dnaN

dnaN
168

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

Locus
BSU_00020
Molecular weight
41.94 kDa
Isoelectric point
4.72
Protein length
378 aaSequenceBlast
Gene length
1137 bpSequenceBlast
Function
DNA replication, DNA repair
Product
DNA polymerase  III (beta subunit), beta clamp
Essential
yes
E.C.
2.7.7.7
Synonyms
dnaN, dnaG
Outlinks
BsubCyc SubtiList UniProt STRING Genoscapist PaperBLAST

Genomic Context

List of homologs in different organisms, belongs to COG0592 (Galperin et al., 2021)

This gene is a member of the following regulons

SigA regulon, Spo0A regulon

Gene
Coordinates
1,939  3,075
Phenotypes of a mutant
essential PubMed
The protein
Catalyzed reaction/ biological activity
DnaN overexpression or release from the replisome decreases association of YabA with oriC, increases association of DnaA with oriC PubMed
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
Beta sliding clamp family (single member, according to UniProt)
Structure
4TR6 (PDB) PubMed
6E8D (PDB) (complex with MutL) PubMed
P05649 (AlphaFold)
Localization
nucleoid (mid-cell spot) PubMed PubMed
forms large assemblies on DNA, called clamp zones PubMed
forms foci PubMed
Expression and Regulation
Operons
Genes
dnaA-dnaN
Description
PubMed
Regulation
negatively controlled by DnaA PubMed and Spo0A PubMed
Regulatory mechanism
Spo0A: repression, PubMed, in spo0A regulon
Sigma factors
SigA: sigma factor, PubMed, in sigA regulon
Additional information
term-seq has identified a potential novel regulatory RNA element including an intrinsic transcription terminator upstream of dnaA PubMed
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dnaA→dnaN

