SubtiBank SubtiBank

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International Conference on Bacilli and Gram-positive bacteria

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Categories containing this gene/protein

transcription, sigma factors and their control, cell envelope stress proteins (controlled by SigM, V, W, X, Y), resistance against toxins/ antibiotics

This gene is a member of the following regulons

SigM regulon

The SigM regulon


  • Coordinates on the chromosome (coding sequence): 1,029,577 -> 1,030,068
  • Phenotypes of a mutant

  • SigM is essential for growth and survival in nutrient broth (NB) containing 1.4 M NaCl PubMed
  • sigM mutants form aberrantly shaped cells, which swell and lyse spontaneously during growth in NB medium containing increased levels (0.35-0.7 M) of a wide range of different salts PubMed
  • increased sensitivity towards beta-lactam antibiotics PubMed
  • a sigM murJ double mutant is not viable (due to the lack of both lipid II flippases) PubMed
  • The protein

    Catalyzed reaction/ biological activity

    Protein family

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

    Kinetic information




    Effectors of protein activity

  • expression of CsbB in the absence of YfhO causes constitutive activation of SigM PubMed
  • shortage of available bactoprenol causes SigM activation PubMed
  • Structure



  • SigM-YhdK-YhdL PubMed
  • SigM-RpoB-RpoC
  • Additional information

  • Expression of the SigM regulon in increased in ugtP mutants PubMed
  • Expression and Regulation


  • sigM-yhdL-yhdK PubMed
  • Sigma factor

  • SigA PubMed, SigM PubMed
  • Regulation

  • induced by paraquat (SigM) PubMed
  • induced by glucose PubMed
  • Regulatory mechanism

    Additional information

  • expression of CsbB in the absence of YfhO causes constitutive activation of SigM PubMed
  • shortage of available bactoprenol causes SigM activation PubMed
  • Biological materials


  • 1A906 (sigM::kan), PubMed, available at BGSC
  • BP129 (sigM::aphA3), available in Fabian Commichau's lab
  • Expression vector

    lacZ fusion

    GFP fusion

    two-hybrid system

    FLAG-tag construct


    Labs working on this gene/protein

  • John Helmann, Cornell University, USA Homepage
  • References


    Radeck J, Fritz G, Mascher T

    The cell envelope stress response of Bacillus subtilis: from static signaling devices to dynamic regulatory network

    Curr Genet. 2017 Feb;63(1):79-90. doi: 10.1007/s00294-016-0624-0. Epub 2016 Jun 25. Review. PubMed PMID: 27344142.
    Helmann JD

    Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope

    Curr Opin Microbiol. 2016 Apr;30:122-32. doi: 10.1016/j.mib.2016.02.002. Epub 2016 Feb 20. Review. PubMed PMID: 26901131; PubMed Central PMCID: PMC4821709.
    Souza BM, Castro TL, Carvalho RD, Seyffert N, Silva A, Miyoshi A, Azevedo V

    σ(ECF) factors of gram-positive bacteria: a focus on Bacillus subtilis and the CMNR group

    Virulence. 2014 Jul 1;5(5):587-600. doi: 10.4161/viru.29514. Epub 2014 Jun 12. Review. PubMed PMID: 24921931; PubMed Central PMCID: PMC4105308.

    The SigM regulon

    Eiamphungporn W, Helmann JD

    The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses

    Mol Microbiol. 2008 Feb;67(4):830-48. doi: 10.1111/j.1365-2958.2007.06090.x. Epub 2008 Jan 2. PubMed PMID: 18179421; PubMed Central PMCID: PMC3025603.
    Mascher T, Hachmann AB, Helmann JD

    Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors

    J Bacteriol. 2007 Oct;189(19):6919-27. Epub 2007 Aug 3. PubMed PMID: 17675383; PubMed Central PMCID: PMC2045236.
    Jervis AJ, Thackray PD, Houston CW, Horsburgh MJ, Moir A

    SigM-responsive genes of Bacillus subtilis and their promoters

    J Bacteriol. 2007 Jun;189(12):4534-8. Epub 2007 Apr 13. PubMed PMID: 17434969; PubMed Central PMCID: PMC1913368.

