Markup | Genome Research

Table 1.

List of Protein Spots Influenced by Regulators ς^B (A), ς^H (B), RelA (C), CcpA (D), and CodY (E)

Valid gene name	Gel 1–9	Synonym	B. SubtiList acc no.	Description
A. ς^B-Dependent Genes (Wild type/ς^B-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 ς^B
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 ς^B activity (anti-anti-ς factor)
rsbW	+		BG10734	Negative regulator of ς^B 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. ς^H -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

[i] Plus signs in the column [Gel 1–9] (A) indicate a clear induction in a ς^B-dependent manner at the protein level in the wild type compared to the ς^B-mutant strain (see also Fig. 3). Minus signs show an overlaying effect of additional regulators masking the ς^B 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.