Genomes and Genes
Gene Symbol: dnaE
Description: DNA polymerase III alpha subunit
Alias: ECK0183, JW0179, polC, sdgC
Species: Escherichia coli str. K-12 substr. MG1655
- Maki H, Kornberg A. Proofreading by DNA polymerase III of Escherichia coli depends on cooperative interaction of the polymerase and exonuclease subunits. Proc Natl Acad Sci U S A. 1987;84:4389-92 pubmed
- 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. ..
- 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. ..
- Maki H, Kornberg A. The polymerase subunit of DNA polymerase III of Escherichia coli. II. Purification of the alpha subunit, devoid of nuclease activities. J Biol Chem. 1985;260:12987-92 pubmed..H., and Echols, H. (1984) Proc. Natl. Acad. Sci. U. S. A. 81, 7747-7751). Together with the theta polypeptide (10 kDa), of unknown function, they form a pol III core with greater stability and catalytic efficiency. ..
- Aravind L, Koonin E. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 1998;26:3746-52 pubmed..In these cases, the pyrophosphate may be hydrolyzed by a stand-alone phosphatase, and candidates for such a role were identified among bacterial PHP superfamily members. ..
- Fujii S, Fuchs R. Defining the position of the switches between replicative and bypass DNA polymerases. EMBO J. 2004;23:4342-52 pubmed
- O Donnell M. Replisome architecture and dynamics in Escherichia coli. J Biol Chem. 2006;281:10653-6 pubmed
- Jergic S, Ozawa K, Williams N, Su X, Scott D, Hamdan S, et al. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Nucleic Acids Res. 2007;35:2813-24 pubmed..An N-terminally extended construct, tau(C)24, was found to bind DNA in a salt-sensitive manner while no binding was observed for tau(C)16, suggesting that the processivity switch of the replisome functionally involves Domain IV of tau. ..
- Su X, Jergic S, Keniry M, Dixon N, Otting G. Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit. Nucleic Acids Res. 2007;35:2825-32 pubmed..Analysis of an N-terminally extended construct (tau(C)22) showed that tau(C)14 presents the only part of Domains IVa and V of tau which comprises a globular fold in the absence of other interaction partners. ..
- Wing R, Bailey S, Steitz T. Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. J Mol Biol. 2008;382:859-69 pubmed publisher..Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching. ..
- Kim D, McHenry C. Identification of the beta-binding domain of the alpha subunit of Escherichia coli polymerase III holoenzyme. J Biol Chem. 1996;271:20699-704 pubmed..Deletion of the polymerase domain (or, presumably, its occupancy by DNA) relaxes the COOH-terminal domain, permitting it to assume a conformation with high affinity for beta. ..
- Kim D, McHenry C. Biotin tagging deletion analysis of domain limits involved in protein-macromolecular interactions. Mapping the tau binding domain of the DNA polymerase III alpha subunit. J Biol Chem. 1996;271:20690-8 pubmed..37 nM). However, deletion of 48 amino acids from the COOH terminus totally eliminated tau binding. These results indicate that the COOH-terminal half of the alpha subunit is involved in tau interaction. ..
- Wieczorek A, McHenry C. The NH2-terminal php domain of the alpha subunit of the Escherichia coli replicase binds the epsilon proofreading subunit. J Biol Chem. 2006;281:12561-7 pubmed..These findings suggest that the php domain serves as a platform to enable coordination of proofreading and polymerase activities during chromosomal replication. ..
- Lamers M, Georgescu R, Lee S, O Donnell M, Kuriyan J. Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III. Cell. 2006;126:881-92 pubmed..The structure also suggests a model for interaction of Pol III with the sliding clamp and DNA. ..
- Ozawa K, Jergic S, Park A, Dixon N, Otting G. The proofreading exonuclease subunit epsilon of Escherichia coli DNA polymerase III is tethered to the polymerase subunit alpha via a flexible linker. Nucleic Acids Res. 2008;36:5074-82 pubmed publisher..This distinguishes the alpha : epsilon complex from other proofreading polymerases, which have a more rigid multidomain structure. ..
- 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. ..
