Abstract
The catalytic DNA primase subunit of the DNA polymerase alpha-primase complex is encoded by the essential PRI1 gene in Saccharomyces cerevisiae. To identify factors that functionally interact with yeast DNA primase in living cells, we developed a genetic screen for mutants that are lethal at the permissive temperature in a cold-sensitive pril-2 genetic background. Twenty-four recessive mutations belonging to seven complementation groups were identified. Some mutants showed additional phenotypes, such as increased sensitivity to UV irradiation, methyl methanesulfonate, and hydroxyurea, that were suggestive of defects in DNA repair and/or checkpoint mechanisms. We have cloned and characterized the gene of one complementation group, PIP3, whose product is necessary both for delaying entry into S phase or mitosis when cells are UV irradiated in G1 or G2 phase and for lowering the rate of ongoing DNA synthesis in the presence of methyl methanesulfonate. PIP3 turned out to be the MEC3 gene, previously identified as a component of the G2 DNA damage checkpoint. The finding that Mec3 is also required for the G1- and S-phase DNA damage checkpoints, together with the analysis of genetic interactions between a mec3 null allele and several conditional DNA replication mutations at the permissive temperature, suggests that Mec3 could be part of a mechanism coupling DNA replication with repair of DNA damage, and DNA primase might be involved in this process.
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- Ayyagari R., Impellizzeri K. J., Yoder B. L., Gary S. L., Burgers P. M. A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol Cell Biol. 1995 Aug;15(8):4420–4429. doi: 10.1128/mcb.15.8.4420. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Baker T. A., Kremenstova E., Luo L. Complete transposition requires four active monomers in the mu transposase tetramer. Genes Dev. 1994 Oct 15;8(20):2416–2428. doi: 10.1101/gad.8.20.2416. [DOI] [PubMed] [Google Scholar]
- Bakkenist C. J., Cotterill S. The 50-kDa primase subunit of Drosophila melanogaster DNA polymerase alpha. Molecular characterization of the gene and functional analysis of the overexpressed protein. J Biol Chem. 1994 Oct 28;269(43):26759–26766. [PubMed] [Google Scholar]
- Bender A., Pringle J. R. Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Mar;11(3):1295–1305. doi: 10.1128/mcb.11.3.1295. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brückner A., Stadlbauer F., Guarino L. A., Brunahl A., Schneider C., Rehfuess C., Previes C., Fanning E., Nasheuer H. P. The mouse DNA polymerase alpha-primase subunit p48 mediates species-specific replication of polyomavirus DNA in vitro. Mol Cell Biol. 1995 Mar;15(3):1716–1724. doi: 10.1128/mcb.15.3.1716. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Budd M. E., Campbell J. L. DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Apr;15(4):2173–2179. doi: 10.1128/mcb.15.4.2173. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Campbell J. L. Yeast DNA replication. J Biol Chem. 1993 Dec 5;268(34):25261–25264. [PubMed] [Google Scholar]
- Carr A. M., Hoekstra M. F. The cellular responses to DNA damage. Trends Cell Biol. 1995 Jan;5(1):32–40. doi: 10.1016/s0962-8924(00)88934-5. [DOI] [PubMed] [Google Scholar]
- Costigan C., Gehrung S., Snyder M. A synthetic lethal screen identifies SLK1, a novel protein kinase homolog implicated in yeast cell morphogenesis and cell growth. Mol Cell Biol. 1992 Mar;12(3):1162–1178. doi: 10.1128/mcb.12.3.1162. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cvrcková F., Nasmyth K. Yeast G1 cyclins CLN1 and CLN2 and a GAP-like protein have a role in bud formation. EMBO J. 1993 Dec 15;12(13):5277–5286. doi: 10.1002/j.1460-2075.1993.tb06223.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- D'Urso G., Grallert B., Nurse P. DNA polymerase alpha, a component of the replication initiation complex, is essential for the checkpoint coupling S phase to mitosis in fission yeast. J Cell Sci. 1995 Sep;108(Pt 9):3109–3118. doi: 10.1242/jcs.108.9.3109. [DOI] [PubMed] [Google Scholar]
