Effect of sequence context and direction of replication on AP site bypass in Saccharomyces cerevisiae

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 669, Issue 1-2, 2009, Pages 147-154

  Bao, Gaobin ^a   Kow, Yoke W ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

AP site bypass; Direction of replication; Sequence context; Single strand oligonucleotide transformation

Indexed keywords

OLIGONUCLEOTIDE;

APURINIC SITE; APYRIMIDINIC SITE; ARTICLE; CONTROLLED STUDY; DNA REPLICATION; DNA SEQUENCE; FUNGAL GENETICS; GENETIC TRANSFORMATION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

DNA DAMAGE; DNA REPLICATION; DNA, FUNGAL; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; FRAMESHIFT MUTATION; OLIGONUCLEOTIDES; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 70349101621     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2009.06.006     Document Type: Article

References (47)

1. Dianov G.L., Sleeth K.M., Dianova I.I., and Allinson S.L. Repair of abasic sites in DNA. Mutation Research 531 (2003) 157-163
2. Evans A.R., Limp-Foster M., and Kelley M.R. Going APE over ref-1. Mutation Research 461 (2000) 83-108
3. Loeb L.A., and Preston B.D. Mutagenesis by apurinic/apyrimidinic sites. Annual Review of Genetics 20 (1986) 201-230
4. Loeb L.A., Preston B.D., Snow E.T., and Schaaper R.M. Apurinic sites as common intermediates in mutagenesis. Basic Life Sciences 38 (1986) 341-347
5. Lindahl T., and Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11 (1972) 3610-3618
6. von Sonntag C. The Chemical Basis of Radiation Biology (1987), Taylor & Francis, London
7. Friedberg E.C., Walker G.C., Siede W., Wood R.D., Schultz R.A., and Ellenberger T. DNA Repair and Mutagenesis (2006), ASM Press, Washington, DC
8. Wallace S.S. AP endonucleases and DNA glycosylases that recognize oxidative DNA damage. Environmental and Molecular Mutagenesis 12 (1988) 431-477
9. Johnson R.E., Torres-Ramos C.A., Izumi T., Mitra S., Prakash S., and Prakash L. Identification of APN2, the Saccharomyces cerevisiae homolog of the major human AP endonuclease HAP1, and its role in the repair of abasic sites. Genes & Development 12 (1998) 3137-3143
10. Unk I., Haracska L., Johnson R.E., Prakash S., and Prakash L. Apurinic endonuclease activity of yeast Apn2 protein. The Journal of Biological Chemistry 275 (2000) 22427-22434
11. Unk I., Haracska L., Prakash S., and Prakash L. 3′-Phosphodiesterase and 3′-->5′ exonuclease activities of yeast Apn2 protein and requirement of these activities for repair of oxidative DNA damage. Molecular and Cellular Biology 21 (2001) 1656-1661
12. Boiteux S., and Guillet M. Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae. DNA Repair 3 (2004) 1-12
13. Boiteux S., and Guillet M. Use of yeast for detection of endogenous abasic lesions, their source, and their repair. Methods in Enzymology 408 (2006) 79-91
14. Gibbs P.E., and Lawrence C.W. Novel mutagenic properties of abasic sites in Saccharomyces cerevisiae. Journal of Molecular Biology 251 (1995) 229-236
15. Gibbs P.E., McDonald J., Woodgate R., and Lawrence C.W. The relative roles in vivo of Saccharomyces cerevisiae Pol eta, Pol zeta, Rev1 protein and Pol32 in the bypass and mutation induction of an abasic site, T-T (6-4) photoadduct and T-T cis-syn cyclobutane dimer. Genetics 169 (2005) 575-582
16. Zhao B., Xie Z., Shen H., and Wang Z. Role of DNA polymerase eta in the bypass of abasic sites in yeast cells. Nucleic Acids Research 32 (2004) 3984-3994
17. Kalam M.A., and Basu A.K. Mutagenesis of 8-oxoguanine adjacent to an abasic site in simian kidney cells: tandem mutations and enhancement of G-->T transversions. Chemical Research in Toxicology 18 (2005) 1187-1192
18. Pages V., Johnson R.E., Prakash L., and Prakash S. Mutational specificity and genetic control of replicative bypass of an abasic site in yeast. Proceedings of the National Academy of Sciences of the United States of America 105 (2008) 1170-1175
19. Otsuka C., Kobayashi K., Kawaguchi N., Kunitomi N., Moriyama K., Hata Y., Iwai S., Loakes D., Noskov V.N., Pavlov Y., and Negishi K. Use of yeast transformation by oligonucleotides to study DNA lesion bypass in vivo. Mutation Research 502 (2002) 53-60
20. Otsuka C., Sanadai S., Hata Y., Okuto H., Noskov V.N., Loakes D., and Negishi K. Difference between deoxyribose- and tetrahydrofuran-type abasic sites in the in vivo mutagenic responses in yeast. Nucleic Acids Research 30 (2002) 5129-5135
21. Kow Y.W., Bao G., Minesinger B., Jinks-Robertson S., Siede W., Jiang Y.L., and Greenberg M.M. Mutagenic effects of abasic and oxidized abasic lesions in Saccharomyces cerevisiae. Nucleic Acids Research 33 (2005) 6196-6202