    Other original publications

    Ogura M, Asai K

    Glucose Induces ECF Sigma Factor Genes, sigX and sigM, Independent of Cognate Anti-sigma Factors through Acetylation of CshA in Bacillus subtilis

    Front Microbiol. 2016 Nov 29;7:1918. eCollection 2016. PubMed PMID: 27965645; PubMed Central PMCID: PMC5126115.
    Seki T, Mineshima R, Hashimoto M, Matsumoto K, Hara H, Matsuoka S

    Repression of the activities of two extracytoplasmic function σ factors, σM and σV, of Bacillus subtilis by glucolipids in Escherichia coli cells

    Genes Genet Syst. 2015;90(2):109-14. doi: 10.1266/ggs.90.109. PubMed PMID: 26399770.
    Meeske AJ, Sham LT, Kimsey H, Koo BM, Gross CA, Bernhardt TG, Rudner DZ

    MurJ and a novel lipid II flippase are required for cell wall biogenesis in Bacillus subtilis

    Proc Natl Acad Sci U S A. 2015 May 19;112(20):6437-42. doi: 10.1073/pnas.1504967112. Epub 2015 Apr 27. PubMed PMID: 25918422; PubMed Central PMCID: PMC4443310.
    Inoue H, Suzuki D, Asai K

    A putative bactoprenol glycosyltransferase, CsbB, in Bacillus subtilis activates SigM in the absence of co-transcribed YfhO

    Biochem Biophys Res Commun. 2013 Jun 21;436(1):6-11. doi: 10.1016/j.bbrc.2013.04.064. Epub 2013 Apr 28. PubMed PMID: 23632331.
    Hashimoto M, Seki T, Matsuoka S, Hara H, Asai K, Sadaie Y, Matsumoto K

    Induction of extracytoplasmic function sigma factors in Bacillus subtilis cells with defects in lipoteichoic acid synthesis

    Microbiology. 2013 Jan;159(Pt 1):23-35. doi: 10.1099/mic.0.063420-0. Epub 2012 Oct 25. PubMed PMID: 23103977.
    Lee YH, Nam KH, Helmann JD

    A mutation of the RNA polymerase β' subunit (rpoC) confers cephalosporin resistance in Bacillus subtilis

    Antimicrob Agents Chemother. 2013 Jan;57(1):56-65. doi: 10.1128/AAC.01449-12. Epub 2012 Oct 15. PubMed PMID: 23070162; PubMed Central PMCID: PMC3535988.
    Matsuoka S, Chiba M, Tanimura Y, Hashimoto M, Hara H, Matsumoto K

    Abnormal morphology of Bacillus subtilis ugtP mutant cells lacking glucolipids

    Genes Genet Syst. 2011;86(5):295-304. PubMed PMID: 22362028.
    Luo Y, Helmann JD

    Analysis of the role of Bacillus subtilis σ(M) in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis

    Mol Microbiol. 2012 Feb;83(3):623-39. doi: 10.1111/j.1365-2958.2011.07953.x. Epub 2012 Jan 4. PubMed PMID: 22211522; PubMed Central PMCID: PMC3306796.
    Luo Y, Asai K, Sadaie Y, Helmann JD

    Transcriptomic and phenotypic characterization of a Bacillus subtilis strain without extracytoplasmic function σ factors

    J Bacteriol. 2010 Nov;192(21):5736-45. doi: 10.1128/JB.00826-10. Epub 2010 Sep 3. PubMed PMID: 20817771; PubMed Central PMCID: PMC2953670.
    Rukmana A, Morimoto T, Takahashi H, Giyanto, Ogasawara N

