Experimental Rugged Fitness Landscape in Protein Sequence Space
Yuuki Hayashi1, Takuyo Aita2,3, Hitoshi Toyota4, Yuzuru Husimi3, Itaru Urabe4, Tetsuya Yomo1,5,6*
1 Department of Bioinformatic Engineering, Osaka University, Suita, Osaka, Japan, 2 Rational Evolutionary Design of Advanced Biomolecules (REDS) Group/JST, Saitama Small Enterprise Promotion Corporation SKIP City, Kawaguchi, Saitama, Japan, 3 Department of Functional Materials Science, Saitama University, Saitama, Japan, 4 Department of Biotechnology, Osaka University, Suita, Osaka, Japan, 5 Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan, 6 Expoloratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Suita, Osaka, Japan
Abstract
The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitromolecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.
Citation: Hayashi Y, Aita T, Toyota H, Husimi Y, Urabe I, et al. (2006) Experimental Rugged Fitness Landscape in Protein Sequence Space. PLoS ONE 1(1): e96. doi:10.1371/journal.pone.0000096
Academic Editor: Suzannah Rutherford, Fred Hutchinson Cancer Research Center, United States of America
Received: August 7, 2006; Accepted: October 1, 2006; Published: December 20, 2006
Copyright: © 2006 Hayashi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This research was supported in part by "The 21st Century Center of Excellence Program" and "Special Coordination Funds for Promoting Science and Technology: Yuragi Project" of the Ministry of Education, Culture, Sports, Science and Technology, Japan.
Competing interests: The authors have declared that no competing interests exist.
* To whom correspondence should be addressed.
E-mail: yomo@ist.osaka-u.ac.jp
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EXCERTO INTERESSANTE DO ARTIGO:
"By extrapolation, we estimated that adaptive walking requires a library size of 10^70 [a one followed by 70 zeros] with 35 substitutions to reach comparable fitness. Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination."
