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Regulation of Saccharomyces cerevisiae DNA polymerase η transcript and protein

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Abstract

RAD30-encoded DNA polymerase η functions as a translesion polymerase that can bypass the most frequent types of UV-induced pyrimidine photoproducts in an error-free manner. Although its transcript is UV-inducible in Saccharomyces cerevisiae, Rad30 (studied as a Rad30-Myc fusion) is a stable protein whose levels do not fluctuate following UV treatment or during cell cycle progression. Rad30 protein is subject to monoubiquitination whose level is upregulated in G1 and downregulated during S-phase reentry. This downregulation is accelerated in UV-treated cells. A missense mutation (L577Q) of the ubiquitin binding domain (UBZ) confers a reduced degree of ubiquitination outside of G1 and a complete failure to stably interact with ubiquitinated substrates. This mutation confers a phenotype resembling a complete RAD30 deletion, thus attesting to the significance of the UBZ motif for polymerase η function in vivo.

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References

  1. Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, Ellenberger T (2005) DNA repair and mutagenesis, 2nd edn. American Society of Microbiology Press, Washington, D.C

    Google Scholar 

  2. Friedberg EC (2005) Suffering in silence: the tolerance of DNA damage. Nat Rev Mol Cell Biol 6:943–953

    Article  Google Scholar 

  3. Prakash S, Johnson RE, Prakash L (2005) Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu Rev Biochem 74:317–353

    Article  Google Scholar 

  4. Ohmori H, Friedberg EC, Fuchs RPP, Goodman MF, Hanaoka F, Hinkle D, Kunkel TA, Lawrence CW, Livneh Z, Nohmi T, Prakash L, Prakash S, Todo T, Walker GC, Wang Z, Woodgate R (2001) The Y-family of DNA polymerases. Mol Cell 8:7–8

    Article  Google Scholar 

  5. Yu S-L, Johnson RE, Prakash S, Prakash L (2001) Requirement of DNA polymerase η for error-free bypass of UV-induced CC and TT photoproducts. Mol Cell Biol 21:185–188

    Article  Google Scholar 

  6. Johnson RE, Prakash S, Prakash L (1999) Efficient bypass of a thymine–thymine dimer by yeast DNA polymerase, Polη. Science 283:1001–1004

    Article  ADS  Google Scholar 

  7. Johnson RE, Kondratick CM, Prakash S, Prakash L (1999) hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285:263–265

    Article  Google Scholar 

  8. Masutani C, Kusumoto R, Yamada A, Dohmae N, Yokoi M, Yuasa M, Araki M, Iwai S, Takio K, Hanaoka F (1999) The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399:700–704

    Article  ADS  Google Scholar 

  9. Masutani C, Araki M, Yamada A, Kusumoto R, Nogimori T, Maekawa T, Iwai S, Hanaoka F (1999) Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass polymerase activity. EMBO J 18:3491–3501

    Article  Google Scholar 

  10. Matsuda T, Bebenek K, Masutani C, Rogozin IB, Hanaoka F, Kunkel TA (2001) Error rate and specificity of human and murine DNA polymerase η. J Mol Biol 312:335–346

    Article  Google Scholar 

  11. Matsuda T, Bebenek K, Masutani C, Hanaoka F, Kunkel TA (2000) Low fidelity DNA synthesis by human DNA polymerase-η. Nature 404:1011–1013

    Article  ADS  Google Scholar 

  12. Roush AA, Suarez M, Friedberg EC, Radman M, Siede W (1998) Deletion of the Saccharomyces cerevisiae gene RAD30 encoding an Escherichia coli DinB homolog confers UV radiation sensitivity and altered mutability. Mol Gen Genet 257:686–692

    Article  Google Scholar 

  13. McDonald JP, Levine AS, Woodgate R (1997) The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free postreplication repair mechanism. Genetics 147:1557–1568

    Google Scholar 

  14. Yamada A, Masutani C, Iwai S, Hanaoka F (2000) Complementation of defective translesion synthesis and UV light sensitivity in xeroderma pigmentosum variant cells by human and mouse DNA polymerase η. Nucleic Acids Res 28:2473–2480

    Article  Google Scholar 

  15. Liu G, Chen X (2006) DNA polymerase η, the product of the Xeroderma Pigmentosum variant gene and a target of p53, modulates the DNA damage checkpoint and p53 activation. Mol Cell Biol 26:1398–1413

