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. 2002 Sep;184(17):4881–4890. doi: 10.1128/JB.184.17.4881-4890.2002

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
a

Gene 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.

b

Ratios 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.

c

Ratios 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.

d

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

e

NO, not determined to be an outlier in our analysis.

f

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

g

Expression 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.

h

Parentheses 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.

i

TCA, tricarboxylic acid.

j

Boldface indicates a match with the consensus promoter sequence.