Pulsatile dynamics in the yeast proteome

Current Biology

Volumn 24, Issue 18, 2014, Pages 2189-2194

  Dalal, Chiraj K ^a   Cai, Long ^a   Lin, Yihan ^a   Rahbar, Kasra ^a   Elowitz, Michael B ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

CELL FUNCTION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE;

CELL PHYSIOLOGICAL PHENOMENA; GENE EXPRESSION REGULATION; PROTEOME; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 84908150919     PISSN: 09609822     EISSN: 18790445     Source Type: Journal    
DOI: 10.1016/j.cub.2014.07.076     Document Type: Article

References (36)

1. J.H. Levine, Y. Lin, and M.B. Elowitz Functional roles of pulsing in genetic circuits Science 342 2013 1193 1200
2. L. Cai, C.K. Dalal, and M.B. Elowitz Frequency-modulated nuclear localization bursts coordinate gene regulation Nature 455 2008 485 490
3. N. Hao, B.A. Budnik, J. Gunawardena, and E.K. O'Shea Tunable signal processing through modular control of transcription factor translocation Science 339 2013 460 464
4. N. Hao, and E.K. O'Shea Signal-dependent dynamics of transcription factor translocation controls gene expression Nat. Struct. Mol. Biol. 19 2012 31 39
5. M. Jacquet, G. Renault, S. Lallet, J. De Mey, and A. Goldbeter Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae J. Cell Biol. 161 2003 497 505
6. O. Medvedik, D.W. Lamming, K.D. Kim, and D.A. Sinclair MSN2 and MSN4 link calorie restriction and TOR to sirtuin-mediated lifespan extension in Saccharomyces cerevisiae PLoS Biol. 5 2007 e261
7. J. Stewart-Ornstein, C. Nelson, J. DeRisi, J.S. Weissman, and H. El-Samad Msn2 coordinates a stoichiometric gene expression program Curr. Biol. 23 2013 2336 2345
8. J. Stewart-Ornstein, J.S. Weissman, and H. El-Samad Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae Mol. Cell 45 2012 483 493
9. N. Yissachar, T. Sharar Fischler, A.A. Cohen, S. Reich-Zeliger, D. Russ, E. Shifrut, Z. Porat, and N. Friedman Dynamic response diversity of NFAT isoforms in individual living cells Mol. Cell 49 2013 322 330
10. J.E. Purvis, K.W. Karhohs, C. Mock, E. Batchelor, A. Loewer, and G. Lahav p53 dynamics control cell fate Science 336 2012 1440 1444
11. J.G. Albeck, G.B. Mills, and J.S. Brugge Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals Mol. Cell 49 2013 249 261
12. A. Warmflash, Q. Zhang, B. Sorre, A. Vonica, E.D. Siggia, and A.H. Brivanlou Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4 Proc. Natl. Acad. Sci. USA 109 2012 E1947 E1956
13. W.K. Huh, J.V. Falvo, L.C. Gerke, A.S. Carroll, R.W. Howson, J.S. Weissman, and E.K. O'Shea Global analysis of protein localization in budding yeast Nature 425 2003 686 691
14. S. Kosugi, M. Hasebe, M. Tomita, and H. Yanagawa Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs Proc. Natl. Acad. Sci. USA 106 2009 10171 10176
15. S.L. Forsburg, and P. Nurse Cell cycle regulation in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe Annu. Rev. Cell Biol. 7 1991 227 256
16. J.M. Cherry, C. Adler, C. Ball, S.A. Chervitz, S.S. Dwight, E.T. Hester, Y. Jia, G. Juvik, T. Roe, and M. Schroeder SGD: Saccharomyces Genome Database Nucleic Acids Res. 26 1998 73 79
17. D. Abdulrehman, P.T. Monteiro, M.C. Teixeira, N.P. Mira, A.B. Lourenço, S.C. dos Santos, T.R. Cabrito, A.P. Francisco, S.C. Madeira, and R.S. Aires YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface Nucleic Acids Res. 39 Database issue 2011 D136 D140
18. J.T. Mettetal, D. Muzzey, C. Gómez-Uribe, and A. van Oudenaarden The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae Science 319 2008 482 484
19. D. Muzzey, C.A. Gómez-Uribe, J.T. Mettetal, and A. van Oudenaarden A systems-level analysis of perfect adaptation in yeast osmoregulation Cell 138 2009 160 171
20. M. Kellis, B.W. Birren, and E.S. Lander Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae Nature 428 2004 617 624
21. J.A. Lewis, and A.P. Gasch Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor G3 (Bethesda) 2 2012 1607 1612
22. S. Tay, J.J. Hughey, T.K. Lee, T. Lipniacki, S.R. Quake, and M.W. Covert Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing Nature 466 2010 267 271
23. A. Hoffmann, A. Levchenko, M.L. Scott, and D. Baltimore The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation Science 298 2002 1241 1245
24. D.E. Nelson, A.E. Ihekwaba, M. Elliott, J.R. Johnson, C.A. Gibney, B.E. Foreman, G. Nelson, V. See, C.A. Horton, and D.G. Spiller Oscillations in NF-kappaB signaling control the dynamics of gene expression Science 306 2004 704 708
25. Y. Wakamoto, N. Dhar, R. Chait, K. Schneider, F. Signorino-Gelo, S. Leibler, and J.D. McKinney Dynamic persistence of antibiotic-stressed mycobacteria Science 339 2013 91 95
26. G.M. Süel, J. Garcia-Ojalvo, L.M. Liberman, and M.B. Elowitz An excitable gene regulatory circuit induces transient cellular differentiation Nature 440 2006 545 550
27. J.H. Levine, M.E. Fontes, J. Dworkin, and M.B. Elowitz Pulsed feedback defers cellular differentiation PLoS Biol. 10 2012 e1001252
28. J.C. Locke, J.W. Young, M. Fontes, M.J. Hernández Jiménez, and M.B. Elowitz Stochastic pulse regulation in bacterial stress response Science 334 2011 366 369
29. G.M. Süel, R.P. Kulkarni, J. Dworkin, J. Garcia-Ojalvo, and M.B. Elowitz Tunability and noise dependence in differentiation dynamics Science 315 2007 1716 1719
30. N. Petrenko, R.V. Chereji, M.N. McClean, A.V. Morozov, and J.R. Broach Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses Mol. Biol. Cell 24 2013 2045 2057
31. A. Roetzer, C. Gregori, A.M. Jennings, J. Quintin, D. Ferrandon, G. Butler, K. Kuchler, G. Ammerer, and C. Schüller Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors Mol. Microbiol. 69 2008 603 620
32. M.A. Sheff, and K.S. Thorn Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae Yeast 21 2004 661 670
33. I. Nachman, A. Regev, and S. Ramanathan Dissecting timing variability in yeast meiosis Cell 131 2007 544 556
34. P.T. Monteiro, N.D. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, N.P. Mira, H. Pais, A.P. Francisco, A.M. Carvalho, and A.B. Lourenço YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae Nucleic Acids Res. 36 Database issue 2008 D132 D136
35. M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira, and I. Sá-Correia The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Nucleic Acids Res. 34 Database issue 2006 D446 D451
36. C. Stark, B.J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers BioGRID: a general repository for interaction datasets Nucleic Acids Res. 34 Database issue 2006 D535 D539