Table 5 P.aeruginosa genes affected in the ΔpppA-ppkA mutant compared to PAO1 wild-type strain under the conditions of oxidative stress
| Â | Â | Â | Â | Â | 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) | Â | 4.4 | 3.5 | 5.9 | 3.7 |
PA0671 | -3.58 | 0.000 | HP | Â | 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) | Â | 5.7 | 3.4 | 7.0 | 3.3 |
PA2288 | -2.24 | 0.003 | HP | Â | 8.7 | 3.2 | 9.9 | 3.7 |
PA3007 (lexA) | -2.02 | 0.023 | repressor protein LexA (Adaptation, protection; Translation, post-translational modification, degradation) | Â | 8.0 | 4.8 | 9.1 | 5.0 |
PA3008 | -2.26 | 0.010 | HP | Â | 7.2 | 3.1 | 8.4 | 2.8 |
PA3617 (recA) | -2.26 | 0.020 | RecA protein (DNA replication, recombination, modification and repair) | Â | 10.1 | 7.6 | 11.2 | 7.5 |
PA0911 | 2.81 | 0.010 | HP | Â | 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) | Â | 11.9 | 11.3 | 12.8 | 10.2 |
PA0140 (ahpF) | -2.73 | 0.044 | alkyl hydroperoxide reductase subunit F (Adaptation, protection) | Â | 6.7 | 3.8 | 8.1 | 3.6 |
PA0848 | -7.13 | 0.001 | Pr. alkyl hydroperoxide reductase (Adaptation, protection; Putative enzymes) | Â | 4.9 | 2.5 | 7.7 | 2.8 |
PA2825 | -3.08 | 0.001 | Pr. transcriptional regulator (Two-component regulatory systems) | Â | 6.8 | 3.7 | 8.4 | 3.7 |
PA2826 | -2.32 | 0.018 | Pr. glutathione peroxidase (Adaptation, protection) | Â | 8.2 | 5.4 | 9.4 | 5.3 |
PA2868 | -7.76 | 0.001 | HP (Membrane proteins) | Â | 4.4 | 2.8 | 7.3 | 2.9 |
PA4400 | -2.60 | 0.012 | Pr. pyrophosphohydrolase (DNA replication, recombination, modification and repair) | Â | 3.2 | 3.0 | 4.5 | 2.9 |
PA4612 (ankB) | -2.79 | 0.042 | CHP | Â | 3.7 | 2.4 | 5.2 | 2.5 |
PA1127 | -3.07 | 0.032 | Pr. oxidoreductase (Adaptation, protection; Putative enzymes) | Â | 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) | Â | 8.9 | 10.8 | 7.2 | 10.4 |
PA4469 (orfX) | 9.73 | 0.001 | HP | Â | 9.4 | 11.8 | 6.1 | 11.1 |
PA4470 (fumC1) | 7.86 | 0.002 | fumarate hydratase (Energy metabolism) | Â | 8.8 | 11.3 | 5.8 | 10.5 |
PA4471 (fagA) | 13.62 | 0.005 | fagA/HP | Â | 9.5 | 10.7 | 5.8 | 10.3 |
Genes of pyocin synthesis | ||||||||
PA0614 | 3.60 | 0.009 | HP | Â | 6.6 | 3.9 | 4.7 | 4.0 |
PA0617 | 4.79 | 0.002 | Pr. bacteriophage protein | Â | 7.4 | 4.6 | 5.2 | 4.9 |
PA0618 | 3.05 | 0.027 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 7.1 | 5.0 | 5.5 | 5.1 |
PA0619 | 3.53 | 0.039 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 7.8 | 5.3 | 5.9 | 4.9 |
PA0620 | 2.51 | 0.035 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 6.7 | 4.9 | 5.4 | 4.8 |
