Mutational consequences of dNTP pool imbalances in E. coli

DNA Repair

Volumn 12, Issue 1, 2013, Pages 73-79

  Schaaper, Roel M ^a   Mathews, Christopher K ^b  

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

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

DCTP deaminase; DNA polymerase; DNA replication fidelity; DNTP pools; Nucleoside diphosphate kinase

Indexed keywords

5' DEOXYNUCLEOSIDE TRIPHOSPHATE; NUCLEOSIDE TRIPHOSPHATE; RIFAMPICIN; UNCLASSIFIED DRUG;

ARTICLE; CARBON SOURCE; DNA REPLICATION; ESCHERICHIA COLI; IN VITRO STUDY; IN VIVO STUDY; MISMATCH REPAIR; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL;

ADENOSINE TRIPHOSPHATASES; DEOXYRIBONUCLEOTIDES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MUTAGENESIS; MUTATION RATE; NUCLEOSIDE-DIPHOSPHATE KINASE; NUCLEOTIDE DEAMINASES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84871714881     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2012.10.011     Document Type: Article

References (48)

1. Kunkel T.A. DNA replication fidelity. J. Biol. Chem. 2004, 279:16895-16898.
2. Kunkel T.A., Bebenek K. DNA replication fidelity. Annu. Rev. Biochem. 2000, 69:497-529.
3. Nordlund P., Reichard P. Ribonucleotide reductases. Annu. Rev. Biochem. 2006, 75:681-706.
4. Friedberg E.C. DNA Repair and Mutagenesis 2006, ASM Press, Washington, DC. 2nd ed.
5. Bessman M.J., Frick D.N., O'Handley S.F. The MutT proteins or Nudix hydrolases, a family of versatile, widely distributed, housecleaning enzymes. J. Biol. Chem. 1996, 271:25059-25062.
6. Galperin M.Y., Moroz O.V., Wilson K.S., Murzin A.G. House cleaning, a part of good housekeeping. Mol. Microbiol. 2006, 59:5-19.
7. Maki H., Sekiguchi M. MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature 1992, 355:273-275.
8. Wheeler L.J., Rajagopal I., Mathews C.K. Stimulation of mutagenesis by proportional deoxyribonucleoside triphosphate accumulation in Escherichia coli. DNA Repair 2005, 4:1450-1456.
9. Mathews C.K., Ji J. DNA precursor asymmetries, replication fidelity, and variable genome evolution. BioEssays 1992, 14:295-301.
10. Song S., Pursell Z.F., Copeland W.C., Longley M.J., Kunkel T.A., Mathews C.K. DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:4990-4995.
11. Wheeler L.J., Mathews C.K. Nucleoside triphosphate pool asymmetry in mammalian mitochondria. J. Biol. Chem. 2011, 286:16992-16996.
12. Ahluwalia D., Bienstock R.J., Schaaper R.M. Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates. DNA Repair 2012, 11:480-487.
13. Kumar D., Abdulovic A.L., Viberg J., Nilsson A.K., Kunkel T.A., Chabes A. Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools. Nucleic Acids Res. 2011, 39:1360-1371.
14. Gon S., Napolitano R., Rocha W., Coulon S., Fuchs R.P. Increase in dNTP pool size during the DNA damage response plays a key role in spontaneous and induced-mutagenesis in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:19311-19316.
15. Wang L., Weiss B. dcd (dCTP deaminase) gene of Escherichia coli: mapping, cloning, sequencing, and identification as a locus of suppressors of lethal dut (dUTPase) mutations. J. Bacteriol. 1992, 174:5647-5653.
16. Hama H., Almaula N., Lerner C.G., Inouye S., Inouye M. Nucleoside diphosphate kinase from Escherichia coli; its overproduction and sequence comparison with eukaryotic enzymes. Gene 1991, 105:31-36.
17. Hama H., Lerner C., Inouye S., Inouye M. Location of the gene (ndk) for nucleoside diphosphate kinase on the physical map of the Escherichia coli chromosome. J. Bacteriol. 1991, 173:3276.
18. Neuhard J., Thomassen E. Altered deoxyribonucleotide pools in P2 eductants of Escherichia coli K-12 due to deletion of the dcd gene. J. Bacteriol. 1976, 126:999-1001.
19. O'Donovan G.A., Edlin G., Fuchs J.A., Neuhard J., Thomassen E. Deoxycytidine triphosphate deaminase: characterization of an Escherichia coli mutant deficient in the enzyme. J. Bacteriol. 1971, 105:666-672.
20. Lacombe M.L., Milon L., Munier A., Mehus J.G., Lambeth D.O. The human Nm23/nucleoside diphosphate kinases. J. Bioenerg. Biomembr. 2000, 32:247-258.
21. Lu Q., Inouye M. Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:5720-5725.
