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It's time for some 'site'-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana

Alan Walton (UGent) , Elisabeth Stes (UGent) , Nicolas Cybulski (UGent) , Michiel Van Bel (UGent) , Sabrina Iñigo (UGent) , Astrid Nagels Durand (UGent) , Evy Timmerman (UGent) , Jefri Heyman (UGent) , Laurens Pauwels (UGent) , Lieven De Veylder (UGent) , et al.
(2016) PLANT CELL. 28(1). p.6-16
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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.
Keywords
BOX PROTEIN, GROWTH, UBIQUITYLATION TARGETS, PROTEASOMAL DEGRADATION, E3 LIGASE KEEP, REGULATED GENE-EXPRESSION, TANDEM AFFINITY PURIFICATION, BRASSINOSTEROID SIGNALING PATHWAY, IDENTIFICATION, BIOSYNTHESIS

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Chicago
Walton, Alan, Elisabeth Stes, Nicolas Cybulski, Michiel Van Bel, Sabrina Iñigo, Astrid Nagels Durand, Evy Timmerman, et al. 2016. “It’s Time for Some ‘Site’-seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis Thaliana.” Plant Cell 28 (1): 6–16.
APA
Walton, A., Stes, E., Cybulski, N., Van Bel, M., Iñigo, S., Nagels Durand, A., Timmerman, E., et al. (2016). It’s time for some “site”-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana. PLANT CELL, 28(1), 6–16.
Vancouver
1.
Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Nagels Durand A, et al. It’s time for some “site”-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana. PLANT CELL. 2016;28(1):6–16.
MLA
Walton, Alan, Elisabeth Stes, Nicolas Cybulski, et al. “It’s Time for Some ‘Site’-seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis Thaliana.” PLANT CELL 28.1 (2016): 6–16. Print.
@article{7170071,
  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.},
  author       = {Walton, Alan and Stes, Elisabeth and Cybulski, Nicolas and Van Bel, Michiel and I{\~n}igo, Sabrina and Nagels Durand, Astrid and Timmerman, Evy and Heyman, Jefri and Pauwels, Laurens and De Veylder, Lieven and Goossens, Alain and De Smet, Ive and Coppens, Frederik and Goormachtig, Sofie and Gevaert, Kris},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {BOX PROTEIN,GROWTH,UBIQUITYLATION TARGETS,PROTEASOMAL DEGRADATION,E3 LIGASE KEEP,REGULATED GENE-EXPRESSION,TANDEM AFFINITY PURIFICATION,BRASSINOSTEROID SIGNALING PATHWAY,IDENTIFICATION,BIOSYNTHESIS},
  language     = {eng},
  number       = {1},
  pages        = {6--16},
  title        = {It's time for some 'site'-seeing: novel tools to monitor the ubiquitin landscape in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1105/tpc.15.00878},
  volume       = {28},
  year         = {2016},
}

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