title: It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana.
abstract: 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.
authors.affiliation: 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.
authors.forename: Alan
authors.initials: A
authors.lastname: Walton
authors.affiliation: 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.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Stes
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Cybulski
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Bel
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Sabrina
authors.identifier: http://orcid.org/0000-0001-5820-7109
authors.initials: S
authors.lastname: Iñigo
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Astrid Nagels
authors.initials: AN
authors.lastname: Durand
authors.affiliation: Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.
authors.forename: Evy
authors.initials: E
authors.lastname: Timmerman
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Jefri
authors.initials: J
authors.lastname: Heyman
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Laurens
authors.initials: L
authors.lastname: Pauwels
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Lieven
authors.initials: L
authors.lastname: De Veylder
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Alain
authors.identifier: http://orcid.org/0000-0002-1599-551X
authors.initials: A
authors.lastname: Goossens
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Ive
authors.identifier: http://orcid.org/0000-0003-4607-8893
authors.initials: I
authors.lastname: De Smet
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Frederik
authors.identifier: http://orcid.org/0000-0001-6565-5145
authors.initials: F
authors.lastname: Coppens
authors.affiliation: 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.
authors.forename: Sofie
authors.identifier: http://orcid.org/0000-0001-6195-9889
authors.initials: S
authors.lastname: Goormachtig
authors.affiliation: 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.
authors.forename: Kris
authors.identifier: http://orcid.org/0000-0002-4237-0283
authors.initials: K
authors.lastname: Gevaert
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D025801:Ubiquitin