Genomes and Genes
Gene Symbol: dnaN
Description: DNA polymerase III, beta subunit
Alias: ECK3693, JW3678
Species: Escherichia coli str. K-12 substr. MG1655
- Lopez de Saro F, O Donnell M. Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I. Proc Natl Acad Sci U S A. 2001;98:8376-80 pubmed
- Indiani C, McInerney P, Georgescu R, Goodman M, O Donnell M. A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol Cell. 2005;19:805-15 pubmed..These polymerase dynamics within the beta toolbelt complex restrict the action of the error-prone Pol IV to only the area on DNA where it is required. ..
- Sutton M, Walker G. Managing DNA polymerases: coordinating DNA replication, DNA repair, and DNA recombination. Proc Natl Acad Sci U S A. 2001;98:8342-9 pubmed..In particular, we discuss these issues in the context of the Gram-negative bacterium, Escherichia coli, that contains a DNA polymerase (Pol V) known to participate in most, if not all, of these processes. ..
- Heltzel J, Maul R, Scouten Ponticelli S, Sutton M. A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp. Proc Natl Acad Sci U S A. 2009;106:12664-9 pubmed publisher..Taken together, our findings challenge the toolbelt model and suggest instead that Pol IV contacts the rim of the clamp adjacent to the cleft that is bound by Pol III* before gaining control of the same cleft that is bound by Pol III*. ..
- Kelman Z, O Donnell M. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem. 1995;64:171-200 pubmed..This review summarizes our present knowledge about the function of the 10 subunits of this replicating machine and how they coordinate their actions for smooth duplication of chromosomes. ..
- Oakley A, Prosselkov P, Wijffels G, Beck J, Wilce M, Dixon N. Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III. Acta Crystallogr D Biol Crystallogr. 2003;59:1192-9 pubmed..This suggests that these residues are likely to be relatively mobile in solution. Some implications of this flexibility for the function of beta are discussed...
- Jeruzalmi D, Yurieva O, Zhao Y, Young M, Stewart J, Hingorani M, et al. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell. 2001;106:417-28 pubmed..Structural comparisons and molecular dynamics simulations suggest a spring-loaded mechanism in which the beta ring opens spontaneously once a dimer interface is perturbed by the delta wrench. ..
- López de Saro F, Marinus M, Modrich P, O Donnell M. The beta sliding clamp binds to multiple sites within MutL and MutS. J Biol Chem. 2006;281:14340-9 pubmed..In light of these results, we propose roles for the beta clamp in orchestrating the sequence of events that lead to mismatch repair in the cell. ..
- Georgescu R, Yurieva O, Kim S, Kuriyan J, Kong X, O Donnell M. Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc Natl Acad Sci U S A. 2008;105:11116-21 pubmed publisher..The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target. ..
- Leu F, Hingorani M, Turner J, O Donnell M. The delta subunit of DNA polymerase III holoenzyme serves as a sliding clamp unloader in Escherichia coli. J Biol Chem. 2000;275:34609-18 pubmed..Since pol III* and gamma complex occur in much lower quantities and perform several DNA metabolic functions in replication and repair, the delta subunit probably aids beta clamp recycling during DNA replication. ..
- Yao N, Leu F, Anjelkovic J, Turner J, O Donnell M. DNA structure requirements for the Escherichia coli gamma complex clamp loader and DNA polymerase III holoenzyme. J Biol Chem. 2000;275:11440-50 pubmed..The possible biological significance of these structural constraints is discussed. ..
- Furukohri A, Goodman M, Maki H. A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp. J Biol Chem. 2008;283:11260-9 pubmed publisher..Our study suggests a model in which the interaction between pol III* and the beta clamp is mediated by pol IV to ensure that DNA replication proceeds with minimal interruption. ..
- Jeruzalmi D, O Donnell M, Kuriyan J. Clamp loaders and sliding clamps. Curr Opin Struct Biol. 2002;12:217-24 pubmed..Crystallographic and electron microscopic views of clamp loaders from bacteria, archaebacteria and eukaryotes emphasize their common architecture and have produced models of how ATPbinding might be coupled to clamp opening/loading. ..
