Quantitative proteomic comparison of stationary/G 0 phase cells and tetrads in budding yeast

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Kumar, Ravinder ^a   Srivastava, Sanjeeva ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BMH1 PROTEIN, S CEREVISIAE; BMH2 PROTEIN, S CEREVISIAE; HEAT SHOCK PROTEIN; HSP12 PROTEIN, S CEREVISIAE; HSP26 PROTEIN, S CEREVISIAE; IME1 PROTEIN, S CEREVISIAE; NUCLEAR PROTEIN; PROTEIN 14 3 3; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

CELL CYCLE G0 PHASE; CYTOLOGY; FLOW CYTOMETRY; FUNGUS SPORE; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MEIOSIS; METABOLISM; OSMOTIC PRESSURE; PHYSIOLOGY; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

14-3-3 PROTEINS; FLOW CYTOMETRY; GENE EXPRESSION REGULATION, FUNGAL; HEAT-SHOCK PROTEINS; MEIOSIS; NUCLEAR PROTEINS; OSMOTIC PRESSURE; PROTEOMICS; RESTING PHASE, CELL CYCLE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPORES, FUNGAL; TRANSCRIPTION FACTORS;

EID: 84984673695     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep32031     Document Type: Article

References (64)

1. Lewis, D. L. & Gattie, D. K. The ecology of quiescent microbes. ASM News 57, 27-32 (1991).
2. Nicholson, W. L., Munakata, N., Horneck, G., Melosh, H. J. & Setlow, P. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol Mol Biol Rev 64, 548-572 (2000).
3. Setlow, P. Spores of Bacillus subtilis: their resistance to radiation, heat and chemicals. J Appl. Microbiol. 101, 514-525 (2006).
4. Setlow, P. Spore germination. Curr Opin Microbiol 6, 550-556 (2003).
5. Moir, A. How do spores germinate? J Appl Microbiol 101, 386-389 (2006).
6. Pringle, J. R. & Hartwell, L. H. The Saccharomyces cerevisiae cell cycle. Cold Spring Harbor Monograph Archive 11, 97-142 (1981).
7. Hartwell, L. H., Culotti, J., Pringle, J. R. & Reid, B. J. Genetic control of the cell division cycle in yeast. Science 183, 46-51 (1974).
8. Govin, J. & Berger, S. L. Genome reprogramming during sporulation. Int J Dev Biol. 53, 425-432 (2009).
9. Freese, E. B., Chu, M. I. & Freese, E. Initiation of yeast sporulation of partial carbon, nitrogen, or phosphate deprivation. J Bacteriol 149, 840-851 (1982).
10. Esposito, R. E. & Klapholz, S. The Molecular Biology of the Yeast Saccharomyces: Life Cycle and Inheritance (ed Strathern. et al.) p. 211-287. (Cold Spring Harbor Laboratory Press, NY, 1981).
11. Werner-Washburne, M., Braun, E., Johnston, G. C. & Singer, R. A. Stationary phase in the yeast Saccharomyces cerevisiae. Microbiol. Rev. 57, 383-401 (1993).
12. Herman, P. K. Stationary phase in yeast. Curr Opin Microbiol. 5, 602-607 (2002).
13. Gray, J. V. et al. "Sleeping beauty": quiescence in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 68, 187-206 (2004).
14. Lewis, K. Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 64, 503-533 (2000).
15. Gasch, A. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11, 4241-4257 (2000).
16. Ashrafi, K., Sinclair, D., Gordon, J. I. & Guarente, L. Passage through stationary-phase advances replicative aging in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 96, 9100-9105 (1999).
17. Ross, P. L. et al. "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents". Mol. Cell. Proteomics 3, 1154-1169 (2004).
18. Wei, W., Nurse, P. & Broek, D. Yeast cells can enter a quiescent state through G1, S, G2, or M phase of the cell cycle. Cancer Res. 53, 1867-1870 (1993).
19. Miller, J. J. The yeasts. (ed Rose. et al.) p. 489-550. (Academic Press, Inc., San Diego, Calif, 1989).
