10
Views
37
CrossRef citations to date
0
Altmetric
DNA Dynamics and Chromosome Structure

Novel Function of Rad27 (FEN-1) in Restricting Short-Sequence Recombination

, , , &
Pages 2349-2358 | Received 01 Dec 2000, Accepted 15 Jan 2001, Published online: 27 Mar 2023

REFERENCES

  • Alani, E., L. Cao, and N. Kleckner. 1987. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116:541–545.
  • Bailis, A. M., and S. Maines. 1996. Nucleotide excision repair gene function in short-sequence recombination. J. Bacteriol. 173:2136–2140.
  • Bailis, A. M., S. Maines, and M. C. Negritto. 1995. The essential helicase gene RAD3 suppresses short-sequence recombination in Saccharomyces cerevisiae. Mol. Cell. Biol. 15:3998–4008.
  • Bailis, A. M., and R. Rothstein. 1990. A defect in mismatch repair in Saccharomyces cerevisiae stimulates ectopic recombination between homologous genes by an excision repair dependent process. Genetics 126:535–547.
  • Bambara, R. A., R. S. Murante, and R. A. Henricksen. 1997. Enzymes and reactions at the eukaryotic DNA replication fork. J. Biol. Chem. 272:4647–4650.
  • Bardwell, A. J., L. Bardwell, A. E. Tomkinson, and E. C. Friedberg. 1994. Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonuclease. Science 265:2062–2065.
  • Boeke, J. D., F. LaCroute, and G. R. Fink. 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197:345–346.
  • Britten, R. J., and D. E. Kohne. 1968. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 161:529–540.
  • Budd, M. E., and J. L. Campbell. 1997. A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function. Mol. Cell. Biol. 17:2136–2142.
  • Chen, C., and R. D. Kolodner. 1999. Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination deficient mutants. Nat. Genet. 23:81–85.
  • Cheng, D. M., M. M. Dhingra, and R. H. Sarma. 1978. Spatial configuration of deoxyribotrinucleoside diphosphate in aqueous solution. Nucleic Acids Res. 5:4399–4416.
  • Deininger, P. L., and M. A. Batzer. 1999. Alu repeats and human disease. Mol. Genet. Metab. 68:183–193.
  • de Laat, W. L., N. G. J. Jaspers, and J. H. J. Hoeijmakers. 1999. Molecular mechanism of nucleotide excision repair. Genes Dev. 13:768–785.
  • Feaver, W. J., J. Q. Svejstrup, L. Bardwell, A. J. Bardwell, S. Buratowski, K. D. Gulyas, T. F. Donahue, E. C. Friedberg, and R. D. Kornberg. 1993. Dual roles of a multiprotein complex from Saccharomyces cerevisiae in transcription and DNA repair. Cell 75:1379–1387.
  • Fikus, M. U., P. A. Mieczkowski, P. Koprowski, J. Rytka, E. Sledziewska-Gojska, and Z. Ciesla. 2000. The product of the DNA damage-inducible gene of Saccharomyces cerevisiae, DIN7, specifically functions in mitochondria. Genetics 154:73–81.
  • Fiorentini, P., K. N. Huang, D. X. Tishkoff, R. D. Kolodner, and L. S. Symington. 1997. Exonuclease I of Saccharomyces cerevisiae functions in mitotic recombination in vivo and in vitro. Mol. Cell. Biol. 17:2764–2773.
  • Fishman-Lobell, J., and J. E. Haber. 1992. Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science 258:480–484.
  • Frank, G., J. Qiu, M. Somsouk, Y. Weng, L. Somsouk, J. P. Nolan, and B. Shen. 1998. Partial functional deficiency of E160D flap endonuclease-1 mutant in vitro and in vivo is due to defective cleavage of DNA substrates. J. Biol. Chem. 273:33064–33072.
  • Freudenreich, C. H., S. M. Kantrow, and V. A. Zakian. 1998. Expansion and length-dependent fragility of CTG repeats in yeast. Science 279:853–856.
  • Habraken, Y., P. Sung, L. Prakash, and S. Prakash. 1993. Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature 366:365–368.
  • Harrington, J. J., and M. R. Lieber. 1994. The characterization of a mammalian DNA structure-specific endonuclease. EMBO J. 13:1235–1246.
  • Holmes, A., and J. E. Haber. 1999. Double-strand break repair requires both leading and lagging strand DNA polymerases. Cell 96:415–424.
  • Hosfield, D. J., C. D. Mol, B. Shen, and J. A. Tainer. 1998. Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 95:135–146.
  • Hwang, Y. H., K. Baek, H.-Y. Kim, and Y. Cho. 1998. The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat. Struct. Biol. 5:707–713.
  • Jinks-Robertson, S., M. Michelitch, and S. Ramcharan. 1993. Substrate length requirements for efficient mitotic recombination in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:3937–3950.
