Table 1.
Expression ratios of genes and gene clusters in catabolic modules for “Energy and Primary and Secondary Electron Flow.”
| Locus tag | Gene product | Predicted function | Relative expression ratios | |||
|---|---|---|---|---|---|---|
| NH+4–I/S | NH2OH–I/S | S/C | NH+4–I/C | |||
| Noc2503 | AmoC | Ammonia monooxygenase subunit C | −1.11 | −1.10 | 1.05 | −1.06 |
| Noc2502 | AmoA | Ammonia monooxygenase subunit A | 1.22 (1.60) | 1.12 (11.5) | −1.32 | −1.09 |
| Noc2501 | AmoB | Ammonia monooxygenase subunit B | 1.41 | 1.22 | −1.47 | −1.04 |
| Noc2500 | AmoD | Periplasmic membrane protein (1 TMS) | 21.91 | 11.43 | −10.91 | 2.00 |
| Noc2499 | Hyp | Hypothetical periplasmic protein | 13.28 | 9.21 | −5.39 | 2.46 |
| Noc2498 | Hyp | Integral transmembrane protein (4TMS) | 2.43 | 1.86 | −1.56 | 1.56 |
| Noc0089 | NirK | Nitrite reductase nirK (EC:1.7.2.1) | −1.16 (10.10) | −1.17 (7.80) | −1.01 | −1.17 |
| Noc0889 | Mco | Multi-copper oxidase | 6.12 | 1.65 | −2.34 | 2.64 |
| Noc0890 | CytL | Cytochrome c P460 (NO & NH2OH detox) | 6.80 | 5.75 | −2.62 | 2.59 |
| (Noc0891) | GntR | Transcriptional regulator | 1.88 | 1.15 | 1.15 | 1.73 |
| Noc0892 | HaoA | Hydroxylamine DH (EC:1.7.2.6, [HaoA]3) | 3.88 (7.20) | 3.61 (15.3) | −3.31 | 1.17 |
| Noc0893 | HaoB | Unknown [HaoA]3-associated protein | 10.97 | 10.07 | −6.34 | 1.73 |
| Noc0894 | CycA | Cytochrome c554 | 2.77 | 2.76 | −2.28 | 1.21 |
| Noc0895 | CycB | Cytochrome cM552 | 9.40 | 9.45 | −4.13 | 2.28 |
| Noc0299 | [Fe-S] | Rieske protein (CIII, EC:1.10.2.4) | 11.85 (13.10) | 10.55 (49.60) | −4.39 | 2.70 |
| Noc0298 | CytB | Cytochrome b (CIII, EC:1.10.2.3) | 4.00 | 3.66 | −2.31 | 1.70 |
| Noc0297 | Cytc1 | Cytochrome c1 (CIII, EC:1.10.2.2) | 3.57 | 3.59 | −2.15 | 1.65 |
| Noc0552 | CccA | Di-heme c552 (COG 2010; class IV) | 13.19 | 5.79 | −2.52 | 5.22 |
| Noc0551 | DsbA | DsbA oxidoreductase | 7.15 | 2.44 | −1.40 | 5.10 |
| Noc0751 | c552 | Mono-heme c552 (COG 2863; class I) | 12.22 (3.90) | 4.69 (2.90) | −2.18 | 5.60 |
| Noc1089 | Pgb | Protoglobin (heme binds O2, CO & NO) | 8.25 | 4.58 | −3.45 | 2.41 |
| Noc1090 | NcyA | Nitrosocyanin | 29.27 | 10.76 | −14.23 | 2.06 |
| (Noc2967) | NsrR | Transcriptional regulator | 2.32 (1.50) | 1.64 (2.10) | −1.37 | 1.69 |
| Noc2969 | SenC | Nitric oxide reductase sNOR (coxBA-senC) | 8.54 | 2.82 | −1.64 | 5.22 |
| Noc2970 | NorY | Nitric oxide reductase sNOR (coxBA-senC) | 2.74 | 2.00 | −2.43 | 1.12 |
| Noc2971 | NorS | Nitric Oxide reductase sNOR (coxBA-senC) | 9.56 | 7.04 | −7.02 | 1.36 |
| Noc3044 | SU III | Type-A Complex IV HCO-1 (EC:1.9.3.1) | 3.61 | 1.55 | −2.85 | 1.27 |
| Noc3045 | SU IV | Type-A Complex IV HCO-1 (Assembly) | 6.93 | 3.00 | −5.10 | 1.36 |
| Noc3046 | SU I | Type-A Complex IV HCO-1 (EC:1.9.3.1) | 6.40 | 2.93 | −5.16 | 1.24 |
| Noc3047 | SU II | Type-A Complex IV HCO-1 (EC:1.9.3.1) | 4.73 (9.70) | 2.71 (5.00) | −4.51 | 1.05 |
| Noc3048 | Hyp | Cytoplasmic membrane protein (2 TMS) | 17.99 | 6.79 | −11.79 | 1.53 |
| Noc3049 | c552 | Mono-heme c552 (COG 2863; class I) | 27.72 | 7.35 | −12.61 | 2.20 |
| Noc3050 | c552 | Mono-heme c552 (COG 2863; class I) | 7.24 (17.10) | 3.58 (7.00) | −5.28 | 1.37 |
| Noc3073 | AtpE | FoF1-Type ATP Synthase (EC:3.6.3.14) | 9.62 | 3.73 | −3.22 | 2.99 |
