DnaN

• 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 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: BSU00020

Phenotypes of a mutant

essential PubMed

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

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:

• Interactions:
  • DnaA-YabA-DnaN PubMed
  • part of the replisome: PolC-HolA-HolB-DnaX-DnaN-DnaG-DnaC-DnaI-DnaD-SsbA-DnaE-PriA-DnaB PubMed
  • PolY1-DnaN, PolY2-DnaN (required for untargeted mutagenesis) PubMed
  • PolY1-PolA-DnaN PubMed
  • MutL (C-terminal domain)-DnaN PubMed
  • MutS-DnaN PubMed
  • DnaE-DnaN PubMed
  • DnaN forms dimers PubMed

• Localization:
  • nucleoid (mid-cell spot) PubMed PubMed
  • forms large assemblies on DNA, called "clamp zones" PubMed
  • forms foci PubMed

Database entries

• Structure:

• UniProt: P05649

• KEGG entry: [3]

• E.C. number: 2.7.7.7

Expression and regulation

• Operon: dnaA-dnaN PubMed

• Expression browser: 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:

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion: PubMed PubMed

• two-hybrid system:

• Antibody:

Labs working on this gene/protein

Philippe Noirot, Jouy-en-Josas, France homepage

References

Original publications

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)