Biochemical evolution of DNA polymerase η: Properties of plant, human, and yeast proteins

Biochemistry

Volumn 47, Issue 16, 2008, Pages 4583-4596

  Hoffman, Peter D ^a   Curtis, Marc J ^a   Iwai, Shigenori ^b   Hays, John B ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; DNA; ESCHERICHIA COLI; MAMMALS; PLANTS (BOTANY); YEAST;

CYCLOBUTANE THYMINE DIMERS; POLYMERASE DOMAINS; SYNTHETIC PRIMERS;

ENZYME KINETICS;

CYCLOBUTANE; DIMER; DNA DIRECTED DNA POLYMERASE ETA; NUCLEOTIDE; PYRIMIDINE DERIVATIVE; THYMINE;

ARABIDOPSIS; ARTICLE; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME PURIFICATION; ESCHERICHIA COLI; EVOLUTION; GENETIC CONSERVATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; SUN EXPOSURE; THERMOSTABILITY; ULTRAVIOLET B RADIATION;

AMINO ACID SEQUENCE; ARABIDOPSIS; BASE SEQUENCE; BIOCHEMISTRY; CONSERVED SEQUENCE; DNA-DIRECTED DNA POLYMERASE; EVOLUTION, MOLECULAR; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PHOTOCHEMISTRY; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT;

ARABIDOPSIS THALIANA; ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 42349084043     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701781p     Document Type: Article

References (27)