| Noc3074 | AtpB-F1 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 8.73 | 4.71 | −4.05 | 2.15 |
| Noc3075 | AtpC-F1 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 5.94 | 3.56 | −4.01 | 1.48 |
| Noc3076 | AtpA-F1 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 11.70 | 4.55 | −5.17 | 2.27 |
| Noc3077 | AtpD-F1 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 7.08 | 3.47 | −4.63 | 1.53 |
| Noc3078 | AtpB-F0 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 17.44 | 4.79 | −5.68 | 3.07 |
| Noc3079 | AtpC-F0 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 3.76 | 2.26 | −3.05 | 1.23 |
| Noc3080 | AtpA-F0 | FoF1-Type ATP Synthase (EC:3.6.3.14) | 1.61 | 1.20 | −1.48 | 1.08 |
| Noc2552 | NuoN | NDH-1 (Reverse Complex-I) | 1.34 | −1.39 | −1.15 | 1.17 |
| Noc2553 | NuoM | NDH-1 (Reverse Complex-I) | −1.26 | −1.71 | 1.03 | −1.22 |
| Noc2554 | NuoL | NDH-1 (Reverse Complex-I) | 1.49 | −1.35 | −1.04 | 1.43 |
| Noc2555 | NuoK | NDH-1 (Reverse Complex-I) | 3.17 | 1.09 | −1.15 | 2.74 |
| Noc2556 | NuoJ | NDH-1 (Reverse Complex-I) | 3.75 | 1.51 | −1.48 | 2.54 |
| Noc2557 | NuoI | NDH-1 (Reverse Complex-I) | 3.33 | 1.46 | −1.20 | 2.76 |
| Noc2558 | NuoH | NDH-1 (Reverse Complex-I) | −1.12 | −1.18 | 1.05 | −1.07 |
| Noc2559 | NuoG | NDH-1 (Reverse Complex-I) | 2.66 | 1.32 | −1.07 | 2.47 |
| Noc2560 | NuoF | NDH-1 (Reverse Complex-I) | 1.57 | 1.36 | −1.12 | 1.40 |
| Noc2561 | NuoE | NDH-1 (Reverse Complex-I) | 5.35 | 1.69 | −1.28 | 4.19 |
| Noc2562 | NuoD | NDH-1 (Reverse Complex-I) | 2.07 | 1.33 | −1.28 | 1.62 |
| Noc2563 | NuoC | NDH-1 (Reverse Complex-I) | 3.54 | 1.94 | −1.59 | 2.23 |
| Noc2564 | NuoB | NDH-1 (Reverse Complex-I) | 2.58 | 1.38 | −1.25 | 2.07 |
| Noc2565 | NuoA | NDH-1 (Reverse Complex-I) | 4.15 | 1.38 | −1.28 | 3.25 |
| Noc0474 | NuoA | NuoAHJKLLMN (C I-membrane arm) | −1.89 | −1.45 | 1.09 | −1.73 |
| Noc0475 | NuoH | NuoAHJKLLMN (C I-membrane arm) | −12.29 | −2.02 | 1.23 | −9.98 |
| Noc0476 | NuoJ | NuoAHJKLLMN (C I-membrane arm) | −8.88 | −2.01 | 1.29 | −6.90 |
| Noc0477 | NuoK | NuoAHJKLLMN (C I-membrane arm) | −3.39 | −1.43 | 1.23 | −2.75 |
| Noc0478 | NuoL | NuoAHJKLLMN (C I-membrane arm) | −10.05 | −1.99 | 1.34 | −7.48 |
| Noc0479 | NuoL | NuoAHJKLLMN (C I-membrane arm) | −11.52 | −2.08 | 1.39 | −8.27 |
| Noc0480 | NuoM | NuoAHJKLLMN (C I-membrane arm) | −5.23 | −2.06 | 1.23 | −4.24 |
| Noc0481 | NuoN | NuoAHJKLLMN (C I-membrane arm) | −3.50 | −1.71 | 1.20 | −2.93 |
| Noc1797 | Cyt_C | Mono-heme cytochrome c protein | −7.34 | −1.37 | 9.24 | 1.25 |
| Noc1798 | Cyt_C | Mono-heme cytochrome c protein | −7.52 | −1.51 | 6.86 | −1.10 |
| Noc1799 | NemA | NADH-flavin oxidoreductase (EC:1.3.1.34) | −9.95 | −1.43 | 12.43 | 1.25 |
| Noc1800 | Cyt_C | Di-heme cytochrome c protein | −15.51 | −1.49 | 13.70 | −1.13 |
Values represent average ratios from four hybridization experiments per gene, per treatment. Bolded ratios indicate those that are considered to have significant differences (changes greater than 5-fold) in gene expression between compared treatments. Values in parentheses represent ratios from qPCR experiments reported previously (Graham et al., 2011) employing the same RNA preparations as used for the microarray hybridizations. Values in bold indicate that both methods yielded consistent results.