Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III τ subunit

Molecular Microbiology

Volumn 59, Issue 4, 2006, Pages 1149-1161

  Pham, Phuong T ^a,b   Zhao, Wei ^a   Schaaper, Roel M ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA DIRECTED DNA POLYMERASE GAMMA; HOLOENZYME;

ALLELE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHROMOSOME REPLICATION; CHROMOSOME SUBSTITUTION; CONTROLLED STUDY; DNA REPLICATION; DNA SEQUENCE; ENZYME SUBUNIT; ESCHERICHIA COLI; FRAMESHIFT MUTATION; GENETIC CODE; GENETIC ORGANIZATION; HETEROZYGOTE; MISSENSE MUTATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUANTUM YIELD; TEMPERATURE SENSITIVE MUTANT;

ALLELES; AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; BASE SEQUENCE; DNA POLYMERASE III; DNA REPLICATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FRAMESHIFT MUTATION; HOLOENZYMES; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTATION, MISSENSE; TRANSCRIPTION FACTORS;

ESCHERICHIA COLI;

EID: 33645081480     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2005.05011.x     Document Type: Article

References (65)

1. Beard WA. Wilson SH. 2003 Structural insights into the origins of DNA polymerase fidelity Structure 11 489 496
2. Beard WA. Shock DD. Vande Berg BJ. Wilson SH. 2002 Efficiency of correct nucleotide insertion governs DNA polymerase fidelity J Biol Chem 277 47393 47398
3. Bebenek K. Kunkel TA. 1990 Frameshift errors initiated by nucleotide misincorporation Proc Natl Acad Sci USA 87 4946 4950
4. Blinkova A. Hervas C. Stukenberg PT. Onrust R. O'Donnell M. Walker JR. 1993 The Escherichia coli DNA polymerase III holoenzyme contains both products of the dnaX gene, τ and γ, but only τ is essential J Bacteriol 175 6018 6027
5. Blinkowa AL. Walker JR. 1990 Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III γ subunit from within the τ subunit reading frame Nucleic Acids Res 18 1725 1729
6. Bloom LB. Chen X. Fygenson DK. Turner J. O'Donnell M. Goodman MF. 1997 Fidelity of Escherichia coli DNA polymerase III holoenzyme. The effects of β, γ complex processivity proteins and ε proofreading exonuclease on nucleotide misincorporation efficiencies J Biol Chem 272 27919 27930
7. Creighton S. Goodman MF. 1995 Gel kinetic analysis of DNA polymerase fidelity in the presence of proofreading using bacteriophage T4 DNA polymerase J Biol Chem 270 4759 4774
8. Cupples C. Miller JH. 1989 A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions Proc Natl Acad Sci USA 86 5345 5349
9. Dallmann HG. McHenry CS. 1995 DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Physical characterization of the DnaX subunits and complexes J Biol Chem 270 29563 29569
10. Dallmann HG. Kim S. Pritchard AE. Marians KJ. McHenry CS. 2000 Characterization of the unique C terminus of the Escherichia coliτ DnaX protein. Monomeric C-τ binds α and DnaB and can partially replace τ in reconstituted replication forks J Biol Chem 275 15512 15519
11. Fijalkowska IJ. Schaaper RM. 1995 Effects of Escherichia coli dnaE antimutator alleles in a proofreading-deficient mutD5 strain J Bacteriol 177 5979 5986
12. Fijalkowska IJ. Schaaper RM. 1996 Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe Proc Natl Acad Sci USA 93 2856 2861
13. Fijalkowska IJ. Dunn RL. Schaaper RM. 1997 Genetic requirements and mutational specificity of the Escherichia coli SOS mutator activity J Bacteriol 179 7435 7445
14. Fijalkowska IJ. Jonczyk P. Tkaczyk MM. Bialoskorska M. Schaaper RM. 1998 Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome Proc Natl Acad Sci USA 95 10020 10025
15. Flower AM. McHenry CS. 1986 The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame Nucleic Acids Res 14 8091 8101
