Mutant power: using mutant allele collections for yeast functional genomics

Abstract

The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology.

Keywords: Candida albicans; Saccharomyces cerevisiae; functional genomics; overexpression; transposon; yeast.

Figure 1

Summary of transposon-based approaches for functional genomics in S. cerevisiae and C. albicans. Diagrammatic representation of a Tn7-derived transposon insertion library for mutagenesis of a desired yeast genetic background. Transposon features are not drawn to scale.

Figure 2

Application of shuttle mutagenesis to generate double heterozygous mutants for large-scale analysis of complex haploinsufficiency in C. albicans. In this illustration, complex haploinsufficiency is assessed with respect to hyphal growth. YFG1, Your Favorite Gene.

Figure 3

Overview of approaches to systematically generate hypomorphic alleles of essential yeast genes. (A) Diagram illustrating a degron-based method to conditionally target a protein of interest for degradation. (B) DAmP constructs for the generation of hyphomorphic alleles through reduced transcript stability. A variation of the approach utilizing a TAP tag and the Degron cassette is also illustrated. DNA elements are not drawn to scale.