Genomes and Genes
Gene Symbol: dnaX
Description: DNA polymerase III/DNA elongation factor III, tau and gamma subunits
Alias: ECK0464, JW0459, dnaZ
Species: Escherichia coli str. K-12 substr. MG1655
- Kim S, Dallmann H, McHenry C, Marians K. tau couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork. J Biol Chem. 1996;271:21406-12 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. ..
- Schaeffer P, Headlam M, Dixon N. Protein--protein interactions in the eubacterial replisome. IUBMB Life. 2005;57:5-12 pubmed..coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7. ..
- O Donnell M. Replisome architecture and dynamics in Escherichia coli. J Biol Chem. 2006;281:10653-6 pubmed
- 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. ..
- Studwell Vaughan P, O Donnell M. Constitution of the twin polymerase of DNA polymerase III holoenzyme. J Biol Chem. 1991;266:19833-41 pubmed..The significance of these results with respect to the organization of subunits within the holoenzyme is discussed. ..
- Bullard J, Pritchard A, Song M, Glover B, Wieczorek A, Chen J, et al. A three-domain structure for the delta subunit of the DNA polymerase III holoenzyme delta domain III binds delta' and assembles into the DnaX complex. J Biol Chem. 2002;277:13246-56 pubmed..This approach, starting with Escherichia coli delta, leads not only to the identification of delta but also to the DnaX and delta' subunits of the DnaX complex and other AAA(+)-class ATPases...
- Blinkova A, Hervas C, Stukenberg P, Onrust R, O Donnell M, Walker J. The Escherichia coli DNA polymerase III holoenzyme contains both products of the dnaX gene, tau and gamma, but only tau is essential. J Bacteriol. 1993;175:6018-27 pubmed..Of these seven, tau and gamma are products of one replication gene, dnaX. The shorter gamma is created from within the tau reading frame by a programmed ribosomal -1 frameshift over codons ..
- 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. ..
- 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. ..
- McHenry C. Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences. Mol Microbiol. 2003;49:1157-65 pubmed..The asymmetry of the holoenzyme is created by the DnaX complex, a heptamer that includes tau and gamma products of the dnaX gene...
- Blinkowa A, Walker J. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res. 1990;18:1725-9 pubmedThe Escherichia coli dnaX gene encodes both the tau and gamma subunits of DNA polymerase III holoenzyme in one reading frame. The 71.1 kDa tau and the shorter gamma share N-terminal sequences...
- Snyder A, Williams C, Johnson A, O Donnell M, Bloom L. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the beta and DNA binding activities of the gamma complex. J Biol Chem. 2004;279:4386-93 pubmed..Additionally, these results show that the "arginine fingers" play a structural role in facilitating the formation of a conformation that has high affinity for beta and DNA. ..
- López de Saro F, Georgescu R, O Donnell M. A peptide switch regulates DNA polymerase processivity. Proc Natl Acad Sci U S A. 2003;100:14689-94 pubmed..Therefore, DNA sensing by tau switches the polymerase peptide tail on and off the clamp and coordinates the dynamic turnover of polymerase during lagging strand synthesis. ..
- Ason B, Handayani R, Williams C, Bertram J, Hingorani M, O Donnell M, et al. Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp. J Biol Chem. 2003;278:10033-40 pubmed
- Yuzhakov A, Kelman Z, O Donnell M. Trading places on DNA--a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell. 1999;96:153-63 pubmed..The conservation of this three-point switch, in which two proteins exchange places on DNA via mutually exclusive interaction with a third protein, is discussed. ..
- 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. ..
- Gao D, McHenry C. Tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain III, shared by gamma and tau, binds delta delta ' and chi psi. J Biol Chem. 2001;276:4447-53 pubmedThe DnaX complex of the DNA polymerase holoenzyme assembles the beta(2) processivity factor onto the primed template enabling highly processive replication...
- 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. ..
- Kodaira M, Biswas S, Kornberg A. The dnaX gene encodes the DNA polymerase III holoenzyme tau subunit, precursor of the gamma subunit, the dnaZ gene product. Mol Gen Genet. 1983;192:80-6 pubmedThe E. coli dnaX and dnaZ gene products, essential for E. coli DNA replication, serve in chain elongation. Both genes, located at 10.4 min and previously cloned into a lambda vector and a ColE1 plasmid, were subcloned into pBR322 (pMK212)...