20. Fuge, E. K., Braun, E. L. & Werner-Washburne, M. Protein synthesis in long term stationary-phase cultures of Saccharomyces cerevisiae. J Bact 176, 5802-5813 (1994).
21. Boucherie, H. Protein synthesis during transition and stationary phases under glucose limitation in Saccharomyces cerevisiae. J. Bacteriol. 161, 385-392 (1985).
22. Laporte, D. et al. Metabolic status rather than cell cycle signals control quiescence entry and exit. J of Cell Biology. 122, 949-957 (2011).
23. Deutschbauer, A. M. & Davis, R. W. Quantitative trait loci mapped to single- nucleotide resolution in yeast. Nat Genet 37, 1333-1340 (2005).
24. Plesset, J., Ludwig, J., Cox, B. & McLaughin, C. Effect of cell position on thermotolerance in Saccharomyces cerevisiae. J. Bacteriol. 169, 779-784 (1987).
25. Breeden, L. L. Alpha-factor synchronization of budding yeast. Methods Enzymol. 283, 332-341 (1997).
26. Lillie, S. H. & Pringle, J. R. Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation. J. Bacteriol. 143, 1384-1394 (1980).
27. Delobel, P. & Tesniere, C. A simple FCM method to avoid misinterpretation in Saccharomyces cerevisiae cell cycle assessment between G0 and sub-G1. PLoS One. 9, e84645 (2014).
28. Kassir, Y., Granot, D. & Simchen, G. IME1, a positive regulator gene of meiosis in S. cerevisiae. Cell. 52, 853-862 (1988).
29. Kupiec, M., Byers, B., Esposito, R. E. A. P. & Mitchell, A. P. The Molecular and Cellular Biology of the Yeast Saccharomyces (ed Pringle. et al.) p. 889-1039 (Cold Spring Harbor Laboratory Press, NY, 1997).
30. Honigberg, S. M. & Purnapatre, K. Signal pathway integration in the switch from the mitotic cell cycle to meiosis in yeast. J. Cell Sci. 116, 2137-2147 (2003).
31. Piekarska, I., Rytka, J. & Rempola, B. Regulation of sporulation in the yeast Saccharomyces cerevisiae. Acta Biochim. Pol. 57, 241-250 (2010).
32. Purnapatre, K., Piccirillo, S., Schneider. B. L. & Honigberg, S. M. The CLN3/SWI6/CLN2 pathway and SNF1 act sequentially to regulate meiotic initiation in Saccharomyces cerevisiae. Genes Cells 7, 675-691 (2002).
33. Kassir, Y. et al. Transcriptional regulation of meiosis in budding yeast. Int Rev Cytol 224, 111-171 (2003).
34. Redddy Panga, Jaipal et al. A simple protein extraction method for proteomic analysis of diverse biological specimens. Curr Proteomics 10, 298-311 (2013).
35. Slubowski, C. J., Paulissen, S. M. & Huang, L. S. The GCKIII kinase Sps1 and the 14-3-3 isoforms, Bmh1 and Bmh2, cooperate to ensure proper sporulation in Saccharomyces cerevisiae. PLoS One 9, e113528 (2014).
36. Praekelt, M. & Meacock, A. HSP12, a new small heat shock gene of Saccharomyces cerevisiae: analysis of structure, regulation and function. Mol Gen Genet 223, 97-106 (1990).
37. Liu, X. et al. Genetic and comparative transcriptome analysis of bromodomain factor 1 in the salt stress response of Saccharomyces cerevisiae. Curr Microbiol 54, 325-330 (2007).
38. Martijn, R., Albertyn, J. & Thevelein, J. M. Different signaling pathways contribute to the control of GPD1 gene expression by osmotic stress in Saccharomyces cerevisiae. Microbiology 145, 715-727 (1999).
39. Hirayama, T., Maeda, T., Saito, H. & Shinozaki, K. Cloning and characterization of seven cDNAs for hyperosmolarity-responsive (HOR) genes of Saccharomyces cerevisiae. Mol Gen Genet. 249, 127-138 (1995).
40. Posas, F. et al. The transcriptional response of yeast to saline stress. J Biol Chem 275, 17249-17255 (2000).
41. Choder, M. A general topoisomerase I-dependent transcriptional repression in the stationary-phase of yeast. Genes Dev. 5, 2315-2326 (1991).
