DNA Damage and DNA Replication Stress in Yeast Models of Aging

  • William C. BurhansEmail author
  • Martin Weinberger
Part of the Subcellular Biochemistry book series (SCBI, volume 57)


DNA damage is an important factor in aging in all eukaryotes. Although connections between DNA damage and aging have been extensively investigated in complex organisms, only a relatively few studies have investigated DNA damage as an aging factor in the model organism S. cerevisiae. Several of these studies point to DNA replication stress as a cause of age-dependent DNA damage in the replicative model of aging, which measures how many times budding yeast cells divide before they senesce and die. Even fewer studies have investigated how DNA damage contributes to aging in the chronological aging model, which measures how long cells in stationary phase cultures retain reproductive capacity. DNA replication stress also has been implicated as a factor in chronological aging . Since cells in stationary phase are generally considered to be “post-mitotic” and to reside in a quiescent G0/G1 state, the notion that defects in DNA replication might contribute to chronological aging appears to be somewhat paradoxical. However, the results of recent studies suggest that a significant fraction of cells in stationary phase cultures are not quiescent, especially in experiments that employ defined medium, which is frequently employed to assess chronological lifespan. Most cells that fail to achieve quiescence remain in a viable, but non-dividing state until they eventually die, similar to the senescent state in mammalian cells. In this chapter we discuss the role of DNA damage and DNA replication stress in both replicative and chronological aging in S. cerevisiae. We also discuss the relevance of these findings to the emerging view that DNA damage and DNA replication stress are important components of the senescent state that occurs at early stages of cancer.


DNA damage DNA replication stress Replicative aging Chronological aging Genome instability 


  1. Aguilaniu H, Gustafsson L, Rigoulet M, Nystrom T (2003) Asymmetric inheritance of oxidatively damaged proteins during cytokinesis. Science 299:1751–1753PubMedCrossRefGoogle Scholar
  2. Allen C, Buttner S, Aragon AD, Thomas JA, Meirelles O, Jaetao JE, Benn D, Ruby SW, Veenhuis M, Madeo F et al (2006) Isolation of quiescent and nonquiescent cells from yeast stationary-phase cultures. J Cell Biol 174:89–100PubMedCrossRefGoogle Scholar
  3. Aragon AD, Rodriguez AL, Meirelles O, Roy S, Davidson GS, Tapia PH, Allen C, Joe R, Benn D, Werner-Washburne M (2008) Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures. Mol Biol Cell 19:1271–1280PubMedCrossRefGoogle Scholar
  4. Barros MH, Bandy B, Tahara EB, Kowaltowski AJ (2004) Higher respiratory activity decreases mitochondrial reactive oxygen release and increases life span in Saccharomyces cerevisiae. J Biol Chem 279:49883–49888PubMedCrossRefGoogle Scholar
  5. Bartkova J, Horejsi Z, Koed K, Kramer A, Tort F, Zieger K, Guldberg P, Sehested M, Nesland JM, Lukas C et al (2005) DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 434:864–870PubMedCrossRefGoogle Scholar
  6. Bester AC, Roniger M, Oren YS, Im MM, Sarni D, Chaoat M, Bensimon A, Zamir G, Shewach DS, Kerem B (2011) Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell 145:435–446PubMedCrossRefGoogle Scholar
