Table 1. Compositions of the RpoHI and RpoHII regulons.
| Mainrole§ | Subrole† | Locus‡ |
| RpoHI/II regulon (45 genes) | ||
| Energy metabolism | Electron transport | RSP_0100, RSP_0101, RSP_0102, RSP_0103, RSP_0104, RSP_0105, RSP_0106, RSP_0107, RSP_2805 |
| Other | RSP_0472 | |
| Protein synthesis/fate | Degradation of proteins, peptides, and glycopeptides | RSP_0665, RSP_1076, RSP_1174, RSP_2710, RSP_2806 |
| Other | RSP_1825 | |
| Protein folding and stabilization | RSP_1207 | |
| Ribosomal proteins: synthesis and modification | RSP_0570 | |
| Serine family | RSP_2481 | |
| Fatty acid and cell envelope | Biosynthesis | RSP_0473 |
| Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides | RSP_2569 | |
| Other | RSP_3601 | |
| DNA metabolism | DNA replication, recombination, and repair | RSP_2388, RSP_2966 |
| Central intermediary metabolism | Phosphorus compounds | RSP_0013 |
| Cellular processes | Adaptations to atypical conditions | RSP_2617 |
| Signal transduction | Two-component systems | RSP_0847 |
| Unknown function | Unknown function | RSP_2718, RSP_0011, RSP_0370, RSP_1025, RSP_1239, RSP_1760, RSP_2218, RSP_2421, RSP_2625, RSP_2973, RSP_3327, RSP_3599, RSP_0870, RSP_1026, RSP_1421, RSP_1840, RSP_2261, RSP_2265 |
| RpoHI regulon (130 genes) | ||
| Protein synthesis/fate | Amino acid biosynthesis | RSP_0244, RSP_0377, RSP_1475 |
| Degradation of proteins, peptides, and glycopeptides | RSP_0357, RSP_0554, RSP_1408, RSP_1531, RSP_1742, RSP_2412, RSP_2649 | |
| Protein and peptide secretion and trafficking | RSP_1169, RSP_1797, RSP_1798, RSP_1799, RSP_1843, RSP_2540, RSP_2541 | |
| Protein folding and stabilization | RSP_1016, RSP_1173, RSP_1532, RSP_1572, RSP_1805, RSP_4043 | |
| Protein modification and repair | RSP_0559, RSP_0872, RSP_0873, RSP_0874, RSP_0923 | |
| tRNA aminoacylation | RSP_0875 | |
| Energy metabolism | Amino acids and amines | RSP_3957 |
| Electron transport | RSP_0296, RSP_0610, RSP_1194, RSP_1489, RSP_1529, RSP_1576, RSP_2375, RSP_2685, RSP_2945 | |
| Glycolysis/gluconeogenesis | RSP_0361 | |
| Fatty acid and cell envelope | Biosynthesis | RSP_0720, RSP_0929, RSP_2776 |
| Biosynthesis and degradation of murein sacculus and peptidoglycan | RSP_1240 | |
| Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides | RSP_0125, RSP_3187 | |
| Degradation | RSP_0409 | |
| Other | RSP_1889 | |
| Biosynthesis of cofactors, prosthetic groups, and carriers | Folic acid | RSP_0930 |
| Lipoate | RSP_2783 | |
| Molybdopterin | RSP_0235, RSP_1071, RSP_1072 | |
| Other | RSP_2658 | |
| Pyridoxine | RSP_1672 | |
| Regulatory functions | DNA interactions | RSP_0014, RSP_2200 |
| Other | RSP_2236 | |
| Protein interactions | RSP_4193 | |
| Transcription factors | RSP_2410 | |
| Transport and binding proteins | Amino acids, peptides and amines | RSP_1564 |
| Cations and iron carrying compounds | RSP_2542, RSP_2891 | |
| Unknown substrate | RSP_2696, RSP_2897 | |
| DNA metabolism | DNA replication, recombination, and repair | RSP_1074, RSP_2815, RSP_4199 |
| Purine ribonucleotide biosynthesis | RSP_2454 | |
| Cellular processes | Adaptations to atypical conditions | RSP_4198 |
| Detoxification | RSP_0890, RSP_1058 | |
| Central intermediary metabolism | Other | RSP_1196, RSP_1949 |
| Sulfur metabolism | RSP_2738 | |
| Signal transduction | Two-component systems | RSP_2130, RSP_3105 |
