The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures

Molecular Biology of the Cell

Volumn 22, Issue 7, 2011, Pages 988-998

  Davidson, George S ^a,b   Joe, Ray M ^a   Roy, Sushmita ^c   Meirelles, Osorio ^a   Allen, Chris P ^d   Wilson, Melissa R ^a   Tapia, Phillip H ^d   Manzanilla, Elaine E ^a   Dodson, Anne E ^a   Chakraborty, Swagata ^a   Carter, Mark ^d   Young, Susan ^d   Edwards, Bruce ^d   Sklar, Larry ^d   Werner Washburne, Margaret ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c University of New Mexico   (United States)

^d UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN;

ARTICLE; CELL DIFFERENTIATION; CELL SUBPOPULATION; FLOW CYTOMETRY; FUNCTIONAL PROTEOMICS; FUNGAL STRAIN; NONHUMAN; PRIORITY JOURNAL;

CELL CYCLE; FLOW CYTOMETRY; GENE EXPRESSION REGULATION, FUNGAL; GREEN FLUORESCENT PROTEINS; OXYGEN CONSUMPTION; PROTEOMICS; RECOMBINANT FUSION PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 79953317636     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E10-06-0499     Document Type: Article

References (55)

1. Aerts AM, Zabrocki P, Govaert G, Mathys J, Carmona-Gutierrez D, Madeo Winderickx J, Cammue BPA, Thevissen K (2009). Mitochondrial dysfunction leads to reduced chronological lifespan and increased apoptosis in yeast. FEBS Lett 583, 113-117.
2. Aguilera A (1986). Deletion of the phosphoglucose isomerase structural gene makes growth and sporulation glucose dependent in Saccharomyces cerevisiae. Mol Gen Genet 204, 310-316.
3. Allen C et al.(2006). Isolation of quiescent and nonquiescent cells from stationary-phase yeast cultures. J Cell Biol 174, 89-100. (Pubitemid 43992899)
4. Aragon AD, Quiñones GA, Thomas EV, Roy S, Werner-Washburne M (2006). Release of extraction-resistant mRNA in stationary-phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress. Genome Biol 7, 403-407.
5. 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 stationaryphase cultures. Mol Biol Cell 19, 1271-1280. (Pubitemid 351481838)
6. Auesukaree C, Damnernsawad A, Kruatrachue M, Pokethitiyook P, Boonchird C, Kaneko Y, Harashima S (2009). Genome-wide identification of genes involved in tolerance to various environmental stresses in S. cerevisiae. J Appl Genet 50, 301-310.
7. Bagnat M, Keranen S, Shevchenko A, Simons K (2000). Lipid rafts function in biosynthetic delivery of proteins to the cell surface in yeast. Proc Natl Acad Sci USA 97, 3254-3259. (Pubitemid 30183288)
8. Benbadis L, Cot M, Rigoulet M, Francois J (2009). Isolation of two cell populations from yeast during high-level alcoholic fermentation that resemble quiescent and nonquiescent cells from the stationary phase on glucose. Fems Yeast Res 9, 1172-1186.
9. Brachmann CB, Davies A, Cost GJ, Caputo E, Li JC, Hieter P, Boeke JD (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14, 115-132. (Pubitemid 28062863)
10. Coyle S, Kroll E (2008). Starvation induces genomic rearrangements and starvation-resilient phenotypes in yeast. Mol Biol Evol 25, 310-318. (Pubitemid 351231602)
11. Deshaies RJ, Koch BD, Werner-Washburne M, Craig EA, Schekman R (1988). A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides. Nature 332, 800-805.
12. DeVirgilio C, Burckert N, Barth G, Neuhaus JM, Boller T, Wiemken A (1992). Cloning and disruption of a gene required for growth on acetate but not on ethanol: the acetyl-coenzyme-A synthetase gene of Saccharomyces cerevisiae. Yeast 8, 1043-1051. (Pubitemid 23015125)
