SubtiBank SubtiBank

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Categories containing this gene/protein

biofilm formation, sporulation/ other

This gene is a member of the following regulons


  • Coordinates on the chromosome (coding sequence): 1,768,941 -> 1,769,735
  • Phenotypes of a mutant

  • strong overexpression of hag PubMed
  • defective in biofilm formation PubMed
  • the phenotypes of the ymdB mutant can be suppressed by overexpression of slrR PubMed
  • inactivation of ymdB restores beta-lactam resistance in a sigM mutant PubMed
  • increased expression of genes encoding small acid-soluble proteins PubMed
  • increased intracellular levels of cyclic AMP PubMed
  • abberant colony development, reduced colony size PubMed
  • reduced formation of nanotubes PubMed
  • inactivation of ymdB reduces sporulation efficiency to 11.4% that of wild type cells PubMed
  • The protein

    Catalyzed reaction/ biological activity

  • phosphodiesterase activity toward 2,3-cAMP PubMed
  • Protein family

    Paralogous protein(s)

    Kinetic information




    Effectors of protein activity


  • 4B2O PubMed
  • Localization


  • forms tetramers PubMed
  • Additional information

    Expression and Regulation


  • rny-ymdB (weak readthrough transcription) PubMed
  • Sigma factor


  • constitutive
  • Regulatory mechanism

    Additional information

  • there is a terminator between rny and ymdB, most transcripts terminate there PubMed
  • the transcription terminator between rny and ymdB is strong and NusA-independent Reference
  • Biological materials


  • MGNA-B070 (ymdB::erm), available at the NBRP B. subtilis, Japan
  • GP583 (spc), available in Jörg Stülke's lab PubMed
  • GP922 (cat), available in Jörg Stülke's lab PubMed
  • GP921 (spc) NCIB3610 derivate, available in Jörg Stülke's lab PubMed
  • GP969 (ymdB(E39Q)-cat) inactive enzyme, available in Jörg Stülke's lab PubMed
  • GP1558 (aphA3; cassette w/o terminator), available in Jörg Stülke's lab
  • GP1573 (aphA3), available in Jörg Stülke's lab
  • GP1848 (replacement of ymdB-spoVS by a spc cassette), available in Jörg Stülke's lab
  • Expression vector

  • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Jörg Stülke's lab
  • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Jörg Stülke's lab
  • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Jörg Stülke's lab
  • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Jörg Stülke's lab PubMed
  • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Jörg Stülke's lab
  • lacZ fusion

    GFP fusion

    two-hybrid system

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

  • GP1018 (spc, based on pGP1331), available in Jörg Stülke's lab
  • Antibody

    Labs working on this gene/protein

  • Jörg Stülke, University of Göttingen, Germany
  • Homepage
  • References


    Matange N(1), Podobnik M(2), Visweswariah SS(1).

    Metallophosphoesterases: structural fidelity with functional promiscuity.

    Biochem J. 2015 Apr 15;467(2):201-16. doi: 10.1042/BJ20150028.

    Original Publications

    Dubey GP, Malli Mohan GB, Dubrovsky A, Amen T, Tsipshtein S, Rouvinski A, Rosenberg A, Kaganovich D, Sherman E, Medalia O, Ben-Yehuda S

    Architecture and Characteristics of Bacterial Nanotubes

    Dev Cell. 2016 Feb 22;36(4):453-61. doi: 10.1016/j.devcel.2016.01.013. PubMed PMID: 26906740.
    Mamou G, Malli Mohan GB, Rouvinski A, Rosenberg A, Ben-Yehuda S

    Early Developmental Program Shapes Colony Morphology in Bacteria

    Cell Rep. 2016 Mar 1;14(8):1850-7. doi: 10.1016/j.celrep.2016.01.071. Epub 2016 Feb 18. PubMed PMID: 26904951; PubMed Central PMCID: PMC4785774.
    Meeske AJ, Rodrigues CD, Brady J, Lim HC, Bernhardt TG, Rudner DZ

    High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis

    PLoS Biol. 2016 Jan 6;14(1):e1002341. doi: 10.1371/journal.pbio.1002341. eCollection 2016 Jan. PubMed PMID: 26735940; PubMed Central PMCID: PMC4703394.
    Diethmaier C, Newman JA, Kovács AT, Kaever V, Herzberg C, Rodrigues C, Boonstra M, Kuipers OP, Lewis RJ, Stülke J

    The YmdB phosphodiesterase is a global regulator of late adaptive responses in Bacillus subtilis

    J Bacteriol. 2014 Jan;196(2):265-75. doi: 10.1128/JB.00826-13. Epub 2013 Oct 25. PubMed PMID: 24163345; PubMed Central PMCID: PMC3911264.
    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.
    Pozsgai ER, Blair KM, Kearns DB

    Modified mariner transposons for random inducible-expression insertions and transcriptional reporter fusion insertions in Bacillus subtilis

    Appl Environ Microbiol. 2012 Feb;78(3):778-85. doi: 10.1128/AEM.07098-11. Epub 2011 Nov 23. PubMed PMID: 22113911; PubMed Central PMCID: PMC3264109.
    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.

    Functional and structural analysis of orthologs in other organisms

    Zemansky J, Kline BC, Woodward JJ, Leber JH, Marquis H, Portnoy DA

    Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype

    J Bacteriol. 2009 Jun;191(12):3950-64. doi: 10.1128/JB.00016-09. Epub 2009 Apr 17. PubMed PMID: 19376879; PubMed Central PMCID: PMC2698408.
    Shin DH, Proudfoot M, Lim HJ, Choi IK, Yokota H, Yakunin AF, Kim R, Kim SH

    Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans

    Proteins. 2008 Feb 15;70(3):1000-9. PubMed PMID: 17847097.
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