Theory of evolutionary molecular engineering through simultaneous accumulation of advantageous mutations

We examined the effectiveness of an "adaptive leap" strategy using the "mut ation scrambling" method as an efficient optimization technique (Uchiyama, 2000; J. Biochem. 128, 441-447) for cases where mutational (rough) additivi ty holds in fitness. The mutation scrambling method is composed of the foll owing three processes: (1) preliminary selection of several advantageous si ngle-point mutations introduced in a wild-type sequence; (2) preparation of various multiple-point mutants incorporating the advantageous mutant resid ue or wild-type residue at each of the selected sites, by scrambling the mu tant residues and wild-type residues (this process is called mutation scram bling); and (3) selection of the fittest through screening of the mutant po ol. 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 eff iciently 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 reali stic cases. Particularly, this strategy works well in cases where the numbe r of component mutations is large and the size of the population to be scre ened is small. Analysis of the mutant fitness distributions with various mi xing ratios is also useful to explore local fitness landscapes. (C) 2000 Ac ademic Press.