  7. Bhattacharyya S, Rolfsmeier ML, Dixon MJ, Wagoner K, Lahue RS (2002) Identification of RTG2 as a modifier gene for CTG*CAG repeat instability in Saccharomyces cerevisiae. Genetics 162:579–589PubMedGoogle Scholar
  8. Blagosklonny MV (2011) Cell cycle arrest is not senescence. Aging (Albany NY) 3:94–101Google Scholar
  9. Borghouts C, Benguria A, Wawryn J, Jazwinski SM (2004) Rtg2 protein links metabolism and genome stability in yeast longevity. Genetics 166:765–777PubMedCrossRefGoogle Scholar
  10. Burhans WC, Weinberger M (2007) DNA replication stress, genome instability and aging. Nucleic Acids Res 35:7545–7556PubMedCrossRefGoogle Scholar
  11. Burhans WC, Weinberger M (2010) Histone genes, DNA replication, apoptosis and aging: what are the connections? Cell Cycle 9:4047–4048CrossRefGoogle Scholar
  12. Burtner CR, Murakami CJ, Kennedy BK, Kaeberlein M (2009) A molecular mechanism of chronological aging in yeast. Cell Cycle 8:1256–1270PubMedCrossRefGoogle Scholar
  13. Casper AM, Mieczkowski PA, Gawel M, Petes TD (2008) Low levels of DNA polymerase alpha induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae. PLoS Genet 4:e1000105PubMedCrossRefGoogle Scholar
  14. Chaudhuri L, Sarsour EH, Goswami PC (2010) 2-(4-Chlorophenyl)benzo-1,4-quinone induced ROS-signaling inhibits proliferation in human non-malignant prostate epithelial cells. Environ Int 36:924–930PubMedCrossRefGoogle Scholar
  15. Chen JH, Hales CN, Ozanne SE (2007) DNA damage, cellular senescence and organismal ageing: causal or correlative? Nucleic Acids Res 35:7417–7428PubMedCrossRefGoogle Scholar
  16. Dang W, Steffen KK, Perry R, Dorsey JA, Johnson FB, Shilatifard A, Kaeberlein M, Kennedy BK, Berger SL (2009) Histone H4 lysine 16 acetylation regulates cellular lifespan. Nature 459:802–807PubMedCrossRefGoogle Scholar
  17. Desany BA, Alcasabas AA, Bachant JB, Elledge SJ (1998) Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway. Genes Dev 12:2956–2970PubMedCrossRefGoogle Scholar
  18. Di Micco R, Fumagalli M, Cicalese A, Piccinin S, Gasparini P, Luise C, Schurra C, Garre M, Nuciforo PG, Bensimon A et al (2006) Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 444:638–642PubMedCrossRefGoogle Scholar
  19. Fabrizio P, Battistella L, Vardavas R, Gattazzo C, Liou LL, Diaspro A, Dossen JW, Gralla EB, Longo VD (2004) Superoxide is a mediator of an altruistic aging program in Saccharomyces cerevisiae. J Cell Biol 166:1055–1067PubMedCrossRefGoogle Scholar
  20. Fabrizio P, Longo VD (2008) Chronological aging-induced apoptosis in yeast. Biochim Biophys Acta 1783:1280–1285PubMedCrossRefGoogle Scholar
  21. Fasullo M, Tsaponina O, Sun M, Chabes A (2010) Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants. Nucleic Acids Res 38:1195–1203PubMedCrossRefGoogle Scholar
  22. Freitas AA, de Magalhaes JP (2011) A review and appraisal of the DNA damage theory of ageing. Mutat Res 728:12–22PubMedCrossRefGoogle Scholar
  23. Ganley AR, Ide S, Saka K, Kobayashi T (2009) The effect of replication initiation on gene amplification in the rDNA and its relationship to aging. Mol Cell 35:683–693PubMedCrossRefGoogle Scholar
  24. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257PubMedGoogle Scholar
  25. Granot D, Levine A, Dor-Hefetz E (2003) Sugar-induced apoptosis in yeast cells. FEMS Yeast Res 4:7–13PubMedCrossRefGoogle Scholar
  26. Guarente L (2000) Sir2 links chromatin silencing, metabolism, and aging. Genes Dev 14:1021–1026PubMedGoogle Scholar
