30
Views
73
CrossRef citations to date
0
Altmetric
DNA Dynamics and Chromosome Structure

Palm Mutants in DNA Polymerases α and η Alter DNA Replication Fidelity and Translesion Activity

, , , , , , , & show all
Pages 2734-2746 | Received 08 Sep 2003, Accepted 11 Dec 2003, Published online: 27 Mar 2023

REFERENCES

  • Ayyagari, R., Impellizzeri K. J., Yoder B. L., Gary S. L., and Burgers P. M.. 1995. A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol. Cell. Biol. 15:4420–4429.
  • Blasco, M. A., Lazaro J. M., Blanco L., and Salas M.. 1993. Phi 29 DNA polymerase active site. The conserved amino acid motif “Kx3NSxYG” is involved in template-primer binding and dNTP selection. J. Biol. Chem. 268:16763–16770.
  • Boudsocq, F., Ling H., Yang W., and Woodgate R.. 2002. Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass. DNA Repair (Amsterdam) 1:343–358.
  • Braithwaite, D. K., and Ito J.. 1993. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21:787–802.
  • Capizzi, R. L., and Jameson J. W.. 1973. A table for the estimation of the spontaneous mutation rate of cells in culture. Mutat. Res. 17:147–148.
  • Chen, C., Merrill B. J., Lau P. J., Holm C., and Kolodner R. D.. 1999. Saccharomyces cerevisiaepol30 (proliferating cell nuclear antigen) mutations impair replication fidelity and mismatch repair. Mol. Cell. Biol. 19:7801–7815.
  • Copeland, W. C., Lam N. K., and Wang T. S.. 1993. Fidelity studies of the human DNA polymerase alpha. The most conserved region among alpha-like DNA polymerases is responsible for metal-induced infidelity in DNA synthesis. J. Biol. Chem. 268:11041–11049.
  • Datta, A., Schmeits J. L., Amin N. S., Lau P. J., Myung K., and Kolodner R. D.. 2000. Checkpoint-dependent activation of mutagenic repair in Saccharomyces cerevisiae pol3-01 mutants. Mol. Cell 6:593–603.
  • Earley, M. C., and Crouse G. F.. 1998. The role of mismatch repair in the prevention of base pair mutations in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 95:15487–15491.
  • Franklin, M. C., Wang J., and Steitz T. A.. 2001. Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105:657–667.
  • Glick, E., Chau J. S., Vigna K. L., McCulloch S. D., Adman E. T., Kunkel T. A., and Loeb L. A.. 2003. Amino acid substitutions at conserved tyrosine 52 alter fidelity and bypass efficiency of human DNA polymerase eta. J. Biol. Chem. 278:19341–19346.
  • Glick, E., Vigna K. L., and Loeb L. A.. 2001. Mutations in human DNA polymerase eta motif II alter bypass of DNA lesions. EMBO J. 20:7303–7312.
  • Goldsby, R. E., Hays L. E., Chen X., Olmsted E. A., Slayton W. B., Spangrude G. J., and Preston B. D.. 2002. High incidence of epithelial cancers in mice deficient for DNA polymerase delta proofreading. Proc. Natl. Acad. Sci. USA 99:15560–15565.
  • Goldsby, R. E., Lawrence N. A., Hays L. E., Olmsted E. A., Chen X., Singh M., and Preston B. D.. 2001. Defective DNA polymerase-delta proofreading causes cancer susceptibility in mice. Nat. Med. 7:638–639.
  • Goodman, M. F., Creighton S., Bloom L. B., and Petruska J.. 1993. Biochemical basis of DNA replication fidelity. Crit. Rev. Biochem. Mol. Biol. 28:83–126.
  • Habraken, Y., Sung P., Prakash L., and Prakash S.. 1997. Enhancement of MSH2-MSH3-mediated mismatch recognition by the yeast MLH1-PMS1 complex. Curr. Biol. 7:790–793.
  • Harfe, B. D., and Jinks-Robertson S.. 2000. DNA mismatch repair and genetic instability. Annu. Rev. Genet. 34:359–399.
  • Johnson, R. E., Kovvali G. K., Guzder S. N., Amin N. S., Holm C., Habraken Y., Sung P., Prakash L., and Prakash S.. 1996. Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair. J. Biol. Chem. 271:27987–27990.
