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Table 5 P.aeruginosa genes affected in the ΔpppA-ppkA mutant compared to PAO1 wild-type strain under the conditions of oxidative stress

From: A eukaryotic-type signalling system of Pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence

      Normalized gene signalsd
Gene (name) Fold changeb P -value Protein (function)c Other regulators Δ
H2O2
Δ wt
H2O2
wt
Oxidative stress-responsive genes
Genes of SOS regulon
PA0669 -2.85 0.027 Pr. DNA polymerase alpha chain (DNA replication, recombination, modification and repair; Putative enzymes)   4.4 3.5 5.9 3.7
PA0671 -3.58 0.000 HP   6.1 2.4 8.0 2.4
PA0923 (dinB) -2.42 0.037 DNA damage inducible protein P (DNA replication, recombination, modification and repair; Adaptation, protection)   5.7 3.4 7.0 3.3
PA2288 -2.24 0.003 HP   8.7 3.2 9.9 3.7
PA3007 (lexA) -2.02 0.023 repressor protein LexA (Adaptation, protection; Translation, post-translational modification, degradation)   8.0 4.8 9.1 5.0
PA3008 -2.26 0.010 HP   7.2 3.1 8.4 2.8
PA3617 (recA) -2.26 0.020 RecA protein (DNA replication, recombination, modification and repair)   10.1 7.6 11.2 7.5
PA0911 2.81 0.010 HP   4.4 2.7 2.9 2.8
Genes of protective cellular mechanisms
PA0139 (ahpC)a -1.91 0.090 alkyl hydroperoxide reductase subunit C (Adaptation, protection)   11.9 11.3 12.8 10.2
PA0140 (ahpF) -2.73 0.044 alkyl hydroperoxide reductase subunit F (Adaptation, protection)   6.7 3.8 8.1 3.6
PA0848 -7.13 0.001 Pr. alkyl hydroperoxide reductase (Adaptation, protection; Putative enzymes)   4.9 2.5 7.7 2.8
PA2825 -3.08 0.001 Pr. transcriptional regulator (Two-component regulatory systems)   6.8 3.7 8.4 3.7
PA2826 -2.32 0.018 Pr. glutathione peroxidase (Adaptation, protection)   8.2 5.4 9.4 5.3
PA2868 -7.76 0.001 HP (Membrane proteins)   4.4 2.8 7.3 2.9
PA4400 -2.60 0.012 Pr. pyrophosphohydrolase (DNA replication, recombination, modification and repair)   3.2 3.0 4.5 2.9
PA4612 (ankB) -2.79 0.042 CHP   3.7 2.4 5.2 2.5
PA1127 -3.07 0.032 Pr. oxidoreductase (Adaptation, protection; Putative enzymes)   6.0 6.5 7.6 8.3
PA3287 -6.70 0.001 CHP RpoS 6.6 3.9 9.4 4.0
PA4468 (sodM) 3.36 0.015 superoxide dismutase (Adaptation, protection)   8.9 10.8 7.2 10.4
PA4469 (orfX) 9.73 0.001 HP   9.4 11.8 6.1 11.1
PA4470 (fumC1) 7.86 0.002 fumarate hydratase (Energy metabolism)   8.8 11.3 5.8 10.5
PA4471 (fagA) 13.62 0.005 fagA/HP   9.5 10.7 5.8 10.3
Genes of pyocin synthesis
PA0614 3.60 0.009 HP   6.6 3.9 4.7 4.0
PA0617 4.79 0.002 Pr. bacteriophage protein   7.4 4.6 5.2 4.9
PA0618 3.05 0.027 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   7.1 5.0 5.5 5.1
PA0619 3.53 0.039 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   7.8 5.3 5.9 4.9
PA0620 2.51 0.035 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   6.7 4.9 5.4 4.8
PA0622 2.56 0.029 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   7.0 5.8 5.7 5.2
PA0623 3.44 0.042 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   8.4 6.5 6.6 5.9
PA0624 3.01 0.014 HP (Related to phage, transposon, or plasmid)   6.9 4.7 5.3 4.4
PA0625 3.02 0.009 HP (Related to phage, transposon, or plasmid)   5.5 4.2 3.9 4.0
PA0626a 2.35 0.053 HP (Related to phage, transposon, or plasmid)   5.5 3.8 4.3 3.5
