Protein expression regulation under oxidative stress

Molecular and Cellular Proteomics

Volumn 10, Issue 12, 2011, Pages

  Vogel, Christine ^a,b   Silva, Gustavo Monteiro ^a   Marcotte, Edward M ^b  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; OXIDOREDUCTASE; PROTEINASE; PROTEOME; RNA BINDING PROTEIN; TRANSCRIPTOME; PEROXIDASE; SACCHAROMYCES CEREVISIAE PROTEIN; TSA1 PROTEIN, S CEREVISIAE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; HALF LIFE TIME; NONHUMAN; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEOMICS; RNA TRANSCRIPTION; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN SYNTHESIS; RNA STABILITY;

GENE EXPRESSION REGULATION, FUNGAL; HALF-LIFE; OXIDATIVE STRESS; PEROXIDASES; PROTEIN BIOSYNTHESIS; PROTEIN STABILITY; PROTEOME; RNA STABILITY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTOME;

EID: 83055163866     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.009217     Document Type: Article

References (103)

1. Halliwell, B., and Gutteridge, J. M. (2007) Free Radicals in Biology and Medicine, Oxford University Press, New York, 246-251
2. Sohal, R. S. (2002) Role of oxidative stress and protein oxidation in the aging process. Free Radic. Biol. Med. 33, 37-44
3. Costa, V., Quintanilha, A., and Moradas-Ferreira, P. (2007) Protein oxidation, repair mechanisms and proteolysis in Saccharomyces cerevisiae. IUBMB Life 59, 293-298 (Pubitemid 46763761)
4. Oyadomari, S., Araki, E., and Mori, M. (2002) Endoplasmic reticulum stress-mediated apoptosis in pancreatic beta-cells. Apoptosis 7, 335-345 (Pubitemid 34832258)
5. Terro, F., Czech, C., Esclaire, F., Elyaman, W., Yardin, C., Baclet, M. C., Touchet, N., Tremp, G., Pradier, L., and Hugon, J. (2002) Neurons overexpressing mutant presenilin-1 are more sensitive to apoptosis induced by endoplasmic reticulum-Golgi stress. J. Neurosci. Res. 69, 530-539 (Pubitemid 34831413)
6. Li, H., and Guo, M. (2009) Protein degradation in Parkinson disease revisited: It's complex. J. Clin. Invest. 119, 442-445
7. Pockley, A. G. (2002) Heat shock proteins, inflammation, and cardiovascular disease. Circulation 105, 1012-1017
8. van Tijn, P., Hol, E. M., van Leeuwen, F. W., and Fischer, D. F. (2008) The neuronal ubiquitin-proteasome system: murine models and their neurological phenotype. Prog. Neurobiol. 85, 176-193
9. Grune, T., Jung, T., Merker, K., and Davies, K. J. (2004) Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and 'aggresomes' during oxidative stress, aging, and disease. Int. J. Biochem. Cell Biol. 36, 2519-2530 (Pubitemid 39119763)
10. Stadtman, E. R. (2006) Protein oxidation and aging. Free Radic. Res. 40, 1250-1258
11. Visconti, R., and Grieco, D. (2009) New insights on oxidative stress in cancer. Curr. Opin. Drug Discov. Dev. 12, 240-245
12. Franssens, V., Boelen, E., Anandhakumar, J., Vanhelmont, T., Büttner, S., and Winderickx, J. (2010) Yeast unfolds the road map toward alphasynuclein-induced cell death. Cell Death Differ. 17, 746-753
13. Barros, M. H., da Cunha, F. M., Oliveira, G. A., Tahara, E. B., and Kowaltowski, A. J. (2010) Yeast as a model to study mitochondrial mechanisms in ageing. Mech. Ageing Dev. 131, 494-502
14. 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 celsls to environmental changes. Mol. Biol. Cell 11, 4241-4257
15. Smirnova, J. B., Selley, J. N., Sanchez-Cabo, F., Carroll, K., Eddy, A. A., McCarthy, J. E., Hubbard, S. J., Pavitt, G. D., Grant, C. M., and Ashe, M. P. (2005) Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol. Cell Biol. 25, 9340-9349 (Pubitemid 41507835)
