Network reconstruction reveals new links between aging and calorie restriction in yeast

HFSP Journal

Volumn 4, Issue 3-4, 2010, Pages 94-99

  Balázsi, Gábor ^a  

^a UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; METAZOA; SACCHAROMYCES CEREVISIAE;

EID: 79955946232     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.3366829     Document Type: Article

References (33)

1. Aoki, SK, Pamma, R, Hernday, AD, Bickham, JE, Braaten, BA, and Low, DA (2005). "Contact-dependent inhibition of growth in Escherichia coli. " Science 309, 1245-1248.
2. Avery, SV (2006). "Microbial cell individuality and the underlying sources of heterogeneity. " Nat. Rev. Microbiol. 4, 577-587.
3. Balázsi, G, Barabási, AL, and Oltvai, ZN (2005). "Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. " Proc. Natl. Acad. Sci. U.S.A. 102, 7841-7846.
4. Balázsi, G, Heath, AP, Shi, L, and Gennaro, ML (2008). "The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. " Mol. Syst. Biol. 4, 225.
5. Balázsi, G, and Oltvai, ZN (2005). "Sensing your surroundings: how transcription-regulatory networks of the cell discern environmental signals. " Sci. STKE 2005, pe20.
6. Bassler, BL, and Losick, R (2006). "Bacterially speaking. " Cell 125, 237-246.
7. Becskei, A, Kaufmann, BB, and van Oudenaarden, A (2005). "Contributions of low molecule number and chromosomal positioning to stochastic gene expression. " Nat. Genet. 37, 937-944.
8. Bennett, MR, Pang, WL, Ostroff, NA, Baumgartner, BL, Nayak, S, Tsimring, LS, and Hasty, J (2008). "Metabolic gene regulation in a dynamically changing environment. " Nature (London) 454, 1119-1122.
9. Blake, WJ, Balázsi, G, Kohanski, MA, Isaacs, FJ, Murphy, KF, Kuang, Y, Cantor, CR, Walt, DR, and Collins, JJ (2006). "Phenotypic consequences of promoter-mediated transcriptional noise. " Mol. Cell 24, 853-865.
10. Blake, WJ, KÆrn, M, Cantor, CR, and Collins, JJ (2003). "Noise in eukaryotic gene expression. " Nature (London) 422, 633-637.
11. Danchin, A (2009). "Natural selection and immortality. " Biogerontology 10, 503-516.
12. Fabrizio, P, Gattazzo, C, Battistella, L, Wei, M, Cheng, C, McGrew, K, and Longo, VD (2005). "Sir2 blocks extreme life-span extension. " Cell 123, 655-667.
13. Fabrizio, P, and Longo, VD (2003). "The chronological life span of Saccharomyces cerevisiae. " Aging Cell 2, 73-81.
14. Faith, JJ, Hayete, B, Thaden, JT, Mogno, I, Wierzbowski, J, Cottarel, G, Kasif, S, Collins, JJ, and Gardner, TS (2007). "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. " PLoS Biol. 5, e8.
15. Finkel, SE (2006). "Long-term survival during stationary phase: evolution and the GASP phenotype. " Nat. Rev. Microbiol. 4, 113-120.
16. Gardner, TS, di Bernardo, D, Lorenz, D, and Collins, JJ (2003). "Inferring genetic networks and identifying compound mode of action via expression profiling. " Science 301, 102-105.
17. Guarente, L, and Kenyon, C (2000). "Genetic pathways that regulate ageing in model organisms. " Nature (London) 408, 255-262.
18. Hedbacker, K, and Carlson, M (2008). "SNF1/AMPK pathways in yeast. " Front. Biosci. 13, 2408-2420.
19. Longo, VD, Gralla, EB, and Valentine, JS (1996). "Superoxide dismutase activity is essential for stationary phase survival in Saccharomyces cerevisiae: Mitochondrial production of toxic oxygen species in vivo. " J. Biol. Chem. 271, 12275-12280.
20. Lorenz, DR, Cantor, CR, and Collins, JJ (2009). "A network biology approach to aging in yeast. " Proc. Natl. Acad. Sci. U.S.A. 106, 1145-1150.
21. Madia, F, Gattazzo, C, Fabrizio, P, and Longo, VD (2007). "A simple model system for age-dependent DNA damage and cancer. " Mech. Ageing Dev. 128, 45-49.
22. Mortimer, RK, and Johnston, JR (1959). "Life span of individual yeast cells. " Nature (London) 183, 1751-1752.
23. Nevozhay, D, Adams, RM, Murphy, KF, Josic, K, and Balázsi, G (2009). "Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. " Proc. Natl. Acad. Sci. U.S.A. 106, 5123-5128.
24. Orgel, LE (1963). "The maintenance of the accuracy of protein synthesis and its relevance to ageing. " Proc. Natl. Acad. Sci. U.S.A. 49, 517-521.
25. Patil, CK, Mian, IS, and Campisi, J (2005). "The thorny path linking cellular senescence to organismal aging. " Mech. Ageing Dev. 126, 1040-1045.
26. Rosenfeld, N, Young, JW, Alon, U, Swain, PS, and Elowitz, MB (2005). "Gene regulation at the single-cell level. " Science 307, 1962-1965.
27. Skinner, AM, and Turker, MS (2005). "Oxidative mutagenesis, mismatch repair, and aging. " Sci. SAGE KE 2005, re3.
28. Stark, GR, Kerr, IM, Williams, BR, Silverman, RH, and Schreiber, RD (1998). "How cells respond to interferons. " Annu. Rev. Biochem. 67, 227-264.
29. Steinkraus, KA, Kaeberlein, M, and Kennedy, BK (2008). "Replicative aging in yeast: the means to the end. " Annu. Rev. Cell Dev. Biol. 24, 29-54.
30. Stewart, EJ, Madden, R, Paul, G, and Taddei, F (2005). "Aging and death in an organism that reproduces by morphologically symmetric division. " PLoS Biol. 3, e45.
31. Veiga, DF, Dutta, B, and Balázsi, G (2010). "Network inference and network response identification: moving genome-scale data to the next level of biological discovery. " Mol. Biosyst. 6, 469-480.
32. Wahl, LM (2002). "The division of labor: genotypic versus phenotypic specialization. " Am. Nat. 160, 135-145.
33. Wolpert, L, and Szathmáry, E (2002). "Multicellularity: evolution and the egg. " Nature (London) 420, 745.