- Dornreiter I., Copeland W. C., Wang T. S. Initiation of simian virus 40 DNA replication requires the interaction of a specific domain of human DNA polymerase alpha with large T antigen. Mol Cell Biol. 1993 Feb;13(2):809–820. doi: 10.1128/mcb.13.2.809. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dornreiter I., Erdile L. F., Gilbert I. U., von Winkler D., Kelly T. J., Fanning E. Interaction of DNA polymerase alpha-primase with cellular replication protein A and SV40 T antigen. EMBO J. 1992 Feb;11(2):769–776. doi: 10.1002/j.1460-2075.1992.tb05110.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Foiani M., Liberi G., Lucchini G., Plevani P. Cell cycle-dependent phosphorylation and dephosphorylation of the yeast DNA polymerase alpha-primase B subunit. Mol Cell Biol. 1995 Feb;15(2):883–891. doi: 10.1128/mcb.15.2.883. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Foiani M., Marini F., Gamba D., Lucchini G., Plevani P. The B subunit of the DNA polymerase alpha-primase complex in Saccharomyces cerevisiae executes an essential function at the initial stage of DNA replication. Mol Cell Biol. 1994 Feb;14(2):923–933. doi: 10.1128/mcb.14.2.923. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Francesconi S., De Recondo A. M., Baldacci G. DNA polymerase delta is required for the replication feedback control of cell cycle progression in Schizosaccharomyces pombe. Mol Gen Genet. 1995 Mar 10;246(5):561–569. doi: 10.1007/BF00298962. [DOI] [PubMed] [Google Scholar]
- Francesconi S., Longhese M. P., Piseri A., Santocanale C., Lucchini G., Plevani P. Mutations in conserved yeast DNA primase domains impair DNA replication in vivo. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3877–3881. doi: 10.1073/pnas.88.9.3877. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Garvik B., Carson M., Hartwell L. Single-stranded DNA arising at telomeres in cdc13 mutants may constitute a specific signal for the RAD9 checkpoint. Mol Cell Biol. 1995 Nov;15(11):6128–6138. doi: 10.1128/mcb.15.11.6128. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
- Hartwell L. H., Kastan M. B. Cell cycle control and cancer. Science. 1994 Dec 16;266(5192):1821–1828. doi: 10.1126/science.7997877. [DOI] [PubMed] [Google Scholar]
- Hartwell L. H., Smith D. Altered fidelity of mitotic chromosome transmission in cell cycle mutants of S. cerevisiae. Genetics. 1985 Jul;110(3):381–395. doi: 10.1093/genetics/110.3.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hartwell L. H., Weinert T. A. Checkpoints: controls that ensure the order of cell cycle events. Science. 1989 Nov 3;246(4930):629–634. doi: 10.1126/science.2683079. [DOI] [PubMed] [Google Scholar]
- Hofmann J. F., Beach D. cdt1 is an essential target of the Cdc10/Sct1 transcription factor: requirement for DNA replication and inhibition of mitosis. EMBO J. 1994 Jan 15;13(2):425–434. doi: 10.1002/j.1460-2075.1994.tb06277.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Howell E. A., McAlear M. A., Rose D., Holm C. CDC44: a putative nucleotide-binding protein required for cell cycle progression that has homology to subunits of replication factor C. Mol Cell Biol. 1994 Jan;14(1):255–267. doi: 10.1128/mcb.14.1.255. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jansen R., Tollervey D., Hurt E. C. A U3 snoRNP protein with homology to splicing factor PRP4 and G beta domains is required for ribosomal RNA processing. EMBO J. 1993 Jun;12(6):2549–2558. doi: 10.1002/j.1460-2075.1993.tb05910.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnston L. H., Lowndes N. F. Cell cycle control of DNA synthesis in budding yeast. Nucleic Acids Res. 1992 May 25;20(10):2403–2410. doi: 10.1093/nar/20.10.2403. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kelly T. J., Martin G. S., Forsburg S. L., Stephen R. J., Russo A., Nurse P. The fission yeast cdc18+ gene product couples S phase to START and mitosis. Cell. 1993 Jul 30;74(2):371–382. doi: 10.1016/0092-8674(93)90427-r. [DOI] [PubMed] [Google Scholar]