16. Shenton, D., Smirnova, J. B., Selley, J. N., Carroll, K., Hubbard, S. J., Pavitt, G. D., Ashe, M. P., and Grant, C. M. (2006) Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J. Biol. Chem. 281, 29011-29021 (Pubitemid 44507045)
17. Nika, J., Yang, W., Pavitt, G. D., Hinnebusch, A. G., and Hannig, E. M. (2000) Purification and kinetic analysis of eIF2B from Saccharomyces cerevisiae. J. Biol. Chem. 275, 26011-26017
18. Lee, J. H., Pestova, T. V., Shin, B. S., Cao, C., Choi, S. K., and Dever, T. E. (2002) Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc. Natl. Acad. Sci. U.S.A. 99, 16689-16694 (Pubitemid 36034034)
19. Abdelmohsen, K., Kuwano, Y., Kim, H. H., and Gorospe, M. (2008) Post-transcriptional gene regulation by RNA-binding proteins during oxidative stress: Implications for cellular senescence. Biol. Chem. 389, 243-255 (Pubitemid 351329020)
20. Breusing, N., and Grune, T. (2008) Regulation of proteasome-mediated protein degradation during oxidative stress and aging. Biol. Chem. 389, 203-209 (Pubitemid 351329027)
21. Hosler, M. R., Wang-Su, S. T., and Wagner, B. J. (2003) Targeted disruption of specific steps of the ubiquitin-proteasome pathway by oxidation in lens epithelial cells. Int. J. Biochem. Cell Biol. 35, 685-697 (Pubitemid 36369516)
22. Ding, Q., Reinacker, K., Dimayuga, E., Nukala, V., Drake, J., Butterfield, D. A., Dunn, J. C., Martin, S., Bruce-Keller, A. J., and Keller, J. N. (2003) Role of the proteasome in protein oxidation and neural viability following low-level oxidative stress. FEBS Lett. 546, 228-232 (Pubitemid 36782416)
23. Weeks, M. E., Sinclair, J., Butt, A., Chung, Y. L., Worthington, J. L., Wilkinson, C. R., Griffiths, J., Jones, N., Waterfield, M. D., and Timms, J. F. (2006) A parallel proteomic and metabolomic analysis of the hydrogen peroxide- and Sty1p-dependent stress response in Schizosaccharomyces pombe. Proteomics 6, 2772-2796
24. Mirzaei, H., and Regnier, F. (2006) Protein-RNA cross-linking in the ribosomes of yeast under oxidative stress. J. Proteome Res. 5, 3249-3259 (Pubitemid 44904316)
25. Kusch, H., Engelmann, S., Albrecht, D., Morschhäuser, J., and Hecker, M. (2007) Proteomic analysis of the oxidative stress response in Candida albicans. Proteomics 7, 686-697 (Pubitemid 46450647)
26. García-Leiro, A., Cerdán, M. E., and González-Siso, M. I. (2010) Proteomic analysis of the oxidative stress response in Kluyveromyces lactis and effect of glutathione reductase depletion. J. Proteome Res. 9, 2358-2376
27. Flory, M. R., Lee, H., Bonneau, R., Mallick, P., Serikawa, K., Morris, D. R., and Aebersold, R. (2006) Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics 6, 6146-6157 (Pubitemid 44935504)
28. Fournier, M. L., Paulson, A., Pavelka, N., Mosley, A. L., Gaudenz, K., Bradford, W. D., Glynn, E., Li, H., Sardiu, M. E., Fleharty, B., Seidel, C., Florens, L., and Washburn, M. P. (2010) Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol. Cell. Proteomics 9, 271-284
29. Shalem, O., Dahan, O., Levo, M., Martinez, M. R., Furman, I., Segal, E., and Pilpel, Y. (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol. Syst. Biol. 4, 223
30. Halbeisen, R. E., and Gerber, A. P. (2009) Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol. 7, e105
31. Timmermann, B., Jarolim, S., Russmayer, H., Kerick, M., Michel, S., Krüger, A., Bluemlein, K., Laun, P., Grillari, J., Lehrach, H., Breitenbach, M., and Ralser, M. (2010) A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging. Aging 2, 475-486
