Studying the interactome with the yeast two‐hybrid system and mass spectrometry

Abstract I. Introduction 00 II. The Yeast Two‐Hybrid System 00 A. A Brief History 00 1. Basis of Yeast Two‐Hybrid System 00 2. Development of the System 00 B. Current Systems 00 1. The GAL4 and LexA Systems 00 2. The Sos Recruitment System 00 3. The Split‐Ubiquitin System 00 4. The Dual‐Bait System 00 5. Other Two‐Hybrid Systems 00 6. Variations on a Theme 00 C. Applications of Yeast Two‐Hybrid 00 III. Studying Protein Interactions by MS 00 IV. Genome‐Wide Analysis of Protein–Protein Interactions 00 A. Yeast Two‐Hybrid 00 B. Mass Spectrometry 00 C. Comparison of the Two Approaches 00 D. Placing Interactions in Context 00 V. Emerging Technologies 00 VI. Conclusions 00 Acknowledgments 00 Abbreviations 00 References 00 Protein interactions are crucial to the life of a cell. The analysis of such interactions is allowing biologists to determine the function of uncharacterized proteins and the genes that encode them. The yeast two‐hybrid system has become one of the most popular and powerful tools to study protein–protein interactions. With the advent of proteomics, the two‐hybrid system has found a niche in interactome mapping. However, it is clear that only by combining two‐hybrid data with that from complementary approaches such as mass spectrometry (MS) can the interactome be analyzed in full. This review introduces the yeast two‐hybrid system to those unfamiliar with the technique, and discusses how it can be used in combination with MS to unravel the network of protein interactions that occur in a cell. © 2004 Wiley Periodicals, Inc., Mass Spec Rev