Extracting characteristic properties of fitness landscape from in vitro molecular evolution: a case study on infectivity of fd phage to E.coli.
We have developed a methodology for extracting characteristic properties of a fitness landscape of interest by analyzing fitness data on an in vitro molecular evolution. The in vitro evolution is required to be conducted as the following "adaptive walk": a single parent sequence generates N mutant sequences as its offsprings, and the fittest individual among the N offsprings will become a new parent in the next generation. N is the library size of mutants to be screened in a single generation. Our theory of the adaptive walk on the "NK landscape" suggests the following: the adaptive walker starting from a random sequence climbs the landscape easily in an early stage, and then reaches a stationary phase in which the mutation-selection-random drift balance sets in. The stationary fitness value is nearly proportional to square root of ln N. Our analysis is performed from the following points: (1) stationary fitness values, (2) time series of fitness in the transitional state, (3) mutant's fitness distribution, and (4) the strength of selection pressure. Applying our methodology, we analyzed experimental data on the in vitro evolution of a random polypeptide (139 amino acids) toward acquiring infectivity (= ability to infect) of fd phage. As a result, we estimated that k is about 27 in this system, indicating that an arbitrary residue in a sequence is affected from other 23% residues. In this article, we demonstrated that the experimental data is consistent with our theoretical equations quantitatively, and that our methodology for extracting characteristic properties of a fitness landscape may be effective.
Aita
Takuyo
T
Rational Evolutionary Design of Advanced Biomolecules(REDS) Group/JST, Saitama Small Enterprise Promotion Corporation SKIP City, Kawaguchi 333-0844, Japan. sts028@saitama-j.or.jp
Hayashi
Yuuki
Y
Toyota
Hitoshi
H
Husimi
Yuzuru
Y
Urabe
Itaru
I
Yomo
Tetsuya
T
D017104:Bacteriophage M13 / Q000235:genetics*; D004926:Escherichia coli / Q000821:virology*; D019143:Evolution, Molecular; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D012641:Selection, Genetic