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Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast

Graumann, Johannes and Dunipace, Leslie A. and Seol, Jae Hong and McDonald, W. Hayes and Yates, John R., III and Wold, Barbara J. and Deshaies, Raymond J. (2004) Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Molecular and Cellular Proteomics, 3 (3). pp. 226-237. ISSN 1535-9476. http://resolver.caltech.edu/CaltechAUTHORS:GRAmcp04

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Abstract

A combined multidimensional chromatography-mass spectrometry approach known as "MudPIT" enables rapid identification of proteins that interact with a tagged bait while bypassing some of the problems associated with analysis of polypeptides excised from SDS-polyacrylamide gels. However, the reproducibility, success rate, and applicability of MudPIT to the rapid characterization of dozens of proteins have not been reported. We show here that MudPIT reproducibly identified bona fide partners for budding yeast Gcn5p. Additionally, we successfully applied MudPIT to rapidly screen through a collection of tagged polypeptides to identify new protein interactions. Twenty-five proteins involved in transcription and progression through mitosis were modified with a new tandem affinity purification (TAP) tag. TAP-MudPIT analysis of 22 yeast strains that expressed these tagged proteins uncovered known or likely interacting partners for 21 of the baits, a figure that compares favorably with traditional approaches. The proteins identified here comprised 102 previously known and 279 potential physical interactions. Even for the intensively studied Swi2p/Snf2p, the catalytic subunit of the Swi/Snf chromatin remodeling complex, our analysis uncovered a new interacting protein, Rtt102p. Reciprocal tagging and TAP-MudPIT analysis of Rtt102p revealed subunits of both the Swi/Snf and RSC complexes, identifying Rtt102p as a common interactor with, and possible integral component of, these chromatin remodeling machines. Our experience indicates it is feasible for an investigator working with a single ion trap instrument in a conventional molecular/cellular biology laboratory to carry out proteomic characterization of a pathway, organelle, or process (i.e. "pathway proteomics") by systematic application of TAP-MudPIT.


Item Type:Article
Additional Information:© 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Received, September 17, 2003, and in revised form, November 30, 2003. Originally published In Press as doi:10.1074/mcp.M300099-MCP200 on December 5, 2003. We thank Erin O’Shea (University of California, San Francisco, CA) for the gift of RJD2067. J. G. thanks all members of the Yates laboratory (The Scripps Research Institute, La Jolla, CA) and Eberhard Dürr (Sidney Kimmel Cancer Center, San Diego, CA) for introduction into mass spectrometry and SEQUEST and D. A. Gold, E. E. Griffin, and A. Mah (Caltech, Pasadena, CA) for critical reading of the manuscript.
Subject Keywords:HISTONE ACETYLTRANSFERASE COMPLEX; SACCHAROMYCES-CEREVISIAE GENOME; CODON ADAPTATION INDEX; PROTEIN COMPLEXES; MASS-SPECTROMETRY; SWI/SNF COMPLEX; GENE DELETION; DATABASE; IDENTIFICATION; POLYMERASE
Record Number:CaltechAUTHORS:GRAmcp04
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:GRAmcp04
Alternative URL:http://dx.doi.org/10.1074/mcp.M300099-MCP200
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4503
Collection:CaltechAUTHORS
Deposited By: Lindsay Cleary
Deposited On:25 Aug 2006
Last Modified:26 Dec 2012 08:59

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