  • Johnson, R. E., Prakash S., and Prakash L.. 1999. Requirement of DNA polymerase activity of yeast Rad30 protein for its biological function. J. Biol. Chem. 274:15975–15977.
  • Kai, M., and Wang T. S.. 2003. Checkpoint activation regulates mutagenic translesion synthesis. Genes Dev. 17:64–76.
  • Kim, B., Hathaway T. R., and Loeb L. A.. 1996. Human immunodeficiency virus reverse transcriptase. Functional mutants obtained by random mutagenesis coupled with genetic selection in Escherichia coli. J. Biol. Chem. 271:4872–4878.
  • Kokoska, R. J., Stefanovic L., DeMai J., and Petes T. D.. 2000. Increased rates of genomic deletions generated by mutations in the yeast gene encoding DNA polymerase δ or by decreases in the cellular levels of DNA polymerase δ. Mol. Cell. Biol. 20:7490–7504.
  • Kunkel, T. A., and Bebenek K.. 2000. DNA replication fidelity. Annu. Rev. Biochem. 69:497–529.
  • Kusumoto, R., Masutani C., Iwai S., and Hanaoka F.. 2002. Translesion synthesis by human DNA polymerase eta across thymine glycol lesions. Biochemistry 41:6090–6099.
  • Li, Y., Korolev S., and Waksman G.. 1998. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J. 17:7514–7525.
  • Limsirichaikul, S., Ogawa M., Niimi A., Iwai S., Murate T., Yoshida S., and Suzuki M.. 2003. The Gly952 residue of Saccharomyces cerevisiae DNA polymerase alpha is important in discriminating correct deoxyribonucleotides from incorrect ones. J. Biol. Chem. 278:19079–19086.
  • Ling, H., Boudsocq F., Plosky B. S., Woodgate R., and Yang W.. 2003. Replication of a cis-syn thymine dimer at atomic resolution. Nature 424:1083–1087.
  • Ling, H., Boudsocq F., Woodgate R., and Yang W.. 2001. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107:91–102.
  • Liu, V. F., Bhaumik D., and Wang T. S.. 1999. Mutator phenotype induced by aberrant replication. Mol. Cell. Biol. 19:1126–1135.
  • Loeb, L. A., and Kunkel T. A.. 1982. Fidelity of DNA synthesis. Annu. Rev. Biochem. 51:429–457.
  • Luria, S. E., and Delbruck M.. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491–511.
  • Masutani, C., Kusumoto R., Iwai S., and Hanaoka F.. 2000. Mechanisms of accurate translesion synthesis by human DNA polymerase eta. EMBO J. 19:3100–3109.
  • Matray, T. J., and Kool E. T.. 1999. A specific partner for abasic damage in DNA. Nature 399:704–708.
  • Matsuda, T., Bebenek K., Masutani C., Hanaoka F., and Kunkel T. A.. 2000. Low fidelity DNA synthesis by human DNA polymerase-eta. Nature 404:1011–1013.
  • Matsuda, T., Bebenek K., Masutani C., Rogozin I. B., Hanaoka F., and Kunkel T. A.. 2001. Error rate and specificity of human and murine DNA polymerase eta. J. Mol. Biol. 312:335–346.
  • Mendelman, L. V., Petruska J., and Goodman M. F.. 1990. Base mispair extension kinetics. Comparison of DNA polymerase alpha and reverse transcriptase. J. Biol. Chem. 265:2338–2346.
  • Morrison, A., Bell J. B., Kunkel T. A., and Sugino A.. 1991. Eukaryotic DNA polymerase amino acid sequence required for 3′-5′ exonuclease activity. Proc. Natl. Acad. Sci. USA 88:9473–9477.
  • Morrison, A., Johnson A. L., Johnston L. H., and Sugino A.. 1993. Pathway correcting DNA replication errors in Saccharomyces cerevisiae. EMBO J. 12:1467–1473.
  • Morrison, A., and Sugino A.. 1994. The 3′→5′ exonucleases of both DNA polymerases delta and epsilon participate in correcting errors of DNA replication in Saccharomyces cerevisiae. Mol. Gen. Genet. 242:289–296.
  • Ni, T. T., Marsischky G. T., and Kolodner R. D.. 1999. MSH2 and MSH6 are required for removal of adenine misincorporated opposite 8-oxo-guanine in S. cerevisiae. Mol. Cell 4:439–444.