- Kelman Z., O'Donnell M. DNA replication: enzymology and mechanisms. Curr Opin Genet Dev. 1994 Apr;4(2):185–195. doi: 10.1016/s0959-437x(05)80044-9. [DOI] [PubMed] [Google Scholar]
- Koshland D., Kent J. C., Hartwell L. H. Genetic analysis of the mitotic transmission of minichromosomes. Cell. 1985 Feb;40(2):393–403. doi: 10.1016/0092-8674(85)90153-9. [DOI] [PubMed] [Google Scholar]
- Kranz J. E., Holm C. Cloning by function: an alternative approach for identifying yeast homologs of genes from other organisms. Proc Natl Acad Sci U S A. 1990 Sep;87(17):6629–6633. doi: 10.1073/pnas.87.17.6629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Longhese M. P., Jovine L., Plevani P., Lucchini G. Conditional mutations in the yeast DNA primase genes affect different aspects of DNA metabolism and interactions in the DNA polymerase alpha-primase complex. Genetics. 1993 Feb;133(2):183–191. doi: 10.1093/genetics/133.2.183. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Longhese M. P., Plevani P., Lucchini G. Replication factor A is required in vivo for DNA replication, repair, and recombination. Mol Cell Biol. 1994 Dec;14(12):7884–7890. doi: 10.1128/mcb.14.12.7884. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lucchini G., Francesconi S., Foiani M., Badaracco G., Plevani P. Yeast DNA polymerase--DNA primase complex; cloning of PRI 1, a single essential gene related to DNA primase activity. EMBO J. 1987 Mar;6(3):737–742. doi: 10.1002/j.1460-2075.1987.tb04815.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lucchini G., Muzi Falconi M., Pizzagalli A., Aguilera A., Klein H. L., Plevani P. Nucleotide sequence and characterization of temperature-sensitive pol1 mutants of Saccharomyces cerevisiae. Gene. 1990 May 31;90(1):99–104. doi: 10.1016/0378-1119(90)90444-v. [DOI] [PubMed] [Google Scholar]
- Lydall D., Weinert T. Yeast checkpoint genes in DNA damage processing: implications for repair and arrest. Science. 1995 Dec 1;270(5241):1488–1491. doi: 10.1126/science.270.5241.1488. [DOI] [PubMed] [Google Scholar]
- Mitchell D. A., Marshall T. K., Deschenes R. J. Vectors for the inducible overexpression of glutathione S-transferase fusion proteins in yeast. Yeast. 1993 Jul;9(7):715–722. doi: 10.1002/yea.320090705. [DOI] [PubMed] [Google Scholar]
- Miyazawa H., Izumi M., Tada S., Takada R., Masutani M., Ui M., Hanaoka F. Molecular cloning of the cDNAs for the four subunits of mouse DNA polymerase alpha-primase complex and their gene expression during cell proliferation and the cell cycle. J Biol Chem. 1993 Apr 15;268(11):8111–8122. [PubMed] [Google Scholar]
- Murakami H., Okayama H. A kinase from fission yeast responsible for blocking mitosis in S phase. Nature. 1995 Apr 27;374(6525):817–819. doi: 10.1038/374817a0. [DOI] [PubMed] [Google Scholar]
- Murakami Y., Hurwitz J. DNA polymerase alpha stimulates the ATP-dependent binding of simian virus tumor T antigen to the SV40 origin of replication. J Biol Chem. 1993 May 25;268(15):11018–11027. [PubMed] [Google Scholar]
- Muzi Falconi M., Piseri A., Ferrari M., Lucchini G., Plevani P., Foiani M. De novo synthesis of budding yeast DNA polymerase alpha and POL1 transcription at the G1/S boundary are not required for entrance into S phase. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10519–10523. doi: 10.1073/pnas.90.22.10519. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Navas T. A., Zhou Z., Elledge S. J. DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell. 1995 Jan 13;80(1):29–39. doi: 10.1016/0092-8674(95)90448-4. [DOI] [PubMed] [Google Scholar]
- Nurse P. Ordering S phase and M phase in the cell cycle. Cell. 1994 Nov 18;79(4):547–550. doi: 10.1016/0092-8674(94)90539-8. [DOI] [PubMed] [Google Scholar]
- Paulovich A. G., Hartwell L. H. A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage. Cell. 1995 Sep 8;82(5):841–847. doi: 10.1016/0092-8674(95)90481-6. [DOI] [PubMed] [Google Scholar]
- Rothstein R. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 1991;194:281–301. doi: 10.1016/0076-6879(91)94022-5. [DOI] [PubMed] [Google Scholar]