2025-04-04 23:37:11

Christoph.elfmann

186

FC7A5B55195EC7707116A1123DA93544D5A1F065

81C2E69BE3D31EEDD50657B28531619FA62B93FD

Biological materials
Two-hybrid system
B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Fabian Commichau's lab
GFP fusion
PubMed  PubMed
References
Reviews
Jameson KH, Wilkinson AJ Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli. Genes. 2017 Jan 10; 8(1). pii:E22. doi:10.3390/genes8010022. PMID:28075389
Lenhart JS, Pillon MC, Guarné A, Biteen JS, Simmons LA Mismatch repair in Gram-positive bacteria. Research in microbiology. 2016 Jan; 167(1):4-12. doi:10.1016/j.resmic.2015.08.006. pii:S0923-2508(15)00146-1. PMID:26343983
Lenhart JS, Schroeder JW, Walsh BW, Simmons LA DNA repair and genome maintenance in Bacillus subtilis. Microbiology and molecular biology reviews : MMBR. 2012 Sep; 76(3):530-64. doi:10.1128/MMBR.05020-11. PMID:22933559
Katayama T, Ozaki S, Keyamura K, Fujimitsu K Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nature reviews. Microbiology. 2010 Mar; 8(3):163-70. doi:10.1038/nrmicro2314. PMID:20157337
Original Publications
O'Reilly FJ, Graziadei A, Forbrig C, Bremenkamp R, Charles K, Lenz S, Elfmann C, Fischer L, Stülke J, Rappsilber JProtein complexes in cells by AI-assisted structural proteomics.Molecular systems biology. 2023 Feb 23; :e11544. PMID: 36815589
Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic acids research. 2019 Mar 27; . pii:gkz115. doi:10.1093/nar/gkz115. PMID:30916336
Liu L, Ortiz Castro MC, Rodríguez González J, Pillon MC, Guarné A The endonuclease domain of Bacillus subtilis MutL is functionally asymmetric. DNA repair. 2018 Oct 24; . pii:S1568-7864(18)30146-0. doi:10.1016/j.dnarep.2018.10.003. PMID:30391220
Paschalis V, Le Chatelier E, Green M, Képès F, Soultanas P, Janniere L Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity. Open biology. 2017 Sep; 7(9). pii:170146. doi:10.1098/rsob.170146. PMID:28878042
Fukui K, Baba S, Kumasaka T, Yano T Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL. The Journal of biological chemistry. 2016 Aug 12; 291(33):16990-7000. doi:10.1074/jbc.M116.739664. PMID:27369079
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 research. 2016 Jan 08; 44(1):449-63. doi:10.1093/nar/gkv1318. PMID:26615189
Pillon MC, Babu VM, Randall JR, Cai J, Simmons LA, Sutton MD, Guarné A The sliding clamp tethers the endonuclease domain of MutL to DNA. Nucleic acids research. 2015 Dec 15; 43(22):10746-59. doi:10.1093/nar/gkv918. PMID:26384423
Wolff P, Amal I, Oliéric V, Chaloin O, Gygli G, Ennifar E, Lorber B, Guichard G, Wagner J, Dejaegere A, Burnouf DY Differential modes of peptide binding onto replicative sliding clamps from various bacterial origins. Journal of medicinal chemistry. 2014 Sep 25; 57(18):7565-76. doi:10.1021/jm500467a. PMID:25170813
Wolff P, Amal I, Oliéric V, Chaloin O, Gygli G, Ennifar E, Lorber B, Guichard G, Wagner J, Dejaegere A, Burnouf DY Differential modes of peptide binding onto replicative sliding clamps from various bacterial origins. Journal of medicinal chemistry. 2014 Sep 25; 57(18):7565-76. doi:10.1021/jm500467a. PMID:25170813
Scholefield G, Murray H YabA and DnaD inhibit helix assembly of the DNA replication initiation protein DnaA. Molecular microbiology. 2013 Oct; 90(1):147-59. doi:10.1111/mmi.12353. PMID:23909787
Seco EM, Zinder JC, Manhart CM, Lo Piano A, McHenry CS, Ayora S Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro. Nucleic acids research. 2013 Feb 01; 41(3):1711-21. doi:10.1093/nar/gks1290. PMID:23268446
Lenhart JS, Sharma A, Hingorani MM, Simmons LA DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication. Molecular microbiology. 2013 Feb; 87(3):553-68. doi:10.1111/mmi.12115. PMID:23228104
Klocko AD, Schroeder JW, Walsh BW, Lenhart JS, Evans ML, Simmons LA Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Molecular microbiology. 2011 Nov; 82(3):648-63. doi:10.1111/j.1365-2958.2011.07841.x. PMID:21958350
Merrikh H, Grossman AD Control of the replication initiator DnaA by an anti-cooperativity factor. Molecular microbiology. 2011 Oct; 82(2):434-46. doi:10.1111/j.1365-2958.2011.07821.x. PMID:21895792
Su'etsugu M, Errington J The replicase sliding clamp dynamically accumulates behind progressing replication forks in Bacillus subtilis cells. Molecular cell. 2011 Mar 18; 41(6):720-32. doi:10.1016/j.molcel.2011.02.024. PMID:21419346
Pillon MC, Miller JH, Guarné A The endonuclease domain of MutL interacts with the β sliding clamp. DNA repair. 2011 Jan 02; 10(1):87-93. doi:10.1016/j.dnarep.2010.10.003. PMID:21050827
Dupes NM, Walsh BW, Klocko AD, Lenhart JS, Peterson HL, Gessert DA, Pavlick CE, Simmons LA Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. Journal of bacteriology. 2010 Jul; 192(13):3452-63. doi:10.1128/JB.01435-09. PMID:20453097
McKenney PT, Driks A, Eskandarian HA, Grabowski P, Guberman J, Wang KH, Gitai Z, Eichenberger P A distance-weighted interaction map reveals a previously uncharacterized layer of the Bacillus subtilis spore coat. Current biology : CB. 2010 May 25; 20(10):934-8. doi:10.1016/j.cub.2010.03.060. PMID:20451384
Sanders GM, Dallmann HG, McHenry CS Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases. Molecular cell. 2010 Jan 29; 37(2):273-81. doi:10.1016/j.molcel.2009.12.025. PMID:20122408
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. Molecular microbiology. 2009 Oct; 74(2):454-66. doi:10.1111/j.1365-2958.2009.06876.x. PMID:19737352
Soufo CD, Soufo HJ, Noirot-Gros MF, Steindorf A, Noirot P, Graumann PL Cell-cycle-dependent spatial sequestration of the DnaA replication initiator protein in Bacillus subtilis. Developmental cell. 2008 Dec; 15(6):935-41. doi:10.1016/j.devcel.2008.09.010. PMID:19081080
Berkmen MB, Grossman AD Spatial and temporal organization of the Bacillus subtilis replication cycle. Molecular microbiology. 2006 Oct; 62(1):57-71. . PMID:16942601
Meile JC, Wu LJ, Ehrlich SD, Errington J, Noirot P Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory. Proteomics. 2006 Apr; 6(7):2135-46. . PMID:16479537
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. Proceedings of the National Academy of Sciences of the United States of America. 2006 Feb 14; 103(7):2368-73. . PMID:16461910
Duigou S, Ehrlich SD, Noirot P, Noirot-Gros MF DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis. Molecular microbiology. 2005 Aug; 57(3):678-90. . PMID:16045613
Duigou S, Ehrlich SD, Noirot P, Noirot-Gros MF Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis. Molecular microbiology. 2004 Oct; 54(2):439-51. . PMID:15469515
Molle V, Fujita M, Jensen ST, Eichenberger P, González-Pastor JE, Liu JS, Losick R The Spo0A regulon of Bacillus subtilis. Molecular microbiology. 2003 Dec; 50(5):1683-701. . PMID:14651647
Molle V, Fujita M, Jensen ST, Eichenberger P, González-Pastor JE, Liu JS, Losick R The Spo0A regulon of Bacillus subtilis. Molecular microbiology. 2003 Dec; 50(5):1683-701. . PMID:14651647
Noirot-Gros MF, Dervyn E, Wu LJ, Mervelet P, Errington J, Ehrlich SD, Noirot P An expanded view of bacterial DNA replication. Proceedings of the National Academy of Sciences of the United States of America. 2002 Jun 11; 99(12):8342-7. . PMID:12060778
Ogura Y, Imai Y, Ogasawara N, Moriya S Autoregulation of the dnaA-dnaN operon and effects of DnaA protein levels on replication initiation in Bacillus subtilis. Journal of bacteriology. 2001 Jul; 183(13):3833-41. . PMID:11395445
Lemon KP, Grossman AD Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science (New York, N.Y.). 1998 Nov 20; 282(5393):1516-9. . PMID:9822387
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 research. 1985 Apr 11; 13(7):2267-79. . PMID:2987848
Fukuoka T, Moriya S, Yoshikawa H, Ogasawara N Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. Journal of biochemistry. 1990 May; 107(5):732-9. . PMID:2168872
Labs working on this gene/protein
Philippe Noirot, Jouy-en-Josas, France homepage

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Time of last update: 2025-04-06 15:51:19

Author of last update: Jstuelk