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Originally published In Press as doi:10.1074/mcp.M400081-MCP200 on July 19, 2004.
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Molecular & Cellular Proteomics 3:1053-1064, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

The Phox Homology (PX) Domain Protein Interaction Network in Yeast*,S

Carolina S. Vollert and Peter Uetz{ddagger}

From the Institut für Genetik, Forschungszentrum Karlsruhe, D-76021 Karlsruhe, Germany

The phox homology (PX) domain is a phosphoinositide-binding domain that is conserved from yeast to human. Here we show for the first time by genome-wide two-hybrid screens and in vitro binding assays that the PX domain is a bona fide protein interaction domain. The yeast PX domain-only proteins Grd19p (YOR357C) and Ypt35p (YHR105W), as well as the isolated PX domains from Mvp1p (YMR004W), Snx42p/Cvt20p/Atg20p (YDL113C), Vam7p (YGL212W), and Vps17p (YOR132W), yielded a total of 40 reproducible two-hybrid interactions. Thirty-five interactions were found for the full-length proteins of Bem1p (YBR200W), Snx42p, Snx4p/Cvt13p (YJL036W), Vam7p, Vps5p (YOR069W), and Vps17p, but these appear not to require the PX domain, because these interactions could not be reproduced with PX-only baits. Interactions of Grd19p, Vam7p, Vps5p, Vps17p, and Ypt35p with members of the Yip1p family of proteins were detected consistently and were verified by in vitro binding assays. The N-terminal cytoplasmic domain of Yip1p and Yif1p mediates these interactions with PX domains. A mutation in the lipid-binding pocket of Ypt35p that reduces lipid binding markedly does not affect these PX domain protein interactions, arguing that lipid binding uses a different interaction surface than protein binding.

{ddagger} To whom correspondence should be addressed: Institut für Genetik, Forschungszentrum Karlsruhe, Box 3640, D-76021 Karlsruhe, Germany. Tel.: 49-7247-82-6103; Fax: 49-7247-82-3354; E-mail: peter.uetz{at}itg.fzk.de


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