Multidimensional protein identification technology (Mud(PIT) analysis of ubiquitinated proteins in plants

Rudy Maor, Alex Jones, Thomas S. Nühse, David J. Studholme, Scott C. Peck, Ken Shirasu

    Research output: Contribution to journalArticlepeer-review


    Protein conjugation with ubiquitin, known as ubiquitination, is a key regulatory mechanism to control protein abundance, localization, and activity in eukaryotic cells. To identify ubiquitin-dependent regulatory steps in plants, we developed a robust affinity purification/ identification system for ubiquitinated proteins. Using GST-tagged ubiquitin binding domains, we performed a large scale affinity purification of ubiquitinated proteins from Arabidopsis cell suspension culture. High molecular weight ubiquitinated proteins were separated by SDS-PAGE, and the trypsin-digested samples were then analyzed by a multidimensional protein identification technology (Mud-PIT) system. A total of 294 proteins specifically bound by the GST-tagged ubiquitin binding domains were identified. From these we determined 85 ubiquitinated lysine residues in 56 proteins, confirming the enrichment of the target class of proteins. Our data provide the first view of the ubiquitinated proteome in plants. We also provide evidence that this technique can be broadly applied to the study of protein ubiquitination in diverse plant species © 2007 by The American Society for Biochemistry and Molecular Biology, Inc.
    Original languageEnglish
    Pages (from-to)601-610
    Number of pages9
    JournalMolecular and Cellular Proteomics
    Issue number4
    Publication statusPublished - Apr 2007


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