32. Tang, H. M., Siu, K. L., Wong, C. M., and Jin, D. Y. (2009) Loss of yeast peroxiredoxin Tsa1p induces genome instability through activation of the DNA damage checkpoint and elevation of dNTP levels. PLoS Genet. 5, e1000697
33. Iraqui, I., Kienda, G., Soeur, J., Faye, G., Baldacci, G., Kolodner, R. D., and Huang, M. E. (2009) Peroxiredoxin Tsa1 is the key peroxidase suppressing genome instability and protecting against cell death in Saccharomyces cerevisiae. PLoS Genet. 5, e1000524
34. Sideri, T. C., Stojanovski, K., Tuite, M. F., and Grant, C. M. (2010) Ribosome-associated peroxiredoxins suppress oxidative stress-induced de novo formation of the [PSI+] prion in yeast. Proc. Natl. Acad. Sci. U.S.A. 107, 6394-6399
35. Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E. M. (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25, 117-124 (Pubitemid 46087910)
36. Alejandro-Osorio, A. L., Huebert, D. J., Porcaro, D. T., Sonntag, M. E., Nillasithanukroh, S., Will, J. L., and Gasch, A. P. (2009) The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol. 10, R57
37. Kim, T. S., Liu, C. L., Yassour, M., Holik, J., Friedman, N., Buratowski, S., and Rando, O. J. (2010) RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast. Genome Biol. 11, R75
38. Vogel, C., de Sousa Abreu, R., Ko, D., Le, S. Y., Shapiro, B., Burns, S. C., Sandhu, D., Boutz, D. R., Marcotte, E. M., and Penalva, L. O. (2010) Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol. Syst. Biol. 6, 400
39. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
40. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (Pubitemid 37082259)
41. Vogel, C., and Marcotte, E. M. (2008) Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat. Protoc. 3, 1444-1451
42. Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S., and Garrels, J. I. (1999) A sampling of the yeast proteome. Mol. Cell. Biol. 19, 7357-7368 (Pubitemid 29493399)
43. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95, 14863-14868 (Pubitemid 29003722)
44. Berriz, G. F., King, O. D., Bryant, B., Sander, C., and Roth, F. P. (2003) Characterizing gene sets with FuncAssociate. Bioinformatics 19, 2502-2504 (Pubitemid 38016661)
45. Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., and Witten, I. H. (2009) The WEKA Data Mining Software: An Update. SIGKDD Explorations 11, 10-18
46. Bailey, T. L., and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36
47. Pelechano, V., and Pérez-Ortín, J. E. (2010) There is a steady-state transcriptome in exponentially growing yeast cells. Yeast 27, 413-422
48. Gsponer, J., Futschik, M. E., Teichmann, S. A., and Babu, M. M. (2008) Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322, 1365-1368 (Pubitemid 352775246)
49. Liao, B., Hu, Y., and Brewer, G. (2007) Competitive binding of AUF1 and TIAR to MYC mRNA controls its translation. Nat. Struct. Mol. Biol. 14, 511-518 (Pubitemid 46871812)
50. Xue, D., Rubinson, D. A., Pannone, B. K., Yoo, C. J., and Wolin, S. L. (2000) U snRNP assembly in yeast involves the La protein. EMBO J. 19, 1650-1660 (Pubitemid 30182171)
51. Pannone, B. K., Xue, D., and Wolin, S. L. (1998) A role for the yeast La protein in U6 snRNP assembly: Evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J. 17, 7442-7453 (Pubitemid 29002711)
52. Inada, M., and Guthrie, C. (2004) Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc. Natl. Acad. Sci. U.S.A. 101, 434-439 (Pubitemid 38084654)
