Disassembly of Lys11 and mixed linkage polyubiquitin conjugates provides insights into function of proteasomal deubiquitinases Rpn11 and Ubp6

Wissam Mansour, Mark A Nakasone, Maximilian von Delbrück, Zanlin Yu, Daria Krutauz, Noa Reis, Oded Kleifeld, Thomas Sommer, David Fushman, Michael H Glickman

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38 Citations (Scopus)
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Abstract

Protein homeostasis is largely dependent on proteolysis by the ubiquitin-proteasome system. Diverse polyubiquitin modifications are reported to target cellular proteins to the proteasome. At the proteasome, deubiquitination is an essential preprocessing event that contributes to degradation efficiency. We characterized the specificities of two proteasome-associated deubiquitinases (DUBs), Rpn11 and Ubp6, and explored their impact on overall proteasome DUB activity. This was accomplished by constructing a panel of well defined ubiquitin (Ub) conjugates, including homogeneous linkages of varying lengths as well as a heterogeneously modified target. Rpn11 and Ubp6 processed Lys(11) and Lys(63) linkages with comparable efficiencies that increased with chain length. In contrast, processing of Lys(48) linkages by proteasome was inversely correlated to chain length. Fluorescently labeled tetra-Ub chains revealed endo-chain preference for Ubp6 acting on Lys(48) and random action for Rpn11. Proteasomes were more efficient at deconjugating identical substrates than their constituent DUBs by roughly 2 orders of magnitude. Incorporation into proteasomes significantly enhanced enzymatic efficiency of Rpn11, due in part to alleviation of the autoinhibitory role of its C terminus. The broad specificity of Rpn11 could explain how proteasomes were more effective at disassembling a heterogeneously modified conjugate compared with homogeneous Lys(48)-linked chains. The reduced ability to disassemble homogeneous Lys(48)-linked chains longer than 4 Ub units may prolong residency time on the proteasome.

Original languageEnglish
Pages (from-to)4688-4704
Number of pages17
JournalJournal of Biological Chemistry
Volume290
Issue number8
Early online date11 Nov 2014
DOIs
Publication statusPublished - 20 Feb 2015

Keywords

  • Endopeptidases/genetics
  • Lysine/genetics
  • Polyubiquitin/genetics
  • Proteasome Endopeptidase Complex/genetics
  • Protein Structure, Tertiary
  • Proteolysis
  • Saccharomyces cerevisiae/genetics
  • Saccharomyces cerevisiae Proteins/genetics

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