PA0622 | 2.56 | 0.029 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 7.0 | 5.8 | 5.7 | 5.2 |
PA0623 | 3.44 | 0.042 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 8.4 | 6.5 | 6.6 | 5.9 |
PA0624 | 3.01 | 0.014 | HP (Related to phage, transposon, or plasmid) | Â | 6.9 | 4.7 | 5.3 | 4.4 |
PA0625 | 3.02 | 0.009 | HP (Related to phage, transposon, or plasmid) | Â | 5.5 | 4.2 | 3.9 | 4.0 |
PA0626a | 2.35 | 0.053 | HP (Related to phage, transposon, or plasmid) | Â | 5.5 | 3.8 | 4.3 | 3.5 |
PA0627 | 3.03 | 0.006 | CHP (Related to phage, transposon, or plasmid) | Â | 5.6 | 3.9 | 4.0 | 3.9 |
PA0628 | 3.97 | 0.004 | CHP (Related to phage, transposon, or plasmid) | Â | 6.8 | 4.8 | 4.8 | 4.0 |
PA0629 | 3.62 | 0.046 | CHP (Related to phage, transposon, or plasmid) | Â | 5.7 | 3.1 | 3.9 | 3.1 |
PA0630 | 3.88 | 0.034 | HP (Related to phage, transposon, or plasmid) | Â | 6.8 | 4.7 | 4.8 | 4.0 |
PA0631 | 4.01 | 0.032 | HP (Related to phage, transposon, or plasmid) | Â | 6.0 | 3.5 | 4.0 | 3.1 |
PA0632 | 2.95 | 0.001 | HP (Related to phage, transposon, or plasmid) | Â | 4.0 | 2.4 | 2.5 | 2.4 |
PA0635 | 3.69 | 0.034 | HP (Related to phage, transposon, or plasmid) | Â | 6.3 | 3.5 | 4.4 | 3.5 |
PA0636 | 4.46 | 0.004 | HP (Related to phage, transposon, or plasmid) | Â | 7.4 | 5.3 | 5.2 | 4.8 |
PA0637 | 2.97 | 0.006 | CHP (Related to phage, transposon, or plasmid) | Â | 5.1 | 3.1 | 3.5 | 2.9 |
PA0638 | 4.28 | 0.003 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 6.0 | 3.6 | 3.9 | 3.3 |
PA0639 | 4.28 | 0.022 | CHP (Related to phage, transposon, or plasmid) | Â | 6.3 | 3.7 | 4.2 | 3.4 |
PA0640 | 3.42 | 0.003 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 4.3 | 2.3 | 2.6 | 2.3 |
PA0641 | 3.02 | 0.008 | Pr. bacteriophage protein (Related to phage, transposon, or plasmid) | Â | 5.2 | 3.2 | 3.6 | 3.1 |
PA0643 | 2.07 | 0.011 | HP (Related to phage, transposon, or plasmid) | Â | 3.7 | 2.5 | 2.7 | 2.4 |
PA0646 | 2.26 | 0.049 | HP (Related to phage, transposon, or plasmid) | Â | 4.4 | 3.2 | 3.3 | 3.0 |
PA3142 | -2.62 | 0.015 | HP (Related to phage, transposon, or plasmid) | Â | 6.7 | 5.9 | 8.1 | 5.5 |
PA3143 | -2.92 | 0.002 | HP (Related to phage, transposon, or plasmid) | Â | 3.4 | 3.0 | 5.0 | 2.9 |
Iron metabolism related genes | ||||||||
Pyoverdine | Â | Â | Â | Â | Â | Â | Â | Â |
PA2381 | 4.72 | 0.023 | HP | Â | 6.9 | 8.4 | 4.7 | 8.7 |
PA2384 | 3.11 | 0.006 | transcriptional regulator | Â | 7.8 | 10.8 | 6.2 | 10.5 |
