Thermal adaptation of viruses and bacteria

Biophysical Journal

Volumn 98, Issue 7, 2010, Pages 1109-1118

  Chen, Peiqiu ^a,b   Shakhnovich, Eugene I ^a  

^a Department of Chemistry and Chemical Biology ^*  (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

BACTERIA; BIOPHYSICS; ESCHERICHIA COLI; EVOLUTION; HEAT; LISTERIA; METABOLISM; PROBABILITY; PROCEDURES; PROTEIN DENATURATION; PROTEIN FOLDING; PSEUDOMONAS; TEMPERATURE; THERMODYNAMICS; TIME; VIRUS;

BACTERIA; BIOLOGICAL EVOLUTION; BIOPHYSICS; ESCHERICHIA COLI; HOT TEMPERATURE; LISTERIA; PROBABILITY; PROTEIN DENATURATION; PROTEIN FOLDING; PSEUDOMONAS; TEMPERATURE; THERMODYNAMICS; TIME FACTORS; VIRUSES;

EID: 77950605529     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.11.048     Document Type: Article

References (45)

1. Bennett, A. F., and R. E. Lenski. 2007. An experimental test of evolutionary trade-offs during temperature adaptation. Prot: Natl. Acad. Sci. USA. 104 (Suppl l):8649-8654. (Pubitemid 47175459)
2. Bronikowski, A. M., A. F. Bennett, and R. E. Lenski. 2001. Evolutionary adaptation to temperature. VIII. Effects of temperature on growth rate in natural isolates of Escherichia coli and Salmonella enterica from, different thermal, environments. Evolution. 55:33-40.
3. Cullum, A. J., A. F. Bennett, and R. E. Lenski. 2001. Evolutionary adaptation to temperature. IX. Preadaptation to novel stressful environments of Escherichia coli adapted to high temperature. Evolution. 55:2194-2202.
4. Knies, J. L., R. Izem, ..., C. L. Burch. 2006. The genetic basis of thermal reaction norm evolution in lab and natural phage populations. PLoS Biol. 4:e201.
5. Travisano, M., and R. E. Lenski. 1996. Long-term experimental evolution, in. Escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics. 143:15-26. (Pubitemid 26136968)
6. Holder, K. K., and J. J. Bull. 2001. Profiles of adaptation in two similar viruses. Genetics. 159:1393-1404.
7. Cooper, V. S., A. F. Bennett, and R. E. Lenski. 2001. Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Evolution. 55:889-896.
8. Leroi, A. M., A. F. Bennett, and R. E. Lenski. 1994. Temperature acclimation and competitive fitness: an experimental test of the beneficial acclimation assumption. Proc. Natl. Acad. Sci. USA. 91:1917-1921.
9. Bennett, A, F., and R. E. Lenski. 1997. Phenotypic and evolutionary adaptation of a model bacterial system to stressful thermal environments. EXS. 83:135-154.
10. Knoll, A. H., and J. Bauld. 1989. The evolution of ecological, tolerance in prokaryotes. Trans. R. Soc. Edinb. Earth Sci. 80:209-223.
11. Xia, X. 1995. Body temperature, rate of biosynthesis, and evolution of genome size. Mol. Biol. Evol. 12:834-842.
12. Ratkowsky, D. A., J. Olley, and T. Ross. 2005. Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins. J. Theor. Biol. 233:351-362.
13. Zeldovich, K. B., P. Chen, and E. I. Shakhnovich. 2007. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Natl. Acad. Sci. USA. 104:16152-16157.
14. Herring, C. D., and F. R, Blattner. 2004. Conditional lethal amber mutations in essential Escherichia coli genes. J. Bacterial. 186:2673-2681.
15. Fraser, A. G., R. S. Kamath,..., J. Ahringer. 2000. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 408:325-330.
16. Bloom, J. D., A. Raval, and C. O. Wilke. 2007. Thermodynamics of neutral protein evolution, Genetics. 175:255-266.
17. Sánchez, I. E., J. Tejero, ..., L. Serrano. 2006. Point mutations in protein globular domains: contributions from function, stability and misfolding. J. Mol. Biol. 363:422-432.
18. Kumar, M. D., K. A. Bava,..., A. Sarai, 2006. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic. Acids Res. 34(Database issue):D204-D206.