    Article  Google Scholar 

  16. Kai M, Wang TS (2003) Checkpoint activation regulates mutagenic translesion synthesis. Genes Dev 17:64–76

    Article  Google Scholar 

  17. Velasco-Miguel S, Richardson JA, Gerlach VL, Lai WC, Gao T, Russell LD, Hladik CL, White CL, Friedberg EC (2003) Constitutive and regulated expression of the mouse Dinb (Polκ) gene encoding DNA polymerase kappa. DNA Repair 2:91–106

    Article  Google Scholar 

  18. Friedberg EC, Lehmann AR, Fuchs RP (2005) Trading places: how do DNA polymerases switch during translesion DNA synthesis? Mol Cell 18:499–505

    Article  Google Scholar 

  19. Hoege C, Pfander B, Moldovan G-L, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419:135–141

    Article  ADS  Google Scholar 

  20. Kannouche PL, Wing J, Lehmann AR (2004) Interaction of human DNA polymerase η with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage. Mol Cell 14:491–500

    Article  Google Scholar 

  21. Stelter P, Ulrich HD (2003) Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425:188–191

    Article  ADS  Google Scholar 

  22. Watanabe K, Tateishi S, Kawasuji M, Tsurimoto T, Inoue H, Yamaizumi M (2004) Rad18 guides polη to replication stalling sites through physical interaction and PCNA monoubiquitination. EMBO J 23:3886–3896

    Article  Google Scholar 

  23. Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR, Hofmann K, Dikic I (2005) Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science 310:1821–1824

    Article  ADS  Google Scholar 

  24. Guo C, Tang T-S, Bienko M, Parker JL, Bielen AB, Sonoda E, Takeda S, Ulrich HD, Dikic I, Friedberg EC (2006) Ubiquitin-binding motifs in REV1 protein are required for its role in the tolerance of DNA damage. Mol Cell Biol 26:8892–8900

    Article  Google Scholar 

  25. Guo C, Sonoda E, Tang T-S, Parker JL, Bielen AB, Takeda S, Ulrich HD, Friedberg EC (2006) REV1 protein interacts with PCNA: significance of the REV1 BRCT domain in vitro and in vivo. Mol Cell 23:265–271

    Article  Google Scholar 

  26. Plosky BS, Vidal AE, de Henestrosa AR, McLenigan MP, McDonald JP, Mead S, Woodgate R (2006) Controlling the subcellular localization of DNA polymerases ι and η via interactions with ubiquitin. EMBO J 25:2847–2855

    Article  Google Scholar 

  27. Haracska L, Johnson RE, Unk I, Phillips BB, Hurwitz J, Prakash L, Prakash S (2001) Targeting of human DNA polymerase ι to the replication machinery via interaction with PCNA. Proc Natl Acad Sci USA 98:14256–14261

    Article  ADS  Google Scholar 

  28. Garg P, Burgers PM (2005) Ubiquitinated proliferating cell nuclear antigen activates translesion DNA polymerases η and REV1. Proc Natl Acad Sci USA 102:18361–18366

    Article  ADS  Google Scholar 

  29. Haracska L, Unk I, Prakash L, Prakash S (2006) Ubiquitylation of yeast proliferating cell nuclear antigen and its implications for translesion DNA synthesis. Proc Natl Acad Sci USA 103:6477–6482

    Article  ADS  Google Scholar 

  30. Longtine MS, McKenzie III A, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961

    Article  Google Scholar 

  31. Amberg DC, Burke DJ, Strathern JN (2005) Methods in yeast genetics: a cold spring harbor laboratory course manual, 2005 edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  32. Wenzel TJ, Teunissen AWRH, Steensma HY (1995) PDA1 mRNA: a standard for quantitation of mRNA in Saccharomyces cerevisiae superior to ACT1 mRNA. Nucleic Acids Res 23:883–884

    Article  Google Scholar 

  33. Hereford LM, Hartwell LH (1973) Role of protein synthesis in the replication of yeast DNA. Nat New Biol 244:129–131

    Article  Google Scholar 

  34. Foiani M, Marini F, Gamba D, Lucchini G, Plevani P (1994) The B subunit of the DNA polymerase α-primase complex in Saccharomyces cerevisiae executes an essential function at the initial stage of DNA replication. Mol Cell Biol 14:923–933

    Google Scholar 

  35. Skoneczna A, McIntyre J, Skoneczny M, Policinska Z, Sledziewska-Gojska E (2007) Polymerase eta is a short-lived, proteasomally degraded protein that is temporarily stabilized following UV irradiation in Saccharomyces cerevisiae. J Mol Biol 366:1074–1086

    Article  Google Scholar 

  36. Parker JL, Bielen AB, Dikic I, Ulrich HD (2007) Contributions of ubiquitin- and PCNA-binding domains to the activity of polymerase η in Saccharomyces cerevisiae. Nucleic Acids Res 35:881–889