| Mobile and extra-chromosomal element functions | Transposon functions | RSP_3007 |
| Unknown function | Unknown function | RSP_0126, RSP_0362, RSP_0363, RSP_0408, RSP_0719, RSP_0999, RSP_1104, RSP_1193, RSP_1204, RSP_1238, RSP_1241, RSP_1360, RSP_1406, RSP_1549, RSP_1563, RSP_1573, RSP_1581, RSP_1615, RSP_1671, RSP_1684, RSP_1743, RSP_1852, RSP_2121, RSP_2125, RSP_2214, RSP_2219, RSP_2387, RSP_2638, RSP_2640, RSP_2641, RSP_2739, RSP_2763, RSP_2764, RSP_2816, RSP_2952, RSP_2953, RSP_3067, RSP_3068, RSP_3378, RSP_3426, RSP_3552, RSP_3597, RSP_3598, RSP_3634, RSP_3809, RSP_3810, RSP_4244, RSP_4245, RSP_4248, RSP_4305 |
| RpoHII regulon (99 genes) | ||
| Energy metabolism | Biosynthesis and degradation of polysaccharides | RSP_0482 |
| Electron transport | RSP_0108, RSP_0109, RSP_0110, RSP_0112, RSP_0474, RSP_2785, RSP_3212, RSP_3305, RSP_3537 | |
| Entner-Doudoroff | RSP_2646 | |
| Fermentation | RSP_3164 | |
| Glycolysis/gluconeogenesis | RSP_2736, RSP_4045, RSP_4211 | |
| Other | RSP_0392, RSP_2294 | |
| Pentose phosphate pathway | RSP_2734, RSP_2735 | |
| Sugars | RSP_2937, RSP_3138 | |
| Biosynthesis of cofactors, prosthetic groups, and carriers | Glutathione and analogs | RSP_3272 |
| Heme, porphyrin, and cobalamin | RSP_1197, RSP_1692, RSP_2831 | |
| Menaquinone and ubiquinone | RSP_1175, RSP_1338, RSP_1492, RSP_1869 | |
| Other | RSP_0750, RSP_0898, RSP_2314 | |
| Transport and binding proteins | Amino acids, peptides and amines | RSP_1542, RSP_3274 |
| Carbohydrates, organic alcohols, and acids | RSP_0149, RSP_0150 | |
| Cations and iron carrying compounds | RSP_1546, RSP_2608 | |
| Unknown substrate | RSP_1895, RSP_2802, RSP_3160 | |
| DNA metabolism | DNA replication, recombination, and repair | RSP_1466, RSP_2083, RSP_2414, RSP_2850, RSP_3077, RSP_3423 |
| Pyrimidine ribonucleotide biosynthesis | RSP_3722 | |
| Fatty acid and cell envelope | Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides | RSP_1491, RSP_2163, RSP_3721 |
| Degradation | RSP_0119 | |
| Other | RSP_0422, RSP_0595, RSP_0855 | |
| Regulatory functions | DNA interactions | RSP_1083, RSP_4210 |
| Other | RSP_0148, RSP_2631, RSP_3430, RSP_3431 | |
| Transcription factors | RSP_0601 | |
| Cellular processes | Detoxification | RSP_1057, RSP_2389, RSP_2693, RSP_3263 |
| Toxin production and resistance | RSP_2803 | |
| Central intermediary metabolism | Other | RSP_0897, RSP_1258, RSP_1397, RSP_3072 |
| Phosphorus compounds | RSP_0782 | |
| Protein synthesis/fate | Amino acid biosynthesis | RSP_0398 |
| Degradation of proteins, peptides, and glycopeptides | RSP_0686, RSP_1490 | |
| Protein folding and stabilization | RSP_1219 | |
| tRNA and rRNA base modification | RSP_2971 | |
| Unknown function | Unknown function | RSP_0151, RSP_0152, RSP_0269, RSP_0423, RSP_0557, RSP_0799, RSP_0896, RSP_1591, RSP_1956, RSP_1985, RSP_2225, RSP_2268, RSP_3075, RSP_3076, RSP_3089, RSP_3310, RSP_3329, RSP_4144, RSP_4209 |
Summary of the functional annotations of members of the RpoHI and RpoHII regulons in R. sphaeroides defined by the intersections of the results from the expression profiling and chromatin immunoprecipitation experiments.
§
Classification of the functional main categories according to the JCVI-CRM database (http://cmr.jcvi.org/).
†
Classification of the functional sub-categories according to the JCVI-CRM database.
‡
Unique locus identifiers for R. sphaeroides 2.4.1.