Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae

Molecular and Cellular Proteomics

Volumn 14, Issue 9, 2015, Pages 2454-2465

  Murphy, J Patrick ^a   Stepanova, Ekaterina ^a   Everley, Robert A ^a   Paulo, Joao A ^a   Gygi, Steven P ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; GLYOXYLIC ACID; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; FUNGAL CELL CULTURE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEOMICS; SACCHAROMYCES CEREVISIAE; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; PROCEDURES;

CHROMATOGRAPHY, LIQUID; GENE EXPRESSION REGULATION, FUNGAL; MASS SPECTROMETRY; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84940529199     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.045849     Document Type: Article

References (33)

1. Botstein, D., and Fink, G. R. (2011) Yeast: an experimental organism for 21st century biology. Genetics 189, 695-704
2. Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., and Coon, J. J. (2014) The one hour yeast proteome. Mol. Cell. Proteomics 13, 339-347
3. Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., and Mann, M. (2014) Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat. Methods 11, 319-324
4. DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686
5. Brauer, M. J., Saldanha, A. J., Dolinski, K., and Botstein, D. (2005) Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol. Biol. Cell 16, 2503-2517
6. Slavov, N., Budnik, B. A., Schwab, D., Airoldi, E. M., and van Oudenaarden, A. (2014) Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis. Cell Reports 7, 705-714
7. McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., and Gygi, S.P. (2012) Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal. Chem. 84, 7469-7478
8. Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K., and Hamon, C. (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904
9. Ting, L., Rad, R., Gygi, S. P., and Haas, W. (2011) MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8, 937-940
10. McAlister, G. C., Nusinow, D. P., Jedrychowski, M. P., Wuhr, M., Huttlin, E. L., Erickson, B. K., Rad, R., Haas, W., and Gygi, S. P. (2014) Multi-Notch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. 86. 7150-7158
11. Senko, M. W., Remes, P. M., Canterbury, J. D., Mathur, R., Song, Q., Eliuk, S. M., Mullen, C., Earley, L., Hardman, M., Blethrow, J. D. Bui, H., Specht, A., Lange, O., Denisov, E., Makarov, A., Horning, S., and Zabrouskov, V. (2013) Novel parallelized quadrupole/linear ion trap/orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. Anal. Chem. 85, 11710-11714
12. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
13. Rappsilber, J., Ishihama, Y., and Mann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670
14. Eng, J. K., McCormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
15. Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
16. Tai, Y.C. (2007) timecourse: Statistical analysis for developmental microarray time course data. R package version 1.38.0 http://www.bioconductor.org
17. Huang, da, W., Sherman, B. T., and Lempicki, R. A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57
18. Teixeira, M. C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A. R., Mira, N. P., Alenquer, M., Freitas, A. T., Oliveira, A. L., and Sa-Correia, I. (2006) The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 34, D446-D451
19. de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
20. Wu, R., Dephoure, N., Haas, W., Huttlin, E. L., Zhai, B., Sowa, M. E., and Gygi, S. P. (2011) Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol. Cell. Proteomics 10, M111. 009654
21. Hebert, A. S., Merrill, A. E., Stefely, J. A., Bailey, D. J., Wenger, C. D., Westphall, M. S., Pagliarini, D. J., and Coon, J. J. (2013) Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol. Cell. Proteomics 12, 3360-3369
22. Boy-Marcotte, E., Perrot, M., Bussereau, F., Boucherie, H., and Jacquet, M. (1998) Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclic AMP in saccharomyces cerevisiae. J. Bacteriol. 180, 1044-1052
23. Boy-Marcotte, E., Lagniel, G., Perrot, M., Bussereau, F., Boudsocq, A., Jacquet, M., and Labarre, J. (1999) The heat shock response in yeast: differential regulations and contributions of the Msn2p/Msn4p and Hsf1p regulons. Mol. Microbiol. 33, 274-283
24. Lai, L. C., Kosorukoff, A. L., Burke, P. V., and Kwast, K. E. (2005) Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol. Cell. Biol. 25, 4075-4091
25. Umekawa, M., and Klionsky, D. J. (2012) Ksp1 kinase regulates autophagy via the target of rapamycin complex 1 (TORC1) pathway. J. Biol. Chem. 287, 16300-16310
26. Castelli, L. M., Lui, J., Campbell, S. G., Rowe, W., Zeef, L. A., Holmes, L. E., Hoyle, N. P., Bone, J., Selley, J. N., Sims, P. F., Ashe, M. P. (2011) Glucose depletion inhibits translation inititaion via eiF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated. Mol. Biol. Cell 22, 3379-3393
27. Wade, J. T., Hall, D. B., and Struhl, K. (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432, 1054-1058
28. Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., and Brown, P. O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257
29. Russell, D. W., Smith, M., Williamson, V. M., and Young, E. T. (1983) Nucleotide sequence of the yeast alcohol dehydrogenase II gene. J. Biol. Chem. 258, 2674-2682
30. Regenberg, B., During-Olsen, L., Kielland-Brandt, M. C., and Holmberg, S. (1999) Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae. Current Genet. 36, 317-328
31. Forsburg, S. L., and Guarente, L. (1989) Communication between mitochondria and the nucleus in regulation of cytochrome genes in the yeast Saccharomyces cerevisiae. Ann. Rev. Cell Biol. 5, 153-180
32. Buschlen, S., Amillet, J. Ä., Guiard, B., Fournier, A., Marcireau, C., and Bolotin-Fukuhara, M. (2003) The S. cerevisiae HAP complex, a key regulator of mitochondrial function, coordinates nuclear and mitochondrial gene expression. Comparative Func. Genomics 4, 37-46
33. Lee, J., Lee, B., Shin, D., Kwak, S. S., Bahk, J. D., Lim, C. O., and Yun, D. J. (2002) Carnitine uptake by AGP2 in yeast Saccharomyces cerevisiae is dependent on Hog1 MAP kinase pathway. Mol. Cells 13, 407-412