- Georgescu R, Kurth I, O Donnell M. Single-molecule studies reveal the function of a third polymerase in the replisome. Nat Struct Mol Biol. 2011;19:113-6 pubmed publisher..Second, tripolymerase replisomes are much more processive than dipolymerase replisomes. These features account for the unexpected three-polymerase-structure of bacterial replisomes. ..
- Kim D, McHenry C. In vivo assembly of overproduced DNA polymerase III. Overproduction, purification, and characterization of the alpha, alpha-epsilon, and alpha-epsilon-theta subunits. J Biol Chem. 1996;271:20681-9 pubmed..and in vivo assembly of DNA polymerase III core, artificial operons containing the three structural genes, dnaE, dnaQ, and holE, were placed in an expression plasmid...
- Pintacuda G, Park A, Keniry M, Dixon N, Otting G. Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes. J Am Chem Soc. 2006;128:3696-702 pubmed..Degeneracies in the mutual orientation of the protein structures were resolved by the use of two different lanthanide ions, Dy3+ and Er3+...
- Perrino F, Harvey S, McNeill S. Two functional domains of the epsilon subunit of DNA polymerase III. Biochemistry. 1999;38:16001-9 pubmed..These data support the concept that epsilon contains a catalytic domain located within the N-terminal region and an alpha-association domain located within the C-terminal region of the protein...
- Silva M, Nevin P, Ronayne E, Beuning P. Selective disruption of the DNA polymerase III ?-? complex by the umuD gene products. Nucleic Acids Res. 2012;40:5511-22 pubmed publisher..We also find that UmuD, but not UmuD', disrupts the ?-? complex. We propose that the interaction between ? and UmuD contributes to the transition between replicative and TLS polymerases by removing ? from the ? clamp. ..
- McHenry C, Crow W. DNA polymerase III of Escherichia coli. Purification and identification of subunits. J Biol Chem. 1979;254:1748-53 pubmed..Our preparation has both the 3' leads to 5' and 5' leads to 3' exonuclease activities previously assigned to DNA polymerase III (Livingston, D., and Richardson, C. (1975) J. Biol. Chem. 250, 470-478). ..
- McCauley M, Shokri L, Sefcikova J, Venclovas C, Beuning P, Williams M. Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. ACS Chem Biol. 2008;3:577-87 pubmed publisher..The results demonstrate that ssDNA binding is localized to the C-terminal region that contains the OB-fold domain, while a tandem helix-hairpin-helix (HhH) 2 motif contributes significantly to dsDNA binding. ..
- Dohrmann P, McHenry C. A bipartite polymerase-processivity factor interaction: only the internal beta binding site of the alpha subunit is required for processive replication by the DNA polymerase III holoenzyme. J Mol Biol. 2005;350:228-39 pubmed..bind beta2, and, if induced to high level expression, could complement a temperature-sensitive conditional lethal dnaE mutation. C-terminal defects that only partially complemented correlated with a defect in binding to tau, not beta2...
- Maki H, Maki S, Kornberg A. DNA Polymerase III holoenzyme of Escherichia coli. IV. The holoenzyme is an asymmetric dimer with twin active sites. J Biol Chem. 1988;263:6570-8 pubmed
- Fijalkowska I, Dunn R, Schaaper R. Genetic requirements and mutational specificity of the Escherichia coli SOS mutator activity. J Bacteriol. 1997;179:7435-45 pubmed..Analysis of the mutator effect in various dnaE strains, including dnaE antimutators, as well as in proofreading-deficient dnaQ (mutD) strains suggests that in ..
- Schaaper R, Dunn R. Effect of Escherichia coli dnaE antimutator mutants on mutagenesis by the base analog N4-aminocytidine. Mutat Res. 1998;402:23-8 pubmedPrevious studies in our laboratory have identified a set of mutations in the Escherichia coli dnaE gene that confer increased accuracy of DNA replication (antimutators)...
- Fijalkowska I, Schaaper R. Antimutator mutations in the alpha subunit of Escherichia coli DNA polymerase III: identification of the responsible mutations and alignment with other DNA polymerases. Genetics. 1993;134:1039-44 pubmedThe dnaE gene of Escherichia coli encodes the DNA polymerase (alpha subunit) of the main replicative enzyme, DNA polymerase III holoenzyme...
