SubtiBank SubtiBank

It will happen very soon:

International Conference on Bacilli and Gram-positive bacteria

June 11 - 15, 2017, Berlin, Germany

Check out the program here

Categories containing this gene/protein

transcription, sigma factors and their control, motility and chemotaxis

This gene is a member of the following regulons

CodY regulon, DegU regulon, SigD regulon, Spo0A regulon

The SigD regulon


  • Coordinates on the chromosome (coding sequence): 1,716,493 -> 1,717,257
  • Phenotypes of a mutant

  • Inactivation of alsR, sigD and sigW increases competitive fitness of Bacillus subtilis under non-sporulating conditions PubMed
  • mucoid phenotype due to the overproduction of poly-gamma-glutamate (because of the loss of motA-motB expression) PubMed
  • not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation 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

  • interaction with FlgM inhibits SigD activity PubMed
  • Structure

  • 1RP3 (SigD-FlgM complex from Aqufex aeolicus, 34% identity) PubMed
  • Localization


  • SigD-FlgM PubMed, SigD-(RpoB-RpoC)
  • Additional information

    Expression and Regulation


  • part of the [[fla-che operon]]
  • flgB-flgC-fliE-fliF-fliG-fliH-fliI-fliJ-ylxF-fliK-flgD-flgE-fliL-fliM-fliY-cheY-fliZ-fliP-fliQ-fliR-flhB-flhA-flhF-flhG-cheB-cheA-cheW-cheC-cheD-sigD-swrB PubMed
  • ylxF-fliK-flgD-flgE-fliL-fliM-fliY-cheY-fliZ-fliP-fliQ-fliR-flhB-flhA-flhF-flhG-cheB-cheA-cheW-cheC-cheD-sigD-swrB PubMed
  • sigD-swrB PubMed
  • Sigma factor

  • flgB: SigA PubMed, SigD PubMed
  • ylxF: SigD PubMed
  • sigD: SigA PubMed
  • Regulation

  • see [[fla-che operon]]
  • Regulatory mechanism

  • see [[fla-che operon]]
  • Additional information

    Biological materials


  • 1A716 ( sigD::cat), PubMed, available at BGSC
  • DS6420 (marker-less in NCIB3610) PubMed
  • Expression vector

    lacZ fusion

    GFP fusion

    two-hybrid system

  • B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • FLAG-tag construct

  • GP948 (ermC, based on pGP1087), available in the Stülke lab
  • Antibody

    Labs working on this gene/protein



    Mukherjee S, Kearns DB

    The structure and regulation of flagella in Bacillus subtilis

    Annu Rev Genet. 2014;48:319-40. doi: 10.1146/annurev-genet-120213-092406. Epub 2014 Sep 10. Review. PubMed PMID: 25251856; PubMed Central PMCID: PMC4869327.
    Veening JW, Kuipers OP

    Gene position within a long transcript as a determinant for stochastic switching in bacteria

    Mol Microbiol. 2010 Apr;76(2):269-72. doi: 10.1111/j.1365-2958.2010.07113.x. Epub 2010 Mar 10. PubMed PMID: 20233302.

    The SigD regulon

    Serizawa M, Yamamoto H, Yamaguchi H, Fujita Y, Kobayashi K, Ogasawara N, Sekiguchi J

    Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses

    Gene. 2004 Mar 31;329:125-36. PubMed PMID: 15033535.
    Márquez LM, Helmann JD, Ferrari E, Parker HM, Ordal GW, Chamberlin MJ

    Studies of sigma D-dependent functions in Bacillus subtilis

    J Bacteriol. 1990 Jun;172(6):3435-43. PubMed PMID: 2111808; PubMed Central PMCID: PMC209155.

    Original publications

    Phillips AM, Calvo RA, Kearns DB

    Functional Activation of the Flagellar Type III Secretion Export Apparatus

    PLoS Genet. 2015 Aug 5;11(8):e1005443. doi: 10.1371/journal.pgen.1005443. eCollection 2015 Aug. PubMed PMID: 26244495; PubMed Central PMCID: PMC4526659.
    Ababneh QO, Herman JK

    CodY Regulates SigD Levels and Activity by Binding to Three Sites in the fla/che Operon

    J Bacteriol. 2015 Sep;197(18):2999-3006. doi: 10.1128/JB.00288-15. Epub 2015 Jul 13. PubMed PMID: 26170408; PubMed Central PMCID: PMC4542168.
    Hölscher T, Bartels B, Lin YC, Gallegos-Monterrosa R, Price-Whelan A, Kolter R, Dietrich LE, Kovács ÁT

