Proteome-wide screens in Saccharomyces cerevisiae using the yeast GFP collection

The budding yeast is a simple and genetically tractable eukaryotic organism. It remains a leading system for functional genomic work and has been the focus of many pioneering efforts, including the systematic construction and analysis of gene deletion mutants. Over the past decade, many large-scale studies have made use of the deletion and other mutant collections to assay genetic interactions, chemical sensitivities, and other phenotypes, contributing enormously to our understanding of gene function. The deletion mutant collection has also been used in cell biological surveys to identify genes that control cell and organelle morphology. One valuable approach for systematic definition of gene function and biological pathways involves global assessment of the localization patterns of the proteins they encode and how these patterns are altered in response to environmental or genetic perturbation. However, proteome-wide, cell biological screens are extremely challenging, from both a technical and computational perspective. The yeast GFP collection, an elegant and unique strain set, is ideal for studying both protein localization and abundance across the proteome ( http://yeastgfp.yeastgenome.org/ ). In this chapter, we outline how the yeast GFP collection has been used to date and discuss approaches for conducting future surveys of the proteome.