  • Ogawa, M., Limsirichaikul S., Niimi A., Iwai S., Yoshida S., and Suzuki M.. 2003. Distinct function of conserved amino acids in the fingers of Saccharomyces cerevisiae DNA polymerase alpha. J. Biol. Chem. 278:19071–19078.
  • Patel, P. H., Kawate H., Adman E., Ashbach M., and Loeb L. A.. 2001. A single highly mutable catalytic site amino acid is critical for DNA polymerase fidelity. J. Biol. Chem. 276:5044–5051.
  • Patel, P. H., and Loeb L. A.. 2001. Getting a grip on how DNA polymerases function. Nat. Struct. Biol. 8:656–659.
  • Patel, P. H., Suzuki M., Adman E., Shinkai A., and Loeb L. A.. 2001. Prokaryotic DNA polymerase I: evolution, structure, and “base flipping” mechanism for nucleotide selection. J. Mol. Biol. 308:823–837.
  • Pavlov, Y. I., Shcherbakova P. V., and Kunkel T. A.. 2001. In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta. Genetics 159:47–64.
  • Perrino, F. W., and Loeb L. A.. 1989. Differential extension of 3′ mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase-alpha. J. Biol. Chem. 264:2898–2905.
  • Shinkai, A., and Loeb L. A.. 2001. In vivo mutagenesis by Escherichia coli DNA polymerase I. Ile(709) in motif A functions in base selection. J. Biol. Chem. 276:46759–46764.
  • Shinkai, A., Patel P. H., and Loeb L. A.. 2001. The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable. J. Biol. Chem. 276:18836–18842.
  • Sommer, S., Coste G., and Bailone A.. 2000. Specific amino acid changes enhance the anti-recombination activity of the UmuD'C complex. Mol. Microbiol. 35:1443–1453.
  • Steitz, T. A. 1999. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274:17395–17398.
  • Sun, L., Wang M., Kool E. T., and Taylor J. S.. 2000. Pyrene nucleotide as a mechanistic probe: evidence for a transient abasic site-like intermediate in the bypass of dipyrimidine photoproducts by T7 DNA polymerase. Biochemistry 39:14603–14610.
  • Suzuki, M., Avicola A. K., Hood L., and Loeb L. A.. 1997. Low fidelity mutants in the O-helix of Thermus aquaticus DNA polymerase I. J. Biol. Chem. 272:11228–11235.
  • Suzuki, M., Baskin D., Hood L., and Loeb L. A.. 1996. Random mutagenesis of Thermus aquaticus DNA polymerase I: concordance of immutable sites in vivo with the crystal structure. Proc. Natl. Acad. Sci. USA 93:9670–9675.
  • Suzuki, M., Yoshida S., Adman E. T., Blank A., and Loeb L. A.. 2000. Thermus aquaticus DNA polymerase I mutants with altered fidelity. Interacting mutations in the O-helix. J. Biol. Chem. 275:32728–32735.
  • Tosaka, A., Ogawa M., Yoshida S., and Suzuki M.. 2001. O-helix mutant T664P of Thermus aquaticus DNA polymerase I: altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides. J. Biol. Chem. 276:27562–27567.
  • Tran, H. T., Gordenin D. A., and Resnick M. A.. 1999. The 3′→5′ exonucleases of DNA polymerases δ and ε and the 5′→3′ exonuclease Exo1 have major roles in postreplication mutation avoidance in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:2000–2007.
  • 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 eta: implications for translesion DNA synthesis. Mol. Cell 8:417–426.
  • Tschumper, G., and Carbon J.. 1980. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene 10:157–166.
  • Umar, A., Buermeyer A. B., Simon J. A., Thomas D. C., Clark A. B., Liskay R. M., and Kunkel T. A.. 1996. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87:65–73.
  • Waga, S., and Stillman B.. 1998. The DNA replication fork in eukaryotic cells Annu. Rev. Biochem. 67:721–751.
  • Wyrick, J. J., Aparicio J. G., Chen T., Barnett J. D., Jennings E. G., Young R. A., Bell S. P., and Aparicio O. M.. 2001. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294:2357–2360.
  • Zhou, B. L., Pata J. D., and Steitz T. A.. 2001. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell 8:427–437.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.