DnaA

• Description: AAA+ ATPase, replication initiation protein
  
  

Gene name	dnaA
Synonyms	dnaH, dnaJ, dnaK
Essential	yes PubMed
Product	replication initiation protein
Function	DNA replication
Gene expression levels in SubtiExpress: dnaA
Interactions involving this protein in SubtInteract: DnaA
MW, pI	50 kDa, 6.035
Gene length, protein length	1338 bp, 446 aa
Immediate neighbours	rpmH, dnaN
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

Spo0A regulon

The gene

Basic information

• Locus tag: BSU00010

Phenotypes of a mutant

essential PubMed

Database entries

• BsubCyc: BSU00010

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• 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):

Extended information on the protein

• Kinetic information:

• Domains: AAA+ domain

• Modification:

• Cofactor(s):

• 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

• Interactions:
  • DnaA assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains PubMed
  • Soj-DnaA PubMed
  • DnaA-YabA PubMed
  • DnaA-YabA-DnaN PubMed
  • DnaA-DnaD PubMed
  • SirA-DnaA (N-terminal domain) PubMed
  • YqaH-DnaA PubMed
  • part of the primosome: DnaA-DnaG-DnaC-DnaI-DnaD-DnaB PubMed

• Localization:
  • throughout the cytoplasm PubMed

Database entries

• BsubCyc: BSU00010

• Structure:

• UniProt: P05648

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon: dnaA-dnaN PubMed

• Expression browser: dnaA 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:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 234 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 1252 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

Labs working on this gene/protein

• Philippe Noirot, Jouy-en-Josas, France homepage
• Peter Graumann, Freiburg University, Germany homepage
• Alan Grossman, MIT, Cambridge, MA, USA
• Heath Murray, Centre for Bacterial Cell Biology, Newcastle, UK homepage

References

Original publications

Janet L Smith, Alan D Grossman
In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.
PLoS Genet: 2015, 11(5);e1005258
[PubMed:26020636] [WorldCat.org] [DOI] (I e)

Heath Murray, Alan Koh
Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis.
PLoS Genet: 2014, 10(10);e1004731
[PubMed:25340815] [WorldCat.org] [DOI] (I e)

Katie H Jameson, Nadia Rostami, Mark J Fogg, Johan P Turkenburg, Anne Grahl, Heath Murray, Anthony J Wilkinson
Structure and interactions of the Bacillus subtilis sporulation inhibitor of DNA replication, SirA, with domain I of DnaA.
Mol Microbiol: 2014, 93(5);975-91
[PubMed:25041308] [WorldCat.org] [DOI] (I p)

Graham Scholefield, Heath Murray
YabA and DnaD inhibit helix assembly of the DNA replication initiation protein DnaA.
Mol Microbiol: 2013, 90(1);147-59
[PubMed:23909787] [WorldCat.org] [DOI] (I p)

Carla Y Bonilla, Alan D Grossman
The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis.
J Bacteriol: 2012, 194(18);5110-7
[PubMed:22821970] [WorldCat.org] [DOI] (I p)

Norbert S Hill, Ryosuke Kadoya, Dhruba K Chattoraj, Petra Anne Levin
Cell size and the initiation of DNA replication in bacteria.
PLoS Genet: 2012, 8(3);e1002549
[PubMed:22396664] [WorldCat.org] [DOI] (I p)

Graham Scholefield, Jeff Errington, Heath Murray
Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA.
EMBO J: 2012, 31(6);1542-55
[PubMed:22286949] [WorldCat.org] [DOI] (I p)

Hajime Okumura, Mika Yoshimura, Mikako Ueki, Taku Oshima, Naotake Ogasawara, Shu Ishikawa
Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis.
Nucleic Acids Res: 2012, 40(1);220-34
[PubMed:21911367] [WorldCat.org] [DOI] (I p)

Houra Merrikh, Alan D Grossman
Control of the replication initiator DnaA by an anti-cooperativity factor.
Mol Microbiol: 2011, 82(2);434-46
[PubMed:21895792] [WorldCat.org] [DOI] (I p)

Lilah Rahn-Lee, Houra Merrikh, Alan D Grossman, Richard Losick
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, 193(6);1302-7
[PubMed:21239581] [WorldCat.org] [DOI] (I p)

