Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence

G3: Genes, Genomes, Genetics

Volumn 5, Issue 1, 2015, Pages 145-155

  Sideri, Theodora ^a   Rallis, Charalampos ^a   Bitton, Danny A ^a   Lages, Bruno M ^a   Suo, Fang ^b   Rodríguez López, María ^a   Du, Li Lin ^b   Bähler, Jürg ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

Author keywords

Cellular aging; Competitive growth; G0 phase; Longevity; Quiescence

Indexed keywords

GENOMIC DNA; MEMBRANE PROTEIN; NITROGEN; FUNGAL DNA;

AGING; ARTICLE; AUTOPHAGY; CELL GROWTH; CELL PROLIFERATION; CELL VIABILITY; DELETION MUTANT; DNA EXTRACTION; FUNGAL CELL; GENE CONTROL; GENE INTERACTION; LIFESPAN; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; QUANTITATIVE ASSAY; SCHIZOSACCHAROMYCES POMBE; DNA BARCODING; GENETICS; GROWTH, DEVELOPMENT AND AGING; MUTATION; SCHIZOSACCHAROMYCES;

SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

DNA BARCODING, TAXONOMIC; DNA, FUNGAL; MUTATION; SCHIZOSACCHAROMYCES;

EID: 84921494761     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.014415     Document Type: Article

References (60)

