Table 1.
The SigR regulon genes.
| Ga | Numberb | Name | Description | Confirmc |
|---|---|---|---|---|
| 3 | SCO0569 | rpmJ | 50S ribosomal protein L36 | |
| 3 | SCO0570* | rpmG3 | 50S ribosomal protein L33 (C-type) | (S1) |
| 8 | SCO0882* | Hypothetical protein, possible dithiol-disulphide isomerase | (S1) | |
| 8 | SCO0884* | Probable oxidoreductase, probable pyridine nucleotide-disulphide oxidoreductases | ||
| 1 | SCO0885* | trxC | Thioredoxin | (S1, A) |
| 8 | SCO0917* | Possible oxygenase | ||
| 7 | SCO0973* | Probable integral membrane protein | ||
| 1 | SCO1084* | trxA4 | Putative thioredoxin | S1 |
| 12 | SCO1085* | Probable phospholipid/glycerol acyltransferase, divergent from trxA4 (1084) | ||
| 8 | SCO1142* | Possible oxidoreductase, probable FAD-dependent pyridine nucleotide-disulphide oxidoreductase | ||
| 5 | SCO1238* | Putative ATP-dependent Clp protease subunit | ||
| 6 | SCO1425* | Possible AsnC-family transcriptional regulatory protein | ||
| 14 | SCO1426* | Hypothetical protein | ||
| 3 | SCO1513* | relA | GTP pyrophosphokinase for ppGpp synthesis | (S1) |
| 3 | SCO1598 | rplT | 50S ribosomal protein L20 | |
| 3 | SCO1599 | rpmI | 50S ribosomal protein L35 | |
| 3 | SCO1600* | infC | Translation initiation factor IF-3 | S1 |
| 6 | SCO1618 | Hypothetical protein, similar to cobalamin binding protein BtuF | ||
| 6 | SCO1619* | Possible transcriptional regulatory protein of HTH-XRE family | ||
| 5 | SCO1643 | prcA | 20S proteasome alpha-subunit | |
| 5 | SCO1644 | prcB | 20S proteasome beta-subunit | |
| 5 | SCO1645 | Hypothetical protein | ||
| 5 | SCO1646 | pup | Prokaryotic ubiquitin-like protein | |
| 5 | SCO1647 | pafD | Proteasome accessory factor | |
| 5 | SCO1648* | mpa | Probable AAA ATPase similar to mycobacterium proteasome-associated ATPase | S1 |
| 3 | SCO1758* | engA | GTP-binding protein with multiple functions | S1 |
| 8 | SCO1869* | Conserved hypothetical, probable protein dithiol-disulphide isomerase | (S1, A) | |
| 11 | SCO1919 | Probable metal-sulphur cluster biosynthetic enzyme | (A) | |
| 11 | SCO1920* | sufU | Similar to NifU in SUF-type Fe-S assembly gene cluster (1926-1919) | (A), S1 |
| 9 | SCO1936* | tal2 | Probable transaldolase, a component of non-oxidative pentose phosphate pathway | S1 |
| 9 | SCO1937 | zwf2 | Glucose 6-phosphate 1-dehydrogenase | |
| 9 | SCO1938 | Hypothetical protein | ||
| 9 | SCO1939 | pgl | 6-phosphogluconolactonase | |
| 10 | SCO1958* | uvrA | ABC excision nuclease subunit A | (A), S1 |
| 14 | SCO1995* | Unknown | (S1, A) | |
| 11 | SCO1996 | coaE | Dephospho-CoA kinase | (A) |
| 11 | SCO1997* | Unknown | (S1, A) | |
| 7 | SCO2124* | Possible hydrophobic membrane spanning regions | ||
| 7 | SCO2154* | Integral membrane protein | ||
| 11 | SCO2161* | sufA | HesB/YadR/Yfh family protein, probable SufA | (S1), S1 |
| 11 | SCO2162* | nadA | Quinolinate synthetase A subunit for nicotinamide synthesis, divergent from sufA (2161). 4Fe-4S enzyme | |
| 11 | SCO2194* | lipA | Putative lipoyl synthase | S1 |
| 7 | SCO2254* | Possible transmembrane efflux protein of MFS(major facilitator superfamily) | S1 | |
| 7 | SCO2310* | Possible transmembrane efflux protein similar to TcmA | ||
| 6 | SCO2331* | Possible MarR family transcriptional regulator | ||
| 6 | SCO2481* | Hypothetical protein, putative transcriptional regulator | ||
| 6 | SCO2537* | Possible DNA-binding protein | (A), S1 | |
| 6 | SCO2538 | Hypothetical protein | ||
| 6 | SCO2539 | era | GTP-binding protein era | |
| 3 | SCO2595* | obgE | GTPase, Obg subfamily, ObgE | S1 |
| 5 | SCO2617 | clpX | ATP-dependent Clp protease ATP binding subunit | |
| 5 | SCO2618 | clpP2 | ATP-dependent Clp protease proteolytic subunit 2 | (A) |
| 5 | SCO2619* | clpP1 | ATP dependent Clp protease proteolytic subunit 1 | (S1, A) |
| 8 | SCO2634* | Hypothetical protein, contains DsbA-like thioredoxin domain | (S1, A) | |