  27. Hakansson P, Hofer A, Thelander L (2006) Regulation of mammalian ribonucleotide reduction and dNTP pools after DNA damage and in resting cells. J Biol Chem 281:7834–7841PubMedCrossRefGoogle Scholar
  28. Hartman J Lt. (2007) Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism. Proc Natl Acad Sci USA 104:11700–11705PubMedCrossRefGoogle Scholar
  29. Heeren G, Rinnerthaler M, Laun P, von Seyerl P, Kossler S, Klinger H, Hager M, Bogengruber E, Jarolim S, Simon-Nobbe B et al (2009) The mitochondrial ribosomal protein of the large subunit, Afo1p, determines cellular longevity through mitochondrial back-signaling via TOR1. Aging (Albany NY) 1:622–636Google Scholar
  30. Heo SJ, Tatebayashi K, Ohsugi I, Shimamoto A, Furuichi Y, Ikeda H (1999) Bloom’s syndrome gene suppresses premature ageing caused by Sgs1 deficiency in yeast. Genes Cells 4:619–625PubMedCrossRefGoogle Scholar
  31. Herker E, Jungwirth H, Lehmann KA, Maldener C, Frohlich KU, Wissing S, Buttner S, Fehr M, Sigrist S, Madeo F (2004) Chronological aging leads to apoptosis in yeast. J Cell Biol 164:501–507PubMedCrossRefGoogle Scholar
  32. Herrero AB, Moreno S (2011) Lsm1 promotes genomic stability by controlling histone mRNA decay. EMBO J 30:2008–2018PubMedCrossRefGoogle Scholar
  33. Hoopes LL, Budd M, Choe W, Weitao T, Campbell JL (2002) Mutations in DNA replication genes reduce yeast life span. Mol Cell Biol 22:4136–4146PubMedCrossRefGoogle Scholar
  34. Jarolim S, Millen J, Heeren G, Laun P, Goldfarb DS, Breitenbach M (2004) A novel assay for replicative lifespan in Saccharomyces cerevisiae. FEMS Yeast Res 5:169–177PubMedCrossRefGoogle Scholar
  35. Jazwinski SM (2005) Rtg2 protein: at the nexus of yeast longevity and aging. FEMS Yeast Res 5:1253–1259PubMedCrossRefGoogle Scholar
  36. Kaeberlein M, Powers RW 3rd, Steffen KK, Westman EA, Hu D, Dang N, Kerr EO, Kirkland KT, Fields S, Kennedy BK (2005) Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 310:1193–1196PubMedCrossRefGoogle Scholar
  37. Laschober GT, Ruli D, Hofer E, Muck C, Carmona-Gutierrez D, Ring J, Hutter E, Ruckenstuhl C, Micutkova L, Brunauer R et al (2010) Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell 9:1084–1097PubMedCrossRefGoogle Scholar
  38. Laun P, Ramachandran L, Jarolim S, Herker E, Liang P, Wang J, Weinberger M, Burhans DT, Suter B, Madeo F et al (2005) A comparison of the aging and apoptotic transcriptome of Saccharomyces cerevisiae. FEMS Yeast Res 5:1261–1272PubMedCrossRefGoogle Scholar
  39. Lengronne A, Schwob E (2002) The yeast CDK inhibitor Sic1 prevents genomic instability by promoting replication origin licensing in late G(1). Mol Cell 9:1067–1078PubMedCrossRefGoogle Scholar
  40. Lesur I, Campbell JL (2004) The transcriptome of prematurely aging yeast cells is similar to that of telomerase-deficient cells. Mol Biol Cell 15:1297–1312PubMedCrossRefGoogle Scholar
  41. Lindstrom DL, Gottschling DE (2009) The mother enrichment program: a genetic system for facile replicative life span analysis in Saccharomyces cerevisiae. Genetics 183:413–422, 411SI–413SIPubMedCrossRefGoogle Scholar
  42. Lindstrom DL, Leverich CK, Henderson KA, Gottschling DE (2011) Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae. PLoS Genet 7:e1002015PubMedCrossRefGoogle Scholar
  43. Lopez Castel A, Cleary JD, Pearson CE (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 11:165–170PubMedCrossRefGoogle Scholar
