TABLE 1.

Genes previously known to be regulated directly by sigma-H

Gene or operonasigH+/sigHbOverexpressionc−35 boxSpacing−10 boxFunction and/or commentsReference(s)
citG (P2)3.52.6AAAGGATTT11GGCGAATTAFumarate hydratase (TCAi cycle), P1 recognized by sigma-A42, 54
dnaG (sigA-P4)3.43.0GAAGGGATT12ATCGAATAADNA primase28, 61
ftsAZ (P2)2.81.6AGAGGATAT11AACGAATATCell division, P1 recognized by sigma-A19
glgBCDAPd4.02.1AAAGGGCTT11TTCGAATAAGlycogen biosynthesis29
kinA3.92.8GAAGGAGAA12AGCGAATCASporulation (phosphorelay)2, 41
phrC1.61.6AGAGGATTT11GTAGCAAAAPhosphatase regulator (promoter within rapC)31
phrE (P1-2)1.6NOeTTAGGAGGC11TTATAATGGPhosphatase regulator (promoter within rapE)37
phrE (P3)1.6NO AGAGGATAG12CAAGAAAATSee above37
phrF2.4NO TGAAGATTT13GGCAAATAAPhosphatase regulator (promoter within rapF)37
phrGNONOfGAAGGAAAA12GCCGAATATPhosphatase regulator (promoter within rapG)37
phrl (P2)NONOfCAAGGAAAT12AATGAATATPhosphatase regulator (promoter within rapI)37
phrKNONOfACAGGAAAG12GGAGAATAAPhosphatase regulator (promoter within rapK)37
sigA (P3)1.62.1GCAGGAGTT12GGAGAATTAMajor sigma factor (promoter within yqxD), P1 recognized by sigma-A8
spo0A (Ps)NONOgAGAGGGTAT11GTCGAATGTTranscriptional regulation of sporulation, Pv recognized by sigma-A41
spo0F (P2)3.22.3AAAGGAAAT11ACAGAATACSporulation (phosphorelay), Spo0A regulated, P1 recognized by sigma-A4, 41
spo0M (ygaI)NONO ATAGGAAAA12AACGAATCTSporulation23
spoIIAA-AB-sigF9.03.2GAAGGAATT12ATCGAAACAForespore gene expression, Spo0A regulated59
spoVG3.02.8GCAGGATTT11GTGGAATTGSporulation (peptidoglycan hydrolysis), AbrB regulated28, 61
spoVS3.12.9GCAGGAATA12AGTGAATATSporulation46
ureABC (P2)1.62.1GAAGGAATT12GTCGAACTAUrease, P3 recognized by sigma-A and repressed by CodY58
yoxA-dacC (pbp)5.35.7GGAGGAAAT12ATTGAATTCUnknown-d-alanyl-d-alanine carboxypeptidase38
ytxG (P2)(3.4)h1.6AAAGGATTT11GGAGAATAGStress, P1 recognized by sigma-B56
yvyD (P2)(2.2)h1.5GCAGGAATT12AGAGAAATAPutative modulator of sigma-L, P1 recognized by sigma-B11
Consensus (24)jR-AGGAwWW11-12R--GAATwwR is A or G, W is A or T25
  • 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.