Defining molecular basis for longevity traits in natural yeast isolates

npj Aging and Mechanisms of Disease

Volumn 1, Issue 1, 2015, Pages

  Kaya, Alaattin ^a   Ma, Siming ^a   Wasko, Brian ^b   Lee, Mitchell ^b   Kaeberlein, Matt ^b   Gladyshev, Vadim N ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85051969408     PISSN: None     EISSN: 20563973     Source Type: Journal    
DOI: 10.1038/npjamd.2015.1     Document Type: Article

References (50)

1. Gladyshev VN. On the cause of aging and control of lifespan: heterogeneity leads to inevitable damage accumulation, causing aging; control of damage composition and rate of accumulation define lifespan. Bioessays 2012; 34: 925–929.
2. Finch CE, Ruvkun G. The genetics of aging. Ann Rev Genomics Hum Genet 2001; 2: 435–462.
3. Kenyon CJ. The genetics of ageing. Nature 2010; 464: 504–512.
4. McCay CM, Crowell MF, Maynard LA. The effect of retarded growth upon the length of life span and upon the ultimate body size. 1935. Nutrition 1989; 5: 155–171.
5. Murakami C, Delaney JR, Chou A, Carr D, Schleit J, Sutphin GL et al. pH neutralization protects against reduction in replicative lifespan following chronological aging in yeast. Cell Cycle 2012; 11: 3087–3096.
6. Botta G, Turn CS, Quintyne NJ, Kirchman PA. Increased iron supplied through Fet3p results in replicative life span extension of Saccharomyces cerevisiae under conditions requiring respiratory metabolism. Exp Gerontol 2011; 46: 827–832.
7. Pitt JN, Leiser SF, Kaeberlein M In:Sprott R(ed) Annual Review of Gerontology and Geriatrics. Springer Publishing, 2014, 59–81.
8. Lopez-Lluch G, Hunt N, Jones B, Zhu M, Jamieson H, Hilmer S et al. Calorie restriction induces mitochondrial biogenesis and bioenergetic efficiency. Proc Natl Acad Sci USA 2006; 103: 1768–1773.
9. Schulz TJ, Zarse K, Voigt A, Urban N, Birringer M, Ristow M. Glucose restriction extends Caenorhabditis elegans life span by inducing mitochondrial respiration and increasing oxidative stress. Cell Metab 2007; 6: 280–293.
10. Lin SJ, Kaeberlein M, Andalis AA, Sturtz LA, Defossez PA, Culotta VC et al. Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration. Nature 2002; 418: 344–348.
11. Johnson SC, Rabinovitch PS, Kaeberlein M. mTOR is a key modulator of ageing and age-related disease. Nature 2013; 493: 338–345.
12. Bonawitz ND, Chatenay-Lapointe M, Pan Y, Shadel GS. Reduced TOR signaling extends chronological life span via increased respiration and upregulation of mitochondrial gene expression. Cell Metab 2007; 5: 265–277.
13. Reznick D, Buckwalter G, Groff J, Elder D. The evolution of senescence in natural populations of guppies (Poecilia reticulata): a comparative approach. Exp Gerontol 2001; 36: 791–812.
14. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA et al. Population genomics of domestic and wild yeasts. Nature 2009; 458: 337–341.
15. Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M et al. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res 2013; 23: 1496–1504.
16. Bergstrom A, Simpson JT, Salinas F, Barre B, Parts L, Zia A et al. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 2014; 31: 872–888.
17. Steffen KK, Kennedy BK, Kaeberlein M. Measuring replicative life span in the budding yeast. J Vis Exp 2009; 25: 1209.
18. Olsen B, Murakami CJ, Kaeberlein M. YODA: software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. BMC Bioinformatics 2010; 11: 141.
19. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria 2013.
20. Pinheiro J, Bates D, DebRoy S, Sarkar DR. Development Core Teamnlme: Linear and Nonlinear Mixed Effects Models. R package 2013.
21. Ho LST, Ane C. A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Syst Biol 2013; 63: 397–408.
22. Regenberg B, Grotkjaer T, Winther O, Fausboll A, Akesson M, Bro C et al. Growth-rate regulated genes have profound impact on interpretation of tran-scriptome profiling in Saccharomyces cerevisiae. Genome Biol 2006; 7: R107.
23. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC et al. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol 2007; 6: 4.
24. Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D et al. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 2008; 19: 352–367.
25. He C, Tsuchiyama SK, Nguyen QT, Plyusnina EN, Terrill SR, Sahibzada S et al. Enhanced longevity by ibuprofen, conserved in multiple species, occurs in yeast through inhibition of tryptophan import. PLoS Genet 2014; 10: e1004860.
26. Felsenstein J. Phylogenies and the comparative method. Am Nat 1985; 125: 1–15.
27. Martins EP, Garland T Jr. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 1991; 45: 534–557.
28. Freckleton RP, Harvey PH, Pagel M. Phylogenetic analysis and comparative data: a test and review of evidence. Am Nat 2002; 160: 712–726.
29. Martin DE, Hall MN. The expanding TOR signaling network. Curr Opin Cell Biol 2005; 17: 158–166.
30. Crespo JL, Powers T, Fowler B, Hall MN. The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine. Proc Natl Acad Sci USA 2002; 99: 6784–6789.
31. Kaeberlein M, Powers RW 3rd, Steffen KK, Westman EA, Hu D, Dang N et al. Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 2005; 310: 1193–1196.
32. Powers RW 3rd, Kaeberlein M, Caldwell SD, Kennedy BK, Fields S. Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Dev 2006; 20: 174–184.
33. Smith ED, Tsuchiya M, Fox LA, Dang N, Hu D, Kerr EO et al. Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. Genome Res 2008; 18: 564–570.
34. Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD et al. A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet 2010; 6: e1000921.
35. Fabrizio P, Hoon S, Shamalnasab M, Galbani A, Wei M, Giaever G et al. Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet 2010; 6: e1001024.
36. Laschober GT, Ruli D, Hofer E, Muck C, Carmona-Gutierrez D, Ring J et al. Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell 2010; 9: 1084–1097.
37. Wang X, Salinas K, Zuo X, Kucejova B, Chen XJ. Dominant membrane uncoupling by mutant adenine nucleotide translocase in mitochondrial diseases. Hum Mol Genet 2008; 17: 4036–4044.
38. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4: 44–57.
39. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J et al. STRING 8—a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009; 37: D412–D416.
40. Liti G, Louis EJ. Advances in quantitative trait analysis in yeast. PLoS Genet 2012; 8: e1002912.
41. Brem RB, Storey JD, Whittle J, Kruglyak L. Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 2005; 436: 701–703.
42. Pan Y, Shadel GS. Extension of chronological life span by reduced TOR signaling requires down-regulation of Sch9p and involves increased mitochondrial OXPHOS complex density. Aging 2009; 1: 131–145.
43. Pan Y, Schroede EA, Ocampo A, Barrientos A, Shadel GS. Regulation of yeast chronological life span by TOR1C via adaptive mitochondrial ROS signaling. Cell Metab 2011; 13: 668–678.
44. Zarse K, Schmeisser S, Groth M, Priebe S, Beuster G, Kuhlow D et al. Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-prolin catabolism to induce a transient ROS signal. Cell Metab 2012; 15: 451–465.
45. Delaney JR, Murakami CJ, Olsen B, Kennedy BK, Kaeberlein M. Quantitative evidence for early life fitness defects from 32 longevity-associated alleles in yeast. Cell Cycle 2011; 10: 156–165.
46. Yang J, Dungrawala H, Hua H, Manukyan A, Abraham L, Lane W et al. Cell size and growth rate are major determinants of replicative lifespan. Cell Cycle 2011; 10: 144–155.
47. Spor A, Nidelet T, Simon J, Bourgais A, de Vienne D, Sicard D. Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae. BMC Evol Biol 2009; 9: 296.
48. Romano GH, Gurvich Y, Lavi O, Ulitsky I, Shamir R, Kupiec M. Different sets of QTLs influence fitness variation in yeast. Mol Syst Biol 2010; 6: 346.
49. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725–2729.
50. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406–425.