PA0627 3.03 0.006 CHP (Related to phage, transposon, or plasmid)   5.6 3.9 4.0 3.9
PA0628 3.97 0.004 CHP (Related to phage, transposon, or plasmid)   6.8 4.8 4.8 4.0
PA0629 3.62 0.046 CHP (Related to phage, transposon, or plasmid)   5.7 3.1 3.9 3.1
PA0630 3.88 0.034 HP (Related to phage, transposon, or plasmid)   6.8 4.7 4.8 4.0
PA0631 4.01 0.032 HP (Related to phage, transposon, or plasmid)   6.0 3.5 4.0 3.1
PA0632 2.95 0.001 HP (Related to phage, transposon, or plasmid)   4.0 2.4 2.5 2.4
PA0635 3.69 0.034 HP (Related to phage, transposon, or plasmid)   6.3 3.5 4.4 3.5
PA0636 4.46 0.004 HP (Related to phage, transposon, or plasmid)   7.4 5.3 5.2 4.8
PA0637 2.97 0.006 CHP (Related to phage, transposon, or plasmid)   5.1 3.1 3.5 2.9
PA0638 4.28 0.003 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   6.0 3.6 3.9 3.3
PA0639 4.28 0.022 CHP (Related to phage, transposon, or plasmid)   6.3 3.7 4.2 3.4
PA0640 3.42 0.003 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   4.3 2.3 2.6 2.3
PA0641 3.02 0.008 Pr. bacteriophage protein (Related to phage, transposon, or plasmid)   5.2 3.2 3.6 3.1
PA0643 2.07 0.011 HP (Related to phage, transposon, or plasmid)   3.7 2.5 2.7 2.4
PA0646 2.26 0.049 HP (Related to phage, transposon, or plasmid)   4.4 3.2 3.3 3.0
PA3142 -2.62 0.015 HP (Related to phage, transposon, or plasmid)   6.7 5.9 8.1 5.5
PA3143 -2.92 0.002 HP (Related to phage, transposon, or plasmid)   3.4 3.0 5.0 2.9
Iron metabolism related genes
Pyoverdine         
PA2381 4.72 0.023 HP   6.9 8.4 4.7 8.7
PA2384 3.11 0.006 transcriptional regulator   7.8 10.8 6.2 10.5
PA2403 -2.96 0.032 HP (Membrane proteins)   3.7 5.9 5.2 5.8
PA2404 -2.19 0.019 HP (Membrane proteins)   6.3 8.2 7.4 7.9
PA2405 -2.14 0.023 HP   5.0 7.5 6.1 7.6
PA2409 -2.58 0.015 Pr. permease of ABC transporter (Membrane proteins; Transport of small molecules)   4.1 6.6 5.4 6.1
Pyochelin         
PA4227 (pchR)a 2.47 0.098 transcriptional regulator PchR (Transcriptional regulators)   7.0 7.2 5.7 7.4
PA4228 (pchD) 6.12 0.029 pyochelin biosynthesis protein PchD (Transport of small molecules; Secreted Factors (toxins, enzymes, alginate))   8.4 10.9 5.7 9.8
PA4229 (pchC) 5.89 0.059 pyochelin biosynthetic protein PchC (Transport of small molecules; Secreted Factors (toxins, enzymes, alginate))   9.1 11.4 6.6 10.5
PA4230 (pchB) 6.08 0.038 salicylate biosynthesis protein PchB (Transport of small molecules; Secreted Factors (toxins, enzymes, alginate))   8.3 11.9 5.7 11.1
Others         
PA1300 3.86 0.028 Pr. sigma-70 factor, ECF subfamily (Transcriptional regulators)   6.4 7.0 4.5 7.3
PA4211 2.74 0.007 Pr. phenazine biosynthesis protein (Secreted Factors (toxins, enzymes, alginate))   4.1 10.8 2.6 10.0
PA4570 5.46 0.011 HP Pr. negative regulator   9.2 11.9 6.7 11.8
PA5505 2.27 0.017 Pr. TonB-dependent receptor (Membrane proteins; Transport of small molecules)   3.8 7.0 2.7 5.8
PA5531 (tonB) 2.25 0.043 TonB protein (Transport of small molecules)   9.2 9.6 8.1 9.6
PA4764 (fur)a -2.44 0.086 ferric uptake regulation protein (Transcriptional regulators)   6.0 7.4 7.3 6.3
PA4895 -2.35 0.039 Pr. transmembrane sensor (Transcriptional regulators; Membrane proteins)   3.2 3.9 4.4 4.4
Primary metabolism
PA0105 (coxB) -2.38 0.048 cytochrome c oxidase, subunit II (Energy metabolism)   8.9 5.7 10.1 4.9
