TABLE 2.

Newly identified sigma-H-regulated geneslegend

Gene or operonasigH+/sigHbOver- expressionc−35 boxSpacing−10 boxDistancedMethodePutative function and/or comments
bsaA-ypgQR2.61.8AGAGGGAAT12ATAGAATGA147PMPutative glutathione peroxidase-unknowns
ccdA2.01.7GAAGGAGTA12GTCAAATTA109HMMLate step of cytochrome c synthesis (33)
gltP2.62.7AAAGGTGTT11CACGAATGA40HMMH+/Glu symport protein
kinE (ykrQ)2.22.7GAAGGAAGT11GTAGAAATA35HMMTwo-component sensor His kinase (27)
vpr9.54.1CAAGGATTT11CAAGAAATA47HMMMinor extracellular serine protease (secretion sequenceg) (50)
ycsN3.11.8AAAGGAAAA12GCCGAATGA50HMMSimilar to aryl-alcohol dehydrogenase
yesL-yesM3.03.2GCAGGAATT11GGAGAAATA43HMMUnknown—similar to two-component sensor histidine kinase
yhaRQ1.81.8AAAGGTTTA12GGGGAATGT44HMMSimilar to enoyl CoAj hydratase-ABC transporter
yhcRSf2.93.0AAAGGAATT12GTCGAAATG45HMMSimilar to 5′-nucleotidase (secretion sequenceg)-unknown
yisK3.96.5AAAGGGATT12AGAGAATAC41HMMSimilar to 5-oxo-1,2,5-TCAk-3-penten acid decarboxylase
yisT2.33.7GAAGGAGAA12AACGAATTT21HMMSimilar to nuclease inhibitor
ykoM3.73.4GAAGGAATT11AGCGAATAC79HMMSimilar to transcriptional regulator (MarR family)
ymaH2.31.9GCAGGAAAA11ATCGAAACT31HMMSimilar to host factor 1 protein, sporulation (MICADO database)
ynaD2.12.2GAAGGATAG12GGAGAATCA143HMMSimilar to ribosomal protein alanine N-acetyltransferase
yobO12.44.2AAAGGAATT11ACAGAATTG84HMMSimilar to phage-related preneck appendage
yoeA2.22.3GAAGGGTTT12GATGAATAA78HMMSimilar to multidrug efflux (Clostridium acetobutylicum), sporulation (MICADO databaseh)
yojLM3.94.0GAAGGGATT12AGAGAATTG292HMMCell wall binding protein (secretion sequenceg)—similar to superoxide dismutase
ypiBF-qcrABC3.22.0AAACGATTT11GATGAATTT80HMMUnknown-unknown-menaquinol:cytochrome c reductase
ypiBF-qcrABC3.22.0GCAGGAATA12GTGGAACAT40HMMAlternative promoter; for function see above
yrvJ2.02.2AAAGGACTT12CAAGAATGC30PMPutative cell wall binding protein (secretion sequenceg); similar to N-acetylmuramoyl-l-alanine amidase
yttP4.9NOiACAGGAACA11CTTGAATAG24HMMSimilar to transcriptional regulator (AcrR/TetR family)
yuxl3.51.6AAAGGAAAA12CACGAATTA33HMMUnknown
yuxL4.45.4AAAGGAGTT12AACGAAATA23HMMSimilar to acylaminoacyl-peptidase
yveKLMNOPQRST- yvfABCDEF3.4NOiTAAGGAATT11ATAAAATTT173PMExopolysaccharide biosynthesis-fruiting body formation
ywfBCDE (FG)1.82.8AAAGGGTTT11TGGGAATAA86HMMUnknown-unknown-similar to Glc-1-dehydrogenase-unknown
ywfFG1.82.8GCAGTAATT11GCTGAATCA53HMMSimilar to efflux protein-similar to Asp aminotransferase
Consensus (24) lR-AGGAwWW11-12R--GAATwwR is A or G, W is A or T
  • a Gene or genes of a potential operon that are regulated by sigma-H.

  • 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 levels 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 The distance is measured from the last base pair of the −10 region to the first base pair of the start codon.

  • e PM, pattern match. HMM, hidden Markov model.

  • f The predicted sigma-H promoter for yhcR overlaps with predicted AUG (SubtiList), but a second AUG is present 60 bp downstream (a possible ribosome binding site is also found just upstream of this second AUG).

  • g Secretion sequence is from reference 55.

  • h MICADO database: http://locus.jouy.inra.fr/cgi-bin/genmic/madbase/progs/madbase.operl.

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

  • j CoA, coenzyme A.

  • k TCA, tricarboxylic acid.

  • legend Boldface indicates a match with the consensus promoter sequence.