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. 2000 Aug;155(4):1593–1606. doi: 10.1093/genetics/155.4.1593

POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae.

M B Schlesinger 1, T Formosa 1
PMCID: PMC1461200  PMID: 10924459

Abstract

Spt16 and Pob3 form stable heterodimers in Saccharomyces cerevisiae, and homologous proteins have also been purified as complexes from diverse eukaryotes. This conserved factor has been implicated in both transcription and replication and may affect both by altering the characteristics of chromatin. Here we describe the isolation and properties of a set of pob3 mutants and confirm that they have defects in both replication and transcription. Mutation of POB3 caused the Spt(-) phenotype, spt16 and pob3 alleles displayed severe synthetic defects, and elevated levels of Pob3 suppressed some spt16 phenotypes. These results are consistent with previous reports that Spt16 and Pob3 act in a complex that modulates transcription. Additional genetic interactions were observed between pob3 mutations and the genes encoding several DNA replication factors, including POL1, CTF4, DNA2, and CHL12. pob3 alleles caused sensitivity to the ribonucleotide reductase inhibitor hydroxyurea, indicating a defect in a process requiring rapid dNTP synthesis. Mutation of the S phase checkpoint gene MEC1 caused pob3 mutants to lose viability rapidly under restrictive conditions, revealing defects in a process monitored by Mec1. Direct examination of DNA contents by flow cytometry showed that S phase onset and progression were delayed when POB3 was mutated. We conclude that Pob3 is required for normal replication as well as for transcription.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bae S. H., Choi E., Lee K. H., Park J. S., Lee S. H., Seo Y. S. Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific endonuclease activity that is able to act on double-stranded DNA in the presence of ATP. J Biol Chem. 1998 Oct 9;273(41):26880–26890. doi: 10.1074/jbc.273.41.26880. [DOI] [PubMed] [Google Scholar]
  3. Boeke J. D., Trueheart J., Natsoulis G., Fink G. R. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 1987;154:164–175. doi: 10.1016/0076-6879(87)54076-9. [DOI] [PubMed] [Google Scholar]
  4. Bonetti B., Fu L., Moon J., Bedwell D. M. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol. 1995 Aug 18;251(3):334–345. doi: 10.1006/jmbi.1995.0438. [DOI] [PubMed] [Google Scholar]
  5. Brewster N. K., Johnston G. C., Singer R. A. Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins that regulates yeast transcriptional activation and chromatin repression. J Biol Chem. 1998 Aug 21;273(34):21972–21979. doi: 10.1074/jbc.273.34.21972. [DOI] [PubMed] [Google Scholar]
  6. Budd M. E., Choe W. C., Campbell J. L. DNA2 encodes a DNA helicase essential for replication of eukaryotic chromosomes. J Biol Chem. 1995 Nov 10;270(45):26766–26769. doi: 10.1074/jbc.270.45.26766. [DOI] [PubMed] [Google Scholar]
  7. Cadwell R. C., Joyce G. F. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 1992 Aug;2(1):28–33. doi: 10.1101/gr.2.1.28. [DOI] [PubMed] [Google Scholar]
  8. Clark-Adams C. D., Norris D., Osley M. A., Fassler J. S., Winston F. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 1988 Feb;2(2):150–159. doi: 10.1101/gad.2.2.150. [DOI] [PubMed] [Google Scholar]
  9. Cullmann G., Fien K., Kobayashi R., Stillman B. Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol Cell Biol. 1995 Sep;15(9):4661–4671. doi: 10.1128/mcb.15.9.4661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Desany B. A., Alcasabas A. A., Bachant J. B., Elledge S. J. Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway. Genes Dev. 1998 Sep 15;12(18):2956–2970. doi: 10.1101/gad.12.18.2956. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Elledge S. J. Cell cycle checkpoints: preventing an identity crisis. Science. 1996 Dec 6;274(5293):1664–1672. doi: 10.1126/science.274.5293.1664. [DOI] [PubMed] [Google Scholar]
  12. Evans D. R., Brewster N. K., Xu Q., Rowley A., Altheim B. A., Johnston G. C., Singer R. A. The yeast protein complex containing cdc68 and pob3 mediates core-promoter repression through the cdc68 N-terminal domain. Genetics. 1998 Dec;150(4):1393–1405. doi: 10.1093/genetics/150.4.1393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Formosa T., Nittis T. Dna2 mutants reveal interactions with Dna polymerase alpha and Ctf4, a Pol alpha accessory factor, and show that full Dna2 helicase activity is not essential for growth. Genetics. 1999 Apr;151(4):1459–1470. doi: 10.1093/genetics/151.4.1459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Hirschman J. E., Durbin K. J., Winston F. Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4608–4615. doi: 10.1128/mcb.8.11.4608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Longhese M. P., Foiani M., Muzi-Falconi M., Lucchini G., Plevani P. DNA damage checkpoint in budding yeast. EMBO J. 1998 Oct 1;17(19):5525–5528. doi: 10.1093/emboj/17.19.5525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lycan D., Mikesell G., Bunger M., Breeden L. Differential effects of Cdc68 on cell cycle-regulated promoters in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Nov;14(11):7455–7465. doi: 10.1128/mcb.14.11.7455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Malone E. A., Clark C. D., Chiang A., Winston F. Mutations in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Nov;11(11):5710–5717. doi: 10.1128/mcb.11.11.5710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Miles J., Formosa T. Evidence that POB1, a Saccharomyces cerevisiae protein that binds to DNA polymerase alpha, acts in DNA metabolism in vivo. Mol Cell Biol. 1992 Dec;12(12):5724–5735. doi: 10.1128/mcb.12.12.5724. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Miles J., Formosa T. Protein affinity chromatography with purified yeast DNA polymerase alpha detects proteins that bind to DNA polymerase. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1276–1280. doi: 10.1073/pnas.89.4.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Newport J. Nuclear reconstitution in vitro: stages of assembly around protein-free DNA. Cell. 1987 Jan 30;48(2):205–217. doi: 10.1016/0092-8674(87)90424-7. [DOI] [PubMed] [Google Scholar]
  22. Okuhara K., Ohta K., Seo H., Shioda M., Yamada T., Tanaka Y., Dohmae N., Seyama Y., Shibata T., Murofushi H. A DNA unwinding factor involved in DNA replication in cell-free extracts of Xenopus eggs. Curr Biol. 1999 Apr 8;9(7):341–350. doi: 10.1016/s0960-9822(99)80160-2. [DOI] [PubMed] [Google Scholar]
  23. Orphanides G., LeRoy G., Chang C. H., Luse D. S., Reinberg D. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell. 1998 Jan 9;92(1):105–116. doi: 10.1016/s0092-8674(00)80903-4. [DOI] [PubMed] [Google Scholar]
  24. Orphanides G., Wu W. H., Lane W. S., Hampsey M., Reinberg D. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature. 1999 Jul 15;400(6741):284–288. doi: 10.1038/22350. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Paulovich A. G., Toczyski D. P., Hartwell L. H. When checkpoints fail. Cell. 1997 Feb 7;88(3):315–321. doi: 10.1016/s0092-8674(00)81870-x. [DOI] [PubMed] [Google Scholar]
  27. Prendergast J. A., Murray L. E., Rowley A., Carruthers D. R., Singer R. A., Johnston G. C. Size selection identifies new genes that regulate Saccharomyces cerevisiae cell proliferation. Genetics. 1990 Jan;124(1):81–90. doi: 10.1093/genetics/124.1.81. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rowley A., Singer R. A., Johnston G. C. CDC68, a yeast gene that affects regulation of cell proliferation and transcription, encodes a protein with a highly acidic carboxyl terminus. Mol Cell Biol. 1991 Nov;11(11):5718–5726. doi: 10.1128/mcb.11.11.5718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Schnell R., D'Ari L., Foss M., Goodman D., Rine J. Genetic and molecular characterization of suppressors of SIR4 mutations in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):29–46. doi: 10.1093/genetics/122.1.29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sikorski R. S., Boeke J. D. In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods Enzymol. 1991;194:302–318. doi: 10.1016/0076-6879(91)94023-6. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. 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]
  33. Weinert T. DNA damage and checkpoint pathways: molecular anatomy and interactions with repair. Cell. 1998 Sep 4;94(5):555–558. doi: 10.1016/s0092-8674(00)81597-4. [DOI] [PubMed] [Google Scholar]
  34. Winston F., Durbin K. J., Fink G. R. The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell. 1984 Dec;39(3 Pt 2):675–682. doi: 10.1016/0092-8674(84)90474-4. [DOI] [PubMed] [Google Scholar]
  35. Wittmeyer J., Formosa T. Identifying DNA replication complex components using protein affinity chromatography. Methods Enzymol. 1995;262:415–430. doi: 10.1016/0076-6879(95)62033-8. [DOI] [PubMed] [Google Scholar]
  36. Wittmeyer J., Formosa T. The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein. Mol Cell Biol. 1997 Jul;17(7):4178–4190. doi: 10.1128/mcb.17.7.4178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Wittmeyer J., Joss L., Formosa T. Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. Biochemistry. 1999 Jul 13;38(28):8961–8971. doi: 10.1021/bi982851d. [DOI] [PubMed] [Google Scholar]
  38. Xu Q., Johnston G. C., Singer R. A. The Saccharomyces cerevisiae Cdc68 transcription activator is antagonized by San1, a protein implicated in transcriptional silencing. Mol Cell Biol. 1993 Dec;13(12):7553–7565. doi: 10.1128/mcb.13.12.7553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Xu Q., Singer R. A., Johnston G. C. Sug1 modulates yeast transcription activation by Cdc68. Mol Cell Biol. 1995 Nov;15(11):6025–6035. doi: 10.1128/mcb.15.11.6025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Zhou Y. H., Zhang X. P., Ebright R. H. Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase. Nucleic Acids Res. 1991 Nov 11;19(21):6052–6052. doi: 10.1093/nar/19.21.6052. [DOI] [PMC free article] [PubMed] [Google Scholar]

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