    Article  Google Scholar 

  37. Bachant JB, Elledge SJ (1998) Regulatory networks that control DNA damage-inducible genes in Saccharomyces cerevisiae. In: Nickoloff JA, Hoekstra MF (eds) DNA damage and repair, vol 1. DNA repair in prokaryotes and lower eukaryotes. Humana Press, Totowa, pp 383–410

  38. Aboussekhra A, Vialard JE, Morrison DE, de la Torre-Ruiz MA, Cernáková L, Fabre F, Lowndes NF (1996) A novel role for the budding yeast RAD9 checkpoint gene in DNA damage-dependent transcription. EMBO J 15:3912–3922

    Google Scholar 

  39. Nyberg KA, Michelson RJ, Putnam CW, Weinert TA (2002) Toward maintaining the genome: DNA damage and replication checkpoints. Annu Rev Genet 36:617–656

    Article  Google Scholar 

  40. Waters LS, Walker GC (2006) The critical mutagenic translesion DNA polymerase Rev1 is highly expressed during G2/M phase rather than S phase. Proc Natl Acad Sci USA 103:8971–8976

    Article  ADS  Google Scholar 

  41. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316:1160–1166

    Article  ADS  Google Scholar 

  42. Raymond WE, Kleckner N (1993) Expression of the Saccharomyces cerevisiae RAD50 gene during meiosis: steady-state transcript levels rise and fall while steady-state protein levels remain constant. Mol Gen Genet 238:390–400

    Article  Google Scholar 

  43. Birrell GW, Brown JA, Wu HI, Giaever G, Chu AM, Davis RW, Brown JM (2002) Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci USA 99:8778–8783

    Article  ADS  Google Scholar 

  44. Begley TJ, Rosenbach AS, Ideker T, Samson LD (2002) Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res 1:103–112

    Google Scholar 

  45. Lee MW, Kim BJ, Choi HK, Ryu MJ, Kim SB, Kang KM, Cho EJ, Youn HD, Huh WK, Kim ST (2007) Global protein expression profiling of budding yeast in response to DNA damage. Yeast 24:145–154

    Article  Google Scholar 

  46. Jelinsky SA, Samson LD (1999) Global response of Saccaromyces cerevisiae to an alkylating agent. Proc Natl Acad Sci USA 96:1486–1491

    Article  ADS  Google Scholar 

  47. Fornace AJ Jr, Zmudzka B, Hollander MC, Wilson SH (1989) Induction of β-polymerase mRNA by DNA damaging agents in Chinese hamster ovary cells. Mol Cell Biol 9:851–853

    Google Scholar 

  48. Lis ET, Romesberg FE (2006) Role of Doa1 in the Saccharomyces cerevisiae DNA damage response. Mol Cell Biol 26:4122–4133

    Article  Google Scholar 

  49. James AP, Kilbey BJ (1977) The timing of UV mutagenesis in yeast: a pedigree analysis of induced recessive mutation. Genetics 87:237–248

    Google Scholar 

  50. Kilbey BJ, Brychcy T, Nasim A (1978) Initiation of UV mutagenesis in Saccharomyces cerevisiae. Nature 274:889–891

    Article  ADS  Google Scholar 

  51. Eckardt F, Haynes RH (1977) Induction of pure and sectored mutant clones in excision-proficient and deficient strains of yeast. Mutat Res 43:327–338

    Google Scholar 

  52. Zhang H, Siede W (2002) UV-induced T→C transition at a TT photoproduct site is dependent on Saccharomyces cerevisiae polymerase η in vivo. Nucleic Acids Res 30:1262–1267

    Article  Google Scholar 

  53. Marchenko ND, Wolff S, Erster S, Becker K, Moll UM (2007) Monoubiquitylation promotes mitochondrial p53 translocation. EMBO J 26:923–934

    Article  Google Scholar 

  54. Bomar MG, Pai MT, Tzeng SR, Li SS, Zhou P (2007) Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase η. EMBO Rep 8:247–251

    Article  Google Scholar 

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Acknowledgments

We appreciate the technical help of Fyalon Kerr. We thank Dr. Graham Walker’s group (Massachusetts Institute of Technology) for communicating unpublished results. Dr. Pei Zhou (Duke University Medical Center) kindly contributed an illustration. This work was supported by Grant ES011163 from the National Institutes of Health.

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Correspondence to Wolfram Siede.

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Pabla, R., Rozario, D. & Siede, W. Regulation of Saccharomyces cerevisiae DNA polymerase η transcript and protein. Radiat Environ Biophys 47, 157–168 (2008). https://doi.org/10.1007/s00411-007-0132-1

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