Networking proteins in yeast

The advent of genome sequencing projects—culminating in the recent reports of the human sequence (1, 2)—has resulted in both the identification of novel genes and proteins as well as the proliferation of the “omes” that come from their analyses: the proteome (the complement of proteins), transcriptome (the complement of mRNA transcripts), metabolome (the complement of metabolites), and so on. These end products of global assays are needed to interpret the large fraction (typically close to half) of predicted proteins for which no proteins of similar structure exist or have been functionally characterized. The report by Ito et al. (3) is the largest contribution to date in the effort to generate the protein interactome, or map of protein–protein interactions, for the yeast Saccharomyces cerevisiae. Yeast has been the major proving ground for functional genomics methods from the time its genome was sequenced in 1996 (4). Most such approaches use the underlying principle of “guilt by association” as the means of elucidating function. For example, genes that are coexpressed or proteins that are found in the same complex or in the same location are likely to be involved in the same or related cellular process. Theoretical methods to deduce function include bioinformatic analyses based on protein homology, phylogenetic relationships, and protein domain fusions (5). Empirical methods elucidate gene function by diverse approaches that include expression profiling, screens for biochemical activity, identification of proteins in macromolecular complexes by mass spectrometry, systematic gene disruptions, and determinations of protein interactions. The most popular means to carry out this last method on a genomewide basis is the yeast two-hybrid system (6), a genetic assay based on the properties of site-specific transcriptional activators. Hybrid proteins are generated in yeast composed of a DNA-binding domain fused with a protein X and a transcriptional activation domain fused …