13. Dickinson JR (1991). Biochemical and genetic studies on the function and relationship between the PGI1-encoded and CDC30-encoded phosphoglucose isomerase in Saccharomyces cerevisiae. J Gen Microbiol 137, 765-770.
14. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D (2002). Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99, 16144-16149. (Pubitemid 35462763)
15. Edwards BS, Oprea T, Prossnitz ER, Sklar LA (2004). Flow cytometry for high-throughput, high-content screening. Curr Opin Chem Biol 8, 392-398. (Pubitemid 38993732)
16. Fabrizio P, Hoon S, Shamalnasab M, Galbani A, Wei M, Giaever G, Nislow C, Longo VD (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.
17. Fabrizio P, Longo VD (2008). Chronological aging-induced apoptosis in yeast. Biochim Biophys Acta 1783, 1280-1285.
18. Fuge EK, Braun EL, Werner-Washburne M (1994). Protein synthesis in longterm stationary-phase cultures of Saccharomyces cerevisiae. J Bact 176, 5802-5813. (Pubitemid 24280515)
19. Futcher B (2006). Metabolic cycle, cell cycle, and the finishing kick to Start. Genome Biol 7, 107.
20. Giaever G et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391. (Pubitemid 34826834)
21. Horton LE, James P, Craig EA, Hensold JO (2001). The yeast hsp70 homologue Ssa is required for translation and interacts with Sis1 and Pab1 on translating ribosomes. J Biol Chem 276, 14426-14433.
22. Huh W-K, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O' Shea EK (2003). Global analysis of protein localization in budding yeast. Nature 425, 686-691. (Pubitemid 37314307)
23. Imai J et al. (2003). The molecular chaperone Hsp90 plays a role in the assembly and maintenance of the 26S proteasome. EMBO J 22, 3557-3567. (Pubitemid 36898333)
24. Izawa S, Maeda K, Miki T, Mano J, Inoue Y, Kimura A (1998). Importance of glucose-6-phosphate dehydrogenase in the adaptive response to hydrogen peroxide in Saccharomyces cerevisiae. Biochem J 330, 811-817. (Pubitemid 28111982)
25. Kaeberlein M, Kirkland KT, Fields S, Kennedy BK (2005). Genes determining yeast replicative life span in a long-lived genetic background. Mech Ageing Dev 126, 491-504. (Pubitemid 40269293)
26. Kim KS, Rosenkrantz MS, Guarente L (1986). Saccharomyces cerevisiae contains two functional citrate synthase genes. Mol Cell Biol 6, 1936-1942.
27. Lee J, Spector D, Godon C, Labarre J, Toledano MB (1999). A new antioxidant with alkyl hydroperoxide defense properties in yeast. J Biol Chem 274, 4537-4544.
28. Lemons JMS, Feng X-J, Bennett BD, Legesse-Miller A, Johnson LE, Raitman I, Pollina EA, Rabitz HA, Rabinowitz JD, Coller HA (2010). Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol 8, e1000514.
29. Le Tallec B et al. (2007). 20S proteasome assembly is orchestrated by two distinct pairs of chaperones in yeast and in mammals. Mol Cell 27, 660-674. (Pubitemid 47243701)
30. Lewis K (2007). Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5, 48-56.
31. Li L, Lu Y, Qin L-X, Bar-Joseph Z, Werner-Washburne M, Breeden LL (2009). Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol Biol Cell 20, 3851-3864.
32. Li W, Dang YJ, Liu JO, Yu BA (2010). Structural and stereochemical requirements of the spiroketal group of hippuristanol for antiproliferative activity. Bioorg Med Chem 20, 3112-3115.
33. Li W, Sun L, Liang Q, Wang J, Mo W, Zhou B (2006). Yeast AMID homologue Ndi1p displays respiration-restricted apoptotic activity and is involved in chronological aging. Mol Biol Cell 17, 1802-1811. (Pubitemid 44011596)
