02

PP_3100

conserved hypothetical protein (type VI)

 

+2.25

2.9 E-04

+2.69

9.6 E-04

PP_3782

hypothetical protein

 

+1.55

1.3 E-02

+1.91

7.6 E-04

PP_3783

conserved hypothetical protein

 

+1.60

2.7 E-03

+1.95

2.8 E-04

PP_3784

conserved domain protein

   

+1.78

7.7 E-03

PP_3785

hypothetical protein

 

+1.65

1.0 E-02

+1.87

3.2 E-03

PP_3786

aminotransferase

 

+1.45*

6.2 E-02

+1.78

7.3 E-03

PP_3787

hypothetical protein

 

+2.10

5.3 E-03

+2.35

9.2 E-04

PP_3788

non-ribosomal peptide synthetase putative

 

+2.35

3.7 E-03

+2.79

4.2 E-05

PP_3790

diaminopimelate epimerase

dapF

  

+1.99

1.4 E-03

Biosynthetic metabolism (amino acids - CO2 production/consumption - glutamate metabolism)

PP_1143

3-hydroxyisobutyrate

 

-1.69

1.0 E-02

-1.95

1.8 E-03

PP_4617

leucine dehydrogenase

 

-1.77

1.9 E-03

-1.62

3.0 E-03

PP_4794

leucyl-tRNA synthetase

leuS

-1.92

3.4 E-04

-1.73

7.5 E-03

PP_0432

N-acetyl-gamma-glutamyl-phosphate reductase

argC

  

+2.03

1.7 E-03

PP_0997

sigma-54 dependent transcriptional regulator/sensory box protein

 

-1.46*

2.0 E-02

-1.88

4.7 E-04

PP_0999

carbamate kinase

arcC

  

-1.72

1.3 E-03

PP_1000

ornithine carbamoyltransferase

argI

  

-1.53

9.6 E-03

PP_1001

arginine deiminase

arcA

  

-1.73

1.9 E-03

PP_1002

arginine/ornithine antiporter

arcD

  

-1.66

1.2 E-02

PP_1079

arginine deiminase

argF

  

+1.69

3.9 E-03

PP_3775*

sarcosine oxidase, putative

   

+1.42

6.8 E-03

PP_3776

rarD protein

rarD-3

  

+1.71

3.6 E-03

PP_3777

hypothetical protein

   

+1.52

2.4 E-02

PP_3780

hypothetical protein

 

+1.44*

8.0 E-03

+1.72

1.4 E-03

PP_4594

cystathionine gamma-lyase

 

-1.69

1.9 E-03

-1.78

1.9 E-02

PP_1631

hypothetical protein (possible lysine decarboxylase)

 

-1.91

3.0 E-03

-1.62

1.3 E-02

PP_3662

decarboxylase family protein (possible lysine decarboxylase)

 

-1.85

4.9 E-03

-1.69

3.9 E-03

PP_1389

carboxyphosphonoenolpyruvate phosphonomutase, putative

 

-1.54

3.7 E-03

  

PP_5346

pyruvate carboxylase subunit B

oadA

-1.58

1.7 E-02

-1.51

1.1 E-01

PP_5347

pyruvate carboxylase subunit A

accC-2

-2.23

1.9 E-03

-2.41

5.6 E-03

PP_5075

glutamate synthase subunit beta

gltD

  

+1.69

1.3 E-02

PP_5409

glucosamine--fructose-6-phosphate aminotransferase

glmS

  

+1.54

1.3 E-02

Electron transport

PP_4265

transcriptional regulator Anr

anr

+1.61

1.2 E-02

-1.99

2.9 E-02

PP_0103

cytochrome c oxidase subunit II

 

-1.41*

1.2 E-02

-1.67

2.3 E-03

PP_0104

cytochrome c oxidase subunit I

   

-1.68

5.6 E-03

PP_0111

electron transport protein SCO1/SenC

 

-1.46*

1.3 E-02

-1.44*

8.7 E-03

PP_0811

cyoups2 protein

cyoups2

+1.79

1.9 E-03

+1.95

7.2 E-04

PP_0812

cytochrome o ubiquinol oxidase subunit II

cyoA

+1.43*

1.3 E-02

+1.59

3.0 E-03

PP_0813

cytochrome o ubiquinol oxidase, subunit I

cyoB

  