PA2403 | -2.96 | 0.032 | HP (Membrane proteins) | Â | 3.7 | 5.9 | 5.2 | 5.8 |
PA2404 | -2.19 | 0.019 | HP (Membrane proteins) | Â | 6.3 | 8.2 | 7.4 | 7.9 |
PA2405 | -2.14 | 0.023 | HP | Â | 5.0 | 7.5 | 6.1 | 7.6 |
PA2409 | -2.58 | 0.015 | Pr. permease of ABC transporter (Membrane proteins; Transport of small molecules) | Â | 4.1 | 6.6 | 5.4 | 6.1 |
Pyochelin | Â | Â | Â | Â | Â | Â | Â | Â |
PA4227 (pchR)a | 2.47 | 0.098 | transcriptional regulator PchR (Transcriptional regulators) | Â | 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)) | Â | 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)) | Â | 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)) | Â | 8.3 | 11.9 | 5.7 | 11.1 |
Others | Â | Â | Â | Â | Â | Â | Â | Â |
PA1300 | 3.86 | 0.028 | Pr. sigma-70 factor, ECF subfamily (Transcriptional regulators) | Â | 6.4 | 7.0 | 4.5 | 7.3 |
PA4211 | 2.74 | 0.007 | Pr. phenazine biosynthesis protein (Secreted Factors (toxins, enzymes, alginate)) | Â | 4.1 | 10.8 | 2.6 | 10.0 |
PA4570 | 5.46 | 0.011 | HP Pr. negative regulator | Â | 9.2 | 11.9 | 6.7 | 11.8 |
PA5505 | 2.27 | 0.017 | Pr. TonB-dependent receptor (Membrane proteins; Transport of small molecules) | Â | 3.8 | 7.0 | 2.7 | 5.8 |
PA5531 (tonB) | 2.25 | 0.043 | TonB protein (Transport of small molecules) | Â | 9.2 | 9.6 | 8.1 | 9.6 |
PA4764 (fur)a | -2.44 | 0.086 | ferric uptake regulation protein (Transcriptional regulators) | Â | 6.0 | 7.4 | 7.3 | 6.3 |
PA4895 | -2.35 | 0.039 | Pr. transmembrane sensor (Transcriptional regulators; Membrane proteins) | Â | 3.2 | 3.9 | 4.4 | 4.4 |
Primary metabolism | ||||||||
PA0105 (coxB) | -2.38 | 0.048 | cytochrome c oxidase, subunit II (Energy metabolism) | Â | 8.9 | 5.7 | 10.1 | 4.9 |
PA0108 (coIII)a | -1.89 | 0.062 | cytochrome c oxidase, subunit III (Energy metabolism) | Â | 9.4 | 6.0 | 10.3 | 4.6 |
PA0250 | -4.17 | 0.001 | CHP | Â | 5.7 | 5.4 | 7.8 | 5.6 |
PA1756 (cysH) | -2.16 | 0.007 | 3'-phosphoadenosine-5'-phosphosulfate reductase (Amino acid biosynthesis and metabolism) | Â | 4.0 | 5.3 | 5.1 | 4.5 |
PA2611 (cysG) | -2.02 | 0.008 | siroheme synthase (Biosynthesis of cofactors, prosthetic groups and carriers) | Â | 4.9 | 4.7 | 5.9 | 4.8 |
PA2869 | -3.36 | 0.000 | HP | Â | 2.6 | 2.6 | 4.4 | 2.7 |
PA0603a | 2.50 | 0.095 | Pr. ATP-binding component of ABC transporter (Transport of small molecules) | Â | 7.9 | 4.8 | 6.5 | 4.1 |
PA0604 | 3.46 | 0.012 | Pr. binding protein component of ABC transporter (Transport of small molecules) | Â | 5.0 | 2.7 | 3.2 | 2.5 |