- Cooper D, Lahue R, Modrich P. Methyl-directed mismatch repair is bidirectional. J Biol Chem. 1993;268:11823-9 pubmed..To our knowledge, these experiments represent the first instance in which exonuclease I, exonuclease VII, and RecJ have been implicated in a particular DNA metabolic pathway. ..
- Naktinis V, Onrust R, Fang L, O Donnell M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J Biol Chem. 1995;270:13358-65 pubmed..The implication of these key features to the clamp loading mechanism of the gamma complex is discussed. ..
- Burgers P, Kornberg A, Sakakibara Y. The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli. Proc Natl Acad Sci U S A. 1981;78:5391-5 pubmedAn Escherichia coli mutant, dnaN59, stops DNA synthesis promptly upon a shift to a high temperature; the wild-type dnaN gene carried in a transducing phage encodes a polypeptide of about 41,000 daltons [Sakakibara, Y. & Mizukami, T...
- Georgescu R, Kim S, Yurieva O, Kuriyan J, Kong X, O Donnell M. Structure of a sliding clamp on DNA. Cell. 2008;132:43-54 pubmed publisher..The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other. ..
- McInerney P, Johnson A, Katz F, O Donnell M. Characterization of a triple DNA polymerase replisome. Mol Cell. 2007;27:527-38 pubmed..We propose that two polymerases can function on the lagging strand and that the third DNA polymerase can act as a reserve enzyme to overcome certain types of obstacles to the replication fork. ..
- Dalrymple B, Kongsuwan K, Wijffels G, Dixon N, Jennings P. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci U S A. 2001;98:11627-32 pubmed..Comparison of the eubacterial, eukaryotic, and archaeal sliding clamp binding motifs suggests that the basic interactions have been conserved across the evolutionary landscape. ..
- Duzen J, Walker G, Sutton M. Identification of specific amino acid residues in the E. coli beta processivity clamp involved in interactions with DNA polymerase III, UmuD and UmuD'. DNA Repair (Amst). 2004;3:301-12 pubmed..coli might coordinate the actions of the umuDC gene products with those of pol III, as well as for how organisms in general might manage the actions of their multiple DNA polymerases. ..
- Sutton M, Duzen J, Maul R. Mutant forms of the Escherichia colibeta sliding clamp that distinguish between its roles in replication and DNA polymerase V-dependent translesion DNA synthesis. Mol Microbiol. 2005;55:1751-66 pubmed..Taken together, these findings indicate that: (i) the beta clamp plays an essential role in pol V-dependent TLS in vivo and (ii) pol III and pol V interact with non-identical surfaces of the beta clamp. ..
- Stukenberg P, Studwell Vaughan P, O Donnell M. Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme. J Biol Chem. 1991;266:11328-34 pubmed..Hence, the high processivity of the holoenzyme is rooted in a "sliding clamp" of beta on DNA that tethers the polymerase to the primed template. Implications for transcription and translation are discussed. ..
- Williams C, Snyder A, Kuzmic P, O Donnell M, Bloom L. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the gamma complex. J Biol Chem. 2004;279:4376-85 pubmed..These results suggest that hydrolysis of 2 molecules of ATP may be coupled to conformational changes that reduce interactions with DNA, whereas hydrolysis of the 3rd is coupled to changes that result in release of beta. ..
- Simonetta K, Kazmirski S, Goedken E, Cantor A, Kelch B, McNally R, et al. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell. 2009;137:659-71 pubmed publisher..By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex. ..
- Maul R, Sanders L, Lim J, Benitez R, Sutton M. Role of Escherichia coli DNA polymerase I in conferring viability upon the dnaN159 mutant strain. J Bacteriol. 2007;189:4688-95 pubmed
- Su etsugu M, Kawakami H, Kurokawa K, Kubota T, Takata M, Katayama T. DNA replication-coupled inactivation of DnaA protein in vitro: a role for DnaA arginine-334 of the AAA+ Box VIII motif in ATP hydrolysis. Mol Microbiol. 2001;40:376-86 pubmed..This residue is highly conserved among DnaA homologues and also in the Box VIII motif of the AAA+ protein family. ..