22. Lu Q., Zhang X., Almaula N., Mathews C.K., Inouye M. The gene for nucleoside diphosphate kinase functions as a mutator gene in Escherichia coli. J. Mol. Biol. 1995, 254:337-341.
23. Miller J.H., Funchain P., Clendenin W., Huang T., Nguyen A., Wolff E., Yeung A., Chiang J.H., Garibyan L., Slupska M.M., Yang H. Escherichia coli strains (ndk) lacking nucleoside diphosphate kinase are powerful mutators for base substitutions and frameshifts in mismatch-repair-deficient strains. Genetics 2002, 162:5-13.
24. Nordman J., Wright A. The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:10197-10202.
25. Nordman J., Wright A. Escherichia coli nucleoside diphosphate kinase mutants depend on translesion DNA synthesis to prevent mutagenesis. J. Bacteriol. 2011, 193:4531-4533.
26. Schaaper R.M., Danforth B.N., Glickman B.W. Rapid repeated cloning of mutant lac repressor genes. Gene 1985, 39:181-189.
27. Fijalkowska I.J., Schaaper R.M. Effects of Escherichia coli dnaE antimutator alleles in a proofreading-deficient mutD5 strain. J. Bacteriol. 1995, 177:5979-5986.
28. Siegel E.C., Wain S.L., Meltzer S.F., Binion M.L., Steinberg J.L. Mutator mutations in Escherichia coli induced by the insertion of phage mu and the transposable resistance elements Tn5 and Tn10. Mutat. Res. 1982, 93:25-33.
29. Cupples C.G., Miller J.H. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc. Natl. Acad. Sci. U.S.A. 1989, 86:5345-5349.
30. Miller J.H. Experiments in Molecular Genetics 1972, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
31. Vogel H.J., Bonner D.M. Acetylornithinase of Escherichia coli: partial purification and some properties. J. Biol. Chem. 1956, 218:97-106.
32. Mathews C.K., Wheeler L.J. Measuring DNA precursor pools in mitochondria. Methods Mol. Biol. 2009, 554:371-381.
33. Ferraro P., Franzolin E., Pontarin G., Reichard P., Bianchi V. Quantitation of cellular deoxynucleoside triphosphates. Nucleic Acids Res. 2010, 38:e85.
34. Mathews C.K. Biochemistry of deoxyribonucleic acid-defective amber mutants of bacteriophage T4. 3. Nucleotide pools. J. Biol. Chem. 1972, 247:7430-7438.
35. Garibyan L., Huang T., Kim M., Wolff E., Nguyen A., Nguyen T., Diep A., Hu K., Iverson A., Yang H., Miller J.H. Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome. DNA Repair 2003, 2:593-608.
36. Neidhardt F.C., Curtiss R. Escherichia coli and Salmonella: Cellular and Molecular Biology 1996, ASM Press, Washington, DC. 2nd ed.
37. Scheuermann R.H., Echols H. A separate editing exonuclease for DNA replication: the epsilon subunit of Escherichia coli DNA polymerase III holoenzyme. Proc. Natl. Acad. Sci. U.S.A. 1984, 81:7747-7751.
38. Taft-Benz S.A., Schaaper R.M. Mutational analysis of the 3'→5' proofreading exonuclease of Escherichia coli DNA polymerase III. Nucleic Acids Res. 1998, 26:4005-4011.
39. Kunkel T.A., Schaaper R.M., Beckman R.A., Loeb L.A. On the fidelity of DNA replication. Effect of the next nucleotide on proofreading. J. Biol. Chem. 1981, 256:9883-9889.
40. Fijalkowska I.J., Jonczyk P., Tkaczyk M.M., Bialoskorska M., Schaaper R.M. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:10020-10025.
41. Fijalkowska I.J., Schaaper R.M., Jonczyk P. DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair. FEMS Microbiol. Rev. 2012.
42. Maliszewska-Tkaczyk M., Jonczyk P., Bialoskorska M., Schaaper R.M., Fijalkowska I.J. SOS mutator activity: unequal mutagenesis on leading and lagging strands. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:12678-12683.
43. Schaaper R.M. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 1993, 268:23762-23765.
44. Fijalkowska I.J., Schaaper R.M. Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:2856-2861.
45. Negishi K., Loakes D., Schaaper R.M. Saturation of DNA mismatch repair and error catastrophe by a base analogue in Escherichia coli. Genetics 2002, 161:1363-1371.
46. Schaaper R.M. Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. Proc. Natl. Acad. Sci. U.S.A. 1988, 85:8126-8130.
47. Duncan B.K., Weiss B. Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 1982, 151:750-755.
48. Schaaper R.M., Loeb L.A. Depurination causes mutations in SOS-induced cells. Proc. Natl. Acad. Sci. U.S.A. 1981, 78:1773-1777.