42. Jona, G., Choder, M. & Gileadi, O. Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochim. Biophys. Acta 1491, 37-48 (2000).
43. Braun, E. L., Fuge, E. K., Padilla, P. A. & Werner-Washburne, M. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. J Bacteriol 178, 6865-6872 (1996).
44. Welker, S. et al. Hsp12 is an intrinsically unstructured stress protein that folds upon membrane association and modulates membrane function. Mol Cell 39, 507-520 (2010).
45. Kolter, R., Siegele, D. A. & Tormo, A. The stationary phase of the bacterial life cycle. Annu. Rev. Microbiol 47, 855-874 (1993).
46. Martinez, M. J. et al. Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol Biol Cell. 15, 5295-5305 (2004).
47. Uppuluri, P. & Chaffin, W. L. Defining Candida albicans stationary phase by cellular and DNA replication, gene expression and regulation. Mol. Microbiol. 64, 1572-1586 (2007).
48. Davidson George, S. et al. The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures. Mol. Bio. of cell. 22, 988-998 (2011).
49. Kakiuchi, K. et al. Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae. Biochemistry 46, 7781-7792 (2007).
50. van Heusden, G. P. & Steensma, H. Y. Yeast 14-3-3 proteins. Yeast 23, 159-171 (2006).
51. Sagot, I., Pinson, B., Salin, B. & Daignan-Fornier, B. Actin bodies in yeast quiescent cells: an immediately available actin reserve? Mol Biol Cell 17, 4645-4655 (2006).
52. Broach, J. R. Nutritional control of growth and development in yeast. Genetics 192, 73-105 (2012).
53. Reed, S. I. The selection of S. cerevisiae mutants defective in the start event of cell division. Genetics 95, 561-577 (1980).
54. Achstetter, T., Ehmann, C. & Wolf, D. H. Proteolysis in eucaryotic cells: aminopeptidases and dipeptidyl aminopeptidases in yeast revisited. Arch. Biochem. Biophys. 226, 292-305 (1983).
55. Jones, E. W. The synthesis and function of proteases in Saccharomyces: genetic approaches. Annu. Rev. Genet. 18, 233-270 (1984).
56. Pifion, R. Folded chromosomes in non-cycling yeast cells. Evidence for a characteristic go form. Chromosoma. 67, 263-274 (1978).
57. Pifion, R. A probe into nuclear events during the cell cycle of Saccharomyces cerevisiae: studies of folded chromosomes in cdc mutants which arrest in G1. Chromosoma 70, 337-352 (1979).
58. Bugeja, V. C., Piggott, J. R. & Carter, B. L. A. Differentiation of Saccharomyces cerevisiae at slow growth rates in glucose-limited chemostat culture. J. Gen. Microbiol. 128, 2707-2714 (1982).
59. Stevens, B. The molecular biology of the yeast Saccharomyces: life cycle and inheritance. (ed Strathern. et al.) p. 471-504. (Cold Spring Harbor Laboratory NY 1981).
60. Matile, P., Moor, H. & Robinow, C. F. The Yeast (ed Rose. et al.) vol. 1. p. 219-302. (Academic Press, Inc., New York, 1969).
61. Cha, R. S., Weiner, B. M., Keeney, S., Dekker, J. & Kleckner N. Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11and positively by Rec8p. Genes Dev 14, 493-503 (2000).
62. Kumar, R., Dhali, S., Srikanth, R., Ghosh, S. K. & Srivastava, S. Comparative proteomics of mitosis and meiosis in Saccharomyces cerevisiae. J Proteomics 109, 1-15 (2014).
63. Reddy, P. J. et al. A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J Proteomics 114, 247-262 (2015).
64. Jain, R., Kulkarni, P., Dhali, S., Rapole S. & Srivastava, S. Quantitative proteomic analysis of global effect of LLL12 on U87 cells proteome: An insight into the molecular mechanism of LLL12. J Proteomics. 113, 127-142 (2015).