Insights into the molecular composition of endogenous unanchored polyubiquitin chains

Joanna Strachan, Lucy Roach, Kleitos Sokratous, David Tooth, Jed Long, Thomas P. Garner, Mark S. Searle, Neil J. Oldham, Robert Layfield

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

The diverse influences of ubiquitin, mediated by its post-translational covalent modification of other proteins, have been extensively investigated. However, more recently roles for unanchored (nonsubstrate linked) polyubiquitin chains have also been proposed. Here we describe the use of ubiquitin-binding domains to affinity purify endogenous unanchored polyubiquitin chains and their subsequent characterization by mass spectrometry (MS). Using the A20 Znf domain of the ubiquitin receptor ZNF216 we isolated a protein from skeletal muscle shown by a combination of nanoLC-MS and LC-MS/MS to represent an unmodified and unanchored K48-linked ubiquitin dimer. Selective purification of unanchored polyubiquitin chains using the Znf UBP (BUZ) domain of USP5/isopeptidase-T allowed the isolation of K48 and K11-linked ubiquitin dimers, as well as revealing longer chains containing as many as 15 ubiquitin moieties, which include the K48 linkage. Top-down nanoLC-MS/MS of the A20 Znf-purified ubiquitin dimer generated diagnostic ions consistent with the presence of the K48 linkage, illustrating for the first time the potential of this approach to probe connectivity within endogenous polyubiquitin modifications. As well as providing initial proteomic insights into the molecular composition of endogenous unanchored polyubiquitin chains, this work also represents the first definition of polyubiquitin chain length in vivo.

Original languageEnglish (US)
Pages (from-to)1969-1980
Number of pages12
JournalJournal of Proteome Research
Volume11
Issue number3
DOIs
StatePublished - Mar 2 2012
Externally publishedYes

Fingerprint

Polyubiquitin
Ubiquitin
Mass spectrometry
Chemical analysis
Dimers
Tandem Mass Spectrometry
Mass Spectrometry
Post Translational Protein Processing
Chain length
Proteomics
Purification
Muscle
Skeletal Muscle
Proteins
Ions

Keywords

  • top-down mass spectrometry
  • ubiquitin
  • unanchored polyubiquitin
  • ZNF216

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Strachan, J., Roach, L., Sokratous, K., Tooth, D., Long, J., Garner, T. P., ... Layfield, R. (2012). Insights into the molecular composition of endogenous unanchored polyubiquitin chains. Journal of Proteome Research, 11(3), 1969-1980. https://doi.org/10.1021/pr201167n

Insights into the molecular composition of endogenous unanchored polyubiquitin chains. / Strachan, Joanna; Roach, Lucy; Sokratous, Kleitos; Tooth, David; Long, Jed; Garner, Thomas P.; Searle, Mark S.; Oldham, Neil J.; Layfield, Robert.

In: Journal of Proteome Research, Vol. 11, No. 3, 02.03.2012, p. 1969-1980.

Research output: Contribution to journalArticle

Strachan, J, Roach, L, Sokratous, K, Tooth, D, Long, J, Garner, TP, Searle, MS, Oldham, NJ & Layfield, R 2012, 'Insights into the molecular composition of endogenous unanchored polyubiquitin chains', Journal of Proteome Research, vol. 11, no. 3, pp. 1969-1980. https://doi.org/10.1021/pr201167n
Strachan, Joanna ; Roach, Lucy ; Sokratous, Kleitos ; Tooth, David ; Long, Jed ; Garner, Thomas P. ; Searle, Mark S. ; Oldham, Neil J. ; Layfield, Robert. / Insights into the molecular composition of endogenous unanchored polyubiquitin chains. In: Journal of Proteome Research. 2012 ; Vol. 11, No. 3. pp. 1969-1980.
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