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. 2002 Apr;160(4):1319–1333. doi: 10.1093/genetics/160.4.1319

Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA replication in Saccharomyces cerevisiae.

Wenge Zhu 1, Irene R Rainville 1, Min Ding 1, Margaret Bolus 1, Nicholas H Heintz 1, David S Pederson 1
PMCID: PMC1462043  PMID: 11973290

Abstract

Clf1p is an essential, highly conserved protein in S. cerevisiae that has been implicated in pre-mRNA splicing. Clf1p's ortholog in Drosophila, Crn, is required for normal cell proliferation. Cells depleted of Clf1p arrest primarily with large buds, a single nucleus, a 2C DNA content, and a short, intact mitotic spindle. We isolated temperature-sensitive clf1 mutants that exhibit similar mitotic defects when released to the restrictive temperature from an early S-phase block. While these mutants also accumulate unspliced pre-mRNA at the restrictive temperature, the mitotic arrest does not appear to result from a failure to splice tubulin pre-mRNA. Moreover, the same mutants exhibit a delayed entry into S phase when released to the restrictive temperature from a G1 phase block. This delay could not be suppressed by disruption of the S-phase CDK inhibitor SIC1, suggesting that Clf1p is involved in DNA replication. Consistent with this possibility, we find that Clf1p (but not the mutant clf1p) interacts with the DNA replication initiation protein Orc2p in two-hybrid and co-immunoprecipitation assays, that Clf1p preferentially associates with origins of DNA replication, and that this association is Orc2p dependent. These observations suggest that Clf1p plays a direct role in the initiation of DNA replication.