53. Hasegawa, Y., Irie, K., and Gerber, A. P. (2008) Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast. RNA 14, 2333-2347
54. Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., and Brown, P. O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 6, e255
55. Godin, K. S., and Varani, G. (2007) How arginine-rich domains coordinate mRNA maturation events. RNA Biol. 4, 69-75 (Pubitemid 350127831)
56. Kessler, S. H., and Sachs, A. B. (1998) RNA recognition motif 2 of yeast Pab1p is required for its functional interaction with eukaryotic translation initiation factor 4G. Mol. Cell. Biol. 18, 51-57 (Pubitemid 28021016)
57. Swisher, K. D., and Parker, R. (2010) Localization to, and effects of Pbp1, Pbp4, Lsm12, Dhh1, and Pab1 on stress granules in Saccharomyces cerevisiae. PLoS ONE 5, e10006
58. Gilbert, W. V., Zhou, K., Butler, T. K., and Doudna, J. A. (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317, 1224-1227
59. Pereira, M. D., Eleutherio, E. C., and Panek, A. D. (2001) Acquisition of tolerance against oxidative damage in Saccharomyces cerevisiae. BMC Microbiol. 1, 11
60. Brown, N. M., Torres, A. S., Doan, P. E., and O'Halloran, T. V. (2004) Oxygen and the copper chaperone CCS regulate posttranslational activation of Cu,Zn superoxide dismutase. Proc. Natl. Acad. Sci. U.S.A. 101, 5518-5523 (Pubitemid 38481189)
61. Mannarino, S. C., Vilela, L. F., Brasil, A. A., Aranha, J. N., Moradas-Ferreira, P., Pereira, M. D., Costa, V., and Eleutherio, E. C. (2011) Requirement of glutathione for Sod1 activation during lifespan extension. Yeast 28, 19-25
62. Terada, T., Oshida, T., Nishimura, M., Maeda, H., Hara, T., Hosomi, S., Mizoguchi, T., and Nishihara, T. (1992) Study on human erythrocyte thioltransferase: Comparative characterization with bovine enzyme and its physiological role under oxidative stress. J. Biochem. 111, 688-692
63. Ghezzi, P., Romines, B., Fratelli, M., Eberini, I., Gianazza, E., Casagrande, S., Laragione, T., Mengozzi, M., and Herzenberg, L. A. (2002) Protein glutathionylation: Coupling and uncoupling of glutathione to protein thiol groups in lymphocytes under oxidative stress and HIV infection. Mol. Immunol. 38, 773-780 (Pubitemid 34158880)
64. Jun, K. O., Song, C. H., Kim, Y. B., An, J., Oh, J. H., and Choi, S. K. (2009) Activation of translation via reduction by thioredoxin-thioredoxin reductase in Saccharomyces cerevisiae. FEBS Lett. 583, 2804-2810
65. Porras, P., McDonagh, B., Pedrajas, J. R., Bárcena, J. A., and Padilla, C. A. (2010) Structure and function of yeast glutaredoxin 2 depend on postranslational processing and are related to subcellular distribution. Biochim. Biophys. Acta 1804, 839-845
66. Luikenhuis, S., Perrone, G., Dawes, I. W., and Grant, C. M. (1998) The yeast Saccharomyces cerevisiae contains two glutaredoxin genes that are required for protection against reactive oxygen species. Mol. Biol. Cell 9, 1081-1091 (Pubitemid 28457301)
67. Discola, K. F., de Oliveira, M. A., Rosa Cussiol, J. R., Monteiro, G., Bárcena, J. A., Porras, P., Padilla, C. A., Guimarães, B. G., and Netto, L. E. (2009) Structural aspects of the distinct biochemical properties of glutaredoxin 1 and glutaredoxin 2 from Saccharomyces cerevisiae. J. Mol. Biol. 385, 889-901
68. Grant, C. M., Luikenhuis, S., Beckhouse, A., Soderbergh, M., and Dawes, I. W. (2000) Differential regulation of glutaredoxin gene expression in response to stress conditions in the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta 1490, 33-42 (Pubitemid 30070131)
