SubtiBank SubtiBank

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Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

Spo0A regulon

The DnaA regulon


  • Coordinates on the chromosome (coding sequence): 410 -> 1,750
  • Phenotypes of a mutant

  • essential PubMed
  • The protein

    Catalyzed reaction/ biological activity

  • binds multiple regions in the oriC region, required for recruitment of proteins needed to load the replicative helicase DnaC
  • Protein family

  • dnaA family (according to Swiss-Prot)
  • Paralogous protein(s)

    Kinetic information


  • AAA + domain
  • Modification


    Effectors of protein activity

  • SirA displaces DnaA from the replication origin PubMed
  • YabA inhibits co-operative binding of DnaA to the oriC DNA PubMed
  • DnaA helix formation (and thus replication initiation) is inhibited by the interaction of either Soj, YabA or DnaN with the AAA domain of DnaA PubMed
  • interaction with DnaD inhibits the ability of DnaA to cooperatively bind to DNA PubMed
  • Structure

  • 2Z4R (from Thermotoga maritima ) PubMed
  • Localization

  • throughout the cytoplasm PubMed
  • Interactions

  • DnaA assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA domains PubMed
  • ParA-DnaA PubMed
  • DnaA-YabA PubMed
  • DnaA-YabA-DnaN PubMed
  • DnaA-DnaD PubMed
  • SirA-DnaA (N-terminal domain) PubMed
  • YqaH-DnaA PubMed
  • DnaA-Rok, to modulate Rok activity PubMed
  • part of the primosome: DnaA-DnaG-DnaC-DnaI-DnaD-DnaB PubMed
  • Additional information

    Expression and Regulation


  • dnaA-dnaN PubMed
  • Sigma factor

  • SigA PubMed
  • Regulation

  • negatively controlled by DnaA PubMed and Spo0A PubMed
  • repressed under conditions that trigger sporulation (Spo0A) PubMed
  • Regulatory mechanism

  • Spo0A: transcription repression PubMed
  • Additional information

  • term-seq has identified a potential novel regulatory RNA element including an intrinsic transcription terminator upstream of dnaA PubMed
  • Biological materials


    Expression vector

    lacZ fusion

    GFP fusion

    two-hybrid system

    FLAG-tag construct


    Labs working on this gene/protein

  • Peter Graumann, Freiburg University, Germany homepage
  • Alan Grossman, MIT, Cambridge, MA, USA
  • Heath Murray, Centre for Bacterial Cell Biology, Newcastle, UK homepage
  • References


    Jameson KH, Wilkinson AJ

    Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli

    Genes (Basel). 2017 Jan 10;8(1). pii: E22. doi: 10.3390/genes8010022. Review. PubMed PMID: 28075389; PubMed Central PMCID: PMC5295017.
    Hajduk IV, Rodrigues CD, Harry EJ

    Connecting the dots of the bacterial cell cycle: Coordinating chromosome replication and segregation with cell division

    Semin Cell Dev Biol. 2016 May;53:2-9. doi: 10.1016/j.semcdb.2015.11.012. Epub 2015 Dec 17. Review. PubMed PMID: 26706151.
    Briggs GS, Smits WK, Soultanas P

    Chromosomal replication initiation machinery of low-G+C-content Firmicutes

    J Bacteriol. 2012 Oct;194(19):5162-70. doi: 10.1128/JB.00865-12. Epub 2012 Jul 13. Review. PubMed PMID: 22797751; PubMed Central PMCID: PMC3457243.
    Chien AC, Hill NS, Levin PA

    Cell size control in bacteria

    Curr Biol. 2012 May 8;22(9):R340-9. doi: 10.1016/j.cub.2012.02.032. Epub 2012 May 7. PubMed PMID: 22575476; PubMed Central PMCID: PMC3350639.
    Leonard AC, Grimwade JE

    Regulation of DnaA assembly and activity: taking directions from the genome

    Annu Rev Microbiol. 2011;65:19-35. doi: 10.1146/annurev-micro-090110-102934. Review. PubMed PMID: 21639790; PubMed Central PMCID: PMC4075013.
    Leonard AC, Grimwade JE

    Regulating DnaA complex assembly: it is time to fill the gaps

    Curr Opin Microbiol. 2010 Dec;13(6):766-72. doi: 10.1016/j.mib.2010.10.001. Epub 2010 Oct 27. Review. PubMed PMID: 21035377; PubMed Central PMCID: PMC3005629.
    Katayama T, Ozaki S, Keyamura K, Fujimitsu K

    Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC

    Nat Rev Microbiol. 2010 Mar;8(3):163-70. doi: 10.1038/nrmicro2314. Review. PubMed PMID: 20157337.

    The DnaA regulon

    Goranov AI(1), Katz L, Breier AM, Burge CB, Grossman AD.

    A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

    Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. Epub 2005 Aug 24.

