DnaN

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  • Description: DNA polymerase III (beta subunit), beta clamp, part of the replisome, also involved in DNA mismatch repair, inhibitor of DnaA oligomerization

Gene name dnaN
Synonyms dnaG, dnaK
Essential yes PubMed
Product DNA polymerase III
(beta subunit), beta clamp
Function DNA replication, DNA repair
Gene expression levels in SubtiExpress: DnaN
Interactions involving this protein in SubtInteract: DnaN
MW, pI 41 kDa, 4.718
Gene length, protein length 1134 bp, 378 aa
Immediate neighbours dnaA, yaaA
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
DnaN expression.png















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: BSU00020

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
    • DnaN overexpression or release from the replisome decreases association of YabA with oriC, increases association of DnaA with oriC PubMed
    • Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
    • recruits MutS to the site of DNA replication (replisome) PubMed
    • required for bacteriophage SPP1 replication PubMed
    • inhibits oligomerization and helix formation of DnaA PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 376 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 2265 PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Fabian Commichau's lab
  • Antibody:

Labs working on this gene/protein

Philippe Noirot, Jouy-en-Josas, France homepage

Your additional remarks

References

Reviews

Justin S Lenhart, Jeremy W Schroeder, Brian W Walsh, Lyle A Simmons
DNA repair and genome maintenance in Bacillus subtilis.
Microbiol Mol Biol Rev: 2012, 76(3);530-64
[PubMed:22933559] [WorldCat.org] [DOI] (I p)

Tsutomu Katayama, Shogo Ozaki, Kenji Keyamura, Kazuyuki Fujimitsu
Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC.
Nat Rev Microbiol: 2010, 8(3);163-70
[PubMed:20157337] [WorldCat.org] [DOI] (I p)

Original publications

Philippe Wolff, Ismail Amal, Vincent Oliéric, Olivier Chaloin, Gudrun Gygli, Eric Ennifar, Bernard Lorber, Gilles Guichard, Jérôme Wagner, Annick Dejaegere, Dominique Y Burnouf
Differential modes of peptide binding onto replicative sliding clamps from various bacterial origins.
J Med Chem: 2014, 57(18);7565-76
[PubMed:25170813] [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)

Elena M Seco, John C Zinder, Carol M Manhart, Ambra Lo Piano, Charles S McHenry, Silvia Ayora
Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro.
Nucleic Acids Res: 2013, 41(3);1711-21
[PubMed:23268446] [WorldCat.org] [DOI] (I p)

Justin S Lenhart, Anushi Sharma, Manju M Hingorani, Lyle A Simmons
DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication.
Mol Microbiol: 2013, 87(3);553-68
[PubMed:23228104] [WorldCat.org] [DOI] (I p)

Andrew D Klocko, Jeremy W Schroeder, Brian W Walsh, Justin S Lenhart, Margery L Evans, Lyle A Simmons
Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork.
Mol Microbiol: 2011, 82(3);648-63
[PubMed:21958350] [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)

Masayuki Su'etsugu, Jeff Errington
The replicase sliding clamp dynamically accumulates behind progressing replication forks in Bacillus subtilis cells.
Mol Cell: 2011, 41(6);720-32
[PubMed:21419346] [WorldCat.org] [DOI] (I p)

Monica C Pillon, Jeffrey H Miller, Alba Guarné
The endonuclease domain of MutL interacts with the β sliding clamp.
DNA Repair (Amst): 2011, 10(1);87-93
[PubMed:21050827] [WorldCat.org] [DOI] (I p)

Nicole M Dupes, Brian W Walsh, Andrew D Klocko, Justin S Lenhart, Heather L Peterson, David A Gessert, Cassie E Pavlick, Lyle A Simmons
Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair.
J Bacteriol: 2010, 192(13);3452-63
[PubMed:20453097] [WorldCat.org] [DOI] (I p)

Peter T McKenney, Adam Driks, Haig A Eskandarian, Paul Grabowski, Jonathan Guberman, Katherine H Wang, Zemer Gitai, Patrick Eichenberger
A distance-weighted interaction map reveals a previously uncharacterized layer of the Bacillus subtilis spore coat.
Curr Biol: 2010, 20(10);934-8
[PubMed:20451384] [WorldCat.org] [DOI] (I p)

Glenn M Sanders, H Garry Dallmann, Charles S McHenry
Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases.
Mol Cell: 2010, 37(2);273-81
[PubMed:20122408] [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)

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)

Melanie B Berkmen, Alan D Grossman
Spatial and temporal organization of the Bacillus subtilis replication cycle.
Mol Microbiol: 2006, 62(1);57-71
[PubMed:16942601] [WorldCat.org] [DOI] (P p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [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)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.
Mol Microbiol: 2005, 57(3);678-90
[PubMed:16045613] [WorldCat.org] [DOI] (P p)

Stéphane Duigou, S Dusko Ehrlich, Philippe Noirot, Marie-Françoise Noirot-Gros
Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis.
Mol Microbiol: 2004, 54(2);439-51
[PubMed:15469515] [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)

Y Ogura, Y Imai, N Ogasawara, S Moriya
Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis.
J Bacteriol: 2001, 183(13);3833-41
[PubMed:11395445] [WorldCat.org] [DOI] (P p)

K P Lemon, A D Grossman
Localization of bacterial DNA polymerase: evidence for a factory model of replication.
Science: 1998, 282(5393);1516-9
[PubMed:9822387] [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)

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