Skip to main content
. 2013 Mar 28;12:30. doi: 10.1186/1475-2859-12-30

Table 3.

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

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

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).

* 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.