34. Lillie SH, Pringle JR (1980). Reserve carbohydrate-metabolism in Saccharomyces cerevisiae: responses to nutrient limitation. J Bacteriol 143, 1384-1394. (Pubitemid 11255509)
35. Lindqvist L, Pelletier J (2009). Inhibitors of translation initiation as cancer therapeutics. Future Med Chem 1, 1709-1722.
36. Martinez MJ, Roy S, Archuletta AB, Wentzell PD, Anna-Arriola SS, Rodriguez AL, Aragon AD, Quiñones GA, Allen C, Werner-Washburne M (2004). Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol Biol Cell 15, 5295-5305. (Pubitemid 39564725)
37. Matecic M, Smith DL, Pan XW, Maqani N, Bekiranov S, Boeke JD, Smith JS (2010). A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet 6, e1000921.
38. McAlister L, Holland M (1982). Targeted deletion of a yeast enolase structural gene. Identification and isolation of yeast enolase isozymes. J Biol Chem 257, 7181-7188.
39. Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846.
40. Planta RJ, Mager WH (1998). The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14, 471-477. (Pubitemid 28138643)
41. Qin SL, Moldave K, McLaughlin CS (1987). Isolation of the yeast gene encoding elongation factor 3 for protein synthesis. J Biol Chem 262, 7802-7807.
42. Raser JM, O'Shea EK (2004). Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814. (Pubitemid 38787899)
43. Raser JM, O'Shea EK (2005). Noise in gene expression: origins, consequences, and control. Science 309, 2010-2013. (Pubitemid 41362308)
44. Reinders J, Zahedi RP, Pfanner N, Meisinger C, Sickmann A (2006). Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5, 1543-1554. (Pubitemid 44036128)
45. Repetto B, Tzagoloff A (1989). Structure and regulation of KGD1, the structural gene for yeast α-ketoglutarate dehydrogenase. Mol Cell Biol 9, 2695-2705.
46. Sales K, Brandt W, Rumbak E, Lindsey G (2000). The LEA-like protein HSP 12 in Saccharomyces cerevisiae has a plasma membrane location and protects membranes against desiccation and ethanol-induced stress. Biochim Biophys Acta 1463, 267-278. (Pubitemid 30081786)
47. Schirmaier F, Philippsen P (1984). Identification of two genes coding for the translation elongation factor eF-1α of S. cerevisiae.. EMBO J 3, 3311-3315.
48. Segal SP, Dunckley T, Parker R (2006). Sbp1p affects translational repression and decapping in Saccharomyces cerevisiae. Mol Cell Biol 26, 5120-5130. (Pubitemid 43955824)
49. Shi L, Sutter B, Xinyue Y, Tu B (2010). Trehalose is a key determinant of the quiescent metabolic state that fuels cell cycle progression upon return to growth. Mol Biol Cell 21, 1982-1990.
50. +)-ATPase. Annu Rev Cell Dev Biol 13, 779-808.
51. Suissa M, Suda K, Schatz G (1984). Isolation of the nuclear yeast genes for citrate synthase and 15 other mitochondrial proteins by a new screening method. EMBO J 3, 1773-1781.
52. Tajbakhsh S, Rocheteau P, Le Roux I (2009). Asymmetric cell divisions and asymmetric cell fates. Annu Rev Cell Dev Biol 25, 671-699.
53. Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005). Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310, 1152-1158. (Pubitemid 41681736)
54. Wright RM, Simpson SL, Lanoil BD (1995). Oxygen regulation of the cytochrome c oxidase subunit VI gene, COX6, in Saccharomyces cerevisiae.. Biochem Biophys Res Commun 216, 676-685.
55. Young SM, Bologa C, Prossnitz ER, Oprea TI, Sklar LA, Edwards BS (2005). High-throughput screening with HyperCyt® flow cytometry to detect small molecule formylpeptide receptor ligands. J Biomol Screen 10, 374-382. (Pubitemid 40800566)