69. Grant, C. M. (2001) Role of the glutathione/glutaredoxin and thioredoxin systems in yeast growth and response to stress conditions. Mol. Microbiol. 39, 533-541
70. Kumar, A., Agarwal, S., Heyman, J. A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., Cheung, K. H., Miller, P., Gerstein, M., Roeder, G. S., and Snyder, M. (2002) Subcellular localization of the yeast proteome. Genes Dev. 16, 707-719 (Pubitemid 34274040)
71. Thorpe, G. W., Fong, C. S., Alic, N., Higgins, V. J., and Dawes, I. W. (2004) Cells have distinct mechanisms to maintain protection against different reactive oxygen species: Oxidative-stress-response genes. Proc. Natl. Acad. Sci. U.S.A. 101, 6564-6569 (Pubitemid 38586014)
72. Slekar, K. H., Kosman, D. J., and Culotta, V. C. (1996) The yeast copper/ zinc superoxide dismutase and the pentose phosphate pathway play overlapping roles in oxidative stress protection. J. Biol. Chem. 271, 28831-28836 (Pubitemid 26382581)
73. Ringnér, M., and Krogh, M. (2005) Folding free energies of 5′-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput. Biol. 1, e72
74. Shringarpure, R., and Davies, K. J. (2002) Protein turnover by the proteasome in aging and disease. Free Radic. Biol. Med. 32, 1084-1089 (Pubitemid 34603346)
75. Shringarpure, R., Grune, T., Mehlhase, J., and Davies, K. J. (2003) Ubiquitin conjugation is not required for the degradation of oxidized proteins by proteasome. J. Biol. Chem. 278, 311-318 (Pubitemid 36043578)
76. Reinheckel, T., Sitte, N., Ullrich, O., Kuckelkorn, U., Davies, K. J., and Grune, T. (1998) Comparative resistance of the 20S and 26S proteasome to oxidative stress. Biochem. J. 335, 637-642
77. Bader, N., and Grune, T. (2006) Protein oxidation and proteolysis. Biol. Chem. 387, 1351-1355 (Pubitemid 44691414)
78. Zong, C., Young, G. W., Wang, Y., Lu, H., Deng, N., Drews, O., and Ping, P. (2008) Two-dimensional electrophoresis-based characterization of post-translational modifications of mammalian 20S proteasome complexes. Proteomics 8, 5025-5037
79. Demasi, M., Silva, G. M., and Netto, L. E. (2003) 20 S proteasome from Saccharomyces cerevisiae is responsive to redox modifications and is S-glutathionylated. J. Biol. Chem. 278, 679-685 (Pubitemid 36043622)
80. Cuervo, A. M., Palmer, A., Rivett, A. J., and Knecht, E. (1995) Degradation of proteasomes by lysosomes in rat liver. Eur. J. Biochem. 227, 792-800
81. Tai, H. C., Besche, H., Goldberg, A. L., and Schuman, E. M. (2010) Characterization of the brain 26S proteasome and its interacting proteins. Front. Mol. Neurosci. 3, 12
82. 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 (Pubitemid 37314318)
83. Hieronymus, H., and Silver, P. A. (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet. 33, 155-161 (Pubitemid 36177066)
84. Hurt, E., Strässer, K., Segref, A., Bailer, S., Schlaich, N., Presutti, C., Tollervey, D., and Jansen, R. (2000) Mex67p mediates nuclear export of a variety of RNA polymerase II transcripts. J. Biol. Chem. 275, 8361-8368 (Pubitemid 30180177)
85. Gong, Y., Kakihara, Y., Krogan, N., Greenblatt, J., Emili, A., Zhang, Z., and Houry, W. A. (2009) An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: Implications to protein folding pathways in the cell. Mol. Syst. Biol. 5, 275
86. Holcik, M., and Sonenberg, N. (2005) Translational control in stress and apoptosis. Nat. Rev. Mol. Cell Biol. 6, 318-327 (Pubitemid 40516898)
