Table 1.
List of Protein Spots Influenced by Regulators ςB (A), ςH (B), RelA (C), CcpA (D), and CodY (E)
| Valid gene name | Gel 1–9 | Synonym | B. SubtiList acc no. | Description |
| A. ςB-Dependent Genes (Wild type/ςB-Mutant Comparison) | ||||
| clpC | − | mecB | BG10148 | Class III stress response-related ATPase |
| clpP | − | yvdN | BG19016 | ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) |
| ctc | + | BG10115 | General stress protein | |
| dps | + | ytkB | BG12584 | Stress- and starvation-induced gene controlled by ςB |
| gsiB | + | BG10826 | General stress protein | |
| gspA | + | ipa-12d ywaG | BG10558 | General stress protein |
| gtaB | + | BG10402 | UTP-glucose-1-phosphate uridylltransferase | |
| katE | + | katB | BG11102 | Catalase 2 |
| katX | + | yxll | BG11945 | Major catalase in spores |
| nadE | + | gsp-81 outB tscBGH | BG10694 | NH3-dependent NAD+ synthetase |
| rsbV | + | BG10733 | Positive regulator of ςB activity (anti-anti-ς factor) | |
| rsbW | + | BG10734 | Negative regulator of ςB activity (switch protein/serine kinase, anti-ς factor) | |
| sigB | + | rpoF | BG10735 | RNA polymerase general stress ς factor |
| sodA | − | yqgD | BG11676 | Superoxide dismutase |
| ycdF | + | BG12761 | Unknown; similar to glucose 1-dehydrogenase | |
| ydaE | + | BG12053 | Unknown | |
| ydbD | + | BG12071 | Unknown; similar to manganese-containing catalase | |
| yfkM | + | BG12929 | Unknown; similar to unknown proteins | |
| yflT | + | BG19020 | Unknown | |
| yhdN | + | BG13020 | Unknown; similar to aldo/keto reductase | |
| yitT | + | yuxA | BG10850 | Unknown; similar to unknown proteins |
| ykzA | + | yzzE | BG19021 | Unknown; similar to organic hydroperoxide resistance protein |
| yocK | + | BG13524 | Unknown; similar to general stress protein | |
| ysnF | + | BG12337 | Unknown; similar to unknown proteins | |
| ytxH | − | csb40 | BG10975 | Unknown; similar to general stress protein |
| yvyD | − | BG10740 | Unknown; similar to ς54 modulating factor of Gram-negative bacteria | |
| B. ςH -Dependent Genes | ||||
| yvyD | □□▪▪▪□▪□□ | BG10740 | General stress protein | |
| spoVG | ▪▪▪▪▪▪▪▪▪ | BG10112 | Sporulation | |
| spo0A | □□▪▪▪▪▪▪□ | sof-1 spo0C spo0G spoIII | BG10765 | Two-component response regulator |
| ytxH | □□▪▪▪▪▪▪▪ | csb40 | BG10975 | Unknown function, similar to general stress protein |
| citG | ▪▪▪▪□□□□□ | BG10384 | Fumarase | |
| C. relA-Dependent Genes Class I: RelA-dependent transcriptional repression (negative regulation) | ||||
| rplA | X | BG10164 | Ribosomal protein L1 | |
| rplJ | ▪▪□□□□□□□ | BG11220 | Ribosomal protein L10 | |
| rpoB | ▪▪□▪□▪▪▪▪ | BG10728 | RNA polymerase (β subunit) | |
| fus | ▪▪□□□□□▪▪ | EF-G | BG11939 | Elongation factor G |
| tufA | ▪▪□□□□□▪▪ | EF-Tu | BG11056 | Elongation factor Tu |
| rplE | X | BG10760 | Ribosomal protein L5 | |
| rplF | X | BG11408 | Ribosomal protein L6 | |
| adk | ▪▪▪□□□□□□ | BG10446 | Adenylate kinase | |
| rpoA | X | BG10732 | RNA polymerase (α subunit) | |
| rpsB | ▪▪□□□□□□□ | BG19004 | Ribosomal protein S2 | |
| tsf | ▪▪□□□□□▪▪ | EF-Ts | BG19025 | Elongation factor Ts |
| frr | weak | BG12587 | Ribosomal recycling factor | |
| rpsF | X | BG10049 | Ribosomal protein S6 | |
| tig | ▪▪□□□□□▪▪ | yzzH | BG19023 | Trigger factor (peptidyl prolyl isomerase) |
| ylaG | ▪▪□□□□□▪▪ | BG13344 | Similar to GTP-binding elongation factor/unknown | |
| yugI | weak | BG12363 | Similar to polyribonucleotide nucleotidyltransferase/unknown | |
| bkdAA | X | bfmb1a bfmbaa bkd | BG10307 | Branched-chain α-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase α subunit) |
| pnpA | ▪▪□□□□□▪▪ | comR | BG11491 | Polynucleotide phosphorylase |
| atpA | ▪▪□▪▪□□▪▪ | BG10819 | ATP synthase (α subunit) | |