22. Kow Y.W., Bao G., Reeves J.W., Jinks-Robertson S., and Crouse G.F. Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands. Proceedings of the National Academy of Sciences of the United States of America 104 (2007) 11352-11357
23. Sherman F. Getting started with yeast. Methods in Enzymology 194 (1991) 3-21
24. Ide H., Tedzuka K., Shimzu H., Kimura Y., Purmal A.A., Wallace S.S., and Kow Y.W. Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry 33 (1994) 7842-7847
25. Kow Y.W. Base excision repair in E. coli-an overview. Annals of the New York Academy of Sciences 726 (1994) 178-180
26. Yao M., and Kow Y.W. Further characterization of Escherichia coli endonuclease. V. Mechanism of recognition for deoxyinosine, deoxyuridine, and base mismatches in DNA. The Journal of Biological Chemistry 272 (1997) 30774-30779
27. Harfe B.D., and Jinks-Robertson S. Removal of frameshift intermediates by mismatch repair proteins in Saccharomyces cerevisiae. Molecular and Cellular Biology 19 (1999) 4766-4773
28. Harfe B.D., and Jinks-Robertson S. Sequence composition and context effects on the generation and repair of frameshift intermediates in mononucleotide runs in Saccharomyces cerevisiae. Genetics 156 (2000) 571-578
29. Sikorski R.S., and Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122 (1989) 19-27
30. Rothstein R. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods in Enzymology 194 (1991) 281-301
31. Kim N., Abdulovic A.L., Gealy R., Lippert M.J., and Jinks-Robertson S. Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication. DNA Repair 6 (2007) 1285-1296
32. Nelson J.R., Lawrence C.W., and Hinkle D.C. Deoxycytidyl transferase activity of yeast REV1 protein. Nature 382 (1996) 729-731
33. Lawrence C.W., and Maher V.M. Eukaryotic mutagenesis and translesion replication dependent on DNA polymerase zeta and Rev1 protein. Biochemical Society Transactions 29 (2001) 187-191
34. Lawrence C.W., and Maher V.M. Mutagenesis in eukaryotes dependent on DNA polymerase zeta and Rev1p. Philosophical Transactions of the Royal Society of London 356 (2001) 41-46
35. Ye N., Holmquist G.P., and O'Connor T.R. Heterogeneous repair of N-methylpurines at the nucleotide level in normal human cells. Journal of Molecular Biology 284 (1998) 269-285
36. Hatahet Z., Zhou M., Reha-Krantz L.J., Ide H., Morrical S.W., and Wallace S.S. In vitro selection of sequence contexts which enhance bypass of abasic sites and tetrahydrofuran by T4 DNA polymerase holoenzyme. Journal of Molecular Biology 286 (1999) 1045-1057
37. Hatahet Z., Zhou M., Reha-Krantz L.J., Morrical S.W., and Wallace S.S. In search of a mutational hotspot. Proceedings of the National Academy of Sciences of the United States of America 95 (1998) 8556-8561
38. Eftedal I., Guddal P.H., Slupphaug G., Volden G., and Krokan H.E. Consensus sequences for good and poor removal of uracil from double stranded DNA by uracil-DNA glycosylase. Nucleic Acids Research 21 (1993) 2095-2101
39. Slupphaug G., Eftedal I., Kavli B., Bharati S., Helle N.M., Haug T., Levine D.W., and Krokan H.E. Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase. Biochemistry 34 (1995) 128-138
40. Nazimiec M., Lee C.S., Tang Y.L., Ye X., Case R., and Tang M. Sequence-dependent interactions of two forms of UvrC with DNA helix-stabilizing CC-1065-N3-adenine adducts. Biochemistry 40 (2001) 11073-11081
41. Mekhovich O., Tang M., and Romano L.J. Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. Biochemistry 37 (1998) 571-579
42. Boosalis M.S., Petruska J., and Goodman M.F. DNA polymerase insertion fidelity. Gel assay for site-specific kinetics. The Journal of Biological Chemistry 262 (1987) 14689-14696
43. Cai H., Bloom L.B., Eritja R., and Goodman M.F. Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase. The Journal of Biological Chemistry 268 (1993) 23567-23572
44. Dosanjh M.K., Galeros G., Goodman M.F., and Singer B. Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences. Biochemistry 30 (1991) 11595-11599
45. Mendelman L.V., Boosalis M.S., Petruska J., and Goodman M.F. Nearest neighbor influences on DNA polymerase insertion fidelity. The Journal of Biological Chemistry 264 (1989) 14415-14423
46. Randall S.K., Eritja R., Kaplan B.E., Petruska J., and Goodman M.F. Nucleotide insertion kinetics opposite abasic lesions in DNA. The Journal of Biological Chemistry 262 (1987) 6864-6870
47. Singer B., Chavez F., Goodman M.F., Essigmann J.M., and Dosanjh M.K. Effect of 3′ flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is used. Proceedings of the National Academy of Sciences of the United States of America 86 (1989) 8271-8274