Introduction

Although the fields of functional genomics and proteomics are relatively young, they have benefited greatly from analysis of the baker's yeast Saccharomyces cerevisiae (1). This single-celled fungus has long been an effective eukaryotic model system for understanding basic cellular processes clue to its ease of manipulation and genetic tractability (2,3). Yeast has a short life cycle of 90 min, it is inexpensive to maintain and grow, it is stable in both the haploid and diploid state, and it is classified as a generally recognized as safe (GRAS) microorganism. Its haploid genome is of relatively low complexity (1.2 × 10⁷ bp) and is packaged into 16 well-characterized chromosomes (4). Furthermore, yeast was the first eukaryotic genome for which genome sequence was reported (5), and its 6466 open reading frames (ORFs) (6,7) exist in a readily usable form (8). Annotated information on the function of these ORFs and their corresponding protein products is available through several databases, including the Saccharomyces Genome Database (SGD; www.yeastgenome.org), the Yeast Protein Database (YPD; www.proteome.com), the Munich Information Center for Protein Sequences (MIPS) Comprehensive Yeast Genome Database (CYGD; mips.gsf.de/genre/proj/yeast/index.jsp), and the Yeast Resource Center (depts. washington.edu/∼yeastrc). In addition, a big advantage of yeast compared with other eukaryotic model organisms is its relatively high rate of recombination between homologous DNA sequences that allows precise insertion of DNA sequences at specific locations within the yeast genome. This phenomenon enables a simple gene knockout technique to be performed in yeast using a PCR-mediated approach and the integration of a selectable marker and/or a mutant allele (9). Similar approaches can be used to introduce regulated promoters upstream of a given ORF (10) or to introduce different epitope tags (11).

Yeast has also been successfully used for many years as a model for mammalian diseases and pathways. In fact, the cellular target of rapamycin, an immunosuppressant used as an anti-rejection drug in tissue transplants, was first discovered in yeast and then subsequently verified in humans (12). Along these lines, yeast is a valuable predictor of human gene function; at least 31% of proteins encoded by yeast genes have human homologs, and conversely, nearly 50% of human genes implicated in heritable diseases have yeast homologs (13). In summary, yeast has definitively improved our understanding of fundamental cellular processes and metabolic pathways in humans and has facilitated the molecular analysis of many disease genes.

In this review, we give a comprehensive overview of the most important yeast-based functional genomic and proteomic technologies that are advancing the utility of yeast as a model organism in modern biomolecular research. These approaches include utilization of the yeast deletion strain collection, large-scale determination of protein localization in vivo, synthetic genetic arrays, variations of the yeast two-hybrid system, protein micro-arrays, and tandem affinity purification (TAP)-tagging.

Applications of the Yeast Deletion Strain Collection

In model organisms, the function of every known gene or predicted ORF can be analyzed by assessing growth defects or other phenotypes when the gene or ORF is deleted or the gene product is inactivated. Systematic generation of null or loss of function mutants and subsequent phenotypic analysis will therefore allow the functional categorization of all genes. Among eukaryotic model organisms, the yeast S. cerevisiae has been most extensively studied by systematic and genome-wide approaches. Undoubtedly, one of the most important milestones for yeast functional genomics was the construction of a complete set of deletion mutants (14,15). This collection of null mutants allowed for the first time a comprehensive and parallel analysis of phenotypes in a model organism. In its final version, 5916 out of the originally annotated approximately 6200 yeast ORFs were successfully deleted for the construction of a heterozygous diploid collection that contains deletions in both essential and nonessential genes (14). In addition, sets of approximately 4800 nonessential deletions have been generated independently as haploid MATa and MATα strains or as homozygous diploids. The collections are available from Research Genetics (ResGen) (www.resgen.com/products/YEASTD.php3) or the Euroscarf consortium (web.uni-frankfurt.de/fb5/mikro/euroscarf/col_index.html).