Theory of Evolutionary Molecular Engineering through Simultaneous Accumulation of Advantageous Mutations

We examined the effectiveness of an “adaptive leap” strategy using the “mutation scrambling” method as an efficient optimization technique (Uchiyama, 2000;J. Biochem.128, 441–447) for cases where mutational (rough) additivity holds in fitness. The mutation scrambling method is composed of the following three processes: (1) preliminary selection of several advantageous single-point mutations introduced in a wild-type sequence; (2) preparation of various multiple-point mutants incorporating the advantageous mutant residue or wild-type residue at each of the selected sites, by scrambling the mutant residues and wild-type residues (this process is called mutation scrambling); and (3) selection of the fittest through screening of the mutant pool. The fitness distribution in the mutant pool is controlled by the mixing ratio of the mutant residues to the wild-type residues. We focused on the mutant fitness distribution and obtained the optimal mixing ratio which efficiently generates superior multiple-point mutants with high fitnesses. As a result, we found that the optimal ratio lies between 7/3 and 9/1 in realistic cases. Particularly, this strategy works well in cases where the number of component mutations is large and the size of the population to be screened is small. Analysis of the mutant fitness distributions with various mixing ratios is also useful to explore local fitness landscapes.