| 5 | SCO2635* | Probable aminopeptidase | ||
| 14 | SCO2642* | Unknown | ||
| 5 | SCO2643* | pepN | Aminopeptidase N | (S1, A) |
| 7 | SCO2763* | ABC transporter protein, ATP-binding component | S1 | |
| 8 | SCO2816* | Conserved hypothetical protein, flavin utilizing monooxygenase superfamily | ||
| 8 | SCO2849* | Conserved hypothetical protein, flavin utilizing monooxygenase superfamily | (S1, A) | |
| 2 | SCO2910 | cysM | Cysteine synthase | (A) |
| 2 | SCO2911* | moaD | Putative MoaD-family protein with ubiquitin fold | (A) |
| 3 | SCOs02* | ssrA | Transfer messenger RNA (tmRNA) | (S1) |
| 7 | SCO3083* | Possible integral membrane protein | (S1, A) | |
| 12 | SCO3091* | cfa | Cyclopropane-fatty-acyl-phospholipid synthase, SAM-dependent methylase | (A), S1 |
| 13 | SCO3162* | Possible esterase, β-lactamase superfamily | (S1, A) | |
| 14 | SCO3187* | Hypothetical protein | (S1) | |
| 7 | SCO3206* | Probable transmembrane efflux protein | (A) | |
| 6 | SCO3207* | TetR family transcriptional regulator | ||
| 8 | SCO3295 | Possible oxidoreductase | ||
| 8 | SCO3296* | Possible oxidoreductase, similar to F420-dependent alcoholdehydrogenase | S1 | |
| 5 | SCO3373* | clpC | Probable Clp-family ATP-binding protease similar to MecB/ClpC | (S1), S1 |
| 11 | SCO3403* | folE | GTP cyclohydrolase I for tetrahydrofolate biosynthesis | (S1) |
| 1 | SCO3442* | mrxB | Glutaredoxin-like protein, probable mycoredoxin | S1 |
| 6 | SCO3449 | rsrA2-1 | Putative ZAS (zinc-containing anti-sigma) factor | |
| 6 | SCO3450* | sigR2 | ECF (group 4) sigma factor close to SigR | |
| 6 | SCO3451* | rsrA2-1 | Putative ZAS (zinc-containing anti-sigma) factor | |
| 14 | SCO3509* | Hypothetical protein | ||
| 7 | SCO3764 | Integral membrane protein | (A) | |
| 7 | SCO3765* | Possible integral membrane protein with CBS domain | ||
| 14 | SCO3766* | Hypothetical protein | ||
| 14 | SCO3767* | Hypothetical protein, similar to tellurite resistance protein TerB | ||
| 1 | SCO3889 | trxA | Thioredoxin | (A) |
| 1 | SCO3890* | trxB | Thioredoxin reductase | (S1, A) |
| 14 | SCO4039* | Unknown | (A) | |
| 14 | SCO4040* | Unknown | ||
| 8 | SCO4109* | Possible oxidoreductase, probable aldo/keto reductases | ||
| 14 | SCO4203* | Hypothetical protein | ||
| 1 | SCO4204* | mshA | Glycosyltransferase for mycothiol synthesis | (S1, A) |
| 1 | SCO4205 | Conserved hypothetical protein | ||
| 8 | SCO4297* | Possible oxidoreductase with FMN binding site, old yellow enzyme family | (A) | |
| 8 | SCO4298 | Carboxylesterase | ||
| 8 | SCO4299 | Integral membrane protein | ||
| 11 | SCO4418 | pdxH2 | Pyridoxamine 5′-phosphate oxidase oxidase | |
| 11 | SCO4419* | pdxH3 | Conserved hypothetical, probable pyridoxamine 5′-phosphate oxidase for pyridoxal phosphate synthesis | |
| 14 | SCO4420* | Hypothetical protein | ||
| 13 | SCO4561* | NLP/P60 family protein | ||
| 4 | SCO4770* | guaB | Inosine 5′ monophosphate dehydrogenase | (S1, A) |
| 4 | SCO4771 | guaB1 | Inosine 5′ monophosphate dehydrogenase | |
| 10 | SCO4797* | uvrD | Probable ATP-dependent DNA helicase | S1 |
| 8 | SCO4833 | Phosphorylmutase | ||
| 8 | SCO4834 | Hypothetical protein | ||
| 8 | SCO4835* | Conserved hypothetical protein with alkylhydroperoxidase-like AhpD/CMD domain | ||
| 2 | SCO4956* | msrA | Probable peptide methionine S-sulphoxide reductase | (S1, A), S1 |
| 14 | SCO4966* | Possible membrane protein | ||
| 1 | SCO4967* | mca | Mycothiol-S-conjugate amidase | (S1, A) |
| 1 | SCO4968 | Hypothetical protein | (A) | |
| 9 | SCO5042* | fumC | Fumarate hydratase, class II family (iron-independent) | (A) |
| 6 | SCO5065* | Possible transcriptional regulator, LuxR family | ||
| 14 | SCO5163* | Unknown | (S1) | |
| 11 | SCO5178* | moeB | Possible sulphurylase related to molybdopterin synthesis | (S1, A) |
| 1 | SCO5187* | mrxA | Glutaredoxin-like protein, probable myc917oredoxin | (S1, A) |