- Lenne Samuel N, Janel Bintz R, Kolbanovskiy A, Geacintov N, Fuchs R. The processing of a Benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli. Mol Microbiol. 2000;38:299-307 pubmed..It is likely that, given the diversity of conformations that can be adopted by lesion-containing replication intermediates, cells use one or several translesional DNA polymerases to achieve TLS. ..
- Helfman W, Hendler S, Smith D. Escherichia coli DNA polymerases II and III: activation by magnesium or by manganous ions. Biochim Biophys Acta. 1976;447:175-87 pubmed..Reactions with poly[d(A-T)] were enhanced by Mn2+ relative to Mg2+, and activity with poly(rA)-poly(dT) was Mn2+ dependent for both enzymes. ..
- O Donnell M, Kornberg A. Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template. J Biol Chem. 1985;260:12875-83 pubmed..Based on these findings, schemes can be considered for holoenzyme action at the replication fork of a duplex chromosome. ..
- Kim D, Pritchard A, McHenry C. Localization of the active site of the alpha subunit of the Escherichia coli DNA polymerase III holoenzyme. J Bacteriol. 1997;179:6721-8 pubmed..The motif Pro-Asp-X-Asp, where X is a hydrophobic amino acid, is shown to be conserved among all known DnaE proteins, including those from Bacillaceae, cyanobacteria, Mycoplasma, and mycobacteria. The E...
- Strauss B, Kelly K, Dincman T, Ekiert D, Biesieda T, Song R. Cell death in Escherichia coli dnaE(Ts) mutants incubated at a nonpermissive temperature is prevented by mutation in the cydA gene. J Bacteriol. 2004;186:2147-55 pubmedCells of the Escherichia coli dnaE(Ts) dnaE74 and dnaE486 mutants die after 4 h of incubation at 40 degrees C in Luria-Bertani medium...
- Livingston D, Hinkle D, Richardson C. Deoxyribonucleic acid polymerase III of Escherichia coli. Purification and properties. J Biol Chem. 1975;250:461-9 pubmed..coli containing the other two known DNA polymerases. Futhermore, the enzyme purified from three different polC mutants exhibits altered polymerase III activity, confirming that polC is the structural gene for DNA polymerase ..
- Saveson C, Lovett S. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics. 1997;146:457-70 pubmed..increased in a dnaQ mutant and sister-strand exchange, producing dimeric replicon products, may be elevated in dnaE mutants...
- Barros T, Guenther J, KELCH B, Anaya J, Prabhakar A, O Donnell M, et al. A structural role for the PHP domain in E. coli DNA polymerase III. BMC Struct Biol. 2013;13:8 pubmed publisher..Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase...
- Sharif F, Bridges B. Mutagenic DNA repair in Escherichia coli. XVII. Effect of temperature-sensitive DnaE proteins on the induction of streptomycin-resistant mutations by UV light. Mutagenesis. 1990;5:31-4 pubmed..These results confirm a role for DnaE protein (the alpha-subunit of DNA polymerase III holoenzyme) in UV mutagenesis...
- Van Dyk T, DeRose E, Gonye G. LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J Bacteriol. 2001;183:5496-505 pubmed publisher..Thus, the promoters of ycgH, intG, rihC, and a putative operon consisting of lpxA, lpxB, rnhB, and dnaE were not generally DNA damage responsive and represent a more specific response to nalidixic acid...
- Su X, Jergic S, Ozawa K, Burns N, Dixon N, Otting G. Measurement of dissociation constants of high-molecular weight protein-protein complexes by transferred 15N-relaxation. J Biomol NMR. 2007;38:65-72 pubmed
- Den Blaauwen T, Aarsman M, Wheeler L, Nanninga N. Pre-replication assembly of E. coli replisome components. Mol Microbiol. 2006;62:695-708 pubmed..DnaB and tau co-labelled in the cell centre, though not at presumed pre-replication assembly sites. By contrast, alpha and tau co-labelled consistently suggesting that they are already associated before replication starts. ..
