Genes induced at pH 9 | Transcriptome4 | Proteome5 | Regulators6 | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
cytoplasma | envelope | membrane | |||||||||||||||
No | gene ID1 | op2 | gene | function | TMH3 | pH 6 | pH 9 | 6 | 7.5 | 9 | 6 | 7.5 | 9 | 6 | 7.5 | 9 | |
1 | cg0077 | Hypothetical protein | 0 | n.d. | 1.04 | -0.6 | - | - | - | - | - | -0.9 | - | - | |||
2 | cg0105 | Hypothetical protein Cgl0077 | 0 | -0.83 | 1.65 | - | - | - | -0.4 | - | - | - | - | - | |||
3 | cg0310 | katA | Catalase | 0 | -0.62 | 1.73 | 4.2 | 5.1 | 6.4 | - | - | 0.0 | - | - | -0.6 | RipA | |
4 | cg0444 | ramB | Regulator of acetate metabolism | 0 | 0.76 | 1.11 | - | - | -0.8 | - | 0.7 | 3.5 | - | - | - | RamA, RamB | |
5 | cg0445 | c | sdhCD | Succinate dehydrogenase component CD | 5 | -1.31 | 1.31 | - | - | - | 1.8 | 1.4 | 2.4 | 3.2 | 4.0 | 5.0 | RipA, DtxR, RamA*, RamB* |
6 | cg0446 | c | sdhA | Succinate dehydrogenase A | 0 | -1.08 | 1.47 | 1.0 | 2.7 | 1.7 | 6.7 | 7.0 | 9.0 | 8.5 | 9.0 | 9.9 | RipA, DtxR, RamA*, RamB* |
7 | cg0447 | c | sdhB | Succinate dehydrogenase B | 0 | -1.43 | 1.14 | - | -0.4 | - | 4.6 | 5.0 | 6.7 | 3.5 | 3.4 | 5.3 | RipA, DtxR, RamA*, RamB* |
8 | cg0448 | c | Conserved hypothetical membrane protein | 2 | -0.98 | 1.18 | - | - | - | -0.4 | 0.8 | 1.7 | - | - | - | RipA*, DtxR, RamB* | |
9 | cg0778 | fecC | putative iron or siderophore ABC-type transporter, permease component | 8 | -0.05 | 1.07 | - | - | - | - | - | - | - | - | - | ||
10 | cg0825 | Dehydrogenases with different specificities | 0 | -0.19 | 1.07 | 4.1 | 4.6 | 5.0 | -0.4 | -0.3 | 1.8 | -0.7 | - | -0.4 | |||
11 | cg0858 | putative gamma subunit of the nitrate reductase | 1 | -0.28 | 1.22 | - | - | - | - | - | - | - | - | - | |||
12 | cg1095 | Hypothetical protein | 0 | 0.32 | 1.28 | - | - | - | - | - | - | - | - | - | |||
13 | cg1136 | Hypothetical protein | 0 | 0.15 | 1.02 | 1.6 | 0.5 | 2.2 | - | - | - | - | - | - | |||
14 | cg1206 | PEP phosphonomutase or related enzyme | 0 | 0.38 | 1.05 | 2.6 | 2.8 | 2.7 | - | - | - | - | - | - | |||
15 | cg1292 | r | Flavin-containing monoxygenase 3 | 0 | n.d. | 3.87 | - | - | 2.4 | - | - | 4.4 | - | - | -0.6 | ||
16 | cg1293 | r | Hypothetical membrane protein | 3 | n.d. | 1.71 | - | - | - | - | - | - | - | - | - | ||
17 | cg1312 | Hypothetical membrane protein | 4 | n.d. | 1.32 | - | - | -0.2 | 1.9 | 2.1 | 4.7 | 5.3 | 4.4 | 6.3 | |||
18 | cg1344 | s | narG | Nitrate dehydrogenases 2 (Fe4S4 containing) | 0 | 1.36 | 1.94 | - | - | -0.6 | - | - | - | - | - | -0.4 | RipA, GlxR* |
19 | cg1345 | s | narK | putative nitrate/nitrite transporter | 12 | n.d. | 1.66 | - | - | - | -0.4 | - | 3.0 | 1.5 | -0.6 | 3.0 | RipA, GlxR* |