1. Backhus, L. E., J. DeRisi, and L. F. Bisson, 2001 Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Res. 1: 111-125.
2. Baryshnikova, A., M. Costanzo, S. Dixon, F. J. Vizeacoumar, C. L. Myers et al., 2010 Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol. 470: 145-179.
3. Bitterman, K. J., R. M. Anderson, H. Y. Cohen, M. Latorre-Esteves, and D. A. Sinclair, 2002 Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. J. Biol. Chem. 277: 45099-45107.
4. Blake, J. A., M. Dolan, H. Drabkin, D. P. Hill, N. Li et al., 2013 Gene Ontology annotations and resources. Nucleic Acids Res. 41: D530-D535.
5. Brauer, M. J., C. Huttenhower, E. M. Airoldi, R. Rosenstein, J. C. Matese et al., 2008 Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol. Biol. Cell 19: 352-367.
6. Breslow, D. K., D. M. Cameron, S. R. Collins, M. Schuldiner, J. Stewart-Ornstein et al., 2008 A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat. Methods 5: 711-718.
7. Cap, M., L. Stepanek, K. Harant, L. Vachova, and Z. Palkova, 2012 Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell 46: 436-448.
8. Castrillo, J. I., L. A. Zeef, D. C. Hoyle, N. Zhang, A. Hayes et al., 2007 Growth control of the eukaryote cell: a systems biology study in yeast. J. Biol. 6: 4.
9. Chen, D., W. M. Toone, J. Mata, R. Lyne, G. Burns et al., 2003 Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14: 214-229.
10. Delaney, J. R., C. J. Murakami, B. Olsen, B. K. Kennedy, and M. Kaeberlein, 2011 Quantitative evidence for early life fitness defects from 32 longevity-associated alleles in yeast. Cell Cycle 10: 156-165.
11. Dziedzic, S. A., and A. B. Caplan, 2012 Autophagy proteins play cytoprotective and cytocidal roles in leucine starvation-induced cell death in Saccharomyces cerevisiae. Autophagy 8: 731-738.
12. Fabrizio, P., S. Hoon, M. Shamalnasab, A. Galbani, M. Wei et al., 2010 Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet. 6: e1001024.
13. Fontana, L., L. Partridge, and V. D. Longo, 2010 Extending healthy life span-from yeast to humans. Science 328: 321-326.
14. Gems, D., and L. Partridge, 2013 Genetics of longevity in model organisms: debates and paradigm shifts. Annu. Rev. Physiol. 75: 621-644.
15. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
16. Hamilton, B., Y. Dong, M. Shindo, W. Liu, I. Odell et al., 2005 A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 19: 1544-1555.
17. Han, T. X., X. Y. Xu, M. J. Zhang, X. Peng, and L. L. Du, 2010 Global fitness profiling of fission yeast deletion strains by barcode sequencing. Genome Biol. 11: R60.
18. Kenyon, C., J. Chang, E. Gensch, A. Rudner, and R. Tabtiang, 1993 A C. elegans mutant that lives twice as long as wild type. Nature 366: 461-464.
19. Kim, D. U., J. Hayles, D. Kim, V. Wood, H. O. Park et al., 2010 Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 28: 617-623.
20. Kohda, T. A., K. Tanaka, M. Konomi, M. Sato, M. Osumi et al., 2007 Fission yeast autophagy induced by nitrogen starvation generates a nitrogen source that drives adaptation processes. Genes Cells 12: 155-170.
21. Kyryakov, P., A. Beach, V. R. Richard, M. T. Burstein, A. Leonov et al., 2012 Caloric restriction extends yeast chronological lifespan by altering a pattern of age-related changes in trehalose concentration. Front Physiol 3: 256.
22. Labunskyy, V. M., M. V. Gerashchenko, J. R. Delaney, A. Kaya, B. K. Kennedy et al., 2014 Lifespan extension conferred by endoplasmic reticulum secretory pathway deficiency requires induction of the unfolded protein response. PLoS Genet. 10: e1004019.
23. Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
24. Lee, W. S., P. Monaghan, and N. B. Metcalfe, 2013 Experimental demonstration of the growth rate-lifespan trade-off. Proc. Biol. Sci. 280: 20122370.
25. Longo, V. D., G. S. Shadel, M. Kaeberlein, and B. Kennedy, 2012 Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab. 16: 18-31.
26. Lopez-Maury, L., S. Marguerat, and J. Bähler, 2008 Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat. Rev. Genet. 9: 583-593.
27. Lopez-Otin, C., M. A. Blasco, L. Partridge, M. Serrano, and G. Kroemer, 2013 The hallmarks of aging. Cell 153: 1194-1217.
28. Marguerat, S., A. Schmidt, S. Codlin, W. Chen, R. Aebersold et al., 2012 Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 151: 671-683.
29. Markaki, M., and N. Tavernarakis, 2013 Metabolic control by target of rapamycin and autophagy during ageing - a mini-review. Gerontology 59: 340-348.
30. Mata, J., R. Lyne, G. Burns, and J. Bähler, 2002 The transcriptional program of meiosis and sporulation in fission yeast. Nat. Genet. 32: 143-147.
31. Matecic, M., D. L. Smith, X. Pan, N. Maqani, S. Bekiranov et al., 2010 A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet. 6: e1000921.
32. Matsuyama, A., R. Arai, Y. Yashiroda, A. Shirai, A. Kamata et al., 2006 ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 24: 841-847.