16. Flower AM. McHenry CS. 1990 The γ subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting Proc Natl Acad Sci USA 87 3713 3717
17. Gao D. McHenry CS. 2001 τ binds and organizes Escherichia coli replication proteins through distinct domains. Partial proteolysis of terminally tagged τ to determine candidate domains and to assign domain V as the α binding domain J Biol Chem 276 4433 4440
18. Garibyan L. Huang T. Kim M. Wolff E. Nguyen A. Nguyen T. et al. 2003 Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome DNA Repair 2 593 608
19. Guerola N. Ingraham JL. Cerda-Olmedo E. 1971 Induction of closely linked multiple mutations by nitrosoguanidine Nat New Biol 230 122 125
20. Henson JM. Chu H. Irwin CA. Walker JR. 1979 Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli Genetics 92 1041 1059
21. Johnson KA. 1993 Conformational coupling in DNA polymerase fidelity Annu Rev Biochem 62 685 713
22. Joyce CM. Sun XC. Grindley NDF. 1992 Reactions at the polymerase active site that contribute to the fidelity of Escherichia coli DNA polymerase I (Klenow fragment) J Biol Chem 267 24485 24500
23. Kelman Z. O'Donnell M. 1995 DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine Annu Rev Biochem 64 171 200
24. Kim DR. McHenry CS. 1996a Biotin tagging deletion analysis of domain limits involved in protein-macromolecular interactions. Mapping the τ binding domain of the DNA polymerase III α subunit J Biol Chem 271 20690 20698
25. Kim DR. McHenry CS. 1996b In vivo assembly of overproduced DNA polymerase III. Overproduction, purification, and characterization of the α, α-ε, and α-ε-θ subunits J Biol Chem 271 20681 20689
26. Kim S. Dallmann HG. McHenry CS. Marians KJ. 1996 τ couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork J Biol Chem 271 21406 21412
27. Kleckner N. Bender J. Gottesman S. 1991 Uses of transposons with emphasis on Tn10 Methods Enzymol 204 139 180
28. Kodaira M. Biswas SB. Kornberg A. 1983 The dnaX gene encodes the DNA polymerase III holoenzyme τ subunit, precursor of the γ subunit, the dnaZ gene product Mol Gen Genet 192 80 86
29. Kohara Y. Akiyama K. Isono K. 1987 The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library Cell 50 495 508
30. Kong X-P. Onrust R. O'Donnell M. Kuriyan J. 1992 Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp Cell 69 425 437
31. Leu FP. Georgescu R. O'Donnell M. 2003 Mechanism of the E. coliτ processivity switch during lagging-strand synthesis Mol Cell 11 315 327
32. Ling H. Boudsocq F. Woodgate R. Yang W. 2001 Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication Cell 197 91 102
33. López de Saro FJ. Georgescu RE. Goodman MF. O'Donnell M. 2003a Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair EMBO J 22 6408 6418
34. López de Saro FJ. Georgescu RE. O'Donnell M. 2003b A peptide switch regulates DNA polymerase processivity Proc Natl Acad Sci USA 100 14689 14694
35. McHenry CS. 1982 Purification and characterization of DNA polymerase III′. Identification of τ as a subunit of the DNA polymerase III holoenzyme J Biol Chem 257 2657 2663
36. McHenry CS. 2003 Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences Mol Microbiol 49 1157 1165
37. McInerney P. O'Donnell M. 2004 Functional uncoupling of twin polymerases. Mechanism of polymerase dissociation from a lagging-strand block J Biol Chem 279 21543 21551
38. Mendelman LV. Petruska J. Goodman MF. 1990 Base mispair extension kinetics. Comparison of DNA polymerase alpha and reverse transcriptase J Biol Chem 265 2338 2346
39. Miller JH. 1992 A Short Course in Bacterial Genetics Cold Spring Harbor, New York Cold Spring Harbor Laboratory Press.
40. Miller JH. 1996 Spontaneous mutators in bacteria: insights into pathways of mutagenesis and repair Annu Rev Microbiol 50 625 643