- Dallmann H, Kim S, Pritchard A, Marians K, McHenry C. Characterization of the unique C terminus of the Escherichia coli tau DnaX protein. Monomeric C-tau binds alpha AND DnaB and can partially replace tau in reconstituted replication forks. J Biol Chem. 2000;275:15512-9 pubmed..C-terminal sequences of tau, free of the sequences shared with the alternative gamma frameshifting product of dnaX. We have established that C-tau is a monomer by sedimentation equilibrium and sedimentation velocity ..
- Onrust R, Finkelstein J, Naktinis V, Turner J, Fang L, O Donnell M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. I. Organization of the clamp loader. J Biol Chem. 1995;270:13348-57 pubmed..Naktinis, V., and O'Donnell, M. (1995) J. Biol. Chem. 270, 13378-13383). The single copy subunits within the gamma complex provide the basis for the structural asymmetry inherent within DNA polymerase III holoenzyme. ..
- Pritchard A, Dallmann H, Glover B, McHenry C. A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of deltadelta' with DnaX(4) forms DnaX(3)deltadelta'. EMBO J. 2000;19:6536-45 pubmedWe have constructed a plasmid-borne artificial operon that expresses the six subunits of the DnaX complex of Escherichia coli DNA polymerase III holoenzyme: tau, gamma, delta, delta', chi and psi...
- Mullin D, Woldringh C, Henson J, Walker J. Cloning of the Escherichia coli dnaZX region and identification of its products. Mol Gen Genet. 1983;192:73-9 pubmedThe Escherichia coli DNA replication genes dnaZ and dnaX have previously been localized very near each other at 10.4 to 10.5 min on the chromosome map...
- Jeruzalmi D, O Donnell M, Kuriyan J. Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Cell. 2001;106:429-41 pubmed
- 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. ..
- Turner J, Hingorani M, Kelman Z, O Donnell M. The internal workings of a DNA polymerase clamp-loading machine. EMBO J. 1999;18:771-83 pubmed..Interaction with DNA stimulates ATP hydrolysis which ejects the gamma complex from DNA, leaving the ring to close around the duplex. ..
- 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. ..
- 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. ..
- Gulbis J, Kazmirski S, Finkelstein J, Kelman Z, O Donnell M, Kuriyan J. Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex. Eur J Biochem. 2004;271:439-49 pubmed..The base of the clamp-loader complex has an open C-shaped structure, and the shape of the chi:psi complex is suggestive of a loose docking within the crevice formed by the open faces of the delta and delta' subunits of the clamp-loader. ..
- Kazmirski S, Podobnik M, Weitze T, O Donnell M, Kuriyan J. Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Proc Natl Acad Sci U S A. 2004;101:16750-5 pubmed
- Tsuchihashi Z, Brown P. Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev. 1992;6:511-9 pubmed..holoenzyme depends on precise and efficient translational frameshifting to the -1 frame at a specific site in the dnaX gene of Escherichia coli...
- Pham P, Zhao W, Schaaper R. Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit. Mol Microbiol. 2006;59:1149-61 pubmed..III holoenzyme (HE) in determining chromosomal replication fidelity, we have investigated the role of the dnaX gene...
- Lovett S. Polymerase switching in DNA replication. Mol Cell. 2007;27:523-6 pubmed..New evidence suggests that three DNA polymerases can be accommodated into the replisome and that polymerases and repair factors are dynamically recruited and engaged without dismantling of the replisome. ..
- 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. ..
- Espeli O, Lee C, Marians K. A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. J Biol Chem. 2003;278:44639-44 pubmed..Rescue of a parE temperature-sensitive mutation by overproduction of DnaX, which leads to stabilization of the temperature-sensitive Topo IV, required both the C-terminal domain of FtsK and ..
- Boye E, Blinkova A, Walker J. Defective initiation in an Escherichia coli dnaA(Cs,Sx) mutant. Biochimie. 2001;83:25-32 pubmed..defect and growth inhibition caused by temperature-sensitive (Ts) mutations in the polymerization gene, dnaX, are called Cs,Sx...
