Empirical fitness landscapes reveal accessible evolutionary paths

Nature

Volumn 445, Issue 7126, 2007, Pages 383-386

  Poelwijk, Frank J ^a   Kiviet, Daniel J ^a   Weinreich, Daniel M ^b,c   Tans, Sander J ^a  

^a FOM INSTITUTE AMOLF   (Netherlands)

^b HARVARD UNIVERSITY   (United States)

^c BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CEFOTAXIME;

EMPIRICAL ANALYSIS; FITNESS; LANDSCAPE EVOLUTION;

ANALYSIS; ARTICLE; EVOLUTION; LABORATORY; PRIORITY JOURNAL;

EID: 33846551980     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature05451     Document Type: Article

References (38)

1. Darwin, C. On the Origin of Species by Means of Natural Selection Ch VI (Murray, London, 1859).
2. Pauling, L. & Zuckerkandl, E. Chemical paleogenetics; Molecular "restoration studies" of extinct forms of life. Acta Chem. Scand. A 17, S9-S16 (1963).
3. Maynard Smith, J. Natural selection and the concept of a protein space. Nature 225, 563-564 (1970).
4. Malcolm, B. A. et al. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345, 86-89 (1990).
5. Stackhouse, J., Presnell, S. R., McGeehan, G. M., Nambiar, K. P. & Benner, S. A. The ribonuclease from an extinct bovid ruminant. FEBS Lett. 262, 104-106 (1990).
6. Ugalde, J. A., Chang, B. S. W. & Matz, M. V. Evolution of coral pigments recreated. Science 305, 1433 (2004).
7. Thornton, J. W. Resurrecting ancient genes: Experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366-375 (2004).
8. Wright, S. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc 6th Int. Cong. Genet. 1, 356-366 (1932).
9. Gillespie, J. H. The Causes of Molecular Evolution (Oxford Univ. Press, Oxford, 1991).
10. Kauffman, S. A. The Origins of Order: Self-organization and Selection in Evolution (Oxford Univ. Press, Oxford, 1993).
11. Gavrilets, S. Fitness Landscapes and the Origin of Species (Princeton Univ. Press, Princeton, 2004).
12. van Nimwegen, E. & Crutchfield, J. P. Metastable evolutionary dynamics: crossing fitness barriers or escaping via neutral paths? Bull. Math. Biol. 62, 799-848 (2000).
13. Weinreich, D. M., Watson, R. A. & Chao, L. Sign epistasis and genetic constraint on evolutionary trajectories. Evol. Int. J. Org. Evol. 59, 1165-1174 (2005).
14. Weinreich, D. M., Delaney, N. F., DePristo, M. A. & Hartl, D. L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111-114 (2006).
15. Kimura, M. On the probability of fixation of mutant genes in a population. Genetics 47, 713-719 (1962).
16. Poelwijk, F. J., Kiviet, D. J. & Tans, S. J. Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data. PLoS Comput. Biol. 2, e58 (2006).
17. DePristo, M. A., Weinreich, D. M. & Hartl, D. L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Rev. Genet. 6, 678-687 (2005).
18. Bloom, J. D., Labthavikul, S. T., Otey, C. R. & Arnold, F. H. Protein stability promotes evolvability. Proc. Natl Acad. Sci. USA 103, 5869-5874 (2006).
19. Lunzer, M., Miller, S. P., Felsheim, R. & Dean, A. M. The biochemical architecture of an ancient adaptive landscape. Science 310, 499-501 (2005).
20. Zhu, G., Golding, G. B. & Dean, A. M. The selective cause of an ancient adaptation. Science 307, 1279-1282 (2005).
21. Bridgham, J. T., Carroll, S. M. & Thornton, J. W. Evolution of hormone-receptor complexity by molecular exploitation. Science 312, 97-101 (2006).
22. Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. Mutant lac repressors with new specificities hint at rules for protein-DNA recognition. EMBO J. 9, 615-621 (1990).
23. Barkai, N. & Leibler, S. Robustness in simple biochemical networks. Nature 387, 913-917 (1997).
24. Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl Acad. Sci. USA 95, 8420-8427 (1998).
25. Kitano, H. Biological robustness. Nature Rev. Genet. 5, 826-837 (2004).
26. Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J. III & Doyle, J. Robustness of cellular functions. Cell 118, 675-685 (2004).
27. Thattai, M. & van Oudenaarden, A. Stochastic gene expression in fluctuating environments. Genetics 167, 523-530 (2004).
28. Kussell, E.&Leibler, S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075-2078 (2005).
29. Arnold, F. H., Wintrode, P. C., Miyazaki, K. & Gershenson, A. How enzymes adapt: lessons from directed evolution. Trends Biochem. Sci. 26, 100-106 (2001).
30. Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457-469 (2003).
31. Couñago, R., Chen, S. & Shamoo, Y. In vivo molecular evolution reveals biophysical origins of organismal fitness. Mol. Cell 22, 441-449 (2006).
32. Lenski, R. E. & Travisano, M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl Acad. Sci. USA 91, 6808-6814 (1994).
33. Dekel, E. & Alon, U. Optimality and evolutionary tuning of the expression level of a protein. Nature 436, 588-592 (2005).
34. Hurley, J. H., Dean, A. M., Koshland, D. E. Jr & Stroud, R. M. Catalytic mechanism of NADP(1)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP1 complexes. Biochemistry 30, 8671-8678 (1991).
35. Hurley, J. H., Chen, R. & Dean, A. M. Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ → NAD+ specificity-reversal mutant. Biochemistry 35, 5670-5678 (1996).
36. Kalodimos, C. G. et al. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J. 21, 2866-2876 (2002).
37. Kopke Salinas, R. et al. Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor. ChemBioChem 6, 1628-1637 (2005).
38. Koradi, R., Billeter, M. & Wüthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 (1996).