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Vol. 11, Issue 10, 3425-3439, October 2000
and
*Division of Biology, Caltech, Pasadena, California 91125;
Ubiquitin-dependent proteolysis is catalyzed by the 26S proteasome,
a dynamic complex of 32 different proteins whose mode of assembly and
mechanism of action are poorly understood, in part due to the
difficulties encountered in purifying the intact complex. Here we
describe a one-step affinity method for purifying intact 26S
proteasomes, 19S regulatory caps, and 20S core particles from budding
yeast cells. Affinity-purified 26S proteasomes hydrolyze both model
peptides and the ubiquitinated Cdk inhibitor Sic1. Affinity
purifications performed in the absence of ATP or presence of the poorly
hydrolyzable analog ATP-University of Washington, Seattle, Washington 98195-7730;
Institute for Genetics, University of Cologne, D-50674
Cologne, Germany; and ¶Howard Hughes Medical Institute,
Division of Biology, Caltech, Pasadena, CA 91125
-S unexpectedly revealed that a large number
of proteins, including subunits of the skp1-cullin-F-box protein ligase
(SCF) and anaphase-promoting complex (APC) ubiquitin ligases,
copurify with the 19S cap. To identify these proteasome-interacting proteins, we used a recently developed method that enables the direct analysis of the composition of large protein complexes (DALPC)
by mass spectrometry. Using DALPC, we identified more than 24 putative
proteasome-interacting proteins, including Ylr421c (Daq1), which we
demonstrate to be a new subunit of the budding yeast 19S cap, and
Ygr232w (Nas6), which is homologous to a subunit of the mammalian 19S
cap (PA700 complex). Additional PIPs include the heat shock proteins
Hsp70 and Hsp82, the deubiquitinating enzyme Ubp6, and proteins
involved in transcriptional control, mitosis, tubulin assembly, RNA
metabolism, and signal transduction. Our data demonstrate that
nucleotide hydrolysis modulates the association of many proteins with
the 26S proteasome, and validate DALPC as a powerful tool for rapidly
identifying stoichiometric and substoichiometric components of large
protein assemblies.
3115 Merryfield
Row, Novartis Agricultural Discovery Institute, San Diego, CA 92130;
§Department of Cell Biology, SR11, 10550 North Torrey
Pines Rd., The Scripps Research Institute, La Jolla, CA 92137 and 3115 Merryfield Row, Novartis Agricultural Discovery Institute, San Diego,
CA 92130.
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