    Original publications

    Seid CA, Smith JL, Grossman AD

    Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in Bacillus subtilis

    Mol Microbiol. 2017 Mar;103(5):798-817. doi: 10.1111/mmi.13590. Epub 2017 Jan 3. PubMed PMID: 27902860; PubMed Central PMCID: PMC5323315.
    Duan Y, Huey JD, Herman JK

    The DnaA inhibitor SirA acts in the same pathway as Soj (ParA) to facilitate oriC segregation during Bacillus subtilis sporulation

    Mol Microbiol. 2016 Nov;102(3):530-544. doi: 10.1111/mmi.13477. Epub 2016 Aug 25. PubMed PMID: 27489185.
    Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P, Sorek R

    Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

    Science. 2016 Apr 8;352(6282):aad9822. doi: 10.1126/science.aad9822. PubMed PMID: 27120414.
    Felicori L, Jameson KH, Roblin P, Fogg MJ, Garcia-Garcia T, Ventroux M, Cherrier MV, Bazin A, Noirot P, Wilkinson AJ, Molina F, Terradot L, Noirot-Gros MF

    Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

    Nucleic Acids Res. 2016 Jan 8;44(1):449-63. doi: 10.1093/nar/gkv1318. Epub 2015 Nov 28. PubMed PMID: 26615189; PubMed Central PMCID: PMC4705661.
    Smith JL, Grossman AD

    In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA

    PLoS Genet. 2015 May 28;11(5):e1005258. doi: 10.1371/journal.pgen.1005258. eCollection 2015 May. PubMed PMID: 26020636; PubMed Central PMCID: PMC4447404.
    Murray H, Koh A

    Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis

    PLoS Genet. 2014 Oct 23;10(10):e1004731. doi: 10.1371/journal.pgen.1004731. eCollection 2014 Oct. PubMed PMID: 25340815; PubMed Central PMCID: PMC4207641.
    Jameson KH, Rostami N, Fogg MJ, Turkenburg JP, Grahl A, Murray H, Wilkinson AJ

    Structure and interactions of the Bacillus subtilis sporulation inhibitor of DNA replication, SirA, with domain I of DnaA

    Mol Microbiol. 2014 Sep;93(5):975-91. doi: 10.1111/mmi.12713. Epub 2014 Aug 5. PubMed PMID: 25041308; PubMed Central PMCID: PMC4285326.
    Scholefield G, Murray H

    YabA and DnaD inhibit helix assembly of the DNA replication initiation protein DnaA

    Mol Microbiol. 2013 Oct;90(1):147-59. doi: 10.1111/mmi.12353. Epub 2013 Aug 23. PubMed PMID: 23909787.
    Bonilla CY, Grossman AD

    The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis

    J Bacteriol. 2012 Sep;194(18):5110-7. doi: 10.1128/JB.00958-12. Epub 2012 Jul 20. PubMed PMID: 22821970; PubMed Central PMCID: PMC3430336.
    Hill NS, Kadoya R, Chattoraj DK, Levin PA

    Cell size and the initiation of DNA replication in bacteria

    PLoS Genet. 2012;8(3):e1002549. doi: 10.1371/journal.pgen.1002549. Epub 2012 Mar 1. PubMed PMID: 22396664; PubMed Central PMCID: PMC3291569.
    Scholefield G, Errington J, Murray H

    Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA

    EMBO J. 2012 Mar 21;31(6):1542-55. doi: 10.1038/emboj.2012.6. Epub 2012 Jan 27. PubMed PMID: 22286949; PubMed Central PMCID: PMC3321191.
    Okumura H, Yoshimura M, Ueki M, Oshima T, Ogasawara N, Ishikawa S

    Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis

    Nucleic Acids Res. 2012 Jan;40(1):220-34. doi: 10.1093/nar/gkr716. Epub 2011 Sep 12. PubMed PMID: 21911367; PubMed Central PMCID: PMC3245932.
    Merrikh H, Grossman AD

    Control of the replication initiator DnaA by an anti-cooperativity factor

    Mol Microbiol. 2011 Oct;82(2):434-46. doi: 10.1111/j.1365-2958.2011.07821.x. Epub 2011 Sep 14. PubMed PMID: 21895792; PubMed Central PMCID: PMC3192265.
    Rahn-Lee L, Merrikh H, Grossman AD, Losick R

    The sporulation protein SirA inhibits the binding of DnaA to the origin of replication by contacting a patch of clustered amino acids

    J Bacteriol. 2011 Mar;193(6):1302-7. doi: 10.1128/JB.01390-10. Epub 2011 Jan 14. PubMed PMID: 21239581; PubMed Central PMCID: PMC3067619.
    Smits WK, Merrikh H, Bonilla CY, Grossman AD

    Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis

    J Bacteriol. 2011 Feb;193(3):640-8. doi: 10.1128/JB.01253-10. Epub 2010 Nov 19. PubMed PMID: 21097613; PubMed Central PMCID: PMC3021214.
    Hoover SE, Xu W, Xiao W, Burkholder WF

    Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium

    J Bacteriol. 2010 Aug;192(15):3915-24. doi: 10.1128/JB.00210-10. Epub 2010 May 28. PubMed PMID: 20511500; PubMed Central PMCID: PMC2916362.
    Smits WK, Goranov AI, Grossman AD

    Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo

    Mol Microbiol. 2010 Jan;75(2):452-61. doi: 10.1111/j.1365-2958.2009.06999.x. Epub 2009 Dec 4. PubMed PMID: 19968790; PubMed Central PMCID: PMC2992960.
    Goranov AI, Breier AM, Merrikh H, Grossman AD

    YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress

    Mol Microbiol. 2009 Oct;74(2):454-66. doi: 10.1111/j.1365-2958.2009.06876.x. Epub 2009 Sep 8. PubMed PMID: 19737352; PubMed Central PMCID: PMC2823125.
    Wagner JK, Marquis KA, Rudner DZ

    SirA enforces diploidy by inhibiting the replication initiator DnaA during spore formation in Bacillus subtilis

    Mol Microbiol. 2009 Sep;73(5):963-74. doi: 10.1111/j.1365-2958.2009.06825.x. Epub 2009 Aug 4. PubMed PMID: 19682252; PubMed Central PMCID: PMC2992877.
    Breier AM, Grossman AD

    Dynamic association of the replication initiator and transcription factor DnaA with the Bacillus subtilis chromosome during replication stress

    J Bacteriol. 2009 Jan;191(2):486-93. doi: 10.1128/JB.01294-08. Epub 2008 Nov 14. PubMed PMID: 19011033; PubMed Central PMCID: PMC2620820.
    Murray H, Errington J

    Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA

    Cell. 2008 Oct 3;135(1):74-84. doi: 10.1016/j.cell.2008.07.044. PubMed PMID: 18854156.
    Ozaki S, Kawakami H, Nakamura K, Fujikawa N, Kagawa W, Park SY, Yokoyama S, Kurumizaka H, Katayama T

    A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin

    J Biol Chem. 2008 Mar 28;283(13):8351-62. doi: 10.1074/jbc.M708684200. Epub 2008 Jan 23. PubMed PMID: 18216012.
    Ishikawa S, Ogura Y, Yoshimura M, Okumura H, Cho E, Kawai Y, Kurokawa K, Oshima T, Ogasawara N

    Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method

    DNA Res. 2007 Aug 31;14(4):155-68. Epub 2007 Oct 10. PubMed PMID: 17932079; PubMed Central PMCID: PMC2533591.
    Berkmen MB, Grossman AD

    Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA

    Mol Microbiol. 2007 Jan;63(1):150-65. Epub 2006 Nov 27. PubMed PMID: 17140409.
    Noirot-Gros MF, Velten M, Yoshimura M, McGovern S, Morimoto T, Ehrlich SD, Ogasawara N, Polard P, Noirot P

    Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis

    Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2368-73. Epub 2006 Feb 6. PubMed PMID: 16461910; PubMed Central PMCID: PMC1413692.
    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.
    Noirot-Gros MF, Dervyn E, Wu LJ, Mervelet P, Errington J, Ehrlich SD, Noirot P

    An expanded view of bacterial DNA replication

    Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8342-7. PubMed PMID: 12060778; PubMed Central PMCID: PMC123069.
    Ishigo-Oka D, Ogasawara N, Moriya S

    DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication

    J Bacteriol. 2001 Mar;183(6):2148-50. PubMed PMID: 11222620; PubMed Central PMCID: PMC95117.
    Ishigo-Oka D, Ogasawara N, Moriya S

    DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication

    J Bacteriol. 2001 Mar;183(6):2148-50. PubMed PMID: 11222620; PubMed Central PMCID: PMC95117.
    Burkholder WF, Kurtser I, Grossman AD

    Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis

    Cell. 2001 Jan 26;104(2):269-79. PubMed PMID: 11207367.
    Imai Y, Ogasawara N, Ishigo-Oka D, Kadoya R, Daito T, Moriya S

    Subcellular localization of Dna-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids

    Mol Microbiol. 2000 Jun;36(5):1037-48. PubMed PMID: 10844689.
    Ogasawara N, Moriya S, Yoshikawa H

    Structure and function of the region of the replication origin of the Bacillus subtilis chromosome

    IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames. Nucleic Acids Res. 1985 Apr 11;13(7):2267-79. PubMed PMID: 2987848; PubMed Central PMCID: PMC341154.
    Fukuoka T, Moriya S, Yoshikawa H, Ogasawara N

    Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis

    J Biochem. 1990 May;107(5):732-9. PubMed PMID: 2168872.
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