- 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. ..
- Echtenkamp P, Wilson D, Shuler M. Cell cycle progression in Escherichia coli B/r affects transcription of certain genes: Implications for synthetic genome design. Biotechnol Bioeng. 2009;102:902-9 pubmed publisher..In conclusion, gene position, with regard to the C period, and gene function are important factors to incorporate into design criteria for synthetic bacterial genomes. ..
- Henson J, Chu H, Irwin C, Walker J. Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics. 1979;92:1041-59 pubmed..transducing phages and the hybrid plasmids suggest that dnaX is a different gene from the previously characterized dnaZ gene, which is also near minute 10...
- Scherzinger E, Haring V, Lurz R, Otto S. Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins. Nucleic Acids Res. 1991;19:1203-11 pubmed..In addition, we find that E.coli DNA gyrase, DnaZ protein (gamma subunit of poIIII holoenzyme) and SSB are required for in vitro plasmid synthesis...
- Shavitt O, Livneh Z. The beta subunit modulates bypass and termination at UV lesions during in vitro replication with DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem. 1989;264:11275-81 pubmed..Moreover, it predicts that bypass synthesis under SOS conditions might be associated with an altered form of the beta subunit. ..
- 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. ..
- Burgers P, Kornberg A. The cycling of Escherichia coli DNA polymerase III holoenzyme in replication. J Biol Chem. 1983;258:7669-75 pubmed
- Dallmann H, Thimmig R, McHenry C. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Central role of tau in initiation complex assembly and in determining the functional asymmetry of holoenzyme. J Biol Chem. 1995;270:29555-62 pubmedThe alternative forms of the DnaX protein found in Escherichia coli DNA polymerase III holoenzyme, tau and gamma, were purified from extracts of strains carrying overexpressing plasmids mutated in their frameshifting sequences such that ..
- Larsen B, Wills N, Gesteland R, Atkins J. rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift. J Bacteriol. 1994;176:6842-51 pubmed..and mRNA is shown to be important for the programmed -1 frameshifting utilized in decoding the Escherichia coli dnaX gene...
- Hubscher U, Kornberg A. The delta subunit of Escherichia coli DNA polymerase III holoenzyme is the dnaX gene product. Proc Natl Acad Sci U S A. 1979;76:6284-8 pubmed..A. & Walker, J.R. (1979) Genetics 92, 1,41-1059] that SG133 has two temperature-sensitive mutations, called dnaX and dnaY...
- Fradkin L, Kornberg A. Prereplicative complexes of components of DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem. 1992;267:10318-22 pubmed..Based on these findings, a sequence of stages can be formulated for an activation of the beta subunit that enables it to bind the template-primer and thereby interact with the core to create a processive polymerase. ..
- Maki S, Kornberg A. DNA polymerase III holoenzyme of Escherichia coli. II. A novel complex including the gamma subunit essential for processive synthesis. J Biol Chem. 1988;263:6555-60 pubmed
- Bertram J, Bloom L, Turner J, O Donnell M, Beechem J, Goodman M. Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA. J Biol Chem. 1998;273:24564-74 pubmed..Thus, the assembly of beta around DNA is coupled tightly to the ATPase activity of the gamma complex, and completion of the assembly process requires ATP hydrolysis for turnover of the catalytic clamp loader. ..
- 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. ..
- Kim S, Dallmann H, McHenry C, Marians K. Coupling of a replicative polymerase and helicase: a tau-DnaB interaction mediates rapid replication fork movement. Cell. 1996;84:643-50 pubmed..This finding establishes the existence of both a physical and communications link between the two major replication machines in the replisome: the DNA polymerase and the primosome. ..
- Flower A, McHenry C. The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame. Nucleic Acids Res. 1986;14:8091-101 pubmedThe dnaZ and dnaX loci of Escherichia coli have been genetically defined as separate genes, both of which are essential for DNA replication (1). The 2...
- 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. ..