  44. Luo J, Solimini NL, Elledge SJ (2009) Principles of cancer therapy: oncogene and non-oncogene addiction. Cell 136:823–837PubMedCrossRefGoogle Scholar
  45. Madia F, Gattazzo C, Wei M, Fabrizio P, Burhans WC, Weinberger M, Galbani A, Smith JR, Nguyen C, Huey S et al (2008) Longevity mutation in SCH9 prevents recombination errors and premature genomic instability in a Werner/Bloom model system. J Cell Biol 180:67–81PubMedCrossRefGoogle Scholar
  46. Madia F, Wei M, Yuan V, Hu J, Gattazzo C, Pham P, Goodman MF, Longo VD (2009) Oncogene homologue Sch9 promotes age-dependent mutations by a superoxide and Rev1/Polzeta-dependent mechanism. J Cell Biol 186:509–523PubMedCrossRefGoogle Scholar
  47. McMurray MA, Gottschling DE (2003) An age-induced switch to a hyper-recombinational state. Science 301:1908–1911PubMedCrossRefGoogle Scholar
  48. McVey M, Kaeberlein M, Tissenbaum HA, Guarente L (2001) The short life span of Saccharomyces cerevisiae sgs1 and srs2 mutants is a composite of normal aging processes and mitotic arrest due to defective recombination. Genetics 157:1531–1542PubMedGoogle Scholar
  49. Merker RJ, Klein HL (2002) hpr1Delta affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae. Mol Cell Biol 22:421–429PubMedCrossRefGoogle Scholar
  50. Mesquita A, Weinberger M, Silva A, Sampaio-Marques B, Almeida B, Leao C, Costa V, Rodrigues F, Burhans WC, Ludovico P (2010) Caloric restriction or catalase inactivation extends yeast chronological lifespan by inducing H2O2 and superoxide dismutase activity. Proc Natl Acad Sci USA 107:15123–15128PubMedCrossRefGoogle Scholar
  51. Mortimer RK, Johnston JR (1959) Life span of individual yeast cells. Nature 183:1751–1752PubMedCrossRefGoogle Scholar
  52. Negrini S, Gorgoulis VG, Halazonetis TD (2010) Genomic instability–an evolving hallmark of cancer. Nat Rev Mol Cell Biol 11:220–228PubMedCrossRefGoogle Scholar
  53. Palermo V, Cundari E, Mangiapelo E, Falcone C, Mazzoni C (2010) Yeast lsm pro-apoptotic mutants show defects in S-phase entry and progression. Cell Cycle 9:3991–3996PubMedCrossRefGoogle Scholar
  54. Pasero P, Bensimon A, Schwob E (2002) Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev 16:2479–2484PubMedCrossRefGoogle Scholar
  55. Pichova A, Vondrakova D, Breitenbach M (1997) Mutants in the Saccharomyces cerevisiae RAS2 gene influence life span, cytoskeleton, and regulation of mitosis. Can J Microbiol 43:774–781PubMedCrossRefGoogle Scholar
  56. Powers RW 3rd, Kaeberlein M, Caldwell SD, Kennedy BK, Fields S (2006) Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Dev 20:174–184PubMedCrossRefGoogle Scholar
  57. Pruitt SC, Bailey KJ, Freeland A (2007) Reduced Mcm2 expression results in severe stem/progenitor cell deficiency and cancer. Stem Cells 25:3121–3132PubMedCrossRefGoogle Scholar
  58. Qin H, Lu M, Goldfarb DS (2008) Genomic instability is associated with natural life span variation in Saccharomyces cerevisiae. PLoS One 3:e2670PubMedCrossRefGoogle Scholar
  59. Ramachandran L, Burhans DT, Laun P, Wang J, Liang P, Weinberger M, Wissing S, Jarolim S, Suter B, Madeo F et al (2006) Evidence for ORC-dependent repression of budding yeast genes induced by starvation and other stresses. FEMS Yeast Res 6:763–776PubMedCrossRefGoogle Scholar
  60. Riesen M, Morgan A (2009) Calorie restriction reduces rDNA recombination independently of rDNA silencing. Aging Cell 8:624–632PubMedCrossRefGoogle Scholar