- Reems J, McHenry C. Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer. J Biol Chem. 1994;269:33091-6 pubmed..The addition of core DNA polymerase III to preintiation complexes restored the 30-nucleotide footprint observed with intact holoenzyme. These results suggest that holoenzyme subunits rearrange during initiation complex formation. ..
- Onogi T, Ohsumi K, Katayama T, Hiraga S. Replication-dependent recruitment of the beta-subunit of DNA polymerase III from cytosolic spaces to replication forks in Escherichia coli. J Bacteriol. 2002;184:867-70 pubmed..When chromosome replication is terminated after incubation at nonpermissive temperature in a temperature-sensitive dnaC mutant, the beta-subunit is located in the cytosolic spaces of the cell poles. ..
- Georgescu R, Kurth I, Yao N, Stewart J, Yurieva O, O Donnell M. Mechanism of polymerase collision release from sliding clamps on the lagging strand. EMBO J. 2009;28:2981-91 pubmed publisher..The tau subunit acts as a switch to enhance polymerase binding at a primed site but not at a nick. The OB domain acts as a sensor that regulates the affinity of Pol III to the clamp in the presence of ssDNA. ..
- O Donnell M, Jeruzalmi D, Kuriyan J. Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curr Biol. 2001;11:R935-46 pubmed..coli beta sliding clamp. We also expand upon the implications of the structural findings to the structure and function of the eukaryotic clamp loader, RFC, and the structure of E. coli DNA polymerase III holoenzyme. ..
- Ortenberg R, Gon S, Porat A, Beckwith J. Interactions of glutaredoxins, ribonucleotide reductase, and components of the DNA replication system of Escherichia coli. Proc Natl Acad Sci U S A. 2004;101:7439-44 pubmed..the growth defects of the multiply mutant strain was by mutations in the DNA replication genes, dnaA and dnaN. These mutations substantially increase the expression of ribonucleotide reductase, most likely by altering the ..
- Fuchs R, Fujii S. Translesion synthesis in Escherichia coli: lessons from the NarI mutation hot spot. DNA Repair (Amst). 2007;6:1032-41 pubmed..The beta-clamp, to which all DNA polymerases bind, plays a critical role in allowing the specialized DNA polymerases to synthesize TLS patches that are long enough to resist such "external proofreading" activities. ..
- COHEN FIX O, Livneh Z. In vitro UV mutagenesis associated with nucleotide excision-repair gaps in Escherichia coli. J Biol Chem. 1994;269:4953-8 pubmed..Thus, the processivity subunit of the holoenzyme is not required for type II UV mutagenesis, in agreement with a mechanism involving filling-in of short single-stranded DNA gaps. ..
- Ohmori H, Kimura M, Nagata T, Sakakibara Y. Structural analysis of the dnaA and dnaN genes of Escherichia coli. Gene. 1984;28:159-70 pubmedThe nucleotide sequence of the entire region containing the Escherichia coli dnaA and dnaN genes was determined. Base substitutions by such mutations as dnaA46, dnaA167, dnaN59, and dnaN806 were also identified...
- Tomer G, COHEN FIX O, O Donnell M, Goodman M, Livneh Z. Reconstitution of repair-gap UV mutagenesis with purified proteins from Escherichia coli: a role for DNA polymerases III and II. Proc Natl Acad Sci U S A. 1996;93:1376-80 pubmed..These observations suggest that repair-gap UV mutagenesis is performed by DNA polymerase III, and to a lesser extent by DNA polymerase II, by filling-in of a rare class of excision gaps that contain UV lesions. ..
- Sutton M, Duzen J. Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli. DNA Repair (Amst). 2006;5:312-23 pubmed..In light of this finding, we designed two additional dnaN alleles...
- Flores M, Bidnenko V, Michel B. The DNA repair helicase UvrD is essential for replication fork reversal in replication mutants. EMBO Rep. 2004;5:983-8 pubmed..coli polymerase III mutants, whereas its partners in DNA repair (UvrA/B and MutL/S) are not. We conclude that UvrD participates in replication fork reversal in E. coli. ..
- Borloo J, De Smet L, Vergauwen B, Van Beeumen J, Devreese B. A beta-galactosidase-based bacterial two-hybrid system to assess protein-protein interactions in the correct cellular environment. J Proteome Res. 2007;6:2587-95 pubmed..These benefits demonstrate the relevance of the method as a powerful new tool in the broad spectrum of interaction assessment methods. ..