Wiep Klaas Smits, Houra Merrikh, Carla Yaneth Bonilla, Alan D Grossman
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis.
J Bacteriol: 2011, 193(3);640-8
[PubMed:21097613] [WorldCat.org] [DOI] (I p)

Sharon E Hoover, Weihong Xu, Wenzhong Xiao, William F Burkholder
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, 192(15);3915-24
[PubMed:20511500] [WorldCat.org] [DOI] (I p)

Wiep Klaas Smits, Alexi I Goranov, Alan D Grossman
Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo.
Mol Microbiol: 2010, 75(2);452-61
[PubMed:19968790] [WorldCat.org] [DOI] (I p)

Alexi I Goranov, Adam M Breier, Houra Merrikh, Alan D Grossman
YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress.
Mol Microbiol: 2009, 74(2);454-66
[PubMed:19737352] [WorldCat.org] [DOI] (I p)

Jennifer K Wagner, Kathleen A Marquis, David Z Rudner
SirA enforces diploidy by inhibiting the replication initiator DnaA during spore formation in Bacillus subtilis.
Mol Microbiol: 2009, 73(5);963-74
[PubMed:19682252] [WorldCat.org] [DOI] (I p)

Clarisse Defeu Soufo, Hervé Joël Defeu Soufo, Marie-Françoise Noirot-Gros, Astrid Steindorf, Philippe Noirot, Peter L Graumann
Cell-cycle-dependent spatial sequestration of the DnaA replication initiator protein in Bacillus subtilis.
Dev Cell: 2008, 15(6);935-41
[PubMed:19081080] [WorldCat.org] [DOI] (I p)

Adam M Breier, Alan D Grossman
Dynamic association of the replication initiator and transcription factor DnaA with the Bacillus subtilis chromosome during replication stress.
J Bacteriol: 2009, 191(2);486-93
[PubMed:19011033] [WorldCat.org] [DOI] (I p)

Heath Murray, Jeff Errington
Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA.
Cell: 2008, 135(1);74-84
[PubMed:18854156] [WorldCat.org] [DOI] (I p)

Shu Ishikawa, Yoshitoshi Ogura, Mika Yoshimura, Hajime Okumura, Eunha Cho, Yoshikazu Kawai, Ken Kurokawa, Taku Oshima, Naotake Ogasawara
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.
DNA Res: 2007, 14(4);155-68
[PubMed:17932079] [WorldCat.org] [DOI] (P p)

Melanie B Berkmen, Alan D Grossman
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, 63(1);150-65
[PubMed:17140409] [WorldCat.org] [DOI] (P p)

Marie-Françoise Noirot-Gros, M Velten, M Yoshimura, S McGovern, T Morimoto, S D Ehrlich, N Ogasawara, P Polard, Philippe Noirot
Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2006, 103(7);2368-73
[PubMed:16461910] [WorldCat.org] [DOI] (P p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P p)

Marie-Françoise Noirot-Gros, Etienne Dervyn, Ling Juan Wu, Peggy Mervelet, Jeffery Errington, S Dusko Ehrlich, Philippe Noirot
An expanded view of bacterial DNA replication.
Proc Natl Acad Sci U S A: 2002, 99(12);8342-7
[PubMed:12060778] [WorldCat.org] [DOI] (P p)

D Ishigo-Oka, N Ogasawara, S Moriya
DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication.
J Bacteriol: 2001, 183(6);2148-50
[PubMed:11222620] [WorldCat.org] [DOI] (P p)

W F Burkholder, I Kurtser, A D Grossman
Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis.
Cell: 2001, 104(2);269-79
[PubMed:11207367] [WorldCat.org] [DOI] (P p)

Y Imai, N Ogasawara, D Ishigo-Oka, R Kadoya, T Daito, S Moriya
Subcellular localization of Dna-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids.
Mol Microbiol: 2000, 36(5);1037-48
[PubMed:10844689] [WorldCat.org] [DOI] (P p)

T Fukuoka, S Moriya, H Yoshikawa, N Ogasawara
Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis.
J Biochem: 1990, 107(5);732-9
[PubMed:2168872] [WorldCat.org] [DOI] (P p)

N Ogasawara, S Moriya, H Yoshikawa
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, 13(7);2267-79
[PubMed:2987848] [WorldCat.org] [DOI] (P p)