Abstract
We previously described a 5'-3' exonuclease required for recombination in vitro between linear DNA molecules with overlapping homologous ends. This exonuclease, referred to as exonuclease I (Exo I), has been purified more than 300-fold from vegetatively grown cells and copurifies with a 42-kDa polypeptide. The activity is nonprocessive and acts preferentially on double-stranded DNA. The biochemical properties are quite similar to those of Schizosaccharomyces pombe Exo I. Extracts prepared from cells containing a mutation of the Saccharomyces cerevisiae EXO1 gene, a homolog of S. pombe exo1, had decreased in vitro recombination activity and when fractionated were found to lack the peak of activity corresponding to the 5'-3' exonuclease. The role of EXO1 on recombination in vivo was determined by measuring the rate of recombination in an exo1 strain containing a direct duplication of mutant ade2 genes and was reduced sixfold. These results indicate that EXO1 is required for recombination in vivo and in vitro in addition to its previously identified role in mismatch repair.
Full Text
The Full Text of this article is available as a PDF (1.7 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Alani E., Padmore R., Kleckner N. Analysis of wild-type and rad50 mutants of yeast suggests an intimate relationship between meiotic chromosome synapsis and recombination. Cell. 1990 May 4;61(3):419–436. doi: 10.1016/0092-8674(90)90524-i. [DOI] [PubMed] [Google Scholar]
- Bauer G. A., Heller H. M., Burgers P. M. DNA polymerase III from Saccharomyces cerevisiae. I. Purification and characterization. J Biol Chem. 1988 Jan 15;263(2):917–924. [PubMed] [Google Scholar]
- Burgers P. M., Bauer G. A., Tam L. Exonuclease V from Saccharomyces cerevisiae. A 5'----3'-deoxyribonuclease that produces dinucleotides in a sequential fashion. J Biol Chem. 1988 Jun 15;263(17):8099–8105. [PubMed] [Google Scholar]
- Bähler J., Hagens G., Holzinger G., Scherthan H., Heyer W. D. Saccharomyces cerevisiae cells lacking the homologous pairing protein p175SEP1 arrest at pachytene during meiotic prophase. Chromosoma. 1994 Apr;103(2):129–141. doi: 10.1007/BF00352322. [DOI] [PubMed] [Google Scholar]
- Cao L., Alani E., Kleckner N. A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell. 1990 Jun 15;61(6):1089–1101. doi: 10.1016/0092-8674(90)90072-m. [DOI] [PubMed] [Google Scholar]
- Carter D. M., Radding C. M. The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease. J Biol Chem. 1971 Apr 25;246(8):2502–2512. [PubMed] [Google Scholar]
- Chow T. Y., Resnick M. A. Purification and characterization of an endo-exonuclease from Saccharomyces cerevisiae that is influenced by the RAD52 gene. J Biol Chem. 1987 Dec 25;262(36):17659–17667. [PubMed] [Google Scholar]
- Cooper D. L., Lahue R. S., Modrich P. Methyl-directed mismatch repair is bidirectional. J Biol Chem. 1993 Jun 5;268(16):11823–11829. [PubMed] [Google Scholar]
- Dake E., Hofmann T. J., McIntire S., Hudson A., Zassenhaus H. P. Purification and properties of the major nuclease from mitochondria of Saccharomyces cerevisiae. J Biol Chem. 1988 Jun 5;263(16):7691–7702. [PubMed] [Google Scholar]
- Digilio F. A., Pannuti A., Lucchesi J. C., Furia M., Polito L. C. Tosca: a Drosophila gene encoding a nuclease specifically expressed in the female germline. Dev Biol. 1996 Aug 25;178(1):90–100. doi: 10.1006/dbio.1996.0200. [DOI] [PubMed] [Google Scholar]
- Dölberg M., Baur C. P., Knippers R. Purification and characterization of a novel 5' exodeoxyribonuclease from the yeast Saccharomyces cerevisiae. Eur J Biochem. 1991 Jun 15;198(3):783–787. doi: 10.1111/j.1432-1033.1991.tb16081.x. [DOI] [PubMed] [Google Scholar]
- Goulian M., Richards S. H., Heard C. J., Bigsby B. M. Discontinuous DNA synthesis by purified mammalian proteins. J Biol Chem. 1990 Oct 25;265(30):18461–18471. [PubMed] [Google Scholar]