87. Munhoz, D. C., and Netto, L. E. (2004) Cytosolic thioredoxin peroxidase I and II are important defenses of yeast against organic hydroperoxide insult: Catalases and peroxiredoxins cooperate in the decomposition of H2O2 by yeast. J. Biol. Chem. 279, 35219-35227 (Pubitemid 39100518)
88. Demasi, A. P., Pereira, G. A., and Netto, L. E. (2001) Cytosolic thioredoxin peroxidase I is essential for the antioxidant defense of yeast with dysfunctional mitochondria. FEBS Lett. 509, 430-434 (Pubitemid 34031973)
89. Berry, D. B., and Gasch, A. P. (2008) Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol. Biol. Cell 19, 4580-4587
90. Mewes, H. W., Dietmann, S., Frishman, D., Gregory, R., Mannhaupt, G., Mayer, K. F., Münsterkötter, M., Ruepp, A., Spannagl, M., Stümpflen, V., and Rattei, T. (2008) MIPS: Analysis and annotation of genome information in 2007. Nucleic Acids Res. 36, D196-D201 (Pubitemid 351149721)
91. Hieronymus, H., and Silver, P. A. (2004) A systems view of mRNP biology. Genes Dev 18, 2845-2860 (Pubitemid 39602303)
92. Belle, A., Tanay, A., Bitincka, L., Shamir, R., and O'Shea, E. K. (2006) Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. U.S.A. 103, 13004-13009 (Pubitemid 44338907)
93. Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277
94. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., and Russell, R. B. (2003) Protein disorder prediction: Implications for structural proteomics. Structure 11, 1453-1459 (Pubitemid 37412427)
95. Arava, Y., Boas, F. E., Brown, P. O., and Herschlag, D. (2005) Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res. 33, 2421-2432 (Pubitemid 41511261)
96. Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O., and Herschlag, D. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 100, 3889-3894 (Pubitemid 36418127)
97. Fraser, H. B., Hirsh, A. E., Giaever, G., Kumm, J., and Eisen, M. B. (2004) Noise minimization in eukaryotic gene expression. PLoS Biol. 2, e137
98. Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D., and Brown, P. O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. U.S.A. 99, 5860-5865 (Pubitemid 34493230)
99. Lawless, C., Pearson, R. D., Selley, J. N., Smirnova, J. B., Grant, C. M., Ashe, M. P., Pavitt, G. D., and Hubbard, S. J. (2009) Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics 10, 7
100. Shalgi, R., Lapidot, M., Shamir, R., and Pilpel, Y. (2005) A catalog of stability-associated sequence elements in 3′ UTRs of yeast mRNAs. Genome Biol. 6, R86
101. Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26, 73-79 (Pubitemid 28295265)
102. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K. D., Flaherty, P., Foury, F., Garfinkel, D. J., Gerstein, M., Gotte, D., Güldener, U., Hegemann, J. H., Hempel, S., Herman, Z., Jaramillo, D. F., Kelly, D. E., Kelly, S. L., Kötter, P., LaBonte, D., Lamb, D. C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S. L., Revuelta, J. L., Roberts, C. J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D. D., Sookhai-Mahadeo, S., Storms, R. K., Strathern, J. N., Valle, G., Voet, M., Volckaert, G., Wang, C. Y., Ward, T. R., Wilhelmy, J., Winzeler, E. A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J. D., Snyder, M., Philippsen, P., Davis, R. W., and Johnston, M. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (Pubitemid 34826834)
103. Kertesz, M., Wan, Y., Mazor, E., Rinn, J. L., Nutter, R. C., Chang, H. Y., and Segal, E. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107