TABLE 2.
Relative transcript levels of selected genes of wild-type C. acetobutylicum during oxygen exposure (O2) and of anaerobic C. acetobutylicum lacking PerR
| ORF and functiona | Gene | Protein function | COG class | Fold regulation
|
PerR boxb | |
|---|---|---|---|---|---|---|
| O2 | Lacking PerR | |||||
| Detoxification/redox balance | ||||||
| CAC0327 | bcp | Bacterioferritin comigratory protein, akylhydroperoxidase | O | 5.2 | 16.0 | + |
| CAC0869 | Thioredoxin reductase | O | 4.9 | 8.1 | − | |
| CAC1027 | fprA1 | Flavoprotein FprA1 | C | 4.4 | 16.1 | + |
| CAC1363 | sodC | Superoxide dismutase; Cu/Zn family | P | 0.21 | − | |
| CAC1547 | trxA | Thioredoxin | O | 7.5 | − | |
| CAC1548 | trxB | Thioredoxin reductase | O | 10.3 | − | |
| CAC1549 | bsaA1 | Glutathione peroxidase | O | 23.3 | − | |
| CAC1570 | bsaA2 | Glutathione peroxidase | O | 2.6 | 0.1 | − |
| CAC1571 | bsaA3 | Glutathione peroxidase | O | 5.1 | − | |
| CAC2448 | nror | NROR | C | 7.8 | 16.8 | + |
| CAC2449 | fprA2 | Flavoprotein FprA2 | C | 7.3 | 22.5 | + |
| CAC2450 | dfx | desulfoferrodoxin, superoxide reductase | C | 18.4 | 29.6 | + |
| CAC2567 | sod | Superoxide dismutase; Fe/Mn family | P | − | ||
| CAC2575 | rbr1 | Rubrerythrin | C | 0.42 | − | |
| CAC2777 | Glutaredoxin | O | 3.5 | 6.0 | + | |
| CAC2778 | rd | Rubredoxin | C | 5.2 | 14.4 | + |
| CAC3018 | rbr2 | Rubrerythrin | − | |||
| CAC3306 | tpx | Thiolperoxidase | O | 3.0 | 3.4 | + |
| CAC3597 | rbr3B | Reverse rubrerythrin | C | 5.6 | 26.9 | + |
| Iron metabolism/transport | ||||||
| CAC0447 | feoA1 | FeoA protein; involved in Fe2+ transport | P | 2.3 | − | |
| CAC0448 | feoB2 | Fe2+ transport protein B (FeoB2) | P | 2.8 | − | |
| CAC0788 | Ferrichrome transport permease | P | 3.3 | − | ||
| CAC0789 | fhuB | Permease | P | 3.4 | − | |
| CAC0790 | fhuD | Ferrichrome-binding periplasmic protein | P | 2.6 | − | |
| CAC0791 | fhuC | Ferrichrome ABC transporter; ATP-binding protein | P | 2.3 | − | |
| CAC1029 | FeoA-like protein; involved in iron transport | P | 5.8 | − | ||
| CAC1030 | FeoA-like protein; involved in iron transport | P | 8.1 | − | ||
| CAC1031 | FeoB-like GTPase; responsible for iron uptake | P | 15.9 | − | ||
| CAC1032 | Predicted transcriptional regulator | K | 4.3 | − | ||
| CAC1988 | Ferrichrome-binding periplasmic protein | P | 0.27 | − | ||
| CAC1989 | ABC-type Fe3+ transport system, ATPase component | P | 0.27 | − | ||
| CAC1990 | ABC-type Fe3+ transport system, permease component | P | 0.30 | − | ||
| CAC1991 | Uncharacterized protein, YIIM family | S | 0.32 | − | ||
| CAC1992 | moaC | Mo cofactor biosynthesis protein C | H | 0.30 | − | |
| CAC1993 | moaA | Mo cofactor biosynthesis protein A | H | 0.30 | − | |
| CAC1994 | moaB | Molybdopterin biosynthesis enzyme | H | 0.32 | − | |
| CAC1995 | Hypothetical protein | X | 0.31 | − | ||
| CAC1996 | Hypothetical protein | X | 0.36 | − | ||
| Nucleic acid repair/metabolism | ||||||
| CAC0502 | uvrB | Excinuclease ABC subunit B | L | 2.1 | − | |
| CAC0503 | uvrA | Excinuclease ABC subunit A (ATPase) | L | 4.2 | − | |
| CAC1047 | Ribonucleotide-diphosphate reductase α subunit | F | 9.9 | − | ||
| CAC1390 | purE | Phosphoribosylaminoimidazole carboxylase catalytic subunit | F | 3.2 | − | |
| CAC1391 | purC | Phosphoribosylaminoimidazole-succinocarboxamide synthase | F | 3.1 | − | |
| CAC1392 | purF | Amidophosphoribosyltransferase | F | 2.8 | − | |
| CAC1393 | purM | Phosphoribosylaminoimidazole synthetase | F | 2.9 | − | |
| CAC1394 | purN | Phosphoribosylglycinamide formyltransferase | F | 2.8 | − | |
| CAC1395 | purH | Phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase | F | 2.5 | − | |
| CAC1655 | purQ-purL | Bifunctional phosphoribosylformylglycinamidine synthase | F | 3.5 | − | |
| CAC1815 | recA | Recombinase A | L | 4.0 | − | |
