Ribonucleotides and manganese ions improve non-homologous end joining by human Polm

Nucleic Acids Research

Volumn 41, Issue 4, 2013, Pages 2428-2436

  Martin, Maria Jose ^a,b   Garcia Ortiz, Maria V ^a   Esteban, Veronica ^a   Blanco, Luis ^a  

^a CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT; DEOXYRIBONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE LAMBDA; DNA DIRECTED DNA POLYMERASE MU; GLYCINE; MANGANESE; MUTANT PROTEIN; PHENYLALANINE; RIBONUCLEOTIDE; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA END JOINING REPAIR; DNA TEMPLATE; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SUBSTRATE; GENE INSERTION; GENE MUTATION; GENE OVEREXPRESSION; HUMAN; HUMAN CELL; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; SCHIZOSACCHAROMYCES POMBE;

CATALYTIC DOMAIN; CATIONS; DNA END-JOINING REPAIR; DNA POLYMERASE BETA; DNA-DIRECTED DNA POLYMERASE; HELA CELLS; HUMANS; MANGANESE; RIBONUCLEOTIDES; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS;

EID: 84876401842     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1444     Document Type: Article

References (36)

1. Chen, S., Inamdar, K.V., Pfeiffer, P., Feldmann, E., Hannah, M.F., Yu, Y., Lee, J.W., Zhou, T., Lees-Miller, S.P. and Povirk, L.F. (2001) Accurate in vitro end joining of a DNA double strand break with partially cohesive 30-overhangs and 30-phosphoglycolate termini: effect of Ku on repair fidelity. J. Biol. Chem., 276, 24323-24330.
2. Nick McElhinny, S.A., Havener, J.M., Garcia-Diaz, M., Juarez, R., Bebenek, K., Kee, B.L., Blanco, L., Kunkel, T.A. and Ramsden, D.A. (2005) A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol. Cell, 19, 357-366.
3. Ma, Y., Lu, H., Tippin, B., Goodman, M.F., Shimazaki, N., Koiwai, O., Hsieh, C.L., Schwarz, K. and Lieber, M.R. (2004) A biochemically defined system for mammalian nonhomologous DNA end joining. Mol. Cell, 16, 701-713.
4. Davis, B.J., Havener, J.M. and Ramsden, D.A. (2008) End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining. Nucleic Acids Res., 36, 3085-3094.
5. Mahajan, K.N., Nick McElhinny, S.A., Mitchell, B.S. and Ramsden, D.A. (2002) Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair. Mol. Cell. Biol., 22, 5194-5202.
6. Lee, J.W., Blanco, L., Zhou, T., Garcia-Diaz, M., Bebenek, K., Kunkel, T.A., Wang, Z. and Povirk, L.F. (2004) Implication of DNA polymerase lambda in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts. J. Biol. Chem., 279, 805-811.
7. Ramsden, D.A. (2011) Polymerases in nonhomologous end joining: building a bridge over broken chromosomes. Antioxid. Redox. Signal., 14, 2509-2519.
8. Blanca, G., Shevelev, I., Ramadan, K., Villani, G., Spadari, S., Hubscher, U. and Maga, G. (2003) Human DNA polymerase lambda diverged in evolution from DNA polymerase beta toward specific Mn(++) dependence: a kinetic and thermodynamic study. Biochemistry, 42, 7467-7476.
9. Pelletier, H., Sawaya, M.R., Wolfle, W., Wilson, S.H. and Kraut, J. (1996) A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry, 35, 12762-12777.
10. Loeb, L.A. and Kunkel, T.A. (1982) Fidelity of DNA synthesis. Annu. Rev. Biochem., 51, 429-457.
11. Sirover, M.A. and Loeb, L.A. (1976) Metal-induced infidelity during DNA synthesis. Proc. Natl Acad. Sci. USA, 73, 2331-2335.
12. Dominguez, O., Ruiz, J.F., Lain de Lera, T., Garcia-Diaz, M., Gonzalez, M.A., Kirchhoff, T., Martinez, A.C., Bernad, A. and Blanco, L. (2000) DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells. EMBO J., 19, 1731-1742.
13. Frank, E.G. and Woodgate, R. (2007) Increased catalytic activity and altered fidelity of human DNA polymerase iota in the presence of manganese. J. Biol. Chem., 282, 24689-24696.
14. Traut, T.W. (1994) Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem., 140, 1-22.
15. Ferraro, P., Franzolin, E., Pontarin, G., Reichard, P. and Bianchi, V. (2010) Quantitation of cellular deoxynucleoside triphosphates. Nucleic Acids Res., 38, e85.