| atpD | ▪▪□□□□□□□ | BG10821 | ATP synthase (β subunit) | |
| yjlD | ▪▪□□□□□□□ | BG13203 | Similar to NADH dehydrogenase/unknown | |
| Class II: RelA-dependent transcriptional induction (positive regulation) | ||||
| ilvB | ▪▪□▪▪▪▪▪▪ | BG10670 | Acetolactate synthase (large subunit) | |
| ilvC | ▪▪□□□□□▪▪ | BG10672 | Ketol-acid reductoisomerase | |
| leuA | ▪▪□□□□□▪▪ | BG11948 | 2-Isopropylmalate synthase | |
| leuB | ▪▪□□□□□▪▪ | leuC | BG10675 | 3-Isopropylmalate dehydrogenase |
| leuC | ▪▪□□□□□▪▪ | BG11949 | 3-Isopropylmalate dehydratase (large subunit) | |
| leuD | ▪▪□□□□□▪▪ | BG11950 | 3-Isopropylmalate dehydratase (small subunit) | |
| ywaA | ▪▪□□▪□□▪▪ | ipa-0r | BG10546 | Similar to branched-chain amino acid aminotransferase/unknown |
| guaB | ▪▪▪□□□□□▪ | guaA | BG10073 | Inosine-monophosphate dehydrogenase |
| ald | ▪▪□□□□□▪▪ | spoVN | BG10468 | L-alanine dehydrogenase |
| spoVG | ▪▪▪▪▪▪▪▪▪ | Ipa-12d ywaG | BG10558 | Stage V sporulation protein, required for spore cortex synthesis, inhibitor of sporulation |
| spo0A | □□□□▪▪▪▪▪ | BG14002 | Two-component response regulator | |
| gspA | □□▪▪▪▪▪▪□ | gcaA ybxD | BG10948 | General stress protein |
| yvyD | □□▪▪▪▪▪□□ | BG12558 | Similar to ς54 modulating factor of Gram-negative bacteria, similar to ribosomal proteins | |
| ytxH | □□▪▪▪▪▪▪□ | yfjI | BG12560 | Similar to general stress protein/unknown |
| yurP | ▪▪□□□□□▪▪ | BG12680 | Similar to glutamine-fructose-6-phosphate transaminase/unknown | |
| D. ccpA-Dependent Genes | ||||
| glmS | □□□▪▪▪▪▪□ | gcaA ybxD | BG10948 | L-Glutamine-D-fructose-6-phosphate amidotransferase |
| acoA | □□□▪▪□□□□ | yfjK | BG12558 | Acetoin dehydrogenase E1 component (TPP-dependent α subunit) |
| acoC | □□□▪▪□□□□ | yfjI | BG12560 | Acetoin dehydrogenase E2 component (dihydrolipoamide acetyltransferase) |
| sucC | ▪▪▪▪▪▪▪▪▪ | BG12680 | Succinyl-CoA synthetase (β subunit) | |
| sucD | ▪▪▪□□□□□▪ | BG12681 | Succinyl-CoA synthetase (α subunit) | |
| gapB | □□▪▪▪▪▪□□ | BG12592 | Glyceraldehyde-3-phosphate dehydrogenase | |
| rbsK | n.i. | BG10877 | Ribokinase | |
| rbsA | □□▪▪▪□▪□□ | BG10879 | Ribose ABC transporter (ATP-binding protein) | |
| rocA | □□▪▪□□□□□ | ipa-76d | BG10622 | Pyrroline-5 carboxylate dehydrogenase |
| rocG | n.i. | ipa-75d; yweB | BG10621 | Glutamate dehydrogenase (major) |
| iolH | n.i. | yxdG | BG11123 | Unknown function in myo-inositol catabolism |
| iolA | n.i. | mmsA yxdA | BG11117 | Oxidative decarboxylase in myo-inositol catabolism |
| iolS | n.i. | yxbF | BG11363 | Unknown function in myo-inositol catabolism |
| rocF | □□□▪▪□□□□ | BG10932 | Arginase | |
| rocD | ▪▪▪▪▪□□▪▪ | BG10722 | Ornithine aminotransferase | |
| E. CodY-Dependent Genes | ||||
| dppA | □□▪▪▪▪□□□ | BG10722 | D-alanyl-aminopeptidase | |
| hutI | □□□□□▪□□□ | BG11100 | Imidazolone-5-propionate hydrolase | |
| hutU | □□▪▪▪▪□□□ | BG10668 | Urocanase | |
| hag | ▪▪▪▪▪□□□▪ | BG10655 | Flagellin protein | |
| srfAD | ▪▪▪□▪▪▪▪▪ | BG10171 | Required for competence development, motility, degradative enzyme synthesis, growth at high temperature and sporulation | |
| citB | □□□□□▪▪▪▪ | BG10478 | Aconitate hydratase | |
| spo0A | □□▪▪▪▪▪▪□ | sof-1 spo0C spo0G spoIII | BG10765 | Two-component response regulator |
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Plus signs in the column [Gel 1–9] (A) indicate a clear induction in a ςB-dependent manner at the protein level in the wild type compared to the ςB-mutant strain (see also Fig. 3). Minus signs show an overlaying effect of additional regulators masking the ςB dependency. Filled squares at positions 1 to 9 in the column [Gel 1–9] (B–E) point out high synthesis in the corresponding gels (see Figs. 1 and 2). X signs indicate very weak expression levels of the corresponding spots.