- Mo J, Maki H, Sekiguchi M. Mutational specificity of the dnaE173 mutator associated with a defect in the catalytic subunit of DNA polymerase III of Escherichia coli. J Mol Biol. 1991;222:925-36 pubmed..rpsL- mutations in the mutator strain were analyzed by DNA sequencing, together with 100 mutants recovered from dnaE+ strain, as the control...
- Bryan S, Moses R. Interallelic complementation of dnaE(Ts) mutations. J Bacteriol. 1992;174:4850-2 pubmedSome Escherichia coli dnaE(Ts) alleles will functionally complement in trans. The complementation is not due to copy number and is compatible with dimeric interaction.
- 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. ..
- Bonner C, Stukenberg P, Rajagopalan M, Eritja R, O Donnell M, McEntee K, et al. Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. J Biol Chem. 1992;267:11431-8 pubmed..pol II also shows limited bypass of the abasic site, dependent on the presence of beta,gamma complex and SSB. pol III shows no significant bypass of the abasic site with or without beta,gamma complex. ..
- Pennington J, Rosenberg S. Spontaneous DNA breakage in single living Escherichia coli cells. Nat Genet. 2007;39:797-802 pubmed..Finally, FACS demonstrated two main cell fates after spontaneous DNA damage: viability with or without resumption of proliferation. ..
- Suzuki E, Kondo T, Makise M, Mima S, Sakamoto K, Tsuchiya T, et al. Alteration in levels of unsaturated fatty acids in mutants of Escherichia coli defective in DNA replication. Biol Pharm Bull. 1998;21:657-61 pubmed..As in the case of temperature-sensitive dnaA mutants, temperature-sensitive dnaC and dnaE mutants, which have defects in initiation and elongation, respectively, of DNA replication showed a lower level of ..
- Reems J, Wood S, McHenry C. Escherichia coli DNA polymerase III holoenzyme subunits alpha, beta, and gamma directly contact the primer-template. J Biol Chem. 1995;270:5606-13 pubmed..These data indicate that assembly of holoenzyme onto a primer-template can occur in distinct stages and results in a structural rearrangement during initiation complex formation. ..
- Lindow J, Dohrmann P, McHenry C. DNA Polymerase Î± Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection. J Biol Chem. 2015;290:16851-60 pubmed publisher..Surprisingly, mutations within the Î² binding domain also ablated interaction with Ï„, suggesting a larger Ï„ binding site than previously recognized. ..
- 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. ..
- Filpula D, Fuchs J. Regulation of the synthesis of ribonucleoside diphosphate reductase in Escherichia coli: specific activity of the enzyme in relationship to perturbations of DNA replication. J Bacteriol. 1978;135:429-35 pubmed..a shift to the nonpermissive temperature in Escherichia coli mutants temperature sensitive for DNA elongation (dnaE dnaG dnaZ lig) or DNA initiation (dnaA dnaC dnaI)...
- 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
- Wechsler J, Nüsslein V, Otto B, Klein A, Bonhoeffer F, Herrmann R, et al. Isolation and characterization of thermosensitive Escherichia coli mutants defective in deoxyribonucleic acid replication. J Bacteriol. 1973;113:1381-8 pubmed..This classification is congruent with that obtained by genetic mapping by using cotransduction frequencies with selected markers in P1 transduction analysis. ..
- Kelman Z, Yuzhakov A, Andjelkovic J, O Donnell M. Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J. 1998;17:2436-49 pubmed..These results establish a role for the psi subunit in contacting SSB, thus enhancing the clamp loading and processivity of synthesis of the holoenzyme, presumably by helping to localize the holoenzyme to sites of SSB-coated ssDNA. ..
- Maki S, Kornberg A. DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits. J Biol Chem. 1988;263:6561-9 pubmed
- MontÃ³n Silva A, Lapenta F, Stefan A, Dal Piaz F, Ceccarelli A, Perrone A, et al. Simultaneous ternary extension of DNA catalyzed by a trimeric replicase assembled in vivo. Biochem Biophys Res Commun. 2015;462:14-20 pubmed publisher..Our observations indicate that trimeric DNA replicases reduce the gap between leading and lagging strand synthesis. ..
- Hagensee M, Moses R. Multiple pathways for repair of hydrogen peroxide-induced DNA damage in Escherichia coli. J Bacteriol. 1989;171:991-5 pubmed..These mutants, in order of increasing sensitivity, were recA, polC, xthA, and polA...
