Dataset Information

Large scale site-specific mapping of the Arabidopsis ubiquitinome

ABSTRACT: Post-translational modification of amino acids changes the properties of a protein and increases the functional diversity of the proteome. For example, protein ubiquitination influences almost all cellular processes and can remodel the proteome in a matter of minutes. However, mostly due to technical limitations, global profiling of the plant ubiquitinome and proteome-wide identification of specific ubiquitinated residues remains challenging. Here, we made use of the COFRADIC technology to map ubiquitination sites in Arabidopsis thaliana. Across two biological replicates, we identified a total of 3,009 ubiquitination sites in 1,607 proteins. Our data increases the number of reported ubiquitin conjugation sites in Arabidopsis by a factor of 10. It contains well-known ubiquitination targets, including cell cycle proteins and key transcriptional regulators of phytohormone signaling as well as yet unreported targets, such as the Glutaredoxin S17 for which we provide here evidence of proteasomal degradation Finally, we could detect N-terminal ubiquitin conjugation on 19 proteins, a less commonly described type of protein modification.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Cell Culture

SUBMITTER: Alan Walton

LAB HEAD: Kris Gevaert

PROVIDER: PXD002297 | Pride | 2016-08-08

REPOSITORIES: Pride

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Publications

It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana.

Walton Alan A Stes Elisabeth E Cybulski Nicolas N Van Bel Michiel M Iñigo Sabrina S Durand Astrid Nagels AN Timmerman Evy E Heyman Jefri J Pauwels Laurens L De Veylder Lieven L Goossens Alain A De Smet Ive I Coppens Frederik F Goormachtig Sofie S Gevaert Kris K

The Plant cell 20160107 1

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 iden ...[more]

PMID: 26744219

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Project description:Aiming at the development of a micropollutant biosensor in the frame of the Micro-Ecological Life Support System Alternative (MELiSSA), a pilot study was initiated to identify triclosan (TCS)-responsive biomarker genes in the MELiSSA carbon-mineralizing microorganism, Rhodospirillum rubrum S1H. TCS is a biocide, commonly found in human excrements and is considered an emerging pollutant in wastewater and the environment. Chronic exposure to MELiSSA-relevant concentrations (≥25 µg L-1) TCS caused a significant extension of the lag phase without affecting the growth rate. Analytical determination gave no indication of TCS biodegradation during the growth experiment and flow cytometric viability analyses revealed that TCS is only slightly toxic to R. rubrum. Through microarray analyses, the genetic mechanisms supporting the reversibility of TCS-induced inhibition were scrutinized. Hence, an extremely TCS-responsive cluster of four small adjacent genes was revealed, with up to 34-fold induction at 25 µg L-1. These four genes, for which the name micropollutant-upregulated factor (muf) was proposed; appear to be unique to R. rubrum and are shown for the first time to be involved in the response to stress. Moreover, numerous other systems that are associated with the proton-motive force were shown to be responsive to TCS, but never as highly upregulated as the muf genes. Hence, R. rubrum induced the phage shock protein operon (pspABC), numerous major facilitator efflux systems, cell envelope consolidation mechanisms, oxidative stress response, beta-oxidation, and carbonic anhydrase; while downregulating bacterial conjugation- and carboxysome synthesis genes. The muf genes and three efflux-related genes showed most potential as low-dose biomarkers. The two microarray experiments (10 and 25 µg l-1 Triclosan) were all performed in biological triplicate and containing three (in-slide) technical repeats. For all conditions, the Triclosan exposed sample (Cy5) was compared with the non-exposed solvent control (Cy3) to identify those genes that were differentially expressed upon Triclosan exposure.

Dataset Information

Large scale site-specific mapping of the Arabidopsis ubiquitinome

Publications

It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana.

Similar Datasets

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