Genomes and Genes
Gene Symbol: holD
Description: DNA polymerase III, psi subunit
Alias: ECK4363, JW4334
Species: Escherichia coli str. K-12 substr. MG1655
- Anderson S, Williams C, O Donnell M, Bloom L. A function for the psi subunit in loading the Escherichia coli DNA polymerase sliding clamp. J Biol Chem. 2007;282:7035-45 pubmed..Results from our work and others suggest that the psi subunit may introduce a temporal order to the clamp loading reaction in which clamp binding precedes DNA binding. ..
- Olson M, Dallmann H, McHenry C. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range. J Biol Chem. 1995;270:29570-7 pubmedAn artificial operon that contains tandem holC-holD genes was used to overproduce a complex of the chi and psi subunits of the DNA polymerase III holoenzyme. Normally insoluble by itself, psi forms a tight soluble complex with chi...
- Flores M, Ehrlich S, Michel B. Primosome assembly requirement for replication restart in the Escherichia coli holDG10 replication mutant. Mol Microbiol. 2002;44:783-92 pubmed
- O Donnell M. Accessory protein function in the DNA polymerase III holoenzyme from E. coli. Bioessays. 1992;14:105-11 pubmed..This report summarizes our current understanding of the individual functions of the accessory proteins within the holoenzyme, lending insight into why a chromosomal replicase needs such a complex structure. ..
- Carter J, Franden M, Aebersold R, McHenry C. Identification, isolation, and overexpression of the gene encoding the psi subunit of DNA polymerase III holoenzyme. J Bacteriol. 1993;175:5604-10 pubmedThe gene encoding the psi subunit of DNA polymerase III holoenzyme, holD, was identified and isolated by an approach in which peptide sequence data were used to obtain a DNA hybridization probe. The gene, which maps to 99...
- 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. ..
- 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. ..
- 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
- Nüsslein V, Henke S, Johnston L. Replication of E. coli duplex DNA in vitro. The separation of the DNA containing fractions of a lysate from the soluble enzymes and their complementation properties. Mol Gen Genet. 1976;145:183-90 pubmed..Other factors, that are essential for replicative DNA synthesis, including the dnaG gene product, are washed out of the DNA containing preparations and the system is reconstituted by readdition of the soluble proteins. ..
- Dallmann H, McHenry C. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Physical characterization of the DnaX subunits and complexes. J Biol Chem. 1995;270:29563-9 pubmed..The stoichiometry of the reconstituted DNA polymerase III* component of holoenzyme in this model is (alpha epsilon theta)2DnaX4 delta 1 delta' 1 chi 1 psi 1. ..
- Burgers P, Kornberg A. The cycling of Escherichia coli DNA polymerase III holoenzyme in replication. J Biol Chem. 1983;258:7669-75 pubmed
- Li F, Liu Q, Chen Y, Yu Z, Zhang Z, Zhou Y, et al. Escherichia coli mismatch repair protein MutL interacts with the clamp loader subunits of DNA polymerase III. Mutat Res. 2008;637:101-10 pubmed
- 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. ..
- 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. ..
- Hingorani M, O Donnell M. ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme. J Biol Chem. 1998;273:24550-63 pubmed..open beta ring.DNA intermediate, setting the stage for ring closing and turnover of the clamp loader, steps that may be linked to subsequent hydrolysis of ATP. ..
- Duigou S, Silvain M, Viguera E, Michel B. ssb gene duplication restores the viability of Î”holC and Î”holD Escherichia coli mutants. PLoS Genet. 2014;10:e1004719 pubmed publisherThe HolC-HolD (Ï‡Ïˆ) complex is part of the DNA polymerase III holoenzyme (Pol III HE) clamp-loader. Several lines of evidence indicate that both leading- and lagging-strand synthesis are affected in the absence of this complex...
- Bloom L, Turner J, Kelman Z, Beechem J, O Donnell M, Goodman M. Dynamics of loading the beta sliding clamp of DNA polymerase III onto DNA. J Biol Chem. 1996;271:30699-708 pubmed..The association rate appears to be limited by an intramolecular step occurring prior to the clamp-loading reaction, possibly the opening of the toroidal beta dimer. ..
- Durand A, Sinha A, Dard Dascot C, Michel B. Mutations Affecting Potassium Import Restore the Viability of the Escherichia coli DNA Polymerase III holD Mutant. PLoS Genet. 2016;12:e1006114 pubmed publisherMutants lacking the ? (HolD) subunit of the Escherichia coli DNA Polymerase III holoenzyme (Pol III HE) have poor viability, but a residual growth allows the isolation of spontaneous suppressor mutations that restore ?holD mutant ..
- Bertram J, Bloom L, Hingorani M, Beechem J, O Donnell M, Goodman M. Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when gamma complex loads beta on DNA. J Biol Chem. 2000;275:28413-20 pubmed..The anisotropy data showed that these mutants decrease the steady-state rates of ATP hydrolysis by causing a buildup of "stuck" binary-ternary complexes on the primer/template DNA. ..
- 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. ..
- Witte G, Urbanke C, Curth U. DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. Nucleic Acids Res. 2003;31:4434-40 pubmed..Thus, the binding of EcoSSB to chi at the replication fork prevents premature dissociation of EcoSSB from the lagging strand and thereby enhances the processivity of DNA polymerase III. ..
- Cull M, McHenry C. Purification of Escherichia coli DNA polymerase III holoenzyme. Methods Enzymol. 1995;262:22-35 pubmed
- 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. ..