20 | cg1695 | SAM dependent methyltransferase | 0 | n.d. | 1.72 | - | - | - | - | - | - | - | - | - | |||
21 | cg1737 | acn | Aconitase A | 0 | -0.58 | 1.66 | 4.4 | 5.3 | 6.2 | 4.4 | 5.0 | 4.9 | 2.2 | 2.6 | 2.5 | RipA, RamA*, RamB* | |
22 | cg1759 | x | sufX | Predicted metal-sulfur cluster biosynthetic enzyme | 0 | 0.94 | 1.34 | - | - | -0.8 | -0.4 | - | - | - | - | - | SufR, SigM |
23 | cg1761 | x | nifS2 | Cysteine desulfhydrase, Selenocysteine lyase | 0 | 0.44 | 1.47 | 2.3 | 2.0 | 3.2 | -0.4 | - | - | - | - | - | SufR, SigM |
24 | cg1762 | x | sufC | Suf related ABC-type transporter, ATPase component | 0 | 0.81 | 1.51 | 3.7 | 3.4 | 4.6 | 3.4 | 4.4 | 4.1 | 0.1 | 2.9 | 2.1 | SufR, SigM |
25 | cg1764 | x | sufB | Suf related ABC-type transporter SufB, permease component | 0 | 0.93 | 1.81 | 2.8 | 3.4 | 5.0 | 3.4 | 3.4 | 3.8 | 0.1 | 0.4 | 1.6 | SufR, SigM |
26 | cg1765 | x | sufR | transcriptional regulator SufR | 0 | 0.76 | 1.53 | - | - | - | - | - | - | - | - | - | SufR, SigM |
27 | cg1790 | pgk | Phosphoglycerate kinase | 0 | 0.15 | 1.07 | 4.8 | 4.2 | 5.0 | 5.0 | 4.8 | 5.0 | 2.5 | 2.7 | 3.3 | SigB* | |
28 | cg1884 | putative copper export protein CopC | 2 | -0.39 | 1.12 | - | - | - | - | - | - | - | - | - | LexA | ||
29 | cg1904 | ABC-type transporter, permease component | 6 | 0.09 | 1.12 | - | - | - | - | - | - | - | -0.6 | 1.2 | |||
30 | cg2191 | putative 3-demethylubiquinone-9 3-methyltransferase | 0 | n.d. | 1.02 | - | - | - | - | - | - | - | - | - | |||
31 | cg2274 | ab | Hypothetical protein | 0 | -0.17 | 1.15 | -0.6 | 0.4 | 1.8 | - | - | - | - | - | - | ||
32 | cg2275 | ab | Hypothetical protein | 0 | -0.28 | 1.03 | 1.0 | 2.4 | 1.3 | - | - | - | -0.9 | - | - | ||
33 | cg2320 | ArsR type transcriptional regulator | 0 | -0.26 | 1.25 | - | - | - | - | - | - | - | - | - | |||
34 | cg2572 | Hypothetical protein | 0 | 0.45 | 1.44 | - | - | - | - | - | - | - | - | - | |||
35 | cg2636 | catA1 | Protocatechuate 3,4-dioxygenase beta subunit | 0 | n.d. | 3.09 | - | - | 1.6 | - | - | - | - | - | - | RipA, GlxR* | |
36 | cg2736 | bcp | putative 3-demethylubiquinone-9 3-methyltransferase | 0 | 0.12 | 1.12 | 0.5 | -0.5 | 0.4 | - | - | - | - | - | - | ||
37 | cg2782 | ftn | Ferritin-like protein | 0 | 0.56 | 1.29 | - | - | 0.8 | - | - | - | - | - | - | DtxR | |
38 | cg2853 | Hypothetical protein | 0 | 0.41 | 1.4 | 0.6 | -0.5 | 1.8 | - | - | - | - | - | - | |||
39 | cg3117 | ai | cysX | Hypothetical protein | 0 | 3.5 | 1.08 | - | - | - | - | - | - | - | - | - | DtxR, McbR*, CysR* |
40 | cg3118 | ai | cysI | Sulfite reductase hemoprotein beta-component | 0 | 3.5 | 1.06 | 0.6 | 1.5 | 2.4 | 3.5 | 2.1 | -0.3 | - | - | - | DtxR, McbR, CysR* |