PA0605 | 2.83 | 0.003 | Pr. permease of ABC transporter (Membrane proteins); Transport of small molecules) | Â | 5.6 | 3.0 | 4.1 | 3.0 |
PA1317 (cyoA) | 3.12 | 0.026 | cytochrome o ubiquinol oxidase subunit II (Energy metabolism) | Â | 7.1 | 8.3 | 5.5 | 9.7 |
PA1318 (cyoB) | 2.24 | 0.032 | cytochrome o ubiquinol oxidase subunit I (Energy metabolism) | Â | 4.4 | 5.8 | 3.2 | 7.3 |
PA1319 (cyoC) | 3.10 | 0.026 | cytochrome o ubiquinol oxidase subunit III (Energy metabolism) | Â | 5.2 | 6.1 | 3.6 | 7.4 |
PA1321 (cyoE) | 2.21 | 0.040 | cytochrome o ubiquinol oxidase protein CyoE (Energy metabolism) | Â | 5.7 | 5.7 | 4.6 | 7.5 |
PA2646 (nuoK) | 2.24 | 0.043 | NADH dehydrogenase I chain K (Energy metabolism) | Â | 4.9 | 5.4 | 3.7 | 5.5 |
PA3441 | 7.35 | 0.006 | Pr. molybdopterin-binding protein (Transport of small molecules) | Â | 9.5 | 7.2 | 6.6 | 5.6 |
PA3442a | 2.69 | 0.092 | Pr. ATP-binding component of ABC transporter (Transport of small molecules) | Â | 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) | Â | 8.1 | 7.4 | 6.0 | 6.7 |
PA5171 (arcA) | 2.67 | 0.019 | arginine deiminase (Amino acid biosynthesis and metabolism) | Â | 7.6 | 9.0 | 6.2 | 8.5 |
PA5172 (arcB) | 2.66 | 0.026 | ornithine carbamoyltransferase, catabolic (Amino acid biosynthesis and metabolism) | Â | 7.3 | 8.8 | 5.9 | 8.5 |
Others | Â | Â | Â | Â | Â | Â | Â | Â |
PA3237 | -2.89 | 0.004 | HP | Â | 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) | Â | 6.6 | 5.3 | 5.4 | 5.4 |
QS regulated genes | ||||||||
PA2134-92 locus | ||||||||
PA2134 | 4.16 | 0.032 | HP | Â | 8.7 | 5.6 | 6.6 | 5.7 |
PA2135 | 2.85 | 0.027 | Pr. transporter (Membrane proteins; Transport of small molecules) | Â | 4.7 | 3.0 | 3.2 | 3.4 |
PA2136 | 3.01 | 0.004 | HP | Â | 4.1 | 2.3 | 2.5 | 2.4 |
PA2139 | 6.55 | 0.001 | HP | Â | 6.8 | 2.6 | 4.1 | 2.8 |
PA2140 | 3.74 | 0.018 | Pr. metallothionein (Central intermediary metabolism) | Â | 6.8 | 3.0 | 4.9 | 3.4 |
PA2141 | 5.64 | 0.003 | HP | Â | 6.9 | 2.8 | 4.4 | 2.8 |
PA2142 | 4.05 | 0.029 | Pr. short-chain dehydrogenase (Putative enzymes) | Â | 7.7 | 3.9 | 5.7 | 4.3 |
PA2144 (glgP) | 4.01 | 0.008 | glycogen phosphorylase (Cell wall/LPS/capsule) | Â | 6.8 | 3.7 | 4.8 | 3.6 |
PA2148 | 4.37 | 0.016 | CHP (Membrane proteins) | Â | 8.1 | 4.2 | 6.0 | 4.3 |
PA2149 | 6.01 | 0.011 | HP | Â | 9.4 | 4.6 | 6.9 | 4.7 |
PA2150 | 5.76 | 0.000 | CHP | Â | 5.5 | 2.4 | 2.9 | 2.4 |
PA2151 | 3.46 | 0.041 | CHP | Â | 7.0 | 3.6 | 5.2 | 3.4 |
PA2156 | 2.40 | 0.001 | CHP | Â | 3.6 | 2.4 | 2.4 | 2.4 |
PA2157 | 4.03 | 0.002 | HP | Â | 6.2 | 3.4 | 4.2 | 3.8 |