1. Friedberg, E. C., Wagner, R., and Radman, M. (2002) Specialized DNA polymerases cellular survival, and the genesis of mutations. Science 296, 1627-1630.
2. Trincao, J., Johnson, R. E., Escalante, C. R., Prakash, S., Prakash, L., and Aggarwal, A. K. (2001) Structure of the catalytic core of S. cerevisiae DNA polymerase η: Implications for translesion DNA synthesis. Mol. Cell 8, 417-426.
3. Ohmori, H., Friedberg, E. C., Fuchs, R. P., Goodman, M. F., Hanaoka, F., Hinkle, D., Kunkel, T. A., Lawrence, C. W., Livneh, Z., Nohmi, T., Prakash, L., Prakash, S., Todo, T., Walker, G. C., Wang, Z., and Woodgate, R. (2001) The Y-family of DNA polymerases. Mol. Cell 8, 7-8.
4. Johnson, R. E., Prakash, S., and Prakash, L. (1999) Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Pol η. Science 283, 1001-1004.
5. Masutani, C., Kusomoto, A., Yamada, A., Dohmae, N., Yokoi, M., Yuasa, M., Araki, M., Iwai, S., Takio, K., and Hanaoka, F. (1999) The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399, 700-704.
6. Lehmann, A. R. (1975) Xeroderma pigmentosum cells with normal levels of excision repair have a defect in DNA synthesis after UV-irradiation. Proc. Natl. Acad. Sci. U.S.A. 72, 219-223.
7. Washington, M. T., Johnson, R. E., Prakash, S., and Prakash, L. (2000) Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase η. Proc. Natl. Acad. Sci. U.S.A. 97, 3094-3099.
8. Haracska, L., Yu, S. L., Johnson, R. E., Prakash, L., and Prakash, S. (2000) Efficient and accurate replication in the presence of 7,8-dihydro-8 oxoguanine by DNA polymerase η. Nat. Genet. 25, 458-461.
9. Yuan, F., Zhang, Y., Rajpal, D. K., Wu, X., Guo, D., Wang, M., Taylor, J. S., and Wang, Z. (2000) Specificity of DNA lesion bypass by the yeast DNA polymerase η. J. Biol. Chem. 275, 8233-8239.
10. Murata, T., Iwai, S., and Ohtsuka, E. (1990) Synthesis and characterization of a substrate for T4 endonuclease V containing a phosphorodithioate linkage at the thymine dimer site. Nucleic Acids Res. 18, 7279-7286.
11. Kokoska, R. J., McCulloch, S. D., and Kunkel, T. A. (2003) The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase η and Sulfolobus solfataricus Dpo4. J. Biol. Chem. 278, 50537-50545.
12. Creighton, S., Bloom, L. B., and Goodman, M. F. (1995) Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol. 262, 232-256.
13. Johnson, R. E., Haracska, L., Prakash, S., and Prakash, L. (2001) Role of DNA polymerase η in the bypass of a (6-4) TT photoproduct. Mol. Cell. Biol. 21, 3558-3563.
14. Kusumoto, R., Masutani, C., Shimmyo, S., Iwai, S., and Hanaoka, F. (2004) DNA binding properties of human DNA polymerase η: Implications for fidelity and polymerase switching of translesion synthesis. Genes Cells 9, 1139-1150.
15. McCulloch, S. D., Kokoska, R. J., Matsutani, C., Iwai, S., Hanaoka, F., and Kunkel, T. T. (2004) Preferential cis-syn thymine dimer bypass occurs with biased fidelity. Nature 428, 97-99.
16. McCulloch, S. D., Wood, A., Garg, P., Burgers, P. M., and Kunkel, T. A. (2007) Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saecharomyces cerevisiae DNA polymerase η. Biochemistry 46, 8888-8896.
17. Johnson, R. E., Washington, M. T., Haracska, L., Prakash, S., and Prakash, L. (2000) Eukaryotic polymerase [ι] and [ξ] act sequentially to bypass DNA lesions. Nature 406, 1015-1019.
18. McDonald, J. P., Levine, A. S., and Woodgate, R. (1997) The Saecharomyces cerevisial RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free postreplication repair mechanism. Genetics 147, 1557-1568.
19. Barone, F., McCulloch, S. D., Macpherson, P., Maga, G., Yamada, M., Nohmi, T., Minoprio, A., Mazzei, F., Kunkel, T. A., Karran, P., and Bignami, M. (2007) Replication of 2-hydroxyadenine-containing DNA and recognition by human MutSalpha. DNA Repair 6, 355-366.
20. Prakash, S., Johnson, R. E., and Prakash, L. (2005) Eukaryotic translesion synthesis DNA polymerases: Specificity of structure and function. Annu. Rev. Biochem. 74, 317-353.
21. Lawrence, C., and Christensen, R. (1976) UV Mutagenesis in Radiation-Sensitive Strains of Yeast. Genetics 82, 207-232.
22. Haracska, L., Kondratick, C. M., Unk, I., Prakash, S., and Prakash, L. (2001) Interaction with PCNA is essential for yeast DNA polymerase η function. Mol. Cell 8, 407-415.
23. Santiago, M. J., Alejandre-Duran, E., and Ruiz-Rubio, M. (2006) Analysis of UV-induced mutation spectra in Escherichia coli by DNA polymerase η from Arabidopsis thaliana. Mutat. Res. 601, 51-60.
24. Horsfall, M. J., Borden, A., and Lawrence, C. W. (1997) Mutagenic properties of the T-C cyclobutane dimer. J. Bacteriol. 179, 2835-2839.
25. Tissier, A., McDonald, J. P., Frank, E. G., and Woodgate, R. (2000) Pol iota, a remarkably error-prone human DNA polymerase. Genes Dev. 14, 1642-1650.
26. Vaisman, A., Frank, E. G., Iwai, S., Ohashi, E., Ohmori, H., Hanaoka, F., and Woodgate, R. (2003) Sequence context-dependent replication of DNA templates containing UV-induced lesions by human DNA polymerase ι. DNA Repair 2, 991-1006.
27. Washington, M. T., Johnson, R. E., Prakash, L, and Prakash, S. (1999) Fidelilty and processivity of Saecharomyces cerevisiae DNA polymerase η. J. Biol. Chem. 274, 36835-36838.