Yeast Two-Hybrid Protein–Protein Interaction Networks

The availability of complete genome sequences of numerous model organisms has initiated the development of new approaches in biological research to complement conventional biochemistry and genetics. Consequently, high-throughput methodologies also need to be applied in the emerging field of proteomics. Here, we discuss several methods that have been developed in the past years in order to characterize proteins and their functions on a large scale. We focus on the yeast two-hybrid system, which is the most widely used method to study protein–protein interactions and which has been used several times now to sucessfully map entire interaction networks on a large scale. We discuss small-scale pilot projects and how they have been upscaled to genome-wide screens, such as for the budding yeast Saccharomyces cerevisiae. We then compare the yeast two-hybrid system with several other screening methods that have been developed to investigate interactions between proteins in a high-throughput format, such as affinity purification methods coupled to mass spectrometry. Efficient adaptation of such methods to a high-throughput format, coupled with the increasing use of databases to compare interaction maps generated with different methods, will help in elucidating protein–protein interactions on a scale that would have been unthinkable just a few years ago. DANIEL AUERBACH Dualsystems Biotech Inc., Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. IGOR STAGLJAR Institute of Veterinary Biochemistry andMolecular Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Proteomics and Protein–Protein Interactions: Biology, Chemistry, Bioinformatics, and Drug Design, edited by Waksman. Springer, New York, 2005.