41 | cg3236 | MFS-type transporter | 0 | 1.27 | 1.01 | - | - | -0.8 | - | - | - | - | - | - | |||
42 | cg3331 | ogt | Methylated DNA-protein cysteine methyltransferase | 0 | 0.2 | 1.34 | - | -0.8 | - | -0.1 | - | 1.3 | - | - | - | ||
Genes repressed at pH 9 | |||||||||||||||||
1 | cg0071 | Metallo-beta-lactamase superfamily | 0 | n.d. | -1.01 | - | - | - | - | - | - | - | - | - | |||
2 | cg0133 | abgT | P-aminobenzoyl-glutamate transporter | 13 | -0.86 | -1.02 | - | - | - | - | - | - | 0.3 | 3.7 | 2.1 | ||
3 | cg0202 | iolD | Putative acetolactate synthase | 0 | n.d. | -1.13 | - | - | - | - | - | - | - | - | - | ||
4 | cg0265 | putative ABC-type molybdate transporter, ATPase component | 0 | -0.22 | -1.08 | - | - | - | - | - | - | - | - | - | |||
5 | cg0303 | leuA | 2-isopropylmalate synthase | 0 | -0.97 | -1.06 | 4.3 | 4.7 | 4.5 | - | -0.3 | - | - | - | - | ||
6 | cg0404 | b | putative nitroreductase | 0 | 1.77 | -1.50 | 3.4 | 2.5 | 0.9 | 0.9 | - | - | -0.9 | - | - | ||
7 | cg0467 | ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component | 0 | -0.50 | -1.10 | - | 0.2 | - | - | 0.7 | - | 0.2 | 1.0 | -0.4 | DtxR | ||
8 | cg0527 | ArsR type transcriptional regulator | 0 | -0.32 | -1.13 | - | - | - | - | - | - | - | - | - | DtxR | ||
9 | cg0589 | ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component | 0 | -0.15 | -1.01 | - | - | - | 1.2 | - | - | 0.1 | - | - | DtxR | ||
10 | cg0623 | putative ABC-type cobalt transporter, permease components | 8 | -1.05 | -1.35 | - | - | - | - | - | - | - | - | - | |||
11 | cg0624 | h | Hypothetical membrane protein | 2 | -1.09 | -1.09 | - | - | - | - | - | - | 1.3 | 1.6 | -0.4 | ||
12 | cg0625 | h | putative terpenoide cylase | 1 | -1.28 | -1.04 | - | 2.2 | 0.0 | 2.8 | 3.6 | 2.2 | - | -0.6 | -0.4 | ||
13 | cg0723 | crtE | Geranylgeranyl-pyrophosphate sythase | 0 | 0.66 | -1.01 | - | - | - | - | -0.2 | - | - | - | - | ||
14 | cg0748 | ABC-type Fe3+-siderophores transporter, periplasmic components | 0 | -1.07 | -2.14 | -0.3 | 1.3 | - | 1.2 | 0.7 | - | 0.1 | -0.6 | - | DtxR | ||
15 | cg0756 | cstA | putative carbon starvation protein A | 16 | -0.83 | -1.56 | - | - | - | 1.9 | 2.1 | 1.0 | 2.1 | 2.8 | -0.6 | ||
16 | cg0767 | m | Siderophore-interacting protein | 0 | -0.34 | -2.99 | 0.5 | -0.8 | - | - | - | - | - | - | - | DtxR, RamB* | |
17 | cg0768 | m | ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component | 0 | -0.17 | -2.03 | - | - | - | 1.7 | 1.7 | - | - | -0.6 | - | DtxR, RamB* | |
18 | cg0924 | n | ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component | 0 | -0.60 | -2.91 | 4.8 | 5.2 | 2.7 | 3.6 | 4.1 | 0.7 | 5.1 | 4.5 | 3.4 | DtxR | |
19 | cg0927 | n | ABC-type cobalamin/Fe3+-siderophores transporter, permease component | 9 | -0.10 | -2.08 | - | - | - | 1.2 | -0.2 | 0.0 | 3.0 | 3.3 | - | DtxR | |
