SubtiBank SubtiBank

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Categories containing this gene/protein

transcription, sigma factors and their control, essential genes

This gene is a member of the following regulons

SigD regulon, SigH regulon


  • Coordinates on the chromosome (coding sequence): 2,600,214 -> 2,601,329
  • Phenotypes of a mutant

  • essential PubMed
  • The protein

    Catalyzed reaction/ biological activity

    Protein family

  • sigma-70 factor family (according to Swiss-Prot)
  • Paralogous protein(s)

    Kinetic information




    Effectors of protein activity


  • 3IYD (RNA polymerase from E. coli, 69% identity) PubMed
  • Localization

  • cytoplasm PubMed
  • Interactions

  • Spo0A-SigA PubMed
  • SigA-(RpoB-RpoC) PubMed
  • BsrA-SigA-RNA polymerase
  • BsrB-SigA-RNA polymerase
  • ComA-SigA PubMed
  • Additional information

    Expression and Regulation


  • yqxD-dnaG-sigA PubMed
  • sigA PubMed
  • Sigma factor

  • yqxD: SigA PubMed, SigH PubMed
  • sigA: SigD PubMed
  • Regulation

    Regulatory mechanism

    Additional information

  • An antisense RNA is predicted for sigA PubMed
  • Biological materials


    Expression vector

    lacZ fusion

    GFP fusion

    two-hybrid system

    FLAG-tag construct


    Labs working on this gene/protein

  • Charles Moran, Emory University, NC, USA homepage
  • References


    Steuten B, Schneider S, Wagner R

    6S RNA: recent answers--future questions

    Mol Microbiol. 2014 Feb;91(4):641-8. doi: 10.1111/mmi.12484. Epub 2014 Jan 7. Review. PubMed PMID: 24308327.
    Iyer LM, Aravind L

    Insights from the architecture of the bacterial transcription apparatus

    J Struct Biol. 2012 Sep;179(3):299-319. doi: 10.1016/j.jsb.2011.12.013. Epub 2011 Dec 24. PubMed PMID: 22210308; PubMed Central PMCID: PMC3769190.

    Original publications

    Narula J, Tiwari A, Igoshin OA

    Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks

    PLoS Comput Biol. 2016 Dec 15;12(12):e1005267. doi: 10.1371/journal.pcbi.1005267. eCollection 2016 Dec. PubMed PMID: 27977677; PubMed Central PMCID: PMC5207722.
    Wolf D, Rippa V, Mobarec JC, Sauer P, Adlung L, Kolb P, Bischofs IB

    The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs

    Nucleic Acids Res. 2016 Mar 18;44(5):2160-72. doi: 10.1093/nar/gkv1242. Epub 2015 Nov 17. PubMed PMID: 26582911; PubMed Central PMCID: PMC4797271.
    Lee YH, Helmann JD

    Mutations in the primary sigma factor σA and termination factor rho that reduce susceptibility to cell wall antibiotics

    J Bacteriol. 2014 Nov;196(21):3700-11. doi: 10.1128/JB.02022-14. Epub 2014 Aug 11. PubMed PMID: 25112476; PubMed Central PMCID: PMC4248801.
    Yeh HY, Hsu HT, Chen TC, Chung KM, Liou KM, Chang BY

    The reduction in σ-promoter recognition flexibility as induced by core RNAP is required for σ to discern the optimal promoter spacing

    Biochem J. 2013 Oct 15;455(2):185-93. doi: 10.1042/BJ20130576. PubMed PMID: 23875654.
    Beckmann BM, Hoch PG, Marz M, Willkomm DK, Salas M, Hartmann RK

    A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis

    EMBO J. 2012 Apr 4;31(7):1727-38. doi: 10.1038/emboj.2012.23. Epub 2012 Feb 14. PubMed PMID: 22333917; PubMed Central PMCID: PMC3321203.
    Yeh HY, Chen TC, Liou KM, Hsu HT, Chung KM, Hsu LL, Chang BY

    The core-independent promoter-specific interaction of primary sigma factor

    Nucleic Acids Res. 2011 Feb;39(3):913-25. doi: 10.1093/nar/gkq911. Epub 2010 Oct 8. PubMed PMID: 20935043; PubMed Central PMCID: PMC3035472.
    Ishikawa S, Oshima T, Kurokawa K, Kusuya Y, Ogasawara N

    RNA polymerase trafficking in Bacillus subtilis cells

    J Bacteriol. 2010 Nov;192(21):5778-87. doi: 10.1128/JB.00489-10. Epub 2010 Sep 3. PubMed PMID: 20817769; PubMed Central PMCID: PMC2953687.
    Irnov I, Sharma CM, Vogel J, Winkler WC

    Identification of regulatory RNAs in Bacillus subtilis

    Nucleic Acids Res. 2010 Oct;38(19):6637-51. doi: 10.1093/nar/gkq454. Epub 2010 Jun 4. PubMed PMID: 20525796; PubMed Central PMCID: PMC2965217.
    Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL

    Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

    Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. doi: 10.1073/pnas.0908782106. Epub 2009 Nov 10. PubMed PMID: 19903881; PubMed Central PMCID: PMC2775702.
    Johnston EB, Lewis PJ, Griffith R