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Selected References

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  1. Adams A. E., Pringle J. R. Relationship of actin and tubulin distribution to bud growth in wild-type and morphogenetic-mutant Saccharomyces cerevisiae. J Cell Biol. 1984 Mar;98(3):934–945. doi: 10.1083/jcb.98.3.934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Aparicio O. M., Weinstein D. M., Bell S. P. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell. 1997 Oct 3;91(1):59–69. doi: 10.1016/s0092-8674(01)80009-x. [DOI] [PubMed] [Google Scholar]
  3. Bell S. P., Kobayashi R., Stillman B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science. 1993 Dec 17;262(5141):1844–1849. doi: 10.1126/science.8266072. [DOI] [PubMed] [Google Scholar]
  4. Bell S. P., Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. doi: 10.1038/357128a0. [DOI] [PubMed] [Google Scholar]
  5. Ben-Yehuda S., Dix I., Russell C. S., McGarvey M., Beggs J. D., Kupiec M. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics. 2000 Dec;156(4):1503–1517. doi: 10.1093/genetics/156.4.1503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Boger-Nadjar E., Vaisman N., Ben-Yehuda S., Kassir Y., Kupiec M. Efficient initiation of S-phase in yeast requires Cdc40p, a protein involved in pre-mRNA splicing. Mol Gen Genet. 1998 Nov;260(2-3):232–241. doi: 10.1007/s004380050891. [DOI] [PubMed] [Google Scholar]
  7. Brewer B. J., Fangman W. L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987 Nov 6;51(3):463–471. doi: 10.1016/0092-8674(87)90642-8. [DOI] [PubMed] [Google Scholar]
  8. Brown J. D., Beggs J. D. Roles of PRP8 protein in the assembly of splicing complexes. EMBO J. 1992 Oct;11(10):3721–3729. doi: 10.1002/j.1460-2075.1992.tb05457.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chung S., McLean M. R., Rymond B. C. Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition. RNA. 1999 Aug;5(8):1042–1054. doi: 10.1017/s1355838299990635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cockell M., Renauld H., Watt P., Gasser S. M. Sif2p interacts with Sir4p amino-terminal domain and antagonizes telomeric silencing in yeast. Curr Biol. 1998 Jun 18;8(13):787–790. doi: 10.1016/s0960-9822(98)70304-5. [DOI] [PubMed] [Google Scholar]
  11. Das A. K., Cohen P. W., Barford D. The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J. 1998 Mar 2;17(5):1192–1199. doi: 10.1093/emboj/17.5.1192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Diffley J. F., Cocker J. H., Dowell S. J., Rowley A. Two steps in the assembly of complexes at yeast replication origins in vivo. Cell. 1994 Jul 29;78(2):303–316. doi: 10.1016/0092-8674(94)90299-2. [DOI] [PubMed] [Google Scholar]
  13. Dillin A., Rine J. Roles for ORC in M phase and S phase. Science. 1998 Mar 13;279(5357):1733–1737. doi: 10.1126/science.279.5357.1733. [DOI] [PubMed] [Google Scholar]
  14. Donaldson A. D., Raghuraman M. K., Friedman K. L., Cross F. R., Brewer B. J., Fangman W. L. CLB5-dependent activation of late replication origins in S. cerevisiae. Mol Cell. 1998 Aug;2(2):173–182. doi: 10.1016/s1097-2765(00)80127-6. [DOI] [PubMed] [Google Scholar]
  15. Donovan J. D., Toyn J. H., Johnson A. L., Johnston L. H. P40SDB25, a putative CDK inhibitor, has a role in the M/G1 transition in Saccharomyces cerevisiae. Genes Dev. 1994 Jul 15;8(14):1640–1653. doi: 10.1101/gad.8.14.1640. [DOI] [PubMed] [Google Scholar]
  16. Donovan S., Harwood J., Drury L. S., Diffley J. F. Cdc6p-dependent loading of Mcm proteins onto pre-replicative chromatin in budding yeast. Proc Natl Acad Sci U S A. 1997 May 27;94(11):5611–5616. doi: 10.1073/pnas.94.11.5611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dumas L. B., Lussky J. P., McFarland E. J., Shampay J. New temperature-sensitive mutants of Saccharomyces cerevisiae affecting DNA replication. Mol Gen Genet. 1982;187(1):42–46. doi: 10.1007/BF00384381. [DOI] [PubMed] [Google Scholar]
  18. Engebrecht J., Hirsch J., Roeder G. S. Meiotic gene conversion and crossing over: their relationship to each other and to chromosome synapsis and segregation. Cell. 1990 Sep 7;62(5):927–937. doi: 10.1016/0092-8674(90)90267-i. [DOI] [PubMed] [Google Scholar]
  19. Foss M., McNally F. J., Laurenson P., Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. doi: 10.1126/science.8266071. [DOI] [PubMed] [Google Scholar]
  20. Gatto G. J., Jr, Geisbrecht B. V., Gould S. J., Berg J. M. Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat Struct Biol. 2000 Dec;7(12):1091–1095. doi: 10.1038/81930. [DOI] [PubMed] [Google Scholar]
  21. Geraghty D. S., Ding M., Heintz N. H., Pederson D. S. Premature structural changes at replication origins in a yeast minichromosome maintenance (MCM) mutant. J Biol Chem. 2000 Jun 16;275(24):18011–18021. doi: 10.1074/jbc.M909787199. [DOI] [PubMed] [Google Scholar]