| 10 | SCO5188* | uvrD2 | ATP-dependent DNA helicase (UvrD/REP type), divergent from mrxA (5187) | |
| 6 | SCO5216* | sigR | ECF (group 4) sigma factor sR | (S1, A) |
| 6 | SCO5217 | rsrA | ZAS (zinc-containing antisigma) factor for sR | (A) |
| 14 | SCO5284* | Hypothetical protein | ||
| 5 | SCO5285* | lon | ATP-dependent protease | (S1) |
| 6 | SCO5357* | rho | Transcription termination factor, an RNA–DNA helicase | |
| 3 | SCO5359* | rpmE1 | Ribosomal proteins L31 | (S1, A) |
| 3 | SCO5360 | prfA | Peptide release factor A | |
| 3 | SCO5361 | hemK | Probable release factor-specific methyltransferase | |
| 8 | SCO5465* | Conserved hypothetical, probable F420-dependent NADP oxidoreductase | (S1, A) | |
| 14 | SCO5490* | Hypothetical protein | ||
| 14 | SCO5545* | hypothetical protein | (A) | |
| 6 | SCO5552* | ndgR | IclR family transcription regulator | |
| 3 | SCO5705* | Hypothetical protein, first gene in translation-related gene cluster | S1 | |
| 3 | SCO5706 | infB | Translation initiation factor IF-2 | |
| 3 | SCO5707 | Hypothetical protein | ||
| 3 | SCO5708 | rbfA | Ribosome binding factor | |
| 3 | SCO5709 | truB | Probable tRNA pseudouridine synthase | |
| 10 | SCO5754* | cinA | Competence-DNA damage-induced protein, neighbouring clgR (5755) | (S1, A) |
| 3 | SCO5796* | hflX | Conserved ribosome binding GTPase | (S1, A) |
| 6 | SCO5820* | hrdB | Major vegetative sigma factor | S1 |
| 14 | SCO5864* | Hypothetical protein | ||
| 14 | SCO5865 | Hypothetical protein | ||
| 2 | SCO6061* | msrB | Probable peptide methionine R-sulphoxide reductase | (S1, A), S1 |
| 14 | SCO6126* | Hypothetical protein | ||
| 13 | SCO6127* | Probable carboxylesterase, probable phenylcarbamate hydrolase | ||
| 11 | SCO6423* | Putative lipoate-protein ligase | (A) | |
| 8 | SCO6551* | Probable oxidoreductase, aldo/keto reductase family | (S1, A) | |
| 12 | SCO6759* | phyA/hopE | Probable phytoene (hopanoid) synthase | (S1, A), S1 |
| 12 | SCO6760 | phyB/hopD | Squalene/phytoene synthase | |
| 12 | SCO6761 | Small (52 aa) hypothetical protein of unknown function | ||
| 12 | SCO6762 | phyC/hopC | Squalene/phytoene dehydrogenase | |
| 12 | SCO6763 | phyD/hopB | Polyprenyl diphosphate synthase | |
| 12 | SCO6764 | phyE/hopA | Squalene–hopene cyclase | |
| 12 | SCO6765 | Lipoprotein | ||
| 12 | SCO6766 | Hypothetical protein | ||
| 12 | SCO6767 | ispG | 4-hydroxy-3-methyl-2-en-1-yl diphosphate synthase | |
| 12 | SCO6768 | 1-deoxy-d-xylulose-5-phospate synthase | ||
| 12 | SCO6769 | Aminotransferase | ||
| 12 | SCO6770 | DNA-binding protein | ||
| 12 | SCO6771 | Small hydrophobic protein | ||
| 6 | SCO6775* | Probable transcriptional regulator, TetR family | ||
| 14 | SCO6776* | Unknown | ||
| 6 | SCO7140* | Probable DNA-binding protein | ||
| 14 | SCO7631* | Possible secreted protein | ||
| 1 | SCO7632* | Probable amidase similar to mshB and mca | (A), S1 | |
| 8 | SCO7784* | Possible oxidoreductase, probable nitro/flavin reductase | S1 | |
| 8 | SCO7785 | Transcriptional regulator |
a
Genes were grouped according to predicted functions such as thiol homeostasis (1), sulphur metabolism (2), modulation of ribosome and/or translation (3), guanine nucleotide metabolism (4), protein degradation (5), transcriptional regulators or DNA binding proteins (6), transporter or integral membrane proteins (7), oxidoreductases (8), energy metabolism (9), DNA damage repair and/or recombination (10), cofactor metabolism (11), lipid metabolism (12), others (13), or function unpredictable (14).
b
Genes with SigR-binding promoters were marked with asterisks (*).
c
The genes whose SigR-dependent expression was previously confirmed by S1 or microarray (A) were marked with S1 and A in parenthesis (Paget et al., 2001; Park and Roe, 2008; Kallifidas et al., 2010). Those confirmed in this study were noted with S1.