  • Johnson, R. E., G. K. Kovvali, L. Prakash, and S. Prakash. 1998. Requirement of the yeast Rth1 5′ to 3′ exonuclease for the stability of simple repetitive DNA. Science 269:238–239.
  • Kokoska, R. J., L. Stefanovic, H. T. Tran, M. A. Resnick, D. A. Gordenin, and T. Petes. 1998. Destabilization of yeast micro- and minisatellite DNA sequences by mutations affecting a nuclease involved in Okazaki fragment processing (rad27) and DNA polymerase δ (pol3-t). Mol. Cell. Biol. 18:2779–2788.
  • Lee, B.-S., C. P. Lichtenstein, B. Faiola, L. A. Rinckel, W. Wysock, M. J. Curcio, and D. J. Garfinkel. 1998. Posttranslational inhibition of Ty1 retrotransposition by nucleotide excision repair/transcription factor TFIIH subunits Ssl2p and Rad3p. Genetics 148:1743–1761.
  • Lee, B.-S., L. Bi, D. J. Garfinkel, and A. M. Bailis. 2000. Nucleotide excision repair/TFIIH helicases Rad3 and Ssl2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms. Mol. Cell. Biol. 20:2436–2445.
  • Leung, K. Y., A. Malkova, and J. E. Haber. 1997. Gene targeting by linear duplex DNA frequently occurs by assimilation of a single strand that is subject to preferential mismatch correction. Proc. Natl. Acad. Sci. USA 94:6851–6856.
  • Lieber, M.. 1997. The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. Bioessays 19:233–240.
  • Lobachev, K. S., J. E. Stenger, O. G. Kozyreva, J. Jurka, D. A. Gordenin, and M. A. Resnick. 2000. Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J. 19:3822–3830.
  • Lovett, S. T., and V. A. Sutera Jr.. 1995. Suppression of RecJ exonuclease mutant of Escherichia coli by alterations in DNA helicases II (uvrD) and IV (helD). Genetics 140:27–45.
  • Maines, S., M. C. Negritto, X. Wu, G. M. Manthey, and A. M. Bailis. 1998. Novel mutations in the RAD3 and SSL1 genes perturb genome stability by stimulating recombination between short repeats in Saccharomyces cerevisiae. Genetics 150:963–976.
  • Manivasakam, P., S. C. Weber, J. McElver, and R. H. Schiestl. 1995. Micro-homology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Res. 23:2799–2800.
  • Morrow, D. M., C. Connelly, and P. Hieter. 1997. “Break copy” duplication a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147:371–382.
  • Murante, R. S., L. Rust, and R. A. Bambara. 1995. Calf 5′ to 3′ exo/endonuclease must slide from a 5′ end of the substrate to perform structure-specific cleavage. J. Biol. Chem. 270:30377–30383.
  • Negritto, M. T., X. Wu, T. Kuo, S. Chu, and A. M. Bailis. 1997. Influence of DNA sequence identity on efficiency of targeted gene replacement. Mol. Cell. Biol. 17:278–286.
  • Paques, F., and J. E. Haber. 1999. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63:349–404.
  • Parenteau, J., and R. J. Wellinger. 1999. Accumulation of single-stranded DNA and destabilization of telomeric repeats in yeast mutant strains carrying a deletion of RAD27. Mol. Cell. Biol. 19:4143–4152.
  • Qiu, J., M. X. Guan, A. M. Bailis, and B. Shen. 1998. Saccharomyces cerevisiae exonuclease-1 plays a role in UV resistance that is distinct from nucleotide excision repair. Nucleic Acids Res. 26:3077–3083.
  • Reagan, M. S., C. Pittenger, W. Siede, and E. C. Friedberg. 1995. Characterization of a mutant strain of Saccharomyces cerevisiae with a deletion of the RAD27 gene, a structural homolog of the RAD2 nucleotide excision repair gene. J. Bacteriol. 177:364–371.
  • Rothstein, R.. 1984. Double-strand break repair, gene conversion, and postdivision segregation. Cold Spring Harbor Symp. Quant. Biol. 49:629–638.
  • Rothstein, R.. 1991. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 194:281–301.
  • Rothstein, R., C. Helms, and N. Rosenberg. 1987. Concerted deletions and inversions are caused by mitotic recombination between delta sequences in Saccharomyces cerevisiae. Mol. Cell. Biol. 7:1198–1207.
  • Rubnitz, J., and S. Subramani. 1984. The minimum amount of homology required for homologous recombination in mammalian cells. Mol. Cell. Biol. 4:2253–2258.
  • Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
  • Schweitzer, J. K., and D. M. Livingston. 1998. Expansions of CAG repeat tracts are frequent in a yeast mutant defective in Okazaki fragment maturation. Hum. Mol. Genet. 7:69–74.