  22. Grey M., Düsterhöft A., Henriques J. A., Brendel M. Allelism of PSO4 and PRP19 links pre-mRNA processing with recombination and error-prone DNA repair in Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Oct 15;24(20):4009–4014. doi: 10.1093/nar/24.20.4009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Grizot S., Fieschi F., Dagher M. C., Pebay-Peyroula E. The active N-terminal region of p67phox. Structure at 1.8 A resolution and biochemical characterizations of the A128V mutant implicated in chronic granulomatous disease. J Biol Chem. 2001 Mar 21;276(24):21627–21631. doi: 10.1074/jbc.M100893200. [DOI] [PubMed] [Google Scholar]
  24. Haase S. B., Lew D. J. Flow cytometric analysis of DNA content in budding yeast. Methods Enzymol. 1997;283:322–332. doi: 10.1016/s0076-6879(97)83026-1. [DOI] [PubMed] [Google Scholar]
  25. Hecht A., Grunstein M. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol. 1999;304:399–414. doi: 10.1016/s0076-6879(99)04024-0. [DOI] [PubMed] [Google Scholar]
  26. Hecht A., Strahl-Bolsinger S., Grunstein M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature. 1996 Sep 5;383(6595):92–96. doi: 10.1038/383092a0. [DOI] [PubMed] [Google Scholar]
  27. Hogan E., Koshland D. Addition of extra origins of replication to a minichromosome suppresses its mitotic loss in cdc6 and cdc14 mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):3098–3102. doi: 10.1073/pnas.89.7.3098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Hwang L. H., Murray A. W. A novel yeast screen for mitotic arrest mutants identifies DOC1, a new gene involved in cyclin proteolysis. Mol Biol Cell. 1997 Oct;8(10):1877–1887. doi: 10.1091/mbc.8.10.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Johnston L. H., Thomas A. P. A further two mutants defective in initiation of the S phase in the yeast Saccharomyces cerevisiae. Mol Gen Genet. 1982;186(3):445–448. doi: 10.1007/BF00729467. [DOI] [PubMed] [Google Scholar]
  30. Kamimura Y., Tak Y. S., Sugino A., Araki H. Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. EMBO J. 2001 Apr 17;20(8):2097–2107. doi: 10.1093/emboj/20.8.2097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kang Y. S., Kane J., Kurjan J., Stadel J. M., Tipper D. J. Effects of expression of mammalian G alpha and hybrid mammalian-yeast G alpha proteins on the yeast pheromone response signal transduction pathway. Mol Cell Biol. 1990 Jun;10(6):2582–2590. doi: 10.1128/mcb.10.6.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kassir Y., Kupiec M., Shalom A., Simchen G. Cloning and mapping of CDC40, a Saccharomyces cerevisiae gene with a role in DNA repair. Curr Genet. 1985;9(4):253–257. doi: 10.1007/BF00419952. [DOI] [PubMed] [Google Scholar]
  33. Kilmartin J. V., Wright B., Milstein C. Rat monoclonal antitubulin antibodies derived by using a new nonsecreting rat cell line. J Cell Biol. 1982 Jun;93(3):576–582. doi: 10.1083/jcb.93.3.576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kumar A., Roach C., Hirsh I. S., Turley S., deWalque S., Michels P. A., Hol W. G. An unexpected extended conformation for the third TPR motif of the peroxin PEX5 from Trypanosoma brucei. J Mol Biol. 2001 Mar 16;307(1):271–282. doi: 10.1006/jmbi.2000.4465. [DOI] [PubMed] [Google Scholar]
  35. Lamb J. R., Tugendreich S., Hieter P. Tetratrico peptide repeat interactions: to TPR or not to TPR? Trends Biochem Sci. 1995 Jul;20(7):257–259. doi: 10.1016/s0968-0004(00)89037-4. [DOI] [PubMed] [Google Scholar]
  36. Lapouge K., Smith S. J., Walker P. A., Gamblin S. J., Smerdon S. J., Rittinger K. Structure of the TPR domain of p67phox in complex with Rac.GTP. Mol Cell. 2000 Oct;6(4):899–907. doi: 10.1016/s1097-2765(05)00091-2. [DOI] [PubMed] [Google Scholar]
  37. Li R., Murray A. W. Feedback control of mitosis in budding yeast. Cell. 1991 Aug 9;66(3):519–531. doi: 10.1016/0092-8674(81)90015-5. [DOI] [PubMed] [Google Scholar]
  38. Liang C., Spitzer J. D., Smith H. S., Gerbi S. A. Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A. Genes Dev. 1993 Jun;7(6):1072–1084. doi: 10.1101/gad.7.6.1072. [DOI] [PubMed] [Google Scholar]
  39. Liang C., Stillman B. Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants. Genes Dev. 1997 Dec 15;11(24):3375–3386. doi: 10.1101/gad.11.24.3375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Lindquist S. Regulation of protein synthesis during heat shock. Nature. 1981 Sep 24;293(5830):311–314. doi: 10.1038/293311a0. [DOI] [PubMed] [Google Scholar]
  41. McDonald W. H., Ohi R., Smelkova N., Frendewey D., Gould K. L. Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol. 1999 Aug;19(8):5352–5362. doi: 10.1128/mcb.19.8.5352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Meluh P. B., Broach J. R. Immunological analysis of yeast chromatin. Methods Enzymol. 1999;304:414–430. doi: 10.1016/s0076-6879(99)04025-2. [DOI] [PubMed] [Google Scholar]
  43. Micklem G., Rowley A., Harwood J., Nasmyth K., Diffley J. F. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature. 1993 Nov 4;366(6450):87–89. doi: 10.1038/366087a0. [DOI] [PubMed] [Google Scholar]