PA0108 (coIII)a -1.89 0.062 cytochrome c oxidase, subunit III (Energy metabolism)   9.4 6.0 10.3 4.6
PA0250 -4.17 0.001 CHP   5.7 5.4 7.8 5.6
PA1756 (cysH) -2.16 0.007 3'-phosphoadenosine-5'-phosphosulfate reductase (Amino acid biosynthesis and metabolism)   4.0 5.3 5.1 4.5
PA2611 (cysG) -2.02 0.008 siroheme synthase (Biosynthesis of cofactors, prosthetic groups and carriers)   4.9 4.7 5.9 4.8
PA2869 -3.36 0.000 HP   2.6 2.6 4.4 2.7
PA0603a 2.50 0.095 Pr. ATP-binding component of ABC transporter (Transport of small molecules)   7.9 4.8 6.5 4.1
PA0604 3.46 0.012 Pr. binding protein component of ABC transporter (Transport of small molecules)   5.0 2.7 3.2 2.5
PA0605 2.83 0.003 Pr. permease of ABC transporter (Membrane proteins); Transport of small molecules)   5.6 3.0 4.1 3.0
PA1317 (cyoA) 3.12 0.026 cytochrome o ubiquinol oxidase subunit II (Energy metabolism)   7.1 8.3 5.5 9.7
PA1318 (cyoB) 2.24 0.032 cytochrome o ubiquinol oxidase subunit I (Energy metabolism)   4.4 5.8 3.2 7.3
PA1319 (cyoC) 3.10 0.026 cytochrome o ubiquinol oxidase subunit III (Energy metabolism)   5.2 6.1 3.6 7.4
PA1321 (cyoE) 2.21 0.040 cytochrome o ubiquinol oxidase protein CyoE (Energy metabolism)   5.7 5.7 4.6 7.5
PA2646 (nuoK) 2.24 0.043 NADH dehydrogenase I chain K (Energy metabolism)   4.9 5.4 3.7 5.5
PA3441 7.35 0.006 Pr. molybdopterin-binding protein (Transport of small molecules)   9.5 7.2 6.6 5.6
PA3442a 2.69 0.092 Pr. ATP-binding component of ABC transporter (Transport of small molecules)   7.5 6.4 6.0 5.1
PA5170 (arcD) 4.45 0.049 arginine/ornithine antiporter (Amino acid biosynthesis and metabolism; Membrane proteins; Transport of small molecules)   8.1 7.4 6.0 6.7
PA5171 (arcA) 2.67 0.019 arginine deiminase (Amino acid biosynthesis and metabolism)   7.6 9.0 6.2 8.5
PA5172 (arcB) 2.66 0.026 ornithine carbamoyltransferase, catabolic (Amino acid biosynthesis and metabolism)   7.3 8.8 5.9 8.5
Others         
PA3237 -2.89 0.004 HP   3.9 2.4 5.5 2.5
PA0157 (triB) 2.28 0.001 Pr. RND efflux membrane fusion protein precursor (Transport of small molecules)   6.6 5.3 5.4 5.4
QS regulated genes
PA2134-92 locus
PA2134 4.16 0.032 HP   8.7 5.6 6.6 5.7
PA2135 2.85 0.027 Pr. transporter (Membrane proteins; Transport of small molecules)   4.7 3.0 3.2 3.4
PA2136 3.01 0.004 HP   4.1 2.3 2.5 2.4
PA2139 6.55 0.001 HP   6.8 2.6 4.1 2.8
PA2140 3.74 0.018 Pr. metallothionein (Central intermediary metabolism)   6.8 3.0 4.9 3.4
PA2141 5.64 0.003 HP   6.9 2.8 4.4 2.8
PA2142 4.05 0.029 Pr. short-chain dehydrogenase (Putative enzymes)   7.7 3.9 5.7 4.3
PA2144 (glgP) 4.01 0.008 glycogen phosphorylase (Cell wall/LPS/capsule)   6.8 3.7 4.8 3.6
PA2148 4.37 0.016 CHP (Membrane proteins)   8.1 4.2 6.0 4.3
PA2149 6.01 0.011 HP   9.4 4.6 6.9 4.7
PA2150 5.76 0.000 CHP   5.5 2.4 2.9 2.4
PA2151 3.46 0.041 CHP   7.0 3.6 5.2 3.4
PA2156 2.40 0.001 CHP   3.6 2.4 2.4 2.4
PA2157 4.03 0.002 HP   6.2 3.4 4.2 3.8
PA2158 4.51 0.019 Pr. alcohol dehydrogenase (Zn-dependent) (Putative enzymes)   7.9 4.1 5.7 4.0
PA2159a 2.89 0.062 CHP   5.9 3.2 4.4 3.7
PA2161a 3.33 0.081 HP   5.1 4.3 3.4 4.2
PA2162 2.14 0.049 Pr. glycosyl hydrolase (Putative enzymes)   6.2 4.6 5.1 4.8
PA2163 2.79 0.023 HP   8.3 5.4 6.8 5.3
PA2164 4.66 0.026 Pr. glycosyl hydrolase (Putative enzymes)   9.6 5.7 7.4 5.1
