SubtiBank SubtiBank

Categories containing this gene/protein


genetic competence, transcription factors and their control, phosphoproteins

This gene is a member of the following regulons


AbrB regulon, CodY regulon, ComK regulon, DegU regulon, Rok regulon, Spo0A regulon

The ComK regulon


Gene


  • Coordinates on the chromosome (coding sequence): 1,117,109 -> 1,117,687
  • Phenotypes of a mutant

  • no expression of competence genes, loss of genetic competence PubMed
  • The protein


    Catalyzed reaction/ biological activity

    Protein family

    Paralogous protein(s)

    Kinetic information

    Domains

    Modification

  • phosphorylated on Arg-65, Arg-157, Arg-161, Arg-165, Arg-186, and Arg-191 PubMed
  • Cofactors

    Effectors of protein activity

    Structure

    Localization

    Interactions

  • MecA-ComK PubMed
  • Additional information

    Expression and Regulation


    Operon

  • comK PubMed
  • Sigma factor

  • SigA PubMed
  • Regulation

  • comK has a bistable expression pattern PubMed
  • repressed by casamino acids PubMed
  • repressed by Rok PubMed
  • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
  • repressed during logarithmic growth (AbrB) PubMed
  • induced at the entry to stationary phase (Spo0A-P) PubMed
  • Regulatory mechanism

  • Rok: transcription repression PubMed
  • CodY: transcription repression PubMed
  • AbrB: transcription repression PubMed
  • ComK: transcription activation (autoregulation) PubMed
  • DegU (non-phosphorylated form): transcription activation PubMed
  • Spo0A-P: transcription activation, acts as antagonist of Rok PubMed
  • Additional information

  • degraded by ClpC-ClpP (with MecA as adaptor protein) PubMed
  • half-life of the comK mRNA: 3.9 min, stabilized to 5.4 min in a kre mutant PubMed
  • Biological materials


    Mutant

  • 1A871 (no resistance), PubMed, available at BGSC
  • Expression vector

  • for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab
  • lacZ fusion

    GFP fusion

    two-hybrid system

    FLAG-tag construct

    Antibody

    Labs working on this gene/protein


  • Oscar Kuipers, University of Groningen, The Netherlands
  • Homepage
  • References


    Reviews

    Kampf J, Stülke J

    Minor Cause--Major Effect: A Novel Mode of Control of Bistable Gene Expression

    PLoS Genet. 2015 Jun 25;11(6):e1005229. doi: 10.1371/journal.pgen.1005229. PubMed PMID: 26110607; PubMed Central PMCID: PMC4482365.
    Schultz D, Wolynes PG, Ben Jacob E, Onuchic JN

    Deciding fate in adverse times: sporulation and competence in Bacillus subtilis

    Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21027-34. doi: 10.1073/pnas.0912185106. PubMed PMID: 19995980; PubMed Central PMCID: PMC2795487.
    Hamoen LW, Venema G, Kuipers OP

    Controlling competence in Bacillus subtilis: shared use of regulators

    Microbiology. 2003 Jan;149(Pt 1):9-17. Review. PubMed PMID: 12576575.

    The ComK regulon

    Ogura M, Yamaguchi H, Kobayashi K, Ogasawara N, Fujita Y, Tanaka T

    Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK

    J Bacteriol. 2002 May;184(9):2344-51. PubMed PMID: 11948146; PubMed Central PMCID: PMC134994.
    Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, Cui X, Sloma A, Widner W, Dubnau D

    Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK

    Mol Microbiol. 2002 Mar;43(5):1331-45. PubMed PMID: 11918817.

    Original Publications

    Miras M, Dubnau D

    A DegU-P and DegQ-Dependent Regulatory Pathway for the K-state in Bacillus subtilis

    Front Microbiol. 2016 Nov 22;7:1868. PubMed PMID: 27920766; PubMed Central PMCID: PMC5118428.
    Nguyen A, Prugel-Bennett A, Dasmahapatra S

    A Low Dimensional Approximation For Competence In Bacillus Subtilis

    IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar-Apr;13(2):272-80. doi: 10.1109/TCBB.2015.2440275. PubMed PMID: 27045827.
    Gamba P, Jonker MJ, Hamoen LW

    A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence

    PLoS Genet. 2015 Jun 25;11(6):e1005047. doi: 10.1371/journal.pgen.1005047. PubMed PMID: 26110430; PubMed Central PMCID: PMC4482431.
    Zhang XZ, You C, Zhang YH