    Motility, Chemotaxis and Aerotaxis Contribute to Competitiveness during Bacterial Pellicle Biofilm Development

    J Mol Biol. 2015 Nov 20;427(23):3695-708. doi: 10.1016/j.jmb.2015.06.014. Epub 2015 Jun 26. PubMed PMID: 26122431; PubMed Central PMCID: PMC4804472.
    Liu B, Deikus G, Bree A, Durand S, Kearns DB, Bechhofer DH

    Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains

    Mol Microbiol. 2014 Oct;94(1):41-55. doi: 10.1111/mmi.12748. Epub 2014 Aug 21. PubMed PMID: 25099370; PubMed Central PMCID: PMC4177450.
    Mordini S, Osera C, Marini S, Scavone F, Bellazzi R, Galizzi A, Calvio C

    The role of SwrA, DegU and P(D3) in fla/che expression in B

    subtilis. PLoS One. 2013 Dec 27;8(12):e85065. doi: 10.1371/journal.pone.0085065. eCollection 2013. PubMed PMID: 24386445; PubMed Central PMCID: PMC3874003.
    Chan JM, Guttenplan SB, Kearns DB

    Defects in the flagellar motor increase synthesis of poly-γ-glutamate in Bacillus subtilis

    J Bacteriol. 2014 Feb;196(4):740-53. doi: 10.1128/JB.01217-13. Epub 2013 Dec 2. PubMed PMID: 24296669; PubMed Central PMCID: PMC3911173.
    Luo Y, Helmann JD

    A σD-dependent antisense transcript modulates expression of the cyclic-di-AMP hydrolase GdpP in Bacillus subtilis

    Microbiology. 2012 Nov;158(Pt 11):2732-41. doi: 10.1099/mic.0.062174-0. Epub 2012 Sep 6. PubMed PMID: 22956758; PubMed Central PMCID: PMC4036058.
    Nicholson WL

    Increased competitive fitness of Bacillus subtilis under nonsporulating conditions via inactivation of pleiotropic regulators AlsR, SigD, and SigW

    Appl Environ Microbiol. 2012 May;78(9):3500-3. doi: 10.1128/AEM.07742-11. Epub 2012 Feb 17. PubMed PMID: 22344650; PubMed Central PMCID: PMC3346490.
    Cozy LM, Phillips AM, Calvo RA, Bate AR, Hsueh YH, Bonneau R, Eichenberger P, Kearns DB

    SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σ(D) in Bacillus subtilis

    Mol Microbiol. 2012 Mar;83(6):1210-28. doi: 10.1111/j.1365-2958.2012.08003.x. Epub 2012 Feb 22. PubMed PMID: 22329926; PubMed Central PMCID: PMC3303961.
    Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J

    A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation

    J Bacteriol. 2011 Nov;193(21):5997-6007. doi: 10.1128/JB.05360-11. Epub 2011 Aug 19. PubMed PMID: 21856853; PubMed Central PMCID: PMC3194898.
    Sevim E, Gaballa A, Beldüz AO, Helmann JD

    DNA-binding properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σ(D) proteins

    J Bacteriol. 2011 Jan;193(2):575-9. doi: 10.1128/JB.01193-10. Epub 2010 Nov 19. PubMed PMID: 21097624; PubMed Central PMCID: PMC3019834.
    Cozy LM, Kearns DB

    Gene position in a long operon governs motility development in Bacillus subtilis

    Mol Microbiol. 2010 Apr;76(2):273-85. doi: 10.1111/j.1365-2958.2010.07112.x. Epub 2010 Mar 10. PubMed PMID: 20233303; PubMed Central PMCID: PMC2911795.
    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.
    Kobayashi K

    Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis

    Mol Microbiol. 2007 Oct;66(2):395-409. Epub 2007 Sep 10. PubMed PMID: 17850253.
    Perez AR, Abanes-De Mello A, Pogliano K

    Suppression of engulfment defects in bacillus subtilis by elevated expression of the motility regulon

    J Bacteriol. 2006 Feb;188(3):1159-64. PubMed PMID: 16428420; PubMed Central PMCID: PMC1347344.
    Kearns DB, Losick R

    Cell population heterogeneity during growth of Bacillus subtilis

    Genes Dev. 2005 Dec 15;19(24):3083-94. PubMed PMID: 16357223; PubMed Central PMCID: PMC1315410.
    Werhane H, Lopez P, Mendel M, Zimmer M, Ordal GW, Márquez-Magaña LM

    The last gene of the fla/che operon in Bacillus subtilis, ylxL, is required for maximal sigmaD function

    J Bacteriol. 2004 Jun;186(12):4025-9. PubMed PMID: 15175317; PubMed Central PMCID: PMC419943.
    Sorenson MK, Ray SS, Darst SA

    Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation

    Mol Cell. 2004 Apr 9;14(1):127-38. PubMed PMID: 15068809.
    Molle V, Fujita M, Jensen ST, Eichenberger P, González-Pastor JE, Liu JS, Losick R

    The Spo0A regulon of Bacillus subtilis

    Mol Microbiol. 2003 Dec;50(5):1683-701. PubMed PMID: 14651647.
    Mirel DB, Estacio WF, Mathieu M, Olmsted E, Ramirez J, Márquez-Magaña LM

    Environmental regulation of Bacillus subtilis sigma(D)-dependent gene expression

    J Bacteriol. 2000 Jun;182(11):3055-62. PubMed PMID: 10809682; PubMed Central PMCID: PMC94489.
    Bertero MG, Gonzales B, Tarricone C, Ceciliani F, Galizzi A

    Overproduction and characterization of the Bacillus subtilis anti-sigma factor FlgM

    J Biol Chem. 1999 Apr 23;274(17):12103-7. PubMed PMID: 10207036.
    Estacio W, Anna-Arriola SS, Adedipe M, Márquez-Magaña LM

    Dual promoters are responsible for transcription initiation of the fla/che operon in Bacillus subtilis

    J Bacteriol. 1998 Jul;180(14):3548-55. PubMed PMID: 9657996; PubMed Central PMCID: PMC107321.
    Caramori T, Galizzi A

    The UP element of the promoter for the flagellin gene, hag, stimulates transcription from both SigD- and SigA-dependent promoters in Bacillus subtilis

    Mol Gen Genet. 1998 May;258(4):385-8. PubMed PMID: 9648743.
    Allmansberger R

    Temporal regulation of sigD from Bacillus subtilis depends on a minor promoter in front of the gene

    J Bacteriol. 1997 Oct;179(20):6531-5. PubMed PMID: 9335309; PubMed Central PMCID: PMC179576.
    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.
    Chen YF, Helmann JD

    DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally

    J Mol Biol. 1997 Mar 21;267(1):47-59. PubMed PMID: 9096206.
    Fredrick K, Helmann JD

    FlgM is a primary regulator of sigmaD activity, and its absence restores motility to a sinR mutant

    J Bacteriol. 1996 Dec;178(23):7010-3. PubMed PMID: 8955328; PubMed Central PMCID: PMC178607.
    Rashid MH, Sekiguchi J

    flaD (sinR) mutations affect SigD-dependent functions at multiple points in Bacillus subtilis

    J Bacteriol. 1996 Nov;178(22):6640-3. PubMed PMID: 8932324; PubMed Central PMCID: PMC178554.
    Chen L, Helmann JD

    The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT

    J Bacteriol. 1994 Jun;176(11):3093-101. PubMed PMID: 8195064; PubMed Central PMCID: PMC205476.
    Fredrick KL, Helmann JD

    Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains

    J Bacteriol. 1994 May;176(9):2727-35. PubMed PMID: 8169223; PubMed Central PMCID: PMC205414.
    Márquez-Magaña LM, Chamberlin MJ

    Characterization of the sigD transcription unit of Bacillus subtilis

    J Bacteriol. 1994 Apr;176(8):2427-34. PubMed PMID: 8157612; PubMed Central PMCID: PMC205368.
    Fredrick K, Caramori T, Chen YF, Galizzi A, Helmann JD

    Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element

    Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2582-6. PubMed PMID: 7708689; PubMed Central PMCID: PMC42262.
    Chen YF, Helmann JD

    The Bacillus subtilis flagellar regulatory protein sigma D: overproduction, domain analysis and DNA-binding properties

    J Mol Biol. 1995 Jun 16;249(4):743-53. PubMed PMID: 7602586.
    Helmann JD, Masiarz FR, Chamberlin MJ

    Isolation and characterization of the Bacillus subtilis sigma 28 factor

    J Bacteriol. 1988 Apr;170(4):1560-7. PubMed PMID: 3127378; PubMed Central PMCID: PMC211002.
    Helmann JD, Márquez LM, Chamberlin MJ

    Cloning, sequencing, and disruption of the Bacillus subtilis sigma 28 gene

    J Bacteriol. 1988 Apr;170(4):1568-74. PubMed PMID: 2832368; PubMed Central PMCID: PMC211003.
    Mirel DB, Chamberlin MJ

    The Bacillus subtilis flagellin gene (hag) is transcribed by the sigma 28 form of RNA polymerase

    J Bacteriol. 1989 Jun;171(6):3095-101. PubMed PMID: 2498284; PubMed Central PMCID: PMC210020.
    No login