A mathematical model for adaptive prediction of environmental changes by microorganisms

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 17, 2011, Pages 7271-7276

  Mitchell, Amir ^a,b   Pilpel, Yitzhak ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Adaptation; Conditioning; Evolution

Indexed keywords

ADAPTATION; ARTICLE; ECOLOGY; ENVIRONMENTAL CHANGE; ENVIRONMENTAL STRESS; ESCHERICHIA COLI; HABITAT; MATHEMATICAL MODEL; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; VIBRIO CHOLERAE;

ADAPTATION, BIOLOGICAL; ECOSYSTEM; ESCHERICHIA COLI; MODELS, BIOLOGICAL; VIBRIO CHOLERAE; YEASTS;

ESCHERICHIA COLI; VIBRIO CHOLERAE;

EID: 79955565307     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1019754108     Document Type: Article

References (29)

1. Causton HC, et al. (2001) Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12:323-337. (Pubitemid 33051578)
2. Cheung KJ, Badarinarayana V, Selinger DW, Janse D, Church GM (2003) A microarraybased antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res 13:206-215. (Pubitemid 36575769)
3. Enjalbert B, Nantel A, Whiteway M (2003) Stress-induced gene expression in Candida albicans: Absence of a general stress response. Mol Biol Cell 14:1460-1467. (Pubitemid 36547414)
4. Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257.
5. Tirosh I, Weinberger A, Carmi M, Barkai N (2006) A genetic signature of interspecies variations in gene expression. Nat Genet 38:830-834. (Pubitemid 43980606)
6. Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40:471-475. (Pubitemid 351450880)
7. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004) Bacterial persistence as a phenotypic switch. Science 305:1622-1625. (Pubitemid 39296357)
8. Levins R (1968) Evolution in Changing Environments: Some Theoretical Explorations (Princeton University Press, Princeton).
9. Tagkopoulos I, Liu YC, Tavazoie S (2008) Predictive behavior within microbial genetic networks. Science 320:1313-1317. (Pubitemid 351929462)
10. Mitchell A, et al. (2009) Adaptive prediction of environmental changes by microorganisms. Nature 460:220-224.
11. Schild S, et al. (2007) Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment. Cell Host Microbe 2:264-277. (Pubitemid 47500823)
12. Rodaki A, et al. (2009) Glucose promotes stress resistance in the fungal pathogen Candida albicans. Mol Biol Cell 20:4845-4855.
13. Piper PW (1995) The heat shock and ethanol stress responses of yeast exhibit extensive similarity and functional overlap. FEMS Microbiol Lett 134:121-127.
14. Sanchez Y, Taulien J, Borkovich KA, Lindquist S (1992) Hsp104 is required for tolerance to many forms of stress. EMBO J 11:2357-2364.
15. Lewis JG, Learmonth RP, Watson K (1995) Induction of heat, freezing and salt tolerance by heat and salt shock in Saccharomyces cerevisiae. Microbiology 141:687-694.
16. Delaney JM (1990) Requirement of the Escherichia coli dnaK gene for thermotolerance and protection against H2O2. J Gen Microbiol 136:2113-2118.
17. Berry DB, Gasch AP (2008) Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol Cell 19:4580-4587.
18. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall, London).
19. Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436:588-592. (Pubitemid 41112935)
20. Stoebel DM, Dean AM, Dykhuizen DE (2008) The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178:1653-1660.
21. Kelley R, Ideker T (2009) Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet 5:e1000488.
22. Dykhuizen D, Hartl D (1978) Transport by the lactose permease of Escherichia coli as the basis of lactose killing. J Bacteriol 135:876-882. (Pubitemid 9022267)
23. Gottesman S (1989) Genetics of proteolysis in Escherichia coli. Annu Rev Genet 23: 163-198.
24. Savageau MA (1983) Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am Nat 122:732-744.
25. Savageau MA (1998) Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics 149:1677-1691.
26. Perkins TJ, Swain PS (2009) Strategies for cellular decision-making. Mol Syst Biol 5: 326.
27. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64-68.
28. Muse GW, et al. (2007) RNA polymerase is poised for activation across the genome. Nat Genet 39:1507-1511. (Pubitemid 350191341)
29. Cook A, Lederberg J (1962) Recombination studies of lactose nonfermenting mutants of Escherichia coli K-12. Genetics 47:1335-1353.