Table 1.
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 |
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.