+1.41*

9.6 E-02

PP_0816

protoheme IX farnesyltransferase

cyoE-2

  

+1.41*

2.1 E-02

PP_4119

NADH dehydrogenase I A subunit

nuoA

-1.51

2.0 E-02

-1.66

3.6 E-03

PP_4202

electron transfer flavoprotein beta subunit

 

+1.42*

6.2 E-03

+1.82

1.4 E-03

PP_4250

cytochrome c oxidase cbb3-type, subunit II

ccoN-1

+1.51

7.2 E-02

-1.56

1.0 E-02

PP_4251

cytochrome c oxidase cbb3-type, subunit II

ccoO-1

  

-2.22

1.7 E-03

PP_4252

cytochrome c oxidase, cbb3-type, CcoQ subunit

ccoQ-1

  

-1.65

9.2 E-02

PP_4253

cytochrome c oxidase, cbb3-type, subunit III

ccoP-1

  

-1.69

2.6 E-02

PP_4255

cytochrome c oxidase cbb3-type, subunit I

ccoN-2

-1.39*

3.0 E-02

-1.55

7.4 E-04

PP_4870

azurin

azu

+2.22

1.9 E-03

-1.19

2.0 E-01

Fe-S cluster assembly

      

PP_0841

iron-sulfur cluster assembly transcription factor IscR

iscR

  

+1.67

2.3 E-03

PP_0842

cysteine desulfurase

iscS-1

  

+2.50

5.7 E-05

PP_0843

iron-binding protein IscU

iscU

  

+2.48

1.5 E-04

PP_0844

iron-binding protein IscA

iscA

  

+2.19

1.1 E-04

PP_0845

co-chaperone HscB

hscB

  

+2.46

7.6 E-04

PP_0846

chaperone protein HscA

hscA

  

+1.88

1.7 E-02

PP_0847

ferredoxin, 2Fe-2S

   

+1.72

2.2 E-03

PP_0848

conserved hypothetical protein

 

-1.38

4.6 E-02

+1.52

5.2 E-03

PP_2378

yghI protein

yghI

  

+2.14

1.5 E-04

PP_1082

bacterioferritin

bfr

-1.85

1.3 E-02

-4.20

1.1 E-05

PP_1083

BFD domain protein (2Fe-2S)-binding domain protein

   

+2.35

1.4 E-04

PP_4900

iron-sulfur cluster-binding, putative

 

-1.43*

4.5 E-03

-1.49*

7.3 E-02

PP_5306

ferric siderophore transport system protein ExbB

exbB

  

+1.87

3.0 E-02

PP_5307

ferric siderophore transport system inner membrane protein

exbD

  

+2.30

1.8 E-03

PP_5308

TonB family protein

tonB

  

+1.54

2.4 E-02

PP_0267

outer membrane ferric siderophore receptor putative

 

+1.54

1.2 E-02

+1.73

6.6 E-03

Detoxification

PP_2439

alkyl hydroxide reductase C subunit

ahpC

+1.87

3.8 E-03

+3.89

2.5 E-05

PP_3639

alkylhydroperoxidase

 

-1.68

6.7 E-03

-1.59

2.1 E-03

PP_1684

major facilitator transporter

   

+1.51

7.5 E-03

PP_1686

glutathione peroxidase

   

+2.11

3.1 E-04

PP_3444

glyoxalase/bleomycin resistance protein/dioxygenase

 

-1.57

4.5 E-03

-1.49*

2.9 E-02

PP_2474

glutathione S-transferase family protein

 

+1.69

7.2 E-02

+1.67

6.7 E-02

PP_3742

glutathione S-transferase family protein

   

+1.53

5.1 E-03

  1. The genes were sorted according to their function. Differential expression is expressed in fold change (FC) where positive and negative values indicate how many times the gene transcription is increased and decreased, respectively, compared to the Control. The significance of differential expression is given by the adjusted P-value (Adj. P-val).
  2. * Genes with a fold change slightly below 1.5 but whose differential expression is supported by a low adjusted P-value or by the differential expression of genes belonging to the same operon.
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Microbial Cell Factories

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