  44. Ohi R., Feoktistova A., McCann S., Valentine V., Look A. T., Lipsick J. S., Gould K. L. Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes. Mol Cell Biol. 1998 Jul;18(7):4097–4108. doi: 10.1128/mcb.18.7.4097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Pederson D. S., Yao M. C., Kimmel A. R., Gorovsky M. A. Sequence organization within and flanking clusters of 5S ribosomal RNA genes in Tetrahymena. Nucleic Acids Res. 1984 Mar 26;12(6):3003–3021. doi: 10.1093/nar/12.6.3003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Perkins G., Diffley J. F. Nucleotide-dependent prereplicative complex assembly by Cdc6p, a homolog of eukaryotic and prokaryotic clamp-loaders. Mol Cell. 1998 Jul;2(1):23–32. doi: 10.1016/s1097-2765(00)80110-0. [DOI] [PubMed] [Google Scholar]
  47. Russell C. S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J. D. Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. RNA. 2000 Nov;6(11):1565–1572. doi: 10.1017/s1355838200000984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Scheufler C., Brinker A., Bourenkov G., Pegoraro S., Moroder L., Bartunik H., Hartl F. U., Moarefi I. Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine. Cell. 2000 Apr 14;101(2):199–210. doi: 10.1016/S0092-8674(00)80830-2. [DOI] [PubMed] [Google Scholar]
  49. Schneider B. L., Yang Q. H., Futcher A. B. Linkage of replication to start by the Cdk inhibitor Sic1. Science. 1996 Apr 26;272(5261):560–562. doi: 10.1126/science.272.5261.560. [DOI] [PubMed] [Google Scholar]
  50. Schwab M., Lutum A. S., Seufert W. Yeast Hct1 is a regulator of Clb2 cyclin proteolysis. Cell. 1997 Aug 22;90(4):683–693. doi: 10.1016/s0092-8674(00)80529-2. [DOI] [PubMed] [Google Scholar]
  51. Shea J. E., Toyn J. H., Johnston L. H. The budding yeast U5 snRNP Prp8 is a highly conserved protein which links RNA splicing with cell cycle progression. Nucleic Acids Res. 1994 Dec 25;22(25):5555–5564. doi: 10.1093/nar/22.25.5555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Sprague G. F., Jr Assay of yeast mating reaction. Methods Enzymol. 1991;194:77–93. doi: 10.1016/0076-6879(91)94008-z. [DOI] [PubMed] [Google Scholar]
  54. Stillman B. Cell cycle control of DNA replication. Science. 1996 Dec 6;274(5293):1659–1664. doi: 10.1126/science.274.5293.1659. [DOI] [PubMed] [Google Scholar]
  55. Strahl-Bolsinger S., Hecht A., Luo K., Grunstein M. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 1997 Jan 1;11(1):83–93. doi: 10.1101/gad.11.1.83. [DOI] [PubMed] [Google Scholar]
  56. Tanaka T., Knapp D., Nasmyth K. Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell. 1997 Aug 22;90(4):649–660. doi: 10.1016/s0092-8674(00)80526-7. [DOI] [PubMed] [Google Scholar]
  57. Tyers M. The cyclin-dependent kinase inhibitor p40SIC1 imposes the requirement for Cln G1 cyclin function at Start. Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7772–7776. doi: 10.1073/pnas.93.15.7772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Tyers M., Willems A. R. One ring to rule a superfamily of E3 ubiquitin ligases. Science. 1999 Apr 23;284(5414):601, 603-4. doi: 10.1126/science.284.5414.601. [DOI] [PubMed] [Google Scholar]
  59. Uetz P., Giot L., Cagney G., Mansfield T. A., Judson R. S., Knight J. R., Lockshon D., Narayan V., Srinivasan M., Pochart P. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623–627. doi: 10.1038/35001009. [DOI] [PubMed] [Google Scholar]
  60. Visintin R., Prinz S., Amon A. CDC20 and CDH1: a family of substrate-specific activators of APC-dependent proteolysis. Science. 1997 Oct 17;278(5337):460–463. doi: 10.1126/science.278.5337.460. [DOI] [PubMed] [Google Scholar]
  61. Waga S., Stillman B. The DNA replication fork in eukaryotic cells. Annu Rev Biochem. 1998;67:721–751. doi: 10.1146/annurev.biochem.67.1.721. [DOI] [PubMed] [Google Scholar]
  62. Zhang K., Smouse D., Perrimon N. The crooked neck gene of Drosophila contains a motif found in a family of yeast cell cycle genes. Genes Dev. 1991 Jun;5(6):1080–1091. doi: 10.1101/gad.5.6.1080. [DOI] [PubMed] [Google Scholar]
  63. Zou L., Mitchell J., Stillman B. CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication. Mol Cell Biol. 1997 Feb;17(2):553–563. doi: 10.1128/mcb.17.2.553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. da Silva K. V., de Morais Júnior M. A., Henriques J. A. The PSO4 gene of S. cerevisiae is important for sporulation and the meiotic DNA repair of photoactivated psoralen lesions. Curr Genet. 1995 Feb;27(3):207–212. doi: 10.1007/BF00326150. [DOI] [PubMed] [Google Scholar]
  65. de Morais M. A., Jr, Vicente E. J., Brozmanova J., Schenberg A. C., Henriques J. A. Further characterization of the yeast pso4-1 mutant: interaction with rad51 and rad52 mutants after photoinduced psoralen lesions. Curr Genet. 1996 Feb;29(3):211–218. doi: 10.1007/BF02221550. [DOI] [PubMed] [Google Scholar]

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