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Submitted on December 28, 2004
Revised on February 7, 2005
Accepted on February 7, 2005

Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets

thibault mayor, J. Russell Lipford, Johannes Graumann, Geoffrey T. Smith, and Raymond J. Deshaies

Biology, California Institute of Technology, Pasadena, CA 91125

Corresponding Author: mayor{at}caltech.edu

The poly-ubiquitin receptor Rpn10 targets ubiquitylated Sic1 to the 26S proteasome for degradation. In contrast, turnover of at least one ubiquitin-proteasome system (UPS) substrate, CPY*, is impervious to deletion of RPN10. To distinguish whether RPN10 is involved in the turnover of only a small set of cell cycle regulators that includes Sic1, or plays a more general role in the UPS, we sought to develop a general method that would allow us to survey the spectrum of ubiquitylated proteins that selectively accumulate in rpn10 cells. Poly-ubiquitin conjugates from yeast cells that express hexahistidine-tagged ubiquitin (H6-ubiquitin) were first enriched on a poly-ubiquitin binding protein affinity resin. This material was then denatured and subjected to immobilized metal ion affinity chromatography (IMAC) to retrieve H6-ubiquitin and proteins to which it may be covalently linked. Using this approach we identified 127 proteins that are candidate substrates for the 26S proteasome. We then sequenced ubiquitin conjugates from cells lacking Rpn10 (rpn10) and identified 54 proteins that were uniquely recovered from rpn10 cells. These include two known targets of the UPS: the cell cycle regulator Sic1 and the transcriptional activator Gcn4. Our approach of comparing the ubiquitin conjugate proteome in wild type and mutant cells has the resolving power to identify even an extremely inabundant transcriptional regulatory protein, and should be generally applicable to mapping enzyme–substrate networks in the UPS.


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