    The interaction of Bacillus subtilis sigmaA with RNA polymerase

    Protein Sci. 2009 Nov;18(11):2287-97. doi: 10.1002/pro.239. PubMed PMID: 19735077; PubMed Central PMCID: PMC2788283.
    Yang X, Molimau S, Doherty GP, Johnston EB, Marles-Wright J, Rothnagel R, Hankamer B, Lewis RJ, Lewis PJ

    The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA

    EMBO Rep. 2009 Sep;10(9):997-1002. doi: 10.1038/embor.2009.155. Epub 2009 Aug 14. PubMed PMID: 19680289; PubMed Central PMCID: PMC2750059.
    Seredick SD, Spiegelman GB

    The Bacillus subtilis response regulator Spo0A stimulates sigmaA-dependent transcription prior to the major energetic barrier

    J Biol Chem. 2004 Apr 23;279(17):17397-403. Epub 2004 Feb 18. PubMed PMID: 14976210.
    Kumar A, Brannigan JA, Moran CP Jr

    Alpha-helix E of Spo0A is required for sigmaA- but not for sigmaH-dependent promoter activation in Bacillus subtilis

    J Bacteriol. 2004 Feb;186(4):1078-83. PubMed PMID: 14762002; PubMed Central PMCID: PMC344211.
    Kumar A, Buckner Starke C, DeZalia M, Moran CP Jr

    Surfaces of Spo0A and RNA polymerase sigma factor A that interact at the spoIIG promoter in Bacillus subtilis

    J Bacteriol. 2004 Jan;186(1):200-6. Erratum in: J Bacteriol. 2004 Apr;186(8):2515. PubMed PMID: 14679239; PubMed Central PMCID: PMC303461.
    Rollenhagen C, Antelmann H, Kirstein J, Delumeau O, Hecker M, Yudkin MD

    Binding of sigma(A) and sigma(B) to core RNA polymerase after environmental stress in Bacillus subtilis

    J Bacteriol. 2003 Jan;185(1):35-40. PubMed PMID: 12486038; PubMed Central PMCID: PMC141833.
    Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S

    Sigma A recognition sites in the Bacillus subtilis genome

    Microbiology. 2001 Sep;147(Pt 9):2417-24. PubMed PMID: 11535782.
    Qiu J, Helmann JD

    Adenines at -11, -9 and -8 play a key role in the binding of Bacillus subtilis Esigma(A) RNA polymerase to -10 region single-stranded DNA

    Nucleic Acids Res. 1999 Dec 1;27(23):4541-6. PubMed PMID: 10556308; PubMed Central PMCID: PMC148740.
    Ju J, Mitchell T, Peters H 3rd, Haldenwang WG

    Sigma factor displacement from RNA polymerase during Bacillus subtilis sporulation

    J Bacteriol. 1999 Aug;181(16):4969-77. PubMed PMID: 10438769; PubMed Central PMCID: PMC93986.
    Buckner CM, Schyns G, Moran CP Jr

    A region in the Bacillus subtilis transcription factor Spo0A that is important for spoIIG promoter activation

    J Bacteriol. 1998 Jul;180(14):3578-83. PubMed PMID: 9658000; PubMed Central PMCID: PMC107325.
    Huang X, Lopez de Saro FJ, Helmann JD

    sigma factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA

    Nucleic Acids Res. 1997 Jul 1;25(13):2603-9. PubMed PMID: 9185571; PubMed Central PMCID: PMC146786.
    Fredrick K, Helmann JD

    RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates

    Proc Natl Acad Sci U S A. 1997 May 13;94(10):4982-7. PubMed PMID: 9144176; PubMed Central PMCID: PMC24617.
    Juang YL, Helmann JD

    A promoter melting region in the primary sigma factor of Bacillus subtilis

    Identification of functionally important aromatic amino acids. J Mol Biol. 1994 Feb 4;235(5):1470-88. PubMed PMID: 8107087.
    Rong JC, Helmann JD

    Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting

    J Bacteriol. 1994 Sep;176(17):5218-24. PubMed PMID: 8071196; PubMed Central PMCID: PMC196704.
    Aiyar SE, Juang YL, Helmann JD, deHaseth PL

    Mutations in sigma factor that affect the temperature dependence of transcription from a promoter, but not from a mismatch bubble in double-stranded DNA

    Biochemistry. 1994 Sep 27;33(38):11501-6. PubMed PMID: 7918363.
    Helmann JD

    Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA

    Nucleic Acids Res. 1995 Jul 11;23(13):2351-60. PubMed PMID: 7630711; PubMed Central PMCID: PMC307037.
    Juang YL, Helmann JD

    Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations

    Biochemistry. 1995 Jul 4;34(26):8465-73. Erratum in: Biochemistry 1995 Oct 31;34(43):14270. PubMed PMID: 7599136.
    Carter HL 3rd, Wang LF, Doi RH, Moran CP Jr

    rpoD operon promoter used by sigma H-RNA polymerase in Bacillus subtilis

    J Bacteriol. 1988 Apr;170(4):1617-21. PubMed PMID: 3127379; PubMed Central PMCID: PMC211009.
    Price CW, Doi RH

    Genetic mapping of rpoD implicates the major sigma factor of Bacillus subtilis RNA polymerase in sporulation initiation

    Mol Gen Genet. 1985;201(1):88-95. PubMed PMID: 2997585.
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