May 2011

Spotlight on degradation pathways

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This month, Molecular and Cellular Proteomics features a special issue highlighting recent advances in ubiquitination and protein degradation research. The issue, titled “Protein Degradation and Ubiquitin Pathways” was coordinated by three guest editors, Lan Huang from the University of California, Irvine; Thibault Mayor from The University of British Columbia and Peipei Ping from the University of California, Los Angeles.

The issue features new techniques and developments presented at the 2010 Proteomics of Protein Degradation and Ubiquitin Pathways meeting held in Vancouver, British Columbia, jointly sponsored by the International Forum of Proteomics and PPDUP and organized by the guest editors. The Vancouver meeting was the first in a series the organizers hope will “promote the elucidation of protein degradation pathways and the understanding of downstream physiologic consequences using cutting-edge proteomic tools.”

Ubiquitination and regulated control of protein degradation are fundamental biological processes that play a critical role in virtually every aspect of eukaryotic cellular function. The cell’s system of tagging proteins for trafficking or degradation by attaching ubiquitin remains an important area of study that continues to provide new insights into cell maintenance and the causes of cellular dysfunction. As the guest editors note in their introduction, “The biological insights offered herein have begun to unveil the functional lesions within these pathways and the potential roles they contribute to the pathogenesis of diseases.”

Much of the research featured in the May issue focuses on understanding the fundamental biology at work. Lan Huang’s laboratory reviews advances in understanding proteasome structure and function during oxidative stress and how cells cope with oxidative stress through proteasome-dependent degradation pathways. A group led by Donald Kirkpatrick at Genentech Inc. presents its progress in quantitative mass spectrometry methods for characterizing complex ubiquitin signals. They reveal the complexity of ubiquitin signals in the cellular proteome by showing that polyubiquitinated substrates purified from mammalian cells can be modified by mixtures of K48, K63 and K11 linkages.

Raymond Deshaies and colleagues at the California Institute of Technology describe novel signaling mechanisms for the SCF ubiquitin ligase complex. Using quantitative mass spectrometry-based approaches, they show that inhibiting conjugation by Nedd8, a ubiquitin-like protein that modifies SCF ubiquitin ligases, increases SCF complex levels, suggesting that other mechanisms maintain the cellular pool of SCF ubiquitin ligases in addition to Nedd8.

Jun Qin and colleagues from the Baylor College of Medicine describe an affinity-based reagent for large-scale isolation of polyubiquitinated proteins that identified 294 ubiquitination sites on 223 proteins from human cells, 15 percent of which were mitochondrial. In a separate contribution, Qin and colleagues highlight the central role of unbiased proteomic technologies in pushing forward the field of global ubiquitin profiling in complex systems.

Michael Glickman from the Technion-Israel Institute of Technology and colleagues report on a method for rapid lysis that allows for global profiling of conjugated cellular ubiquitin directly from whole cell extract. They found that almost half of conjugated ubiquitin was nonextended monoubiquitin. Further studies with lysine-less ubiquitin (K0 Ub), which cannot be extended, revealed that K0 Ub was unevenly distributed between the two branches of ubiquitin processing, degradation and trafficking, despite both systems utilizing a common pool of ubiquitin. In a second contribution, Glickman and colleagues review the activation mechanism of the proteasome activator, PA200, thought to regulate proteolytic activity. Crystallographic analysis revealed the detailed interactions of PA200 and the proteasome core particle 20S and suggest that PA200 stabilizes a partially open conformation of 20S.

Other manuscripts feature research that is distinctly disease-related. Daniel Finley and colleagues from Harvard University examine deubiquitinase activities and potential mechanisms for enhancing protein degradation; their findings could have therapeutic implications for diseases involving toxic proteins that are targeted for degradation. A research group led Ugo Mayor at the CIC bioGUNE in Spain report a novel proteomics strategy to isolate ubiquitin conjugates from Drosophila melanogaster embryonic neurons and the identification of 48 novel neuronal ubiquitin substrates, many of which play important roles in synaptogenesis.

Alain Doucet and Christopher Overall from the University of British Columbia describe a novel liquid chromatography-mass spectrometry approach for identifying the amino termini of protein cleavage fragments in solution. Bioactive cleavage products play important cellular regulatory roles, and identifying cleavage sites is critical to understanding the pathology of many diseases.

Matthew Bogyo and colleagues from Stanford University and Scripps Research Institute present the first global map of the proteolytic processing events that occur as Plasmodium falciparum, the parasite that causes malaria, ruptures and emerges from host red blood cells. Their findings will aid the study of proteases that could serve as potential therapeutic targets.

A group led by Peipei Ping describes the first isolation and characterization of functional cardiac 19S complexes, unique among proteasome regulators because they affect both the capacity and specificity of protein degradation. They found that cardiac 19S complexes were heterogeneous, with one subpopulation exhibiting greater sensitivity to Hsp90 inhibition. Identifying these features opened up new avenues for proteasome-targeted therapeutic interventions in cardiovascular diseases.

The next conference will be held Jan. 22 to 25, 2012 in San Diego, Calif., and MCP already has signed on as a sponsor.

Angela Hvitved (

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