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Molecular & Cellular Proteomics 1:561-566, 2002.
© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

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Reviews/Perspectives

Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome^*

Takashi Ito^,,¶, Kazuhisa Ota^,, Hiroyuki Kubota^,||, Yoshihiro Yamaguchi^,, Tomoko Chiba, Kazumi Sakuraba^, and Mikio Yoshida^,**

Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan
Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST), Tokyo 102-0081, Japan
^** INTEC Web and Genome Informatics Corporation, Tokyo 136-0075, Japan

^¶ To whom correspondence should be addressed: Division of Genome Biology, Cancer Research Inst., Kanazawa University, 13-1 Takaramachi, Kanazawa 920-0934, Japan. Tel.: 81-76-265-2726; Fax: 81-76-234-4508; E-mail: titolab{at}kenroku.kanazawa-u.ac.jp

Comprehensive analysis of protein-protein interactions is a challenging endeavor of functional proteomics and has been best explored in the budding yeast. The yeast protein interactome analysis was achieved first by using the yeast two-hybrid system in a proteome-wide scale and next by large-scale mass spectrometric analysis of affinity-purified protein complexes. While these interaction data have led to a number of novel findings and the emergence of a single huge network containing thousands of proteins, they suffer many false signals and fall short of grasping the entire interactome. Thus, continuous efforts are necessary in both bioinformatics and experimentation to fully exploit these data and to proceed another step forward to the goal. Computational tools to integrate existing biological knowledge buried in literature and various functional genomic data with the interactome data are required for biological interpretation of the huge protein interaction network. Novel experimental methods have to be developed to detect weak, transient interactions involving low abundance proteins as well as to obtain clues to the biological role for each interaction. Since the yeast two-hybrid system can be used for the mapping of the interaction domains and the isolation of interaction-defective mutants, it would serve as a technical basis for the latter purpose, thereby playing another important role in the next phase of protein interactome research.

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