PA2165 3.96 0.008 Pr. glycogen synthase (Energy metabolism)   10.3 5.5 8.3 5.3
PA2167 2.72 0.049 HP   6.5 3.0 5.1 2.5
PA2168 2.78 0.049 HP   8.0 4.6 6.5 4.3
PA2178 3.55 0.004 HP   6.6 3.3 4.8 3.9
PA2179 3.16 0.023 HP   5.7 2.5 4.1 2.7
PA2180 3.05 0.032 HP   8.3 4.2 6.6 4.2
PA2181 2.99 0.001 HP   5.3 2.6 3.7 2.8
PA2184 5.62 0.007 CHP   7.6 4.9 5.1 5.0
PA2187 3.01 0.038 HP   7.2 3.4 5.6 3.9
PA2188 2.14 0.032 Pr. alcohol dehydrogenase (Zn-dependent) (Putative enzymes)   4.2 2.8 3.1 2.8
PA2192 2.72 0.020 CHP   5.4 2.9 4.0 3.0
QS regulated virulence factors
PA1246 (aprD)a 2.10 0.066 alkaline protease secretion protein AprD (Secreted Factors (toxins, enzymes, alginate); Protein secretion/export apparatus)   6.4 8.0 5.4 8.1
PA1248 (aprF)a 2.05 0.072 alkaline protease secretion protein AprF (Protein secretion/export apparatus; Secreted Factors (toxins, enzymes, alginate))   6.4 6.8 5.4 6.6
PA1249 (aprA) 3.25 0.042 alkaline metalloproteinase precursor (Secreted Factors (toxins, enzymes, alginate) PhoB 6.6 8.3 4.9 7.2
PA2300 (chiC) 6.31 0.004 chitinase (Carbon compound catabolism) RpoS 5.7 8.3 3.1 7.2
PA2570 (pa1L) 3.37 0.025 PA-I galactophilic lectin (Adaptation, protection; Motility & Attachment) RpoS 6.6 5.8 4.8 4.8
PA3477 (rhlR) 2.25 0.013 transcriptional regulator RhlR (Adaptation, protection; Transcriptional regulators) RpoS 8.9 9.2 7.8 9.3
PA3724 (lasB) 2.37 0.042 elastase LasB (Translation, post-translational modification, degradation; Secreted Factors (toxins, enzymes, alginate)) RpoS PQS 6.0 8.4 4.7 6.6
PhoB regulon         
PA2364 -2.65 0.006 HP RpoS 5.6 5.4 7.0 5.2
PA2560 -2.09 0.039 HP   5.1 3.8 6.2 3.0
PA2931 (cifR) -2.05 0.008 transcriptional regulator (Transcriptional regulators)   5.4 3.6 6.5 4.2
PA3006 (psrA) -2.31 0.049 transcriptional regulator PsrA (Transcriptional regulators)   5.1 4.4 6.3 5.1
PA5360 (phoB) -2.00 0.004 two-component response regulator PhoB (Transcriptional regulators; Two-component regulatory systems)   4.6 3.5 5.6 3.5
PA5365 (phoU) -1.76 0.012 phosphate uptake regulatory protein PhoU (Membrane proteins; Transcriptional regulators)   6.1 4.1 6.9 4.1
PA5369 (pstS) -2.03 0.049 phosphate ABC transporter, periplasmic phosphate-binding protein (Transport of small molecules)   8.3 5.2 9.3 5.3
PA3309 3.88 0.010 CHP   7.7 7.3 5.7 7.2
Other genes         
PA3757 -5.59 0.005 Pr. transcriptional regulator (Transcriptional regulators)   3.4 3.4 5.9 2.8
PA2414 2.70 0.039 L-sorbosone dehydrogenase (Carbon compound catabolism)   6.2 5.2 4.8 4.5
PA2416 (treA) 3.31 0.025 periplasmic trehalase precursor (Carbon compound catabolism)   6.5 3.7 4.8 4.0
PA4139 13.54 0.044 HP   7.2 8.0 3.5 4.2
  1. a p-value > 0.05, only genes from the same transcriptional unit are listed;b Fold changes represent the ratio of the expression levels in the comparison of P. aeruginosa ΔpppA-ppkA and wild type PAO1 under the conditions of oxidative stress. Minus (-) sign indicates a decreased expression in ΔpppA-ppkA mutant strain;c HP - hypothetical protein, CHP- conserved hypothetical protein, Pr. - probabled  Means of normalized gene signals of two replicates; Δ H2O2/Δ - mutant strain signal intensities treated/untreated with 10 mM H2O2; wt H2O2/wt - wild-type PAO1 strain signal intensities treated/untreated with 10 mM H2O2