33. Pancaldi, V., F. Schubert, and J. Bähler, 2010 Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast. Mol. Biosyst. 6: 543-552.
34. Pedruzzi, I., F. Dubouloz, E. Cameroni, V. Wanke, J. Roosen et al., 2003 TOR and PKA signaling pathways converge on the protein kinase Rim15 to control entry into G0. Mol. Cell 12: 1607-1613.
35. Powers, R. W., 3rd, M. Kaeberlein, S. D. Caldwell, B. K. Kennedy, and S. Fields, 2006 Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Dev. 20: 174-184.
36. Rallis, C., S. Codlin, and J. Bähler, 2013 TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast. Aging Cell 12: 563-573.
37. Rallis, C., L. Lopez-Maury, T. Georgescu, V. Pancaldi, and J. Bähler, 2014 Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth. Biol. Open 3: 161-171.
38. Reyes-Turcu, F. E., K. Zhang, M. Zofall, E. Chen, and S. I. Grewal, 2011 Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin. Nat. Struct. Mol. Biol. 18: 1132-1138.
39. Robinson, D. G., W. Chen, J. D. Storey, and D. Gresham, 2014 Design and analysis of Bar-seq experiments. G3 (Bethesda) 4: 11-18.
40. Roux, A. E., G. Arseneault, P. Chartrand, G. Ferbeyre, and L. A. Rokeach, 2010 A screen for genes involved in respiration control and longevity in Schizosaccharomyces pombe. Ann. N. Y. Acad. Sci. 1197: 19-27.
41. Roux, A. E., A. Leroux, M. A. Alaamery, C. S. Hoffman, P. Chartrand et al., 2009 Pro-aging effects of glucose signaling through a G protein-coupled glucose receptor in fission yeast. PLoS Genet. 5: e1000408.
42. Roux, A. E., A. Quissac, P. Chartrand, G. Ferbeyre, and L. A. Rokeach, 2006 Regulation of chronological aging in Schizosaccharomyces pombe by the protein kinases Pka1 and Sck2. Aging Cell 5: 345-357.
43. Ryan, C. J., A. Roguev, K. Patrick, J. Xu, H. Jahari et al., 2012 Hierarchical modularity and the evolution of genetic interactomes across species. Mol. Cell 46: 691-704.
44. Ryu, H. Y., B. H. Rhie, and S. H. Ahn, 2014 Loss of the Set2 histone methyltransferase increases cellular lifespan in yeast cells. Biochem. Biophys. Res. Commun. 446: 113-118.
45. Sajiki, K., M. Hatanaka, T. Nakamura, K. Takeda, M. Shimanuki et al., 2009 Genetic control of cellular quiescence in S. pombe. J. Cell Sci. 122: 1418-1429.
46. Selman, C., J. M. A. Tullet, D. Wieser, E. Irvine, S. J. Lingard et al., 2009 Ribosomal Protein S6 Kinase 1 Signaling Regulates Mammalian Life Span. Science 326: 140-144.
47. Shimanuki, M., L. Uehara, T. Pluskal, T. Yoshida, A. Kokubu et al., 2013 Klf1, a C2H2 zinc finger-transcription factor, is required for cell wall maintenance during long-term quiescence in differentiated G0 phase. PLoS ONE 8: e78545.
48. Shin, S., L. Wolgamott, Y. Yu, J. Blenis, and S. O. Yoon, 2011 Glycogen synthase kinase (GSK)-3 promotes p70 ribosomal protein S6 kinase (p70S6K) activity and cell proliferation. Proc. Natl. Acad. Sci. USA 108: E1204-E1213.
49. Smith, A. M., L. E. Heisler, J. Mellor, F. Kaper, M. J. Thompson et al., 2009 Quantitative phenotyping via deep barcode sequencing. Genome Res. 19: 1836-1842.
50. Sofola, O., F. Kerr, I. Rogers, R. Killick, H. Augustin et al., 2010 Inhibition of GSK-3 ameliorates Abeta pathology in an adult-onset Drosophila model of Alzheimer's disease. PLoS Genet. 6: e1001087.
51. Stephan, J., J. Franke, and A. E. Ehrenhofer-Murray, 2013 Chemical genetic screen in fission yeast reveals roles for vacuolar acidification, mitochondrial fission, and cellular GMP levels in lifespan extension. Aging Cell 12: 574-583.
52. Stephan, J. S., Y. Y. Yeh, V. Ramachandran, S. J. Deminoff, and P. K. Herman, 2009 The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy. Proc. Natl. Acad. Sci. USA 106: 17049-17054.
53. Sun, L. L., M. Li, F. Suo, X. M. Liu, E. Z. Shen et al., 2013 Global analysis of fission yeast mating genes reveals new autophagy factors. PLoS Genet. 9: e1003715.
54. Takeda, K., T. Yoshida, S. Kikuchi, K. Nagao, A. Kokubu et al., 2010 Synergistic roles of the proteasome and autophagy for mitochondrial maintenance and chronological lifespan in fission yeast. Proc. Natl. Acad. Sci. USA 107: 3540-3545.
55. Weisman, R., 2010 Fission yeast TOR and Rapamycin, Vol. 27, pp. 251-269 in The Enzymes, edited by Michael N. Hall and Fuyuhiko Tamanoi.
56. Wilhelm, B. T., S. Marguerat, S. Watt, F. Schubert, V. Wood et al., 2008 Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453: 1239-1243.
57. Wood, V., R. Gwilliam, M. A. Rajandream, M. Lyne, R. Lyne et al., 2002 The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880.
58. Wood, V., M. A. Harris, M. D. McDowall, K. Rutherford, B. W. Vaughan et al., 2012 PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res. 40: D695-D699.
59. Yanagida, M., 2009 Cellular quiescence: are controlling genes conserved? Trends Cell Biol. 19: 705-715.
60. Yoshikawa, K., T. Tanaka, Y. Ida, C. Furusawa, T. Hirasawa et al., 2011 Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae. Yeast 28: 349-361.