41. Mo J-Y. Schaaper RM. 1996 Fidelity and error specificity of the α catalytic subunit of Escherichia coli DNA polymerase III J Biol Chem 271 18947 18953
42. Modrich P. 1991 Mechanisms and biological effects of mismatch repair Annu Rev Genet 25 229 253
43. Mullin DA. Woldringh CL. Henson JM. Walker JR. 1983 Cloning of the Escherichia coli dnaZX region and identification of its products Mol Gen Genet 192 73 79
44. Nakano Y. Yoshida Y. Yamashita Y. Koga T. 1995 Construction of a series of pACYC-derived plasmid vectors Gene 162 157 158
45. Naktinis V. Turner J. O'Donnell M. 1996 A molecular switch in a replication machine defined by an internal competition for protein rings Cell 84 137 145
46. Nghiem Y. Cabrera M. Cupples CG. Miller JH. 1988 The mutY gene: a mutator locus in Escherichia coli that generates G·C→T·A transversions Proc Natl Acad Sci USA 85 2709 2713
47. Onrust R. Finkelstein J. Naktinis V. Turner J. Fang L. O'Donnell M. 1995 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 270 13348 13357
48. Perrino FW. Loeb LA. 1989 Differential extension of 3′ mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase-alpha J Biol Chem 264 2898 2905
49. Pham PT. Olson MW. McHenry CS. Schaaper RM. 1998 The base substitution and frameshift fidelity of Escherichia coli DNA polymerase III holoenzyme in vitro J Biol Chem 273 23575 23584
50. Pham PT. Olson MW. McHenry CS. Schaaper RM. 1999 Mismatch extension by Escherichia coli DNA polymerase III holoenzyme J Biol Chem 274 3705 3710
51. Rangarajan S. Gudmundsson G. Qiu Z. Foster PL. Goodman MF. 1997 Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo Proc Natl Acad Sci USA 94 946 951
52. Schaaper RM. 1988 Mechanism of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair Proc Natl Acad Sci USA 85 8126 8130
53. Schaaper RM. 1993a Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli J Biol Chem 268 23762 23765
54. Schaaper RM. 1993b The mutational specificity of two Escherichia coli dnaE antimutator alleles as determined from lacI mutation spectra Genetics 134 1031 1038
55. Schaaper RM. Dunn RL. 1991 Spontaneous mutation in the Escherichia coli lacI gene Genetics 129 317 326
56. Schaaper RM. Danforth BN. Glickman BW. 1985 Rapid repeated cloning of mutant lac repressor genes Gene 39 181 189
57. Siegel EC. Vaccaro KK. 1978 The reversion of trp frameshift mutations in mut, polA, lig, and dnaE mutant strains of Escherichia coli Mutat Res 50 9 17
58. Siegel EC. Wain SL. Meltzer SF. Binion ML. Steinberg JL. 1982 Mutator mutations in Escherichia coli induced by the insertion of phage mu and the transposable resistance elements Tn5 and Tn10 Mutat Res 93 25 33
59. Singer M. Baker TA. Schnitzler G. Deischel SM. Goel M. Dove M. et al. 1989 A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli Microbiol Rev 53 1 24
60. Studwell-Vaughan PS. O'Donnell M. 1993 DNA polymerase III accessory proteins: θ encoded by holE J Biol Chem 268 1785 11791
61. Stukenberg PT. O'Donnell M. 1995 Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. V. Four different polymerase-clamp complexes on DNA J Biol Chem 270 13384 13391
62. Taft-Benz SA. Schaaper RM. 2004 The θ subunit of Escherichia coli DNA Polymerase III: a role in stabilizing the ε proofreading subunit J Bacteriol 186 2774 2780 /
63. Tsuchihashi Z. Kornberg A. 1990 Translational frameshifting generates the γ subunit of DNA polymerase III holoenzyme Proc Natl Acad Sci USA 87 2516 2520
64. Wagner J. Etienne H. Janel-Bintz R. Fuchs RPP. 2002 Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity DNA Repair 1 159 167
65. Yin K-C. Blinkowa A. Walker JR. 1986 Nucleotide sequence of the Escherichia coli replication gene dnaZX Nucleic Acids Res 14 6541 6549