- Habraken Y., Sung P., Prakash L., Prakash S. A conserved 5' to 3' exonuclease activity in the yeast and human nucleotide excision repair proteins RAD2 and XPG. J Biol Chem. 1994 Dec 16;269(50):31342–31345. [PubMed] [Google Scholar]
- Habraken Y., Sung P., Prakash L., Prakash S. Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature. 1993 Nov 25;366(6453):365–368. doi: 10.1038/366365a0. [DOI] [PubMed] [Google Scholar]
- Harrington J. J., Lieber M. R. Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 1994 Jun 1;8(11):1344–1355. doi: 10.1101/gad.8.11.1344. [DOI] [PubMed] [Google Scholar]
- Harrington J. J., Lieber M. R. The characterization of a mammalian DNA structure-specific endonuclease. EMBO J. 1994 Mar 1;13(5):1235–1246. doi: 10.1002/j.1460-2075.1994.tb06373.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang K. N., Symington L. S. A 5'-3' exonuclease from Saccharomyces cerevisiae is required for in vitro recombination between linear DNA molecules with overlapping homology. Mol Cell Biol. 1993 Jun;13(6):3125–3134. doi: 10.1128/mcb.13.6.3125. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang K. N., Symington L. S. Mutation of the gene encoding protein kinase C 1 stimulates mitotic recombination in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Sep;14(9):6039–6045. doi: 10.1128/mcb.14.9.6039. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ivanov E. L., Sugawara N., White C. I., Fabre F., Haber J. E. Mutations in XRS2 and RAD50 delay but do not prevent mating-type switching in Saccharomyces cerevisiae. Mol Cell Biol. 1994 May;14(5):3414–3425. doi: 10.1128/mcb.14.5.3414. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jacquier A., Legrain P., Dujon B. Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1 and the BAF1 loci and reveals one tRNA gene and several new open reading frames including homologs to RAD2 and kinases. Yeast. 1992 Feb;8(2):121–132. doi: 10.1002/yea.320080207. [DOI] [PubMed] [Google Scholar]
- Johnson A. W., Kolodner R. D. Strand exchange protein 1 from Saccharomyces cerevisiae. A novel multifunctional protein that contains DNA strand exchange and exonuclease activities. J Biol Chem. 1991 Jul 25;266(21):14046–14054. [PubMed] [Google Scholar]
- Keeney S., Kleckner N. Covalent protein-DNA complexes at the 5' strand termini of meiosis-specific double-strand breaks in yeast. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11274–11278. doi: 10.1073/pnas.92.24.11274. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kenny M. K., Balogh L. A., Hurwitz J. Initiation of adenovirus DNA replication. I. Mechanism of action of a host protein required for replication of adenovirus DNA templates devoid of the terminal protein. J Biol Chem. 1988 Jul 15;263(20):9801–9808. [PubMed] [Google Scholar]
- Klein H. L. Different types of recombination events are controlled by the RAD1 and RAD52 genes of Saccharomyces cerevisiae. Genetics. 1988 Oct;120(2):367–377. doi: 10.1093/genetics/120.2.367. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Klein H. L. Genetic control of intrachromosomal recombination. Bioessays. 1995 Feb;17(2):147–159. doi: 10.1002/bies.950170210. [DOI] [PubMed] [Google Scholar]
- Kolodner R., Evans D. H., Morrison P. T. Purification and characterization of an activity from Saccharomyces cerevisiae that catalyzes homologous pairing and strand exchange. Proc Natl Acad Sci U S A. 1987 Aug;84(16):5560–5564. doi: 10.1073/pnas.84.16.5560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kowalczykowski S. C., Dixon D. A., Eggleston A. K., Lauder S. D., Rehrauer W. M. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994 Sep;58(3):401–465. doi: 10.1128/mr.58.3.401-465.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Käslin E., Heyer W. D. A multifunctional exonuclease from vegetative Schizosaccharomyces pombe cells exhibiting in vitro strand exchange activity. J Biol Chem. 1994 May 13;269(19):14094–14102. [PubMed] [Google Scholar]