PA2158 | 4.51 | 0.019 | Pr. alcohol dehydrogenase (Zn-dependent) (Putative enzymes) | Â | 7.9 | 4.1 | 5.7 | 4.0 |
PA2159a | 2.89 | 0.062 | CHP | Â | 5.9 | 3.2 | 4.4 | 3.7 |
PA2161a | 3.33 | 0.081 | HP | Â | 5.1 | 4.3 | 3.4 | 4.2 |
PA2162 | 2.14 | 0.049 | Pr. glycosyl hydrolase (Putative enzymes) | Â | 6.2 | 4.6 | 5.1 | 4.8 |
PA2163 | 2.79 | 0.023 | HP | Â | 8.3 | 5.4 | 6.8 | 5.3 |
PA2164 | 4.66 | 0.026 | Pr. glycosyl hydrolase (Putative enzymes) | Â | 9.6 | 5.7 | 7.4 | 5.1 |
PA2165 | 3.96 | 0.008 | Pr. glycogen synthase (Energy metabolism) | Â | 10.3 | 5.5 | 8.3 | 5.3 |
PA2167 | 2.72 | 0.049 | HP | Â | 6.5 | 3.0 | 5.1 | 2.5 |
PA2168 | 2.78 | 0.049 | HP | Â | 8.0 | 4.6 | 6.5 | 4.3 |
PA2178 | 3.55 | 0.004 | HP | Â | 6.6 | 3.3 | 4.8 | 3.9 |
PA2179 | 3.16 | 0.023 | HP | Â | 5.7 | 2.5 | 4.1 | 2.7 |
PA2180 | 3.05 | 0.032 | HP | Â | 8.3 | 4.2 | 6.6 | 4.2 |
PA2181 | 2.99 | 0.001 | HP | Â | 5.3 | 2.6 | 3.7 | 2.8 |
PA2184 | 5.62 | 0.007 | CHP | Â | 7.6 | 4.9 | 5.1 | 5.0 |
PA2187 | 3.01 | 0.038 | HP | Â | 7.2 | 3.4 | 5.6 | 3.9 |
PA2188 | 2.14 | 0.032 | Pr. alcohol dehydrogenase (Zn-dependent) (Putative enzymes) | Â | 4.2 | 2.8 | 3.1 | 2.8 |
PA2192 | 2.72 | 0.020 | CHP | Â | 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) | Â | 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)) | Â | 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 | Â | Â | Â | Â | Â | Â | Â | Â |
PA2364 | -2.65 | 0.006 | HP | RpoS | 5.6 | 5.4 | 7.0 | 5.2 |
PA2560 | -2.09 | 0.039 | HP | Â | 5.1 | 3.8 | 6.2 | 3.0 |
PA2931 (cifR) | -2.05 | 0.008 | transcriptional regulator (Transcriptional regulators) | Â | 5.4 | 3.6 | 6.5 | 4.2 |
PA3006 (psrA) | -2.31 | 0.049 | transcriptional regulator PsrA (Transcriptional regulators) | Â | 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) | Â | 4.6 | 3.5 | 5.6 | 3.5 |
PA5365 (phoU) | -1.76 | 0.012 | phosphate uptake regulatory protein PhoU (Membrane proteins; Transcriptional regulators) | Â | 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) | Â | 8.3 | 5.2 | 9.3 | 5.3 |
PA3309 | 3.88 | 0.010 | CHP | Â | 7.7 | 7.3 | 5.7 | 7.2 |
Other genes | Â | Â | Â | Â | Â | Â | Â | Â |
PA3757 | -5.59 | 0.005 | Pr. transcriptional regulator (Transcriptional regulators) | Â | 3.4 | 3.4 | 5.9 | 2.8 |
PA2414 | 2.70 | 0.039 | L-sorbosone dehydrogenase (Carbon compound catabolism) | Â | 6.2 | 5.2 | 4.8 | 4.5 |
PA2416 (treA) | 3.31 | 0.025 | periplasmic trehalase precursor (Carbon compound catabolism) | Â | 6.5 | 3.7 | 4.8 | 4.0 |
PA4139 | 13.54 | 0.044 | HP | Â | 7.2 | 8.0 | 3.5 | 4.2 |