- 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. ..
- Xiao H, Crombie R, Dong Z, Onrust R, O Donnell M. DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi. J Biol Chem. 1993;268:11773-8 pubmed..5 min on the chromosome; it encodes a 147-amino acid protein of 16.6 kDa. holD encoding psi lies upstream of rimI at 99.3 min and encodes a 137-amino acid protein of 15.2 kDa...
- 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
- O Donnell M. Accessory proteins bind a primed template and mediate rapid cycling of DNA polymerase III holoenzyme from Escherichia coli. J Biol Chem. 1987;262:16558-65 pubmed..These subunit dynamics suggest mechanisms for polymerase cycling on the lagging strand of replication forks in a growing chromosome. ..
- 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. ..
- 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. ..
- Bloom L. Dynamics of loading the Escherichia coli DNA polymerase processivity clamp. Crit Rev Biochem Mol Biol. 2006;41:179-208 pubmed..This review focuses on the measurement of dynamic and transient interactions required to assemble the Escherichia coli sliding clamp on DNA. ..
- 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. ..
- 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
- Magdalena Coman M, Jin M, Ceapa R, Finkelstein J, O DONNELL M, Chait B, et al. Dual functions, clamp opening and primer-template recognition, define a key clamp loader subunit. J Mol Biol. 2004;342:1457-69 pubmed..A similar analysis of the S.cerevisiae RFC complex suggests that the dual functionality observed for delta in the gamma complex may be true also for clamp loaders from other organisms. ..
- LaDuca R, Fay P, Chuang C, McHenry C, Bambara R. Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III. Biochemistry. 1983;22:5177-88 pubmed..Additionally, a nucleotide composition specificity of pause sites has been observed. ..
- Morag A, Saveson C, Lovett S. Expansion of DNA repeats in Escherichia coli: effects of recombination and replication functions. J Mol Biol. 1999;289:21-7 pubmed..The specific location of such a stall site can also, in theory, account for propensity towards expansion or deletion of repeat arrays. This may have relevance to trinucleotide repeat expansion in human genetic disease. ..
- 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. ..
- 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. ..
- Shwartz H, Livneh Z. Dynamics of termination during in vitro replication of ultraviolet-irradiated DNA with DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem. 1987;262:10518-23 pubmed..We suggest that the inability of the polymerase to bypass photodimers during termination is due to the formation of defective initiation-like complexes with reduced stability at the blocked termini. ..
- 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. ..
- Ason B, Bertram J, Hingorani M, Beechem J, O Donnell M, Goodman M, et al. A model for Escherichia coli DNA polymerase III holoenzyme assembly at primer/template ends. DNA triggers a change in binding specificity of the gamma complex clamp loader. J Biol Chem. 2000;275:3006-15 pubmed..DNA complex. ..
- Song M, McHenry C. Carboxyl-terminal domain III of the delta' subunit of DNA polymerase III holoenzyme binds DnaX and supports cooperative DnaX complex assembly. J Biol Chem. 2001;276:48709-15 pubmed..A domain III-specific anti-delta' monoclonal antibody interfered with DnaX complex formation and abolished the replication activity of DNA polymerase III holoenzyme. ..
- 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. ..
- 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
- 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. ..
- Glover B, Pritchard A, McHenry C. tau binds and organizes Escherichia coli replication proteins through distinct domains: domain III, shared by gamma and tau, oligomerizes DnaX. J Biol Chem. 2001;276:35842-6 pubmed..Thus, domain III not only contains the delta, delta', chi, and psi binding interface, but also the region that enables DnaX to oligomerize. ..
- 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. ..
- 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 pubmed..Thus, domain III of the DnaX proteins not only contains the deltadelta' and chipsi binding sites but also contains the elements required for the positive cooperative assembly of the DnaX complex. ..
- 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. ..
- Goedken E, Levitus M, Johnson A, Bustamante C, O Donnell M, Kuriyan J. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol. 2004;336:1047-59 pubmed
- 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. ..
- Rajagopala S, Sikorski P, Caufield J, Tovchigrechko A, Uetz P. Studying protein complexes by the yeast two-hybrid system. Methods. 2012;58:392-9 pubmed publisher..Finally, we review an Y2H analysis of the human spliceosome which may serve as an example for a dynamic mega-complex...
- 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. ..
- O Donnell M. Replisome architecture and dynamics in Escherichia coli. J Biol Chem. 2006;281:10653-6 pubmed
- 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
- Glover B, McHenry C. The DnaX-binding subunits delta' and psi are bound to gamma and not tau in the DNA polymerase III holoenzyme. J Biol Chem. 2000;275:3017-20 pubmed..Immunodetection of cross-linked species with anti-delta' and anti-psi antibodies revealed that no tau-delta' or tau-psi cross-links had formed, suggesting that the delta' and psi subunits reside only on gamma within holoenzyme. ..
- 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
- Yoshikawa A, Isono S, Sheback A, Isono K. Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12. Mol Gen Genet. 1987;209:481-8 pubmed..There is only a low level of overall homology between the two genes except for a 3' terminal region in which a significant degree of homology was noticed. ..
- Park M, O Donnell M. The clamp loader assembles the beta clamp onto either a 3' or 5' primer terminus: the underlying basis favoring 3' loading. J Biol Chem. 2009;284:31473-83 pubmed publisher..We present evidence that the beta clamp facilitates its own loading specificity for a 3' primed site. Implications to eukaryotic clamp loader complexes are proposed. ..
- 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. ..
- 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. ..