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 |
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.
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.
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.
Sigma-H-dependent regulation has been demonstrated only for Bacillus stearothermophilus (29).
NO, not determined to be an outlier in our analysis.
This phr gene was not detected as an outlier most likely because of its small size (<200 bp).
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.
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.
TCA, tricarboxylic acid.
Boldface indicates a match with the consensus promoter sequence.