  61. Ringvoll J, Uldal L, Roed MA, Reite K, Baynton K, Klungland A, Eide L (2007) Mutations in the RAD27 and SGS1 genes differentially affect the chronological and replicative lifespan of yeast cells growing on glucose and glycerol. FEMS Yeast Res 7:848–859PubMedCrossRefGoogle Scholar
  62. Rodier F, Campisi J (2011) Four faces of cellular senescence. J Cell Biol 192:547–556PubMedCrossRefGoogle Scholar
  63. Rowe LA, Degtyareva N, Doetsch PW (2008) DNA damage-induced reactive oxygen species (ROS) stress response in Saccharomyces cerevisiae. Free Radic Biol Med 45:1167–1177PubMedCrossRefGoogle Scholar
  64. Salmon TB, Evert BA, Song B, Doetsch PW (2004) Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae. Nucleic Acids Res 32:3712–3723PubMedCrossRefGoogle Scholar
  65. Sarsour EH, Venkataraman S, Kalen AL, Oberley LW, Goswami PC (2008) Manganese superoxide dismutase activity regulates transitions between quiescent and proliferative growth. Aging Cell 7:405–417PubMedCrossRefGoogle Scholar
  66. Sinclair DA, Guarente L (1997) Extrachromosomal rDNA circles – a cause of aging in yeast. Cell 91:1033–1042PubMedCrossRefGoogle Scholar
  67. Singh DK, Ahn B, Bohr VA (2009) Roles of RECQ helicases in recombination based DNA repair, genomic stability and aging. Biogerontology 10:235–252PubMedCrossRefGoogle Scholar
  68. Smith DL Jr, Li C, Matecic M, Maqani N, Bryk M, Smith JS (2009) Calorie restriction effects on silencing and recombination at the yeast rDNA. Aging Cell 8:633–642PubMedCrossRefGoogle Scholar
  69. Veatch JR, McMurray MA, Nelson ZW, Gottschling DE (2009) Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect. Cell 137:1247–1258PubMedCrossRefGoogle Scholar
  70. Wang Y, Pierce M, Schneper L, Guldal CG, Zhang X, Tavazoie S, Broach JR (2004) Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol 2:E128PubMedCrossRefGoogle Scholar
  71. Weinberger M, Feng L, Paul A, Smith DL, Hontz RD, Smith JS, Vujcic M, Singh KK, Huberman J, Burhans WC (2007) DNA replication stress is a determinant of chronological lifespan in budding yeast. PLOS One 2:e748PubMedCrossRefGoogle Scholar
  72. Weinberger M, Mesquita A, Caroll T, Marks L, Yang H, Zhang Z, Ludovico P, Burhans WC (2010) Growth signaling promotes chronological aging in budding yeast by inducing superoxide anions that inhibit quiescence. Aging (Albany NY) 2:709–726Google Scholar
  73. Weitao T, Budd M, Campbell JL (2003a) Evidence that yeast SGS1, DNA2, SRS2, and FOB1 interact to maintain rDNA stability. Mutat Res 532:157–172PubMedCrossRefGoogle Scholar
  74. Weitao T, Budd M, Hoopes LL, Campbell JL (2003b) Dna2 helicase/nuclease causes replicative fork stalling and double-strand breaks in the ribosomal DNA of Saccharomyces cerevisiae. J Biol Chem 278:22513–22522PubMedCrossRefGoogle Scholar
  75. Zanetti M, Zwacka R, Engelhardt J, Katusic Z, O’Brien T (2001) Superoxide anions and endothelial cell proliferation in normoglycemia and hyperglycemia. Arterioscler Thromb Vasc Biol 21:195–200PubMedCrossRefGoogle Scholar
  76. Zinzalla V, Graziola M, Mastriani A, Vanoni M, Alberghina L (2007) Rapamycin-mediated G1 arrest involves regulation of the Cdk inhibitor Sic1 in Saccharomyces cerevisiae. Mol Microbiol 63:1482–1494PubMedCrossRefGoogle Scholar

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© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Molecular and Cellular BiologyRoswell Park Cancer InstituteBuffaloUSA

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