TABLE 1.

Genes previously known to be regulated directly by sigma-H

Gene or operona	sigH+/sigHb	Overexpressionc	−35 box	Spacing	−10 box	Function and/or comments	Reference(s)
citG (P2)	3.5	2.6	AAAGGATTT	11	GGCGAATTA	Fumarate hydratase (TCAi cycle), P1 recognized by sigma-A	42, 54
dnaG (sigA-P4)	3.4	3.0	GAAGGGATT	12	ATCGAATAA	DNA primase	28, 61
ftsAZ (P2)	2.8	1.6	AGAGGATAT	11	AACGAATAT	Cell division, P1 recognized by sigma-A	19
glgBCDAPd	4.0	2.1	AAAGGGCTT	11	TTCGAATAA	Glycogen biosynthesis	29
kinA	3.9	2.8	GAAGGAGAA	12	AGCGAATCA	Sporulation (phosphorelay)	2, 41
phrC	1.6	1.6	AGAGGATTT	11	GTAGCAAAA	Phosphatase regulator (promoter within rapC)	31
phrE (P1-2)	1.6	NOe	TTAGGAGGC	11	TTATAATGG	Phosphatase regulator (promoter within rapE)	37
phrE (P3)	1.6	NO	AGAGGATAG	12	CAAGAAAAT	See above	37
phrF	2.4	NO	TGAAGATTT	13	GGCAAATAA	Phosphatase regulator (promoter within rapF)	37
phrG	NO	NOf	GAAGGAAAA	12	GCCGAATAT	Phosphatase regulator (promoter within rapG)	37
phrl (P2)	NO	NOf	CAAGGAAAT	12	AATGAATAT	Phosphatase regulator (promoter within rapI)	37
phrK	NO	NOf	ACAGGAAAG	12	GGAGAATAA	Phosphatase regulator (promoter within rapK)	37
sigA (P3)	1.6	2.1	GCAGGAGTT	12	GGAGAATTA	Major sigma factor (promoter within yqxD), P1 recognized by sigma-A	8
spo0A (Ps)	NO	NOg	AGAGGGTAT	11	GTCGAATGT	Transcriptional regulation of sporulation, Pv recognized by sigma-A	41
spo0F (P2)	3.2	2.3	AAAGGAAAT	11	ACAGAATAC	Sporulation (phosphorelay), Spo0A regulated, P1 recognized by sigma-A	4, 41
spo0M (ygaI)	NO	NO	ATAGGAAAA	12	AACGAATCT	Sporulation	23
spoIIAA-AB-sigF	9.0	3.2	GAAGGAATT	12	ATCGAAACA	Forespore gene expression, Spo0A regulated	59
spoVG	3.0	2.8	GCAGGATTT	11	GTGGAATTG	Sporulation (peptidoglycan hydrolysis), AbrB regulated	28, 61
spoVS	3.1	2.9	GCAGGAATA	12	AGTGAATAT	Sporulation	46
ureABC (P2)	1.6	2.1	GAAGGAATT	12	GTCGAACTA	Urease, P3 recognized by sigma-A and repressed by CodY	58
yoxA-dacC (pbp)	5.3	5.7	GGAGGAAAT	12	ATTGAATTC	Unknown-d-alanyl-d-alanine carboxypeptidase	38
ytxG (P2)	(3.4)h	1.6	AAAGGATTT	11	GGAGAATAG	Stress, P1 recognized by sigma-B	56
yvyD (P2)	(2.2)h	1.5	GCAGGAATT	12	AGAGAAATA	Putative modulator of sigma-L, P1 recognized by sigma-B	11
Consensus (24)j			R-AGGAwWW	11-12	R--GAATww	R is A or G, W is A or T	25

^aGene or genes of an operon that are regulated by sigma-H. If the sigma-H promoter is a secondary promoter, its designation is listed in parentheses. lytE (cwlF), which had been proposed to be under sigma-H control (26), was not included in the table because its suggested promoter matches poorly with the proposed consensus.

^bRatios of relative RNA levels in sigH⁺ versus sigH-null mutant. Ratios are presented from the time point at which the difference was largest (Fig. 2). In cases where multiple genes from an operon are listed, data are presented from the gene with the largest detected effect. Ratios are the averages of at least three independent experiments.

^cRatios of relative RNA from sigH overexpression (+IPTG) compared to comparable time points without overexpression (−IPTG). Ratios are presented from the time point where the largest effect was detected (Fig. 2). In cases where multiple genes from an operon are listed, data are presented from the gene with the largest detected effect. Ratios are the average of at least three independent experiments.

^dSigma-H-dependent regulation has been demonstrated only for Bacillus stearothermophilus (29).

^eNO, not determined to be an outlier in our analysis.

^fThis phr gene was not detected as an outlier most likely because of its small size (<200 bp).

^gExpression of spo0A from Ps (the sigma-H-dependent promoter) is modest relative to the overall level of expression and is probably the reason that we did not detect it.

^hParentheses denote that ytxG and yvyD were more highly produced in the sigH mutant strain, most likely due to activation of a sigma-B-dependent promoter in the absence of sigma-H.

ⁱTCA, tricarboxylic acid.

^jBoldface indicates a match with the consensus promoter sequence.