Ubiquitylation, the covalent attachment of the small protein ubiquitin to other proteins, regulates a host of cellular processes. Protein ubiquitylation has become a synonym for protein degradation, and most of the current research is focused on the role of ubiquitin in targeting proteins for degradation by the 26S proteasome. However, we are beginning to appreciate that a number of proteins are regulated by ubiquitylation in a proteolysis-independent manner. Recent system-wide experiments suggest that only little more than fifty percent of ubiquitylated proteins are efficiently degraded by the proteasome, implying that protein ubiquitylation has widespread signaling functions outside the proteasome pathway. Molecular understanding of these proteolysis-independent ubiquitin signals will be important for basic biomedical research and development of therapeutics targeting the ubiquitin system. Some of the key questions are: Why are some ubiquitylated proteins degraded and others are not? How can ubiquitylation directly affect protein activity? What are the mechanisms of direct protein regulation by ubiquitylation and what are the components mediating regulation? We analyze a system regulated by the cullin-RING ubiquitin ligase complex SCFMet30, which connects metabolic stress to cell cycle regulation. This pathway is particularly suited to probe non-proteolytic signals of ubiquitylation because the same ligase modifies different substrate proteins with the same lysine-48 linked ubiquitin chain, yet some substrates are labeled for degradation while other substrates are regulated in a proteolysis-independent manner. This proposal builds on a plethora of tools available to analyze biochemistry and physiology of this pathway and will address (i) how regulated ubiquitin-binding domains can dictate signal identity and switch between ubiquitin chains signaling for degradation and non-proteolytic regulation (Aim 1);(ii) how a polyubiquitin chain can directly regulate transcription factor activity (Aim 2) and (iii) how ubiquitylation induces active disassembly/remodeling of multisubunit protein complexes to modulate their activities (Aim 3). Ubiquitylation affects many important cellular processes and has been linked to a number of human diseases including cancer, neurodegeneration, and retroviral infection. A contribution of proteolysis-independent ubiquitylation in these diseases is emerging and it will be important to understand the mechanism behind this regulation to design diagnostic tools and treatment strategies. This proposal aims to achieve detailed mechanistic insight into proteolysis-independent ubiquitin signals and to define the concepts of these regulatory ubiquitylation pathways.

Public Health Relevance

Protein modification with ubiquitin controls most if not all functions of living cells and is involved in many human diseases. This project seeks a mechanistic understanding of regulation of protein function by ubiquitylation and regulation of key components of the ubiquitylation machinery. The ubiquitin system is a promising target for therapeutic approaches and findings derived from the proposed studies will therefore be of great significance to human health.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM066164-12
Application #
8704948
Study Section
Membrane Biology and Protein Processing (MBPP)
Program Officer
Gerratana, Barbara
Project Start
2002-08-01
Project End
2016-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
12
Fiscal Year
2014
Total Cost
$428,738
Indirect Cost
$151,238
Name
University of California Irvine
Department
Biochemistry
Type
Schools of Medicine
DUNS #
046705849
City
Irvine
State
CA
Country
United States
Zip Code
92697
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Kaiser, Peter; Mayor, Thibault (2011) Gold for ubiquitin in Vancouver: First Conference on Proteomics of Protein Degradation and Ubiquitin Pathways held June 6-8, 2010 in Vancouver, University of British Columbia, organized By Lan Huang, Thibault Mayor, and Peipei Ping. Mol Cell Proteomics 10:R110.003863
Flick, Karin; Kaiser, Peter (2009) Proteomic revelation: SUMO changes partners when the heat is on. Sci Signal 2:pe45
Meierhofer, David; Wang, Xiaorong; Huang, Lan et al. (2008) Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. J Proteome Res 7:4566-76
Kaiser, Peter; Meierhofer, David; Wang, Xiaorong et al. (2008) Tandem affinity purification combined with mass spectrometry to identify components of protein complexes. Methods Mol Biol 439:309-26
Wang, Xiaorong; Chen, Chi-Fen; Baker, Peter R et al. (2007) Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry 46:3553-65
Tagwerker, Christian; Zhang, Hongwei; Wang, Xiaorong et al. (2006) HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae. Yeast 23:623-32
Guerrero, Cortnie; Tagwerker, Christian; Kaiser, Peter et al. (2006) An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol Cell Proteomics 5:366-78
Kaiser, Peter; Huang, Lan (2005) Global approaches to understanding ubiquitination. Genome Biol 6:233
Yen, James L; Su, Ning-Yuan; Kaiser, Peter (2005) The yeast ubiquitin ligase SCFMet30 regulates heavy metal response. Mol Biol Cell 16:1872-82