- Saka Y., Fantes P., Sutani T., McInerny C., Creanor J., Yanagida M. Fission yeast cut5 links nuclear chromatin and M phase regulator in the replication checkpoint control. EMBO J. 1994 Nov 15;13(22):5319–5329. doi: 10.1002/j.1460-2075.1994.tb06866.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Santocanale C., Foiani M., Lucchini G., Plevani P. The isolated 48,000-dalton subunit of yeast DNA primase is sufficient for RNA primer synthesis. J Biol Chem. 1993 Jan 15;268(2):1343–1348. [PubMed] [Google Scholar]
- Santocanale C., Locati F., Muzi Falconi M., Piseri A., Tseng B. Y., Lucchini G., Plevani P. Overproduction and functional analysis of DNA primase subunits from yeast and mouse. Gene. 1992 Apr 15;113(2):199–205. doi: 10.1016/0378-1119(92)90396-7. [DOI] [PubMed] [Google Scholar]
- Santocanale C., Neecke H., Longhese M. P., Lucchini G., Plevani P. Mutations in the gene encoding the 34 kDa subunit of yeast replication protein A cause defective S phase progression. J Mol Biol. 1995 Dec 8;254(4):595–607. doi: 10.1006/jmbi.1995.0641. [DOI] [PubMed] [Google Scholar]
- Schiestl R. H., Reynolds P., Prakash S., Prakash L. Cloning and sequence analysis of the Saccharomyces cerevisiae RAD9 gene and further evidence that its product is required for cell cycle arrest induced by DNA damage. Mol Cell Biol. 1989 May;9(5):1882–1896. doi: 10.1128/mcb.9.5.1882. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Siede W., Friedberg A. S., Friedberg E. C. RAD9-dependent G1 arrest defines a second checkpoint for damaged DNA in the cell cycle of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7985–7989. doi: 10.1073/pnas.90.17.7985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stadlbauer F., Brueckner A., Rehfuess C., Eckerskorn C., Lottspeich F., Förster V., Tseng B. Y., Nasheuer H. P. DNA replication in vitro by recombinant DNA-polymerase-alpha-primase. Eur J Biochem. 1994 Jun 15;222(3):781–793. doi: 10.1111/j.1432-1033.1994.tb18925.x. [DOI] [PubMed] [Google Scholar]
- Stillman B. Smart machines at the DNA replication fork. Cell. 1994 Sep 9;78(5):725–728. doi: 10.1016/s0092-8674(94)90362-x. [DOI] [PubMed] [Google Scholar]
- Sugino A. Yeast DNA polymerases and their role at the replication fork. Trends Biochem Sci. 1995 Aug;20(8):319–323. doi: 10.1016/s0968-0004(00)89059-3. [DOI] [PubMed] [Google Scholar]
- Waga S., Stillman B. Anatomy of a DNA replication fork revealed by reconstitution of SV40 DNA replication in vitro. Nature. 1994 May 19;369(6477):207–212. doi: 10.1038/369207a0. [DOI] [PubMed] [Google Scholar]
- Wang T. A., Li J. J. Eukaryotic DNA replication. Curr Opin Cell Biol. 1995 Jun;7(3):414–420. doi: 10.1016/0955-0674(95)80098-0. [DOI] [PubMed] [Google Scholar]
- Wang T. S. Eukaryotic DNA polymerases. Annu Rev Biochem. 1991;60:513–552. doi: 10.1146/annurev.bi.60.070191.002501. [DOI] [PubMed] [Google Scholar]
- Weinert T. A., Hartwell L. H. Cell cycle arrest of cdc mutants and specificity of the RAD9 checkpoint. Genetics. 1993 May;134(1):63–80. doi: 10.1093/genetics/134.1.63. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weinert T. A., Hartwell L. H. The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science. 1988 Jul 15;241(4863):317–322. doi: 10.1126/science.3291120. [DOI] [PubMed] [Google Scholar]
- Weinert T. A., Kiser G. L., Hartwell L. H. Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev. 1994 Mar 15;8(6):652–665. doi: 10.1101/gad.8.6.652. [DOI] [PubMed] [Google Scholar]
- Wimmer C., Doye V., Grandi P., Nehrbass U., Hurt E. C. A new subclass of nucleoporins that functionally interact with nuclear pore protein NSP1. EMBO J. 1992 Dec;11(13):5051–5061. doi: 10.1002/j.1460-2075.1992.tb05612.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zheng P., Fay D. S., Burton J., Xiao H., Pinkham J. L., Stern D. F. SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase. Mol Cell Biol. 1993 Sep;13(9):5829–5842. doi: 10.1128/mcb.13.9.5829. [DOI] [PMC free article] [PubMed] [Google Scholar]