    Assessment of transcriptional responses of Bacillus subtilis cells to the antibiotic enduracidin, which interferes with cell wall synthesis, using a high-density tiling chip

    Genes Genet Syst. 2009 Aug;84(4):253-67. Erratum in: Genes Genet Syst. 2009 Oct;84(5):2 p following 395. PubMed PMID: 20057163.
    Hashimoto M, Takahashi H, Hara Y, Hara H, Asai K, Sadaie Y, Matsumoto K

    Induction of extracytoplasmic function sigma factors in Bacillus subtilis cells with membranes of reduced phosphatidylglycerol content

    Genes Genet Syst. 2009 Jun;84(3):191-8. PubMed PMID: 19745567.
    Luo Y, Helmann JD

    Extracytoplasmic function sigma factors with overlapping promoter specificity regulate sublancin production in Bacillus subtilis

    J Bacteriol. 2009 Aug;191(15):4951-8. doi: 10.1128/JB.00549-09. Epub 2009 May 22. PubMed PMID: 19465659; PubMed Central PMCID: PMC2715738.
    Eiamphungporn W, Helmann JD

    Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA

    J Bacteriol. 2009 Feb;191(3):1101-5. doi: 10.1128/JB.01530-08. Epub 2008 Dec 1. PubMed PMID: 19047346; PubMed Central PMCID: PMC2632094.
    Salzberg LI, Helmann JD

    Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition

    J Bacteriol. 2008 Dec;190(23):7797-807. doi: 10.1128/JB.00720-08. Epub 2008 Sep 26. PubMed PMID: 18820022; PubMed Central PMCID: PMC2583605.
    Rietkötter E, Hoyer D, Mascher T

    Bacitracin sensing in Bacillus subtilis

    Mol Microbiol. 2008 May;68(3):768-85. doi: 10.1111/j.1365-2958.2008.06194.x. PubMed PMID: 18394148.
    Minnig K, Lazarevic V, Soldo B, Mauël C

    Analysis of teichoic acid biosynthesis regulation reveals that the extracytoplasmic function sigma factor sigmaM is induced by phosphate depletion in Bacillus subtilis W23

    Microbiology. 2005 Sep;151(Pt 9):3041-9. PubMed PMID: 16151214.
    Cao M, Moore CM, Helmann JD

    Bacillus subtilis paraquat resistance is directed by sigmaM, an extracytoplasmic function sigma factor, and is conferred by YqjL and BcrC

    J Bacteriol. 2005 May;187(9):2948-56. PubMed PMID: 15838020; PubMed Central PMCID: PMC1082808.
    Yoshimura M, Asai K, Sadaie Y, Yoshikawa H

    Interaction of Bacillus subtilis extracytoplasmic function (ECF) sigma factors with the N-terminal regions of their potential anti-sigma factors

    Microbiology. 2004 Mar;150(Pt 3):591-9. PubMed PMID: 14993308.
    Mascher T, Margulis NG, Wang T, Ye RW, Helmann JD

    Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon

    Mol Microbiol. 2003 Dec;50(5):1591-604. PubMed PMID: 14651641.
    Cao M, Helmann JD

    Regulation of the Bacillus subtilis bcrC bacitracin resistance gene by two extracytoplasmic function sigma factors

    J Bacteriol. 2002 Nov;184(22):6123-9. PubMed PMID: 12399481; PubMed Central PMCID: PMC151963.
    Cao M, Wang T, Ye R, Helmann JD

    Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons

    Mol Microbiol. 2002 Sep;45(5):1267-76. PubMed PMID: 12207695.
    Horsburgh MJ, Moir A

    Sigma M, an ECF RNA polymerase sigma factor of Bacillus subtilis 168, is essential for growth and survival in high concentrations of salt

    Mol Microbiol. 1999 Apr;32(1):41-50. PubMed PMID: 10216858.
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