| CAC1856 | RNase HI | R | 2.4 | 4.4 | − | |
| CAC3276 | nrdB | Ribonucleotide-diphosphate reductase β subunit | F | 13.5 | − | |
| CAC3277 | nrdA | Ribonucleotide-diphosphate reductase α subunit | F | 6.5 | − | |
| CAC3358 | dam | Site-specific DNA methylase | L | 6.4 | ||
| CAC3499 | Predicted endonuclease | G | 5.3 | 4.1 | − | |
| Protein turnover/repair | ||||||
| CAC1857 | Metal-dependent peptidase | S | 2.2 | 4.8 | − | |
| CAC3288 | sufC | Fe-regulated ABC transporter ATPase subunit | O | 2.8 | − | |
| CAC3289 | sufB1 | Fe-regulated ABC-type transporter membrane component | O | 2.9 | − | |
| CAC3290 | sufB2 | Fe-regulated ABC-type transporter membrane component | O | 3.3 | − | |
| CAC3291 | Selenocysteine lyase, NifS family | E | 2.6 | − | ||
| CAC3292 | NifU homolog involved in Fe-S cluster formation | C | 2.0 | − | ||
| CAC3624 | 6-Pyruvoyl-tetrahydropterin synthase | H | 8.2 | − | ||
| CAC3625 | Fe-S oxidoreductase of MoaA family | O | 3.1 | − | ||
| Energy conversion | ||||||
| CAP0162 | adhE1 | Aldehyde dehydrogenase (NAD+) | C | 1.9 | 2.2 | − |
| CAP0163 | ctfA | Butyrate-acetoacetate CoA-transferase subunit A | C | 1.9 | 2.1 | − |
| CAP0164 | ctfB | Butyrate-acetoacetate CoA-transferase subunit B | C | 2.0 | 2.2 | − |
| CAC0116 | CO dehydrogenase; beta chain | C | 23.9 | 0.05 | − | |
| CAC0587 | Flavodoxin | C | 11.4 | − | ||
| CAC0711 | tpi | Triosephosphate isomerase | G | 2.1 | 3.2 | − |
| CAC0712 | pgm | Phosphoglyceromutase | G | 2.8 | 9.0 | − |
| CAC0713 | eno | Phosphopyruvate hydratase | G | 3.3 | 6.9 | − |
| CAC2452 | Flavodoxin | C | 3.6 | 11.6 | + | |
| CAC2458 | ofrB | 2-Oxoglutarate ferredoxin oxidoreductase, β-subunit | C | 9.3 | 40.0 | + |
| CAC2459 | ofrA | 2-Oxoacid ferredoxin oxidoreductase, α-subunit | C | 9.1 | 23.8 | + |
| CAC2499 | Pyruvate ferredoxin oxidoreductase | C | 0.3 | − | ||
| CAC2708 | hbd | 3-Hydroxybutyryl-CoA dehydrogenase | I | 0.34 | − | |
| CAC2709 | etfA | Electron transfer flavoprotein α-subunit | C | 0.29 | − | |
| CAC2710 | etfB | Electron transfer flavoprotein β-subunit | C | 0.26 | − | |
| CAC2711 | bcd | Butyryl-CoA dehydrogenase | I | 0.28 | − | |
| CAC2712 | crt | Enoyl-CoA hydratase, crotonase | I | 0.28 | − | |
| CAC2873 | thlA | Thiolase | I | 0.31 | − | |
| CAC3075 | buk | Butyrate kinase | C | 0.41 | − | |
| CAC3076 | ptb | Phosphate acetyltransferase | C | 0.35 | − | |
| CAC3657 | gapN | NADP-GAPDH | C | 19.0 | 26.7 | + |
| CAC3658 | Conserved membrane protein, SapB/MtgC family | S | 4.0 | 12.5 | − | |
| CAC3659 | samX | S-Adenosylmethionine-dependent methyltransferase | Q | 2.1 | 4.7 | − |
| Arginine biosynthesis | ||||||
| CAC0316 | argF-argI | Ornithine carbomoyltransferase | E | 0.15 | − | |
| CAC0376 | N-Dimethylarginine dimethylaminohydrolase | E | 2.4 | 2.1 | − | |
| CAC0973 | argG | Argininosuccinate synthase | E | 0.12 | − | |
| CAC0974 | argH | Argininosuccinate lyase | E | 0.27 | − | |
| CAC2388 | argD | N-Acetylornithine aminotransferase | E | 0.11 | − | |
| CAC2389 | argB | Acetylglutamate kinase | E | 0.18 | − | |
| CAC2390 | argC | N-Acetyl-γ-glutamyl-phosphate reductase | E | 0.29 | − | |
| CAC2391 | argJ | Ornithine acetyltransferase/N-acetylglutamate synthase | E | 0.31 | − | |
a
CAC1547 to CAC1549, CAC1570 and CAC1571, CAC2448 to CAC2450, CAC2777 and CAC2778, CAC0447 and CAC0448, CAC0788 to CAC0791, CAC1029 to CAC1032, CAC1988 to CAC1990, CAC1991 to CAC1996, CAC0502 to CAC0503, CAC1391 to CAC1395, CAC3276 and CAC3277, CAC3288 to CAC3292, CAC3624 and CAC3625, CAP0162 to CAP0164, CAC0711 to CAC0713, CAC2458 and CAC2459, CAC2708 to CAC2712, CAC3075 and CAC3076, CAC3657 to CAC3659, CAC0973 and CAC0974, and CAC2388 to CAC2391 are genes that presumably form a transcriptional unit, respectively.
b
As identified with Virtual Footprint software (48) (see Materials and Methods for details).