- Griep M, McHenry C. The dimer of the beta subunit of Escherichia coli DNA polymerase III holoenzyme is dissociated into monomers upon binding magnesium(II). Biochemistry. 1988;27:5210-5 pubmed..These and other results suggested that the fluorescence increase which accompanies beta dissociation is due to a relief from homoquenching of FM when the beta dimer dissociates into monomers. ..
- Parks A, Li Z, Shi Q, Owens R, Jin M, Peters J. Transposition into replicating DNA occurs through interaction with the processivity factor. Cell. 2009;138:685-95 pubmed publisher..The TnsE interaction with an essential and conserved component of the replication machinery, and a DNA structure reveals a mechanism by which Tn7, and probably other elements, selects target sites associated with DNA replication. ..
- Sako T, Sakakibara Y. Coordinate expression of Escherichia coli dnaA and dnaN genes. Mol Gen Genet. 1980;179:521-6 pubmedThe defects of temperature-sensitive dnaA and dnaN mutants of Escherichia coli are complemented by a recombinant lambda phage, which carries the bacterial DNA segment composed of two EcoRI segments of 1.0 and 3.3 kilobases...
- Onrust R, Finkelstein J, Turner J, Naktinis V, O Donnell M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. III. Interface between two polymerases and the clamp loader. J Biol Chem. 1995;270:13366-77 pubmed..The single copy nature of the delta, delta', chi, and psi subunits confers a structural asymmetry with respect to the two polymerases, presumably for the different functions of replicating the leading and lagging strands. ..
- Saveson C, Lovett S. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics. 1997;146:457-70 pubmed..deletion formation: the alpha polymerase (dnal;), the gamma clamp loader complex (holC, dnaX), and the beta clamp (dnaN) subunits of Pol III and the primosomal proteins, dnaC and priA...
- Villarroya M, Perez Roger I, Macian F, Armengod M. Stationary phase induction of dnaN and recF, two genes of Escherichia coli involved in DNA replication and repair. EMBO J. 1998;17:1829-37 pubmed..The gene encoding beta, dnaN, maps between dnaA and recF, which are involved in initiation of DNA replication at oriC and resumption of DNA ..
- Anderson S, Thompson J, Paschall C, O Donnell M, Bloom L. Temporal correlation of DNA binding, ATP hydrolysis, and clamp release in the clamp loading reaction catalyzed by the Escherichia coli gamma complex. Biochemistry. 2009;48:8516-27 pubmed publisher..Clamp release is relatively slow and likely to be the rate-limiting step in the overall clamp loading reaction cycle. ..
- Kongsuwan K, Dalrymple B, Wijffels G, Jennings P. Cellular localisation of the clamp protein during DNA replication. FEMS Microbiol Lett. 2002;216:255-62 pubmed
- O Donnell M. Replisome architecture and dynamics in Escherichia coli. J Biol Chem. 2006;281:10653-6 pubmed
- Maul R, Sutton M. Roles of the Escherichia coli RecA protein and the global SOS response in effecting DNA polymerase selection in vivo. J Bacteriol. 2005;187:7607-18 pubmed
- Quillardet P, Rouffaud M, Bouige P. DNA array analysis of gene expression in response to UV irradiation in Escherichia coli. Res Microbiol. 2003;154:559-72 pubmed..One gene, dnaN, encoding the beta subunit of DNA polymerase III holoenzyme, was identified as an upregulated gene in a LexA-..
- Livneh Z. Mechanism of replication of ultraviolet-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli. Implications for SOS mutagenesis. J Biol Chem. 1986;261:9526-33 pubmed..Based on these observations a model for SOS-induced UV mutagenesis is proposed. ..
- Ream L, Clark A. Cloning and deletion mapping of the recF dnaN region of the Escherichia coli chromosome. Plasmid. 1983;10:101-10 pubmed..6-kb EcoRI fragment of the Escherichia coli chromosome with pBR322 we located more precisely recF relative to dnaN. By deletion mapping we localized functional recF to a 1...