19. Nishikawa, T., N. Gulbahce, and A. E. Motter. 2008. Spontaneous reaction silencing in metabolic optimization. PLOS Comput. Biol. 4;e1000236.
20. Couñago, R., S. Chen, and Y. Shamoo. 2006. In vivo molecular evolution reveals biophysical origins of organismal fitness. Mol. Cell. 22:441-449.
21. Zeldovich, K. B., P. Chen, ..., E. I. Shakhnovich. 2007. A first-principles model of early evolution: emergence of gene families, species, and preferred protein, folds. PLOS Comput. Biol. 3:el39.
22. Shakhnovich, E. I. 2006. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem. Rev. 106:1559-1588.
23. Sali, A., E. Shakhnovich, and M. Karplus. 1994. How does a protein fold? Nature. 369:248-251. (Pubitemid 24154805)
24. Privalov, P. L. 1979. Stability of proteins: small globular proteins. Adv. Protein Chem, 33:167-241.
25. Makhatadze, G. I., and P. L. Privalov. 1990. Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect. J. Mol. Biol. 213:375-384. (Pubitemid 20176546)
26. Robertson, A. D., and K. P. Murphy. 1997. Protein structure and the energetics of protein stability. Chem. Rev. 97:1251-1268.
27. Privalov, P. L., and S. J. Gill. 1988. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39:191-234.
28. Makhatadze, G. I., and P. L. Privalov. 1995. Energetics of protein structure. Adv. Protein Chem. 47:307-425.
29. Fersht, A. R., M. Bycroft, ..., L. Serrano. 1991. Pathway and stability of protein, folding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 332:171-176.
30. Drake, J. W., B. Charlesworth, ..., J. F. Crow. 1998. Rates of spontaneous mutation. Genetics. 148:1667-1686.
31. Sniegowski, P. D., P. J. Gerrish, and R. E. Lenski. 1997. Evolution of high mutation rates in experimental, populations of E. coli. Nature. 387:703-705. (Pubitemid 27270609)
32. Drake, J. W. 1993. Rates of spontaneous mutation among RNA viruses. Proc. Natl. Acad. Sci. USA. 90:4171-4175.
33. Chen, P., and E. I. Shakhnovich. 2009. Lethal mutagenesis in viruses and bacteria. Genetics. 183:639-650.
34. Forster, A. C., and G. M. Church. 2006. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2:45.
35. Drummond, D. A.,and C. O. Wilke. 2008. Mistranslation-induced protein, misfolding as a dominant constraint on coding-sequence evolution, Cell. 134:341-352.
36. Elena, S. F., C. O. Wilke, ..., R, E. Lenski. 2007. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution. 61:666-674.
37. DePristo, M. A., D. M. Weinreich, and D. L. Hartl. 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6:678-687.
38. Shoichet, B. K., W. A. Baase, ..., B.W. Matthews. 1995. A relationship between protein, stability and protein function, Proc. Natl. Acad. Sci. USA. 92:452-456.
39. Beadle, B. M., and B. K. Shoichet. 2002. Structural bases of stabilityfunction tradeoffs in enzymes. J. Mol. Biol. 321:285-296.
40. Giver, L., A. Gershenson,..., F. H. Arnold. 1998. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA. 95:12809-12813.
41. Bloom, J. D., S. T. Labthavikul, ..., F. H. Arnold. 2006. Protein stability promotes evolvability. Proc. Natl. Acad. Sci. USA. 103:5869-5874.
42. Topping, T. B., and L. M. Gloss. 2004. Stability and folding mechanism, of mesophilic, thermophilic and hyperthermophilic archael tristones: the importance of folding intermediates. J. Mol. Biol. 342:247-260.
43. Li, W. T., R. A. Grayling, ..., J. N. Reeve. 1998. Thermodynamic stability of archaeal histones. Biochemistry. 37:10563-10572.
44. Perl, D., C. Welker,..., F.X.Schmid. 1998. Conservation of rapid twostate folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nat. Struct. Biol. 5:229-235. (Pubitemid 28113755)
45. Woldringh, C. L. 1976. Morphological analysis of nuclear separation and cell division during the life cycle of Escherichia coli. J. Bacterial, 125:248-257.