- Welch M, McHenry C. Cloning and identification of the product of the dnaE gene of Escherichia coli. J Bacteriol. 1982;152:351-6 pubmedWe successively subcloned the dnaE gene of Escherichia coli into pBR322, resulting in a plasmid that contains 4.6 kilobases of E. coli DNA. This plasmid can complement a dnaE temperature-sensitive mutation...
- Shepard D, Oberfelder R, Welch M, McHenry C. Determination of the precise location and orientation of the Escherichia coli dnaE gene. J Bacteriol. 1984;158:455-9 pubmedThe minimal region required for expression of the dnaE gene of Escherichia coli has been determined relative to a detailed restriction endonuclease map...
- Lestini R, Michel B. UvrD controls the access of recombination proteins to blocked replication forks. EMBO J. 2007;26:3804-14 pubmed..A defective UvrD mutant is able to antagonize RecA in cells affected for the Pol IIIh catalytic subunit DnaE. In this mutant, RecA action at blocked forks specifically requires the protein RarA (MgsA)...
- O Grady P, Borden A, Vandewiele D, Ozgenc A, Woodgate R, Lawrence C. Intrinsic polymerase activities of UmuD'(2)C and MucA'(2)B are responsible for their different mutagenic properties during bypass of a T-T cis-syn cyclobutane dimer. J Bacteriol. 2000;182:2285-91 pubmed..allele mutD5, which is deficient in proofreading but is competent in the structural function of epsilon, or the dnaE antimutator allele spq-2...
- 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. ..
- Tomasiewicz H, McHenry C. Sequence analysis of the Escherichia coli dnaE gene. J Bacteriol. 1987;169:5735-44 pubmedWe have determined the sequence of a 4,350-nucleotide region of the Escherichia coli chromosome that contains dnaE, the structural gene for the alpha subunit of DNA polymerase III holoenzyme...
- McCauley M, Williams M. Optical tweezers experiments resolve distinct modes of DNA-protein binding. Biopolymers. 2009;91:265-82 pubmed publisher..These recently developed methods quantify both the binding activity of the ligand as well as the mode of binding. ..
- Kornberg T, Gefter M. Deoxyribonucleic acid synthesis in cell-free extracts. IV. Purification and catalytic properties of deoxyribonucleic acid polymerase III. J Biol Chem. 1972;247:5369-75 pubmed
- Borden A, O Grady P, Vandewiele D, Fernández de Henestrosa A, Lawrence C, Woodgate R. Escherichia coli DNA polymerase III can replicate efficiently past a T-T cis-syn cyclobutane dimer if DNA polymerase V and the 3' to 5' exonuclease proofreading function encoded by dnaQ are inactivated. J Bacteriol. 2002;184:2674-81 pubmed..This mutant polymerase does not replicate past the much more distorted T-T (6-4) photoadduct, however, suggesting that it may only replicate past lesions, like the T-T dimer, that form base pairs normally. ..
- Li S, Cronan J. Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis. J Bacteriol. 1993;175:332-40 pubmed..For example, the accA promoter was localized within the upstream polC gene (which encodes the DNA polymerase III catalytic subunit), suggesting that additional regulatory mechanisms ..
- Naufer M, Murison D, Rouzina I, Beuning P, Williams M. Single-molecule mechanochemical characterization of E. coli pol III core catalytic activity. Protein Sci. 2017;26:1413-1426 pubmed publisher..Thus, binding to an unstable primer is the primary mechanism for mismatch recognition during proofreading, rather than an alternative model of duplex defect recognition. ..
- Liang R, Liu J. In-frame deletion of Escherichia coli essential genes in complex regulon. Biotechniques. 2008;44:209-10, 212-5 pubmed..We selected three essential genes as targets, yaeT, fabZ, and dnaE, which are components of the complex eight-gene regulon yaeT-hlpA-lpxD-fabZ-lpxA-1pxB-rnhB-dnaE...
- Cull M, McHenry C. Purification of Escherichia coli DNA polymerase III holoenzyme. Methods Enzymol. 1995;262:22-35 pubmed