- Tadmor Y, Bergstein M, Skaliter R, Shwartz H, Livneh Z. Beta subunit of DNA polymerase III holoenzyme is induced upon ultraviolet irradiation or nalidixic acid treatment of Escherichia coli. Mutat Res. 1994;308:53-64 pubmed..Mapping of transcription initiation sites of the dnaN gene, encoding the beta subunit, using the S1 nuclease protection assay showed essentially no induction of ..
- Zechner E, Wu C, Marians K. Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size. J Biol Chem. 1992;267:4054-63 pubmed
- Armengod M, Lambíes E. Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences. Gene. 1986;43:183-96 pubmed..start codon of the recF structural gene and resides entirely within the translated region of the preceding gene, dnaN, which encodes for the beta subunit of DNA polymerase III...
- Adachi T, Mizuuchi K, Menzel R, Gellert M. DNA sequence and transcription of the region upstream of the E. coli gyrB gene. Nucleic Acids Res. 1984;12:6389-95 pubmedWe have determined the sequence of a 1498 base-pair region in E. coli that extends from within dnaN through recF and into the gyrB gene. An open reading frame of 1071 base pairs has been identified with the recF structural gene...
- Pomerantz R, O Donnell M. Replisome mechanics: insights into a twin DNA polymerase machine. Trends Microbiol. 2007;15:156-64 pubmed..These studies demonstrate close similarities between the bacterial and eukaryotic replication machineries. ..
- Macian F, Perez Roger I, Armengod M. An improved vector system for constructing transcriptional lacZ fusions: analysis of regulation of the dnaA, dnaN, recF and gyrB genes of Escherichia coli. Gene. 1994;145:17-24 pubmed..We use this system to compare the transcriptional activities of the promoters present in the dnaA-dnaN-recF-gyrB cluster. The order of strength of these promoters is gyrB > dnaA > recF > dnaN...
- Sutton M, Narumi I, Walker G. Posttranslational modification of the umuD-encoded subunit of Escherichia coli DNA polymerase V regulates its interactions with the beta processivity clamp. Proc Natl Acad Sci U S A. 2002;99:5307-12 pubmed..Implications of these structure-function analyses for the checkpoint and translesion DNA synthesis functions of the umuDC gene products are discussed. ..
- Hansen E, Hansen F, von Meyenburg K. The nucleotide sequence of the dnaA gene and the first part of the dnaN gene of Escherichia coli K-12. Nucleic Acids Res. 1982;10:7373-85 pubmedThe nucleotide sequence of the dnaA gene and the first 10% of the dnaN gene was determined. From the nucleotide sequence the amino acid sequence of the dnaA gene product was derived...
- ..In this issue, Parks et al. (2009) find that the beta clamp interacts with the transposition protein TnsE to target the Tn7 transposon to discontinuously replicating DNA at the replication fork. ..
- Motamedi M, Szigety S, Rosenberg S. Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes Dev. 1999;13:2889-903 pubmed..coli; the other half occurs by breakage and reunion, which we show requires resolvases, and is replication-independent. The data also indicate that accumulation of recombination intermediates promotes replication dramatically. ..
- Wagner J, Fujii S, Gruz P, Nohmi T, Fuchs R. The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity. EMBO Rep. 2000;1:484-8 pubmed..In vivo, the beta processivity subunit may target DNA Pol IV to its substrate, generating synthesis tracks much longer than previously thought. ..
- Perez Roger I, García Sogo M, Navarro Avino J, López Acedo C, Macian F, Armengod M. Positive and negative regulatory elements in the dnaA-dnaN-recF operon of Escherichia coli. Biochimie. 1991;73:329-34 pubmed..gene of E coli lies within a cluster of genes which play essential roles in DNA replication; the gene order is dnaA dnaN recF gyrB...
- Baharoglu Z, Petranovic M, Flores M, Michel B. RuvAB is essential for replication forks reversal in certain replication mutants. EMBO J. 2006;25:596-604 pubmed..In contrast, RFR occurs in the absence of RuvAB in the dnaNts mutant, affected for the processivity clamp of Pol III, and in the priA mutant, defective for replication restart. This suggests alternative pathways of RFR. ..