16. Brown, J.A. and Suo, Z. (2011) Unlocking the sugar "steric gate" of DNA polymerases. Biochemistry, 50, 1135-1142.
17. Joyce, C.M. (1997) Choosing the right sugar: how polymerases select a nucleotide substrate. Proc. Natl Acad. Sci. USA, 94, 1619-1622.
18. Brown, J.A., Fiala, K.A., Fowler, J.D., Sherrer, S.M., Newmister, S.A., Duym, W.W. and Suo, Z. (2010) A novel mechanism of sugar selection utilized by a human X-family DNA polymerase. J. Mol. Biol., 395, 282-290.
19. Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. and Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science, 264, 1891-1903.
20. Ruiz, J.F., Juarez, R., Garcia-Diaz, M., Terrados, G., Picher, A.J., Gonzalez-Barrera, S., Fernandez de Henestrosa, A.R. and Blanco, L. (2003) Lack of sugar discrimination by human Pol mu requires a single glycine residue. Nucleic Acids Res., 31, 4441-4449.
21. Nick McElhinny, S.A. and Ramsden, D.A. (2003) Polymerase mu is a DNA-directed DNA/RNA polymerase. Mol. Cell. Biol., 23, 2309-2315.
22. Gonzalez-Barrera, S., Sanchez, A., Ruiz, J.F., Juarez, R., Picher, A.J., Terrados, G., Andrade, P. and Blanco, L. (2005) Characterization of SpPol4, a unique X-family DNA polymerase in Schizosaccharomyces pombe. Nucleic Acids Res., 33, 4762-4774.
23. Nick McElhinny, S.A., Watts, B.E., Kumar, D., Watt, D.L., Lundstrom, E.B., Burgers, P.M., Johansson, E., Chabes, A. and Kunkel, T.A. (2010) Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc. Natl Acad. Sci. USA, 107, 4949-4954.
24. Pitcher, R.S., Brissett, N.C., Picher, A.J., Andrade, P., Juarez, R., Thompson, D., Fox, G.C., Blanco, L. and Doherty, A.J. (2007) Structure and function of a mycobacterial NHEJ DNA repair polymerase. J. Mol. Biol., 366, 391-405.
25. Garcia-Diaz, M., Bebenek, K., Sabariegos, R., Dominguez, O., Rodriguez, J., Kirchhoff, T., Garcia-Palomero, E., Picher, A.J., Juarez, R., Ruiz, J.F. et al. (2002) DNA polymerase lambda, a novel DNA repair enzyme in human cells. J. Biol. Chem., 277, 13184-13191.
26. Moreno, S., Klar, A. and Nurse, P. (1991) Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol., 194, 795-823.
27. Cueille, N., Salimova, E., Esteban, V., Blanco, M., Moreno, S., Bueno, A. and Simanis, V. (2001) Flp1, a fission yeast orthologue of the S. cerevisiae CDC14 gene, is not required for cyclin degradation or rum1p stabilisation at the end of mitosis. J. Cell Sci., 114, 2649-2664.
28. Andrade, P., Martin, M.J., Juarez, R., Lopez de Saro, F. and Blanco, L. (2009) Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ. Proc. Natl Acad. Sci. USA, 106, 16203-16208.
29. Cavanaugh, N.A., Beard, W.A., Batra, V.K., Perera, L., Pedersen, L.G. and Wilson, S.H. (2011) Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J. Biol. Chem., 286, 31650-31660.
30. Ruiz, J.F., Lucas, D., Garcia-Palomero, E., Saez, A.I., Gonzalez, M.A., Piris, M.A., Bernad, A. and Blanco, L. (2004) Overexpression of human DNA polymerase mu (Pol mu) in a Burkitt's lymphoma cell line affects the somatic hypermutation rate. Nucleic Acids Res., 32, 5861-5873.
31. Daley, J.M., Laan, R.L., Suresh, A. and Wilson, T.E. (2005) DNA joint dependence of pol X family polymerase action in nonhomologous end joining. J. Biol. Chem., 280, 29030-29037.
32. Ash, D.E. and Schramm, V.L. (1982) Determination of free and bound manganese(II) in hepatocytes from fed and fasted rats. J. Biol. Chem., 257, 9261-9264.
33. Markesbery, W.R., Ehmann, W.D., Alauddin, M. and Hossain, T.I. (1984) Brain trace element concentrations in aging. Neurobiol. Aging, 5, 19-28.
34. Versieck, J. (1985) Trace elements in human body fluids and tissues. Crit. Rev. Clin. Lab. Sci., 22, 97-184.
35. Goldschmidt, V., Didierjean, J., Ehresmann, B., Ehresmann, C., Isel, C. and Marquet, R. (2006) Mg2+dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance. Nucleic Acids Res., 34, 42-52.
36. Gee, J.B. II, Corbett, R.J., Perlman, J.M. and Laptook, A.R. (2001) Hypermagnesemia does not increase brain intracellular magnesium in newborn swine. Pediatr. Neurol., 25, 304-308.