Get access
Advertisement

Unraveling the ubiquitin-regulated signaling networks by mass spectrometry-based proteomics

Authors

  • Teck Yew Low,

    Corresponding author
    1. The Netherlands Proteomics Center, Utrecht, The Netherlands
    • Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    Search for more papers by this author
  • Roberto Magliozzi,

    1. Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
    Search for more papers by this author
  • Daniele Guardavaccaro,

    1. Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
    Search for more papers by this author
  • Albert J. R. Heck

    Corresponding author
    1. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
    • The Netherlands Proteomics Center, Utrecht, The Netherlands
    Search for more papers by this author

  • Colour Online: See the article online to view Figs. 1–4 in colour.

Correspondence: Dr. Teck Yew Low, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

E-mail: t.y.low@uu.nl

Fax: +31-030-253-6919

Additional corresponding author: Professor Albert J. R. Heck,

E-mail: a.j.r.heck@uu.nl

Abstract

Ubiquitin (Ub) is a small protein modifier that is covalently attached to the ε-amino group of lysine residues of protein substrates, generally targeting them for degradation. Due to the emergence of specific anti-diglycine (-GG) antibodies and the improvement in MS, it is now possible to identify more than 10 000 ubiquitylated sites in a single proteomics study. Besides cataloging ubiquitylated sites, it is equally important to unravel the biological relationship between ubiquitylated substrates and the ubiquitin conjugation machinery. Relevant to this, we discuss the role of affinity purification-MS (AP-MS), in characterizing E3 ligase-substrate complexes. Recently, such strategies have also been adapted to screen for binding partners of both deubiquitylating enzymes (DUBs) and ubiquitin-binding domains (UBDs). The complexity of the “ubiquitome” is further expanded by the fact that Ub itself can be ubiquitylated at any of its seven lysine residues forming polyubiquitin (polyUb), thus diversifying its lengths and topologies to suit a variety of molecular recognition processes. Therefore, applying MS to study polyUb linkages is also becoming an emerging and important area. Finally, we discuss the future of MS-based proteomics in answering important questions with respect to ubiquitylation.

Get access to the full text of this article

Ancillary