Publication Information
Walton et al., 2016
Abstract
Plant Cell. 2016 Jan;28(1):6-16. doi: 10.1105/tpc.15.00878. Epub 2016 Jan 7.
It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape
in Arabidopsis thaliana.
Walton A(1), Stes E(1), Cybulski N(2), Van Bel M(2), Iñigo S(2), Durand AN(2),
Timmerman E(3), Heyman J(2), Pauwels L(2), De Veylder L(2), Goossens A(2), De
Smet I(2), Coppens F(2), Goormachtig S(4), Gevaert K(5).
Author information:
(1)Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of
Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of
Biochemistry, Ghent University, 9000 Ghent, Belgium.
(2)Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of
Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
(3)Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium.
(4)Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of
Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
sofie.goormachtig@psb.vib-ugent.be kris.gevaert@vib-ugent.be.
(5)Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
sofie.goormachtig@psb.vib-ugent.be kris.gevaert@vib-ugent.be.
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to
a target protein, is an important and frequently studied posttranslational
protein modification. Multiple reports provide useful insights into the plant
ubiquitinome, but mostly at the protein level without comprehensive site
identification. Here, we implemented ubiquitin combined fractional diagonal
chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on
Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins,
thereby greatly increasing the number of known ubiquitination sites in this
model plant. Finally, The Ubiquitination Site tool
(http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to
the obtained ubiquitination sites, not only to consult the ubiquitination status
of a given protein, but also to conduct intricate experiments aiming to study
the roles of specific ubiquitination events. Together with the antibodies
recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a
powerful tool to resolve the ubiquitination maps of numerous cellular processes
in plants.
© 2016 American Society of Plant Biologists. All rights reserved.
DOI: 10.1105/tpc.15.00878
PMCID: PMC4746685
PMID: 26744219 [Indexed for MEDLINE]