- Scouten Ponticelli S, Duzen J, Sutton M. Contributions of the individual hydrophobic clefts of the Escherichia coli beta sliding clamp to clamp loading, DNA replication and clamp recycling. Nucleic Acids Res. 2009;37:2796-809 pubmed publisher..five residues of beta (beta(C)) disrupted both clefts, severely impairing interactions of the clamp with the DnaX clamp loader, as well as the replicative DNA polymerase, Pol III...
- 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..These results suggest that the inhibition of DNA replication causes a lower level of unsaturation of fatty acids in Escherichia coli cells. ..
- 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. ..
- 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
- Hagensee M, Moses R. Multiple pathways for repair of hydrogen peroxide-induced DNA damage in Escherichia coli. J Bacteriol. 1989;171:991-5 pubmed..One of these pathways would utilize exonuclease III, DNA polymerase III, and DNA polymerase I, while the other would be DNA polymerase I dependent. The RecA protein seems to have little or no direct function in either repair pathway. ..
- Lee S, Walker J. Escherichia coli DnaX product, the tau subunit of DNA polymerase III, is a multifunctional protein with single-stranded DNA-dependent ATPase activity. Proc Natl Acad Sci U S A. 1987;84:2713-7 pubmedThe dnaZX gene of Escherichia coli directs the synthesis of two proteins, DnaZ and DnaX. These products are confirmed as the gamma and tau subunits of DNA polymerase III because antibody to a synthetic peptide present in both the DnaZ and ..
- Leu F, O Donnell M. Interplay of clamp loader subunits in opening the beta sliding clamp of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem. 2001;276:47185-94 pubmed..The implications of these actions for the workings of the E. coli clamp loading machinery and for eukaryotic RFC and PCNA are discussed. ..
- López de Saro F, Georgescu R, Leu F, O Donnell M. Protein trafficking on sliding clamps. Philos Trans R Soc Lond B Biol Sci. 2004;359:25-30 pubmed..It seems likely that the principles will generalize to a traffic flow of other factors on these circular clamp proteins. ..
- 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
- Cull M, McHenry C. Purification of Escherichia coli DNA polymerase III holoenzyme. Methods Enzymol. 1995;262:22-35 pubmed
- Marceau A, Bahng S, Massoni S, George N, Sandler S, Marians K, et al. Structure of the SSB-DNA polymerase III interface and its role in DNA replication. EMBO J. 2011;30:4236-47 pubmed publisher..Destabilization of the ?/SSB complex in vivo produces cells with temperature-dependent cell cycle defects that appear to arise from replisome instability. ..
- Dohrmann P, Correa R, Frisch R, Rosenberg S, McHenry C. The DNA polymerase III holoenzyme contains Î³ and is not a trimeric polymerase. Nucleic Acids Res. 2016;44:1285-97 pubmed publisher..Two DnaX proteins exist in E. coli, full length Ï„ and a truncated Î³ that is created by ribosomal frameshifting...
- Flower A, McHenry C. Transcriptional organization of the Escherichia coli dnaX gene. J Mol Biol. 1991;220:649-58 pubmedWe have determined the transcriptional organization of the Escherichia coli dnaX gene, the structural gene for both the gamma and tau subunits of DNA polymerase III holoenzyme...
- Kim S, Marians K. DNA and RNA-DNA annealing activity associated with the tau subunit of the Escherichia coli DNA polymerase III holoenzyme. Nucleic Acids Res. 1995;23:1374-9 pubmed..The 71 kDa tau subunit, encoded by dnaX, dimerizes the core polymerase (alpha epsilon theta) to form pol III'[(alpha epsilon theta)2 tau 2]...
- Podobnik M, Weitze T, O Donnell M, Kuriyan J. Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit. Structure. 2003;11:253-63 pubmed..This change would break one of the gamma:gamma interfaces seen in the empty clamp loader complex, and may represent one step in the activation process. ..
- Hingorani M, Bloom L, Goodman M, O Donnell M. Division of labor--sequential ATP hydrolysis drives assembly of a DNA polymerase sliding clamp around DNA. EMBO J. 1999;18:5131-44 pubmed..We also discuss underlying principles of this step-wise mechanism that may apply to the workings of other ATP-fueled biological machines. ..