- Lee Y. S., Shimizu J., Yoda K., Yamasaki M. Molecular cloning of a gene, DHS1, which complements a drug-hypersensitive mutation of the yeast Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 1994 Feb;58(2):391–395. doi: 10.1271/bbb.58.391. [DOI] [PubMed] [Google Scholar]
- Liu J., Wu T. C., Lichten M. The location and structure of double-strand DNA breaks induced during yeast meiosis: evidence for a covalently linked DNA-protein intermediate. EMBO J. 1995 Sep 15;14(18):4599–4608. doi: 10.1002/j.1460-2075.1995.tb00139.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lovett S. T., Clark A. J. Genetic analysis of the recJ gene of Escherichia coli K-12. J Bacteriol. 1984 Jan;157(1):190–196. doi: 10.1128/jb.157.1.190-196.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lovett S. T., Kolodner R. D. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2627–2631. doi: 10.1073/pnas.86.8.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McIntosh E. M. MCB elements and the regulation of DNA replication genes in yeast. Curr Genet. 1993 Sep;24(3):185–192. doi: 10.1007/BF00351790. [DOI] [PubMed] [Google Scholar]
- Meselson M. S., Radding C. M. A general model for genetic recombination. Proc Natl Acad Sci U S A. 1975 Jan;72(1):358–361. doi: 10.1073/pnas.72.1.358. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mueser T. C., Nossal N. G., Hyde C. C. Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell. 1996 Jun 28;85(7):1101–1112. doi: 10.1016/s0092-8674(00)81310-0. [DOI] [PubMed] [Google Scholar]
- Prado F., Aguilera A. Role of reciprocal exchange, one-ended invasion crossover and single-strand annealing on inverted and direct repeat recombination in yeast: different requirements for the RAD1, RAD10, and RAD52 genes. Genetics. 1995 Jan;139(1):109–123. doi: 10.1093/genetics/139.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reagan M. S., Pittenger C., Siede W., Friedberg E. C. 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. 1995 Jan;177(2):364–371. doi: 10.1128/jb.177.2.364-371.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rothstein R. J. One-step gene disruption in yeast. Methods Enzymol. 1983;101:202–211. doi: 10.1016/0076-6879(83)01015-0. [DOI] [PubMed] [Google Scholar]
- Saparbaev M., Prakash L., Prakash S. Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae. Genetics. 1996 Mar;142(3):727–736. doi: 10.1093/genetics/142.3.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schiestl R. H., Prakash S. RAD1, an excision repair gene of Saccharomyces cerevisiae, is also involved in recombination. Mol Cell Biol. 1988 Sep;8(9):3619–3626. doi: 10.1128/mcb.8.9.3619. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schiestl R. H., Prakash S. RAD10, an excision repair gene of Saccharomyces cerevisiae, is involved in the RAD1 pathway of mitotic recombination. Mol Cell Biol. 1990 Jun;10(6):2485–2491. doi: 10.1128/mcb.10.6.2485. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Siede W., Robinson G. W., Kalainov D., Malley T., Friedberg E. C. Regulation of the RAD2 gene of Saccharomyces cerevisiae. Mol Microbiol. 1989 Dec;3(12):1697–1707. doi: 10.1111/j.1365-2958.1989.tb00155.x. [DOI] [PubMed] [Google Scholar]
- Sommers C. H., Miller E. J., Dujon B., Prakash S., Prakash L. Conditional lethality of null mutations in RTH1 that encodes the yeast counterpart of a mammalian 5'- to 3'-exonuclease required for lagging strand DNA synthesis in reconstituted systems. J Biol Chem. 1995 Mar 3;270(9):4193–4196. doi: 10.1074/jbc.270.9.4193. [DOI] [PubMed] [Google Scholar]
- Stevens A. Purification and characterization of a Saccharomyces cerevisiae exoribonuclease which yields 5'-mononucleotides by a 5' leads to 3' mode of hydrolysis. J Biol Chem. 1980 Apr 10;255(7):3080–3085. [PubMed] [Google Scholar]