    Transformation of Bacillus subtilis

    Methods Mol Biol. 2014;1151:95-101. doi: 10.1007/978-1-4939-0554-6_7. PubMed PMID: 24838881.
    Elsholz AK, Turgay K, Michalik S, Hessling B, Gronau K, Oertel D, Mäder U, Bernhardt J, Becher D, Hecker M, Gerth U

    Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis

    Proc Natl Acad Sci U S A. 2012 May 8;109(19):7451-6. doi: 10.1073/pnas.1117483109. PubMed PMID: 22517742; PubMed Central PMCID: PMC3358850.
    Mirouze N, Desai Y, Raj A, Dubnau D

    Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis

    PLoS Genet. 2012;8(3):e1002586. doi: 10.1371/journal.pgen.1002586. PubMed PMID: 22412392; PubMed Central PMCID: PMC3297582.
    Dandach SH, Khammash M

    Analysis of stochastic strategies in bacterial competence: a master equation approach

    PLoS Comput Biol. 2010 Nov 11;6(11):e1000985. doi: 10.1371/journal.pcbi.1000985. PubMed PMID: 21085679; PubMed Central PMCID: PMC2978674.
    Nijland R, Burgess JG, Errington J, Veening JW

    Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence

    PLoS One. 2010 Mar 16;5(3):e9724. doi: 10.1371/journal.pone.0009724. PubMed PMID: 20300532; PubMed Central PMCID: PMC2838798.
    Smits WK, Bongiorni C, Veening JW, Hamoen LW, Kuipers OP, Perego M

    Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis

    Mol Microbiol. 2007 Jul;65(1):103-20. PubMed PMID: 17581123.
    Maamar H, Raj A, Dubnau D

    Noise in gene expression determines cell fate in Bacillus subtilis

    Science. 2007 Jul 27;317(5837):526-9. PubMed PMID: 17569828; PubMed Central PMCID: PMC3828679.
    Prepiak P, Dubnau D

    A peptide signal for adapter protein-mediated degradation by the AAA+ protease ClpCP

    Mol Cell. 2007 Jun 8;26(5):639-47. PubMed PMID: 17560370; PubMed Central PMCID: PMC2041856.
    Smits WK, Hoa TT, Hamoen LW, Kuipers OP, Dubnau D

    Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein

    Mol Microbiol. 2007 Apr;64(2):368-81. PubMed PMID: 17493123; PubMed Central PMCID: PMC3831528.
    Susanna KA, Fusetti F, Thunnissen AM, Hamoen LW, Kuipers OP

    Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants

    Microbiology. 2006 Feb;152(Pt 2):473-83. PubMed PMID: 16436435.
    Susanna KA, den Hengst CD, Hamoen LW, Kuipers OP

    Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer

    Appl Environ Microbiol. 2006 Jan;72(1):404-11. PubMed PMID: 16391071; PubMed Central PMCID: PMC1352259.
    Maamar H, Dubnau D

    Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop

    Mol Microbiol. 2005 May;56(3):615-24. PubMed PMID: 15819619; PubMed Central PMCID: PMC3831615.
    Shimane K, Ogura M

    Mutational analysis of the helix-turn-helix region of Bacillus subtilis response regulator DegU, and identification of cis-acting sequences for DegU in the aprE and comK promoters

    J Biochem. 2004 Sep;136(3):387-97. PubMed PMID: 15598897.
    Nanamiya H, Shiomi E, Ogura M, Tanaka T, Asai K, Kawamura F

    Involvement of ClpX protein in the post-transcriptional regulation of a competence specific transcription factor, ComK protein, of Bacillus subtilis

    J Biochem. 2003 Mar;133(3):295-302. PubMed PMID: 12761164.
    Hamoen LW, Kausche D, Marahiel MA, van Sinderen D, Venema G, Serror P

    The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK

    FEMS Microbiol Lett. 2003 Jan 28;218(2):299-304. PubMed PMID: 12586407.
    Sung HM, Yasbin RE

    Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis

    J Bacteriol. 2002 Oct;184(20):5641-53. PubMed PMID: 12270822; PubMed Central PMCID: PMC139596.
    Ogura M, Hashimoto H, Tanaka T

    Med, a cell-surface localized protein regulating a competence transcription factor gene, comK, in Bacillus subtilis

    Biosci Biotechnol Biochem. 2002 Apr;66(4):892-6. PubMed PMID: 12036071.
    Nakano MM, Nakano S, Zuber P