  • Shen, B., J. P. Nolan, L. A. Sklar, and M. S. Park. 1996. Essential amino acids for substrate binding and catalysis of human flap endonuclease 1. J. Biol. Chem. 271:9173–9176.
  • Shen, B., J. P. Nolan, L. A. Sklar, and M. S. Park. 1997. Functional analysis of point mutations in human flap endonuclease-1 active site. Nucleic Acids Res. 25:3332–3338.
  • Shen, B., J. Qiu, D. Hosfield, and J. A. Tainer. 1998. Flap endonuclease homologs in archaebacteria exist as independent proteins. Trends Biochem. Sci. 23:171–173.
  • Sherman, F., G. R. Fink, and J. B. Hicks. 1987. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
  • Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
  • Sokolsky, T., and E. Alani. 2000. EXO1 and MSH6 are high-copy suppressors of conditional mutations in the MSH2 mismatch repair gene of Saccharomyces cerevisiae. Genetics 155:589–599.
  • Sommers, C. H., E. J. Miller, B. Dujon, S. Prakash, and L. Prakash. 1995. Conditional lethality of null mutations in RTH1 that encodes the yeast counterpart of a mammalian 5′ to 3′ exonuclease required for lagging strand synthesis in reconstituted systems. J. Biol. Chem. 270:4193–4196.
  • Spiro, C., R. Pelletier, M. L. Rolfsmeier, M. J. Dixon, R. S. Lahue, G. Gupta, M. S. Park, X. Chen, S. V. S. Mariappan, and C. T. McMurray. 1999. Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Mol. Cell 4:1079–1085.
  • Sugawara, N., and J. E. Haber. 1992. Characterization of double-strand-break-induced recombination: homology requirements and single-stranded DNA formation. Mol. Cell. Biol. 12:563–575.
  • Sung, P., P. Reynolds, L. Prakash, and S. Prakash. 1993. Purification and characterization of the Saccharomyces cerevisiae Rad1/Rad10 endonuclease. J. Biol. Chem. 26:23691–23699.
  • Symington, L. S.. 1998. Homologous recombination is required for the viability of rad27 mutants. Nucleic Acids Res. 26:5589–5595.
  • Symington, L. S., L. E. Kang, and S. Moreau. 2000. Alteration of gene conversion tract length and associated crossing over during plasmid gap repair in nuclease-deficient strains of Saccharomyces cerevisiae. Nucleic Acids Res. 28:4649–4656.
  • Szankasi, P., C. Gysler, U. Zehntner, U. Leupold, J. Kohli, and P. Munz. 1986. Mitotic recombination between dispersed but related tRNA genes of S. pombe generates a reciprocal translocation. Mol. Gen. Genet. 202:394–402.
  • Thomas, B. J., and R. Rothstein. 1989. The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination of a GAL10 transcriptionally regulated gene. Genetics 123:725–738.
  • Tishkoff, D. X., A. L. Boerger, P. Bertrand, N. Filosi, G. M. Gaida, M. F. Kane, and R. D. Kolodner. 1997. Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2. Proc. Natl. Acad. Sci. USA 94:7487–7492.
  • Tishkoff, D. X., N. Filosi, G. M. Gaida, and R. D. Kolodner. 1997. A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair. Cell 88:253–263.
  • Tomkinson, A. E., A. J. Bardwell, L. Bardwell, N. J. Tappe, and E. C. Friedberg. 1993. Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature 362:860–862.
  • Tran, H. T., D. A. Gordenin, and M. A. Resnick. 1999. The 3′→5′ exonucleases of DNA polymerases δ and ɛ and the 5′→3′ exonuclease Exo1 have major roles in postreplication mutation avoidance in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:2000–2007.
  • Vallen, E. A., and F. R. Cross. 1995. Mutations in RAD27 define a potential link between G1 cyclins and DNA replication. Mol. Cell. Biol. 15:4291–4302.
  • Wach, A., A. Brachat, R. Pohlmann, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based disruptions in Saccharomyces cerevisiae. Yeast 10:1793–1808.
  • Wang, Z., J. Q. Svejstrup, W. J. Feaver, X. Wu, R. D. Kornberg, and E. C. Friedberg. 1994. Transcription factor b (TFIIH) is required during nucleotide excision repair in yeast. Nature 368:74–76.
  • Wu, X., T. E. Wilson, and M. R. Lieber. 1999. A role for FEN-1 in nonhomologous DNA end joining: the order of strand annealing and nucleolytic processing events. Proc. Natl. Acad. Sci. USA 96:1303–1308.
  • Zhu, F. X., E. E. Biswas, and S. B. Biswas. 1997. Purification and characterization of the DNA polymerase α associated exonuclease: the RTH1 gene product. Biochemistry 36:5947–5954.

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.