Global subcellular characterization of protein degradation using quantitative proteomics

Mark Larance, Yasmeen Ahmad, Kathryn J. Kirkwood, Tony Ly, Angus I. Lamond (Lead / Corresponding author)

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    Abstract

    Protein degradation provides an important regulatory mechanism used to control cell cycle progression and many other cellular pathways. To comprehensively analyze the spatial control of protein degradation in U2OS osteosarcoma cells, we have combined drug treatment and SILAC-based quantitative mass spectrometry with subcellular and protein fractionation. The resulting data set analyzed more than 74,000 peptides, corresponding to similar to 5000 proteins, from nuclear, cytosolic, membrane, and cytoskeletal compartments. These data identified rapidly degraded proteasome targets, such as PRR11 and high-lighted a feedback mechanism resulting in translation inhibition, induced by blocking the proteasome. We show this is mediated by activation of the unfolded protein response. We observed compartment-specific differences in protein degradation, including proteins that would not have been characterized as rapidly degraded through analysis of whole cell lysates. Bioinformatic analysis of the entire data set is presented in the Encyclopedia of Proteome Dynamics, a web-based resource, with proteins annotated for stability and subcellular distribution. Molecular & Cellular Proteomics 12: 10.1074/mcp.M112.024547, 638-650, 2013.

    Original languageEnglish
    Pages (from-to)638-650
    Number of pages13
    JournalMolecular & Cellular Proteomics
    Volume12
    Issue number3
    DOIs
    Publication statusPublished - Mar 2013

    Keywords

    • UBIQUITIN
    • LOCALIZATION
    • AMINO-ACIDS
    • QUANTIFICATION
    • PHOSPHORYLATION
    • STABILITY
    • EXPRESSION
    • TURNOVER
    • PROTEASOME
    • SPECTROMETRY-BASED PROTEOMICS

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