20 | cg0928 | n | ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component | 0 | -0.14 | -2.35 | - | -0.8 | - | 3.3 | 4.0 | - | 1.8 | 1.0 | - | DtxR | |
21 | cg0952 | o | mctB | putative monocarboxylate transporter subunit | 2 | -2.55 | -1.32 | - | 0.5 | - | 2.4 | 4.7 | 4.1 | - | 2.1 | -0.6 | RamA, RamB |
22 | cg0953 | o | mctC | monocarboxylate transporter | 13 | -2.44 | -1.01 | - | 3.0 | -0.2 | 1.9 | 4.7 | 4.7 | 3.2 | 4.5 | 3.2 | RamA, RamB |
23 | cg1091 | Hypothetical protein | 0 | 0.95 | -1.18 | - | - | - | - | - | - | - | - | - | SigM* | ||
24 | cg1167 | metS | putative methionine transporter subunit | 0 | -1.04 | -1.43 | - | - | - | - | - | - | -0.9 | - | -0.6 | ||
25 | cg1290 | metE | 5-methyltetrahydropteroyltri-glutamate-homocystein-emethyltransferase | 0 | 0.65 | -1.06 | 8.2 | 6.8 | 6.4 | 8.0 | 8.0 | 6.5 | 6.2 | 6.4 | 4.2 | McbR* | |
26 | cg1365 | t | atpH | F0F1 ATP synthase delta subunit | 0 | -1.26 | -1.03 | 1.9 | 2.3 | 1.3 | 3.9 | 4.8 | 4.7 | 3.2 | 4.1 | 3.4 | SigH* |
27 | cg1367 | t | atpG | F0F1 ATP synthase gamma subunit | 0 | -1.71 | -1.11 | 1.1 | 4.2 | 3.4 | 3.3 | 4.9 | 4.7 | 4.0 | 4.0 | 2.5 | SigH* |
28 | cg1451 | serA | Phosphoglycerate dehydrogenase | 0 | -0.22 | -1.10 | 6.5 | 5.4 | 6.1 | 7.7 | 7.5 | 7.2 | 5.3 | 5.3 | 4.2 | ||
29 | cg1537 | ptsM | PTS system mannose-specific EIIBCA component | 10 | -0.39 | -1.06 | 2.6 | 3.5 | 1.8 | 5.9 | 5.6 | 6.0 | 6.6 | 6.4 | 6.1 | RamB*, GlxR* | |
30 | cg1859 | Putative secreted protein | 0 | 0.04 | -1.34 | - | 1.7 | - | - | 3.6 | 1.5 | 0.1 | 5.0 | -0.4 | |||
31 | cg1930 | z | Putative secreted hydrolase | 0 | -1.18 | -3.26 | - | - | - | - | - | - | - | - | - | DtxR | |
32 | cg1931 | z | Hypothetical protein | 0 | -0.88 | -2.55 | - | - | - | - | - | - | -0.7 | -0.6 | - | DtxR | |
33 | cg2283 | Hypothetical protein | 0 | 0.00 | -1.51 | 4.2 | 4.3 | 3.4 | - | -0.2 | - | - | - | - | |||
34 | cg2336 | Putative secreted protein | 0 | -0.09 | -1.31 | - | - | - | - | 2.1 | - | 3.6 | 3.9 | 1.9 | |||
35 | cg2445 | hmuO | putative heme oxygenase | 0 | -0.93 | -1.19 | -0.2 | 2.5 | - | - | -0.2 | - | - | -0.6 | - | DtxR | |
36 | cg2560 | ad | aceA | Isocitrate lyase | 0 | -2.73 | -2.19 | - | 4.9 | 2.4 | - | -0.3 | - | - | - | - | RamA, RamB |
37 | cg2962 | Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides | 0 | 0.45 | -1.18 | -0.3 | 0.2 | - | - | - | - | - | - | - | |||
38 | cg3156 | htaA | secreted protein implicated in iron acquisition and transport | 0 | -2.50 | -2.76 | - | - | - | - | - | -0.3 | 2.7 | 5.7 | - | DtxR | |
39 | cg3254 | Hypothetical membrane protein | 3 | 0.07 | -1.29 | - | - | - | - | - | - | -0.5 | - | - |