- Sugawara N., Ivanov E. L., Fishman-Lobell J., Ray B. L., Wu X., Haber J. E. DNA structure-dependent requirements for yeast RAD genes in gene conversion. Nature. 1995 Jan 5;373(6509):84–86. doi: 10.1038/373084a0. [DOI] [PubMed] [Google Scholar]
- Sun H., Treco D., Szostak J. W. Extensive 3'-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site. Cell. 1991 Mar 22;64(6):1155–1161. doi: 10.1016/0092-8674(91)90270-9. [DOI] [PubMed] [Google Scholar]
- Symington L. S. Double-strand-break repair and recombination catalyzed by a nuclear extract of Saccharomyces cerevisiae. EMBO J. 1991 Apr;10(4):987–996. doi: 10.1002/j.1460-2075.1991.tb08033.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Szankasi P., Smith G. R. A DNA exonuclease induced during meiosis of Schizosaccharomyces pombe. J Biol Chem. 1992 Feb 15;267(5):3014–3023. [PubMed] [Google Scholar]
- Szankasi P., Smith G. R. A role for exonuclease I from S. pombe in mutation avoidance and mismatch correction. Science. 1995 Feb 24;267(5201):1166–1169. doi: 10.1126/science.7855597. [DOI] [PubMed] [Google Scholar]
- Szankasi P., Smith G. R. A single-stranded DNA exonuclease from Schizosaccharomyces pombe. Biochemistry. 1992 Jul 28;31(29):6769–6773. doi: 10.1021/bi00144a017. [DOI] [PubMed] [Google Scholar]
- Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
- Thomas B. J., Rothstein R. The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene. Genetics. 1989 Dec;123(4):725–738. doi: 10.1093/genetics/123.4.725. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tishkoff D. X., Johnson A. W., Kolodner R. D. Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sep1. Mol Cell Biol. 1991 May;11(5):2593–2608. doi: 10.1128/mcb.11.5.2593. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tishkoff D. X., Rockmill B., Roeder G. S., Kolodner R. D. The sep1 mutant of Saccharomyces cerevisiae arrests in pachytene and is deficient in meiotic recombination. Genetics. 1995 Feb;139(2):495–509. doi: 10.1093/genetics/139.2.495. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Turchi J. J., Huang L., Murante R. S., Kim Y., Bambara R. A. Enzymatic completion of mammalian lagging-strand DNA replication. Proc Natl Acad Sci U S A. 1994 Oct 11;91(21):9803–9807. doi: 10.1073/pnas.91.21.9803. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vallen E. A., Cross F. R. Mutations in RAD27 define a potential link between G1 cyclins and DNA replication. Mol Cell Biol. 1995 Aug;15(8):4291–4302. doi: 10.1128/mcb.15.8.4291. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Villadsen I. S., Bjørn S. E., Vrang A. Exonuclease II from Saccharomyces cerevisiae. An enzyme which liberates 5'-deoxyribomononucleotides from single-stranded DNA by a 5' goes to 3' mode of hydrolysis. J Biol Chem. 1982 Jul 25;257(14):8177–8182. [PubMed] [Google Scholar]
- Waga S., Bauer G., Stillman B. Reconstitution of complete SV40 DNA replication with purified replication factors. J Biol Chem. 1994 Apr 8;269(14):10923–10934. [PubMed] [Google Scholar]
- White C. I., Haber J. E. Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. EMBO J. 1990 Mar;9(3):663–673. doi: 10.1002/j.1460-2075.1990.tb08158.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zassenhaus H. P., Hofmann T. J., Uthayashanker R., Vincent R. D., Zona M. Construction of a yeast mutant lacking the mitochondrial nuclease. Nucleic Acids Res. 1988 Apr 25;16(8):3283–3296. doi: 10.1093/nar/16.8.3283. [DOI] [PMC free article] [PubMed] [Google Scholar]
- de Massy B., Rocco V., Nicolas A. The nucleotide mapping of DNA double-strand breaks at the CYS3 initiation site of meiotic recombination in Saccharomyces cerevisiae. EMBO J. 1995 Sep 15;14(18):4589–4598. doi: 10.1002/j.1460-2075.1995.tb00138.x. [DOI] [PMC free article] [PubMed] [Google Scholar]