Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ

DNA Repair

Volumn 12, Issue 2, 2013, Pages 121-127

  Clausen, Anders R ^a   Zhang, Sufang ^b   Burgers, Peter M ^c   Lee, Marietta Y ^b   Kunkel, Thomas A ^a  

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

^b NEW YORK MEDICAL COLLEGE   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bypass; DNA polymerase delta; Incorporation; Proofreading; Ribonucleotide

Indexed keywords

DNA DIRECTED DNA POLYMERASE ALPHA; DNA DIRECTED DNA POLYMERASE DELTA; DNA DIRECTED DNA POLYMERASE EPSILON; NUCLEOTIDE; RIBONUCLEASE; RIBONUCLEASE H2; RIBONUCLEOTIDE; SPLEEN EXONUCLEASE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BUDDING; CONTROLLED STUDY; DNA METABOLISM; DNA REPLICATION; DNA SYNTHESIS; DNA TEMPLATE; ENZYME STABILITY; GENOME; HUMAN; HUMAN CELL; MAMMAL CELL; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROOFREADING; RIBONUCLEOTIDE INCORPORATION; RNA EDITING;

DNA POLYMERASE III; DNA REPAIR; DNA REPLICATION; HUMANS; MUTATION; RIBONUCLEOTIDES; SACCHAROMYCES CEREVISIAE;

MAMMALIA; MUS; SCHIZOSACCHAROMYCETACEAE;

EID: 84872485372     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2012.11.006     Document Type: Article

References (25)

1. Kornberg A., Baker T.A. DNA Replication 2005, University Science Books, Herndon, VA.
2. Brown J.A., Suo Z.C. Unlocking the sugar steric gate of DNA polymerases. Biochemistry 2011, 50:1135-1142.
3. Joyce C.M. Choosing the right sugar: how polymerases select a nucleotide substrate. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:1619-1622.
4. McElhinny S.A.N., Watts B.E., Kumar D., Watt D.L., Lundstrom E.B., Burgers P.M.J., Johansson E., Chabes A., Kunkel T.A. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:4949-4954.
5. Traut T.W. Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 1994, 140:1-22.
6. McElhinny S.A.N., Kumar D., Clark A.B., Watt D.L., Watts B.E., Lundstrom E.B., Johansson E., Chabes A., Kunkel T.A. Genome instability due to ribonucleotide incorporation into DNA. Nat. Chem. Biol. 2010, 6:774-781.
7. Sparks J.L., Chon H., Cerritelli S.M., Kunkel T.A., Johansson E., Crouch R.J., Burgers P.M. RNase H2-initiated ribonucleotide excision repair. Mol. Cell 2012, 47:980-986.
8. Clark A.B., Lujan S.A., Kissling G.E., Kunkel T.A. Mismatch repair-independent tandem repeat sequence instability resulting from ribonucleotide incorporation by DNA polymerase epsilon. DNA Repair 2011, 10:476-482.
9. Kim N., Huang S.Y.N., Williams J.S., Li Y.C., Clark A.B., Cho J.E., Kunkel T.A., Pommier Y., Jinks-Robertson S. Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science 2011, 332:1561-1564.
10. Miyabe I., Kunkel T.A., Carr A.M. The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved. PLoS Genet. 2011, 7.
11. Williams J.S., Clausen A.R., McElhinny S.A.N., Watts B.E., Johansson E., Kunkel T.A. Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase epsilon. DNA Repair 2012, 11:649-656.
12. Crow Y.J., Leitch A., Hayward B.E., Garner A., Parmar R., Griffith E., Ali M., Semple C., Aicardi J., Babul-Hirji R., Baumann C., Baxter P., Bertini E., Chandler K.E., Chitayat D., Cau D., Dery C., Fazzi E., Goizet C., King M.D., Klepper J., Lacombe D., Lanzi G., Lyall H., Martinez-Frias M.L., Mathieu M., McKeown C., Monier A., Oade Y., Quarrell O.W., Rittey C.D., Rogers R.C., Sanchis A., Stephenson J.B.P., Tacke U., Till M., Tolmie J.L., Tomlin P., Voit T., Weschke B., Woods C.G., Lebon P., Bonthron D.T., Ponting C.P., Jackson A.P. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutiéres syndrome and mimic congenital viral brain infection. Nat. Genet. 2006, 38:910-916.
13. Reijns M.A.M., Rabe B., Rigby R.E., Mill P., Astell K.R., Lettice L.A., Boyle S., Leitch A., Keighren M., Kilanowski F., Devenney P.S., Sexton D., Grimes G., Holt I.J., Hill R.E., Taylor M.S., Lawson K.A., Dorin J.R., Jackson A.P. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 2012, 149:1008-1022.
14. McElhinny S.A.N., Gordenin D.A., Stith C.M., Burgers P.M.J., Kunkel T.A. Division of labor at the eukaryotic replication fork. Mol. Cell 2008, 30:137-144.
15. Fortune J.M., Pavlov Y.I., Welch C.M., Johansson E., Burgers P.M.J., Kunkel T.A. Saccharomyces cerevisiae DNA polymerase delta: high fidelity for base substitutions but lower fidelity for single- and multi-base deletions. J. Biol. Chem. 2005, 280:29980-29987.
16. Burgers P.M.J., Gerik K.J. Structure and processivity of two forms of Saccharomyces cerevisiae DNA polymerase delta. J. Biol. Chem. 1998, 273:19756-19762.
17. Eissenberg J.C., Ayyagari R., Gomes X.V., Burgers P.M.J. Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase delta and DNA polymerase epsilon. Mol. Cell. Biol. 1997, 17:6367-6378.
18. Fazlieva R., Spittle C.S., Morrissey D., Hayashi H., Yan H., Matsumoto Y. Proofreading exonuclease activity of human DNA polymerase and its effects on lesion-bypass DNA synthesis. Nucleic Acids Res. 2009, 37:2854-2866.
19. Xie B., Mazloum N., Liu L., Rahmeh A., Li H., Lee M. Reconstitution and characterization of the human DNA polymerase delta four-subunit holoenzyme. Biochemistry 2002, 41:13133-13142.
20. McElhinny S.A.N., Ramsden D.A. Polymerase Mu is a DNA-directed DNA/RNA polymerase. Mol. Cell. Biol. 2003, 23:2309-2315.
21. Shen Y., Koh K.D., Weiss B., Storici F. Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H. Nat. Struct. Mol. Biol. 2012, 19:98-104.
22. Lazzaro F., Novarina D., Amara F., Watt D.L., Stone J.E., Costanzo V., Burgers P.M., Kunkel T.A., Plevani P., Muzi-Falconi M., Nase R.H. Postreplication repair protect cells from ribonucleotides incorporated in DNA. Mol. Cell 2012, 45:99-110.
23. Watt D.L., Johansson E., Burgers P.M., Kunkel T.A. Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases. DNA Repair 2011, 10:897-902.
24. Cerritelli S.M., Crouch R.J. Ribonuclease H: the enzymes in eukaryotes. FEBS J. 2009, 276:1494-1505.
25. Vengrova S., Dalgaard J.Z. The wild-type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides. EMBO Rep. 2006, 7:59-65.