Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock

Nature Structural Biology

Volumn 10, Issue 12, 2003, Pages 1039-1047

  Preiss, Thomas ^a,b   Baron Benhamou, Julie ^a,c   Ansorge, Wilhelm ^a   Hentze, Matthias ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^c ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA; PHOSPHOTRANSFERASE INHIBITOR; PROTEOME; RAPAMYCIN;

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENE; GENE CONTROL; HEAT SHOCK; IMMUNOBLOTTING; IMMUNOPRECIPITATION; NONHUMAN; OPEN READING FRAME; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE;

1-PHOSPHATIDYLINOSITOL 3-KINASE; ENZYME INHIBITORS; HEAT; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN BIOSYNTHESIS; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIROLIMUS; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0345602742     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb1015     Document Type: Article

References (39)

1. Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499-506 (2002).
2. Keene, J.D. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc. Natl. Acad. Sci. USA 98, 7018-7024 (2001).
3. Jensen, T.H. & Rosbash, M. Co-transcriptional monitoring of mRNP formation. Nat. Struct. Biol. 10, 10-12 (2003).
4. Manley, J.L. Nuclear coupling: RNA processing reaches back to transcription. Nat. Struct. Biol. 9, 790-791 (2002).
5. Proudfoot, N.J., Furger, A. & Dye, M.J. Integrating mRNA processing with transcription. Cell 108, 501-512 (2002).
6. Fong, N. & Bentley, D.L. Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD. Genes Dev. 15, 1783-1795 (2001).
7. Lei, E.P. & Silver, P.A. Intron status and 3′-end formation control cotranscriptional export of mRNA. Genes Dev. 16, 2761-2766 (2002).
8. Strasser, K. et al. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417, 304-308 (2002).
9. Zenklusen, D., Vinciguerra, P., Wyss, J.C. & Stutz, F. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol. Cell. Biol. 22, 8241-8253 (2002).
10. Hentze, M.W. & Kulozik, A.E. A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96, 307-310 (1999).
11. Maquat, L.E. & Carmichael, G.G. Quality control of mRNA function. Cell 104, 173-176 (2001).
12. Li, S. & Wilkinson, M.F. Nonsense surveillance in lymphocytes? Immunity 8, 135-141 (1998).
13. Gygi, S.P., Rochon, Y., Franza, B.R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730 (1999).
14. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
15. Mathews, M.B., Sonenberg, N. & Hershey, J.B.W. Origins and principles of translational control. In Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J.B.W. & Mathews, M.B.) 1-31 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).
16. Pradet-Balade, B., Boulme, F., Beug, H., Mullner, E.W. & Garcia-Sanz, J.A. Translation control: bridging the gap between genomics and proteomics? Trends Biochem. Sci. 26, 225-229 (2001).
17. Gray, N.K. & Wickens, M. Control of translation initiation in animals. Annu. Rev. Cell. Dev. Biol. 14, 399-458 (1998).
18. Kuhn, K.M., DeRisi, J.L., Brown, P.O. & Sarnow, P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21, 916-927 (2001).
19. Brown, V. et al. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107, 477-487 (2001).
20. Zong, Q., Schummer, M., Hood, L. & Morris, D.R. Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc. Natl. Acad. Sci. USA 96, 10632-10636 (1999).
21. Grolleau, A. et al. Global and specific translational control by rapamycin in T cells uncovered by microarrays and proteomics. J. Biol. Chem. 277, 22175-22184 (2002).
22. Muckenthaler, M. et al. Relationships and distinctions in iron regulatory networks responding to interrelated signals. Blood 101, 3690-3698 (2002).
23. Barbet, N.C. et al. TOR controls translation initiation and early G1 progression in yeast. Mol. Biol. Cell 7, 25-42 (1996).
24. Powers, T. & Walter, P. Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol. Biol. Cell 10, 987-1000 (1999).
25. Shamji, A. F., Kuruvilla, F.G. & Schreiber, S.L. Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr. Biol. 10, 1574-1581 (2000).
26. Albig, A.R. & Decker, C.J. The target of rapamycin signaling pathway regulates mRNA turnover in the yeast Saccharomyces cerevisiae. Mol. Biol. Cell 12, 3428-3438 (2001).
27. Berset, C., Trachsel, H. & Altmann, M. The TOR (target of rapamycin) signal transduction pathway regulates the stability of translation initiation factor eIF4G in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 95, 4264-4269 (1998).
28. Wang, Y. et al. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99, 5860-5865 (2002).
29. Gasch, A.P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
30. Schneider, R.J. Translational control during heat shock. In Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J.W.B. & Mathews, M.B.) 581-593 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).
31. Kedersha, N. et al. Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules. Mol. Biol. Cell 13, 195-210 (2002).
32. Kimball, S.R., Horetsky, R.L., Ron, D., Jefferson, L.S. & Harding, H.P. Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes. Am. J. Physiol. Cell. Physiol. 284, C273-C284 (2003).
33. Dunand-Sauthier, I. et al. Suml, a component of the fission yeast eIF3 translation initiation complex, is rapidly relocalized during environmental stress and interacts with components of the 26S proteasome. Mol. Biol. Cell 13, 1626-1640 (2002).
34. Sachs, A.B. & Varani, G. Eukaryotic translation initiation: there are (at least) two sides to every story. Nat. Struct. Biol. 7, 356-361 (2000).
35. Schwartz, D.C. & Parker, R. Interaction of mRNA translation and mRNA degradation in Saccharomyces cerevisiae. In Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J.W.B. & Mathews, M.B.) 807-825 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).
36. Mitchell, P. & Tollervey, D. mRNA turnover. Curr. Opin. Cell. Biol. 13, 320-325 (2001).
37. Preiss, T. & Hentze, M.W. Starting the protein synthesis machine: eukaryotic translation initiation. BioEssays 25, 1201-1210 (2003).
38. Richter, A. et al. Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays. Biotechniques 33, 620-628, 630 (2002).
39. Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).