Characterizing the Fitness Effects of Mutations in the Yeast URA3 Gene

Abstract

The central goal of this project is to study the mechanisms by which changes in gene sequence affect the level of function of the associated protein and therefore, fitness of the organism that carries a particular allele of a gene. In order to study this process, we performed random mutagenesis of the yeast URA3 gene and are currently assaying the mutated sequences for their function by competing yeast strains that have different alleles of the URA3 gene. The results from such a study would allow us to address some long standing issues in genetics--for example, the tolerance of proteins to amino acid substitutions, and secondly, the relative importance of the interaction between mutations as compared to the additive effects of mutations on the fitness of the gene. We are also interested in studying sequence evolution from a computational perspective, and more specifically, evaluating how much information about the structural constraints of a protein can be extracted from many homologous sequences. Using a statistical coupling analysis on a multiple sequence alignment of 620 URA3 sequences from different organisms, we have identified two large co-evolving networks of residues in the enzyme. Our preliminary results indicate that statistical coupling analysis is a powerful tool for identifying mutations that are likely to cause fitness effects.