    Spx (YjbD), a negative effector of competence in Bacillus subtilis, enhances ClpC-MecA-ComK interaction

    Mol Microbiol. 2002 Jun;44(5):1341-9. PubMed PMID: 12028382.
    Hoa TT, Tortosa P, Albano M, Dubnau D

    Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK

    Mol Microbiol. 2002 Jan;43(1):15-26. PubMed PMID: 11849533.
    Jarmer H, Berka R, Knudsen S, Saxild HH

    Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions

    FEMS Microbiol Lett. 2002 Jan 10;206(2):197-200. PubMed PMID: 11814663.
    Nakano MM, Hajarizadeh F, Zhu Y, Zuber P

    Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis

    Mol Microbiol. 2001 Oct;42(2):383-94. PubMed PMID: 11703662.
    Hamoen LW, Van Werkhoven AF, Venema G, Dubnau D

    The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis

    Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9246-51. PubMed PMID: 10908654; PubMed Central PMCID: PMC16853.
    Persuh M, Turgay K, Mandic-Mulec I, Dubnau D

    The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch

    Mol Microbiol. 1999 Aug;33(4):886-94. PubMed PMID: 10447896.
    Ogura M, Liu L, Lacelle M, Nakano MM, Zuber P

    Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis

    Mol Microbiol. 1999 May;32(4):799-812. PubMed PMID: 10361283.
    Turgay K, Hahn J, Burghoorn J, Dubnau D

    Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor

    EMBO J. 1998 Nov 16;17(22):6730-8. PubMed PMID: 9890793; PubMed Central PMCID: PMC1171018.
    Hamoen LW, Van Werkhoven AF, Bijlsma JJ, Dubnau D, Venema G

    The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix

    Genes Dev. 1998 May 15;12(10):1539-50. PubMed PMID: 9585513; PubMed Central PMCID: PMC316842.
    Ogura M, Ohshiro Y, Hirao S, Tanaka T

    A new Bacillus subtilis gene, med, encodes a positive regulator of comK

    J Bacteriol. 1997 Oct;179(20):6244-53. PubMed PMID: 9335269; PubMed Central PMCID: PMC179536.
    Ogura M, Tanaka T

    Bacillus subtilis ComK negatively regulates degR gene expression

    Mol Gen Genet. 1997 Mar 26;254(2):157-65. PubMed PMID: 9108277.
    Turgay K, Hamoen LW, Venema G, Dubnau D

    Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis

    Genes Dev. 1997 Jan 1;11(1):119-28. PubMed PMID: 9000055.
    Hahn J, Luttinger A, Dubnau D

    Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis

    Mol Microbiol. 1996 Aug;21(4):763-75. PubMed PMID: 8878039.
    Serror P, Sonenshein AL

    CodY is required for nutritional repression of Bacillus subtilis genetic competence

    J Bacteriol. 1996 Oct;178(20):5910-5. PubMed PMID: 8830686; PubMed Central PMCID: PMC178446.
    van Sinderen D, ten Berge A, Hayema BJ, Hamoen L, Venema G

    Molecular cloning and sequence of comK, a gene required for genetic competence in Bacillus subtilis

    Mol Microbiol. 1994 Feb;11(4):695-703. PubMed PMID: 8196543.
    van Sinderen D, Venema G

    comK acts as an autoregulatory control switch in the signal transduction route to competence in Bacillus subtilis

    J Bacteriol. 1994 Sep;176(18):5762-70. PubMed PMID: 8083168; PubMed Central PMCID: PMC196780.
    Kong L, Dubnau D

    Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis

    Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5793-7. PubMed PMID: 8016067; PubMed Central PMCID: PMC44083.
    Msadek T, Kunst F, Rapoport G

    MecB of Bacillus subtilis, a member of the ClpC ATPase family, is a pleiotropic regulator controlling competence gene expression and growth at high temperature

    Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5788-92. PubMed PMID: 8016066; PubMed Central PMCID: PMC44082.
    van Sinderen D, Luttinger A, Kong L, Dubnau D, Venema G, Hamoen L

    comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis

    Mol Microbiol. 1995 Feb;15(3):455-62. PubMed PMID: 7783616.
    Haijema BJ(1), Hamoen LW, Kooistra J, Venema G, van Sinderen D.

    Expression of the ATP-dependent deoxyribonuclease of Bacillus subtilis is under competence-mediated control.

    Mol Microbiol. 1995 Jan;15(2):203-11.
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