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Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves

Lam Dai Vu (UGent) , Elisabeth Stes (UGent) , Michiel Van Bel (UGent) , Hilde Nelissen (UGent) , Davy Maddelein (UGent) , Dirk Inzé (UGent) , Frederik Coppens (UGent) , Lennart Martens (UGent) , Kris Gevaert (UGent) and Ive De Smet (UGent)
(2016) JOURNAL OF PROTEOME RESEARCH. 15(12). p.4304-4317
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Protein phosphorylation is one of the most common post-translational modifications (PTMs), which can regulate protein activity and localization as well as proteinprotein interactions in numerous cellular processes. Phosphopeptide enrichment techniques enable plant researchers to acquire insight into phosphorylation-controlled signaling networks in various plant species. Most phosphoproteome analyses of plant samples still involve stable isotope labeling, peptide fractionation, and demand a lot of mass spectrometry (MS) time. Here, we present a simple workflow to probe, map, and catalogue plant phosphoproteomes, requiring relatively low amounts of starting material, no labeling, no fractionation, and no excessive analysis time. Following optimization of the different experimental steps on Arabidopsis thaliana samples, we transferred our workflow to maize, a major monocot crop, to study signaling upon drought stress. In addition, we included normalization to protein abundance to identify true phosphorylation changes. Overall, we identified a set of new phosphosites in both Arabidopsis thaliana and maize, some of which are differentially phosphorylated upon drought. All data are available via ProteomeXchange with identifier PXD003634, but to provide easy access to our model plant and crop data sets, we created an online database, Plant PTM Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), where all phosphosites identified in our study can be consulted.
Keywords
phosphoproteomics, maize, Arabidopsis, drought stress, database, ABIOTIC STRESS, QUANTITATIVE PHOSPHOPROTEOMICS, ARABIDOPSIS-THALIANA, PROTEIN-PHOSPHORYLATION, AFFINITY-CHROMATOGRAPHY, SIGNALING PATHWAYS, DEFENSE-MECHANISMS, SEEDLING LEAVES, OSMOTIC-STRESS, ABSCISIC-ACID

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Chicago
Vu, Lam Dai, Elisabeth Stes, Michiel Van Bel, Hilde Nelissen, Davy Maddelein, Dirk Inzé, Frederik Coppens, Lennart Martens, Kris Gevaert, and Ive De Smet. 2016. “Up-to-date Workflow for Plant (phospho)proteomics Identifies Differential Drought-responsive Phosphorylation Events in Maize Leaves.” Journal of Proteome Research 15 (12): 4304–4317.
APA
Vu, L. D., Stes, E., Van Bel, M., Nelissen, H., Maddelein, D., Inzé, D., Coppens, F., et al. (2016). Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves. JOURNAL OF PROTEOME RESEARCH, 15(12), 4304–4317.
Vancouver
1.
Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, et al. Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves. JOURNAL OF PROTEOME RESEARCH. 2016;15(12):4304–17.
MLA
Vu, Lam Dai, Elisabeth Stes, Michiel Van Bel, et al. “Up-to-date Workflow for Plant (phospho)proteomics Identifies Differential Drought-responsive Phosphorylation Events in Maize Leaves.” JOURNAL OF PROTEOME RESEARCH 15.12 (2016): 4304–4317. Print.
@article{8503091,
  abstract     = {Protein phosphorylation is one of the most common post-translational modifications (PTMs), which can regulate protein activity and localization as well as proteinprotein interactions in numerous cellular processes. Phosphopeptide enrichment techniques enable plant researchers to acquire insight into phosphorylation-controlled signaling networks in various plant species. Most phosphoproteome analyses of plant samples still involve stable isotope labeling, peptide fractionation, and demand a lot of mass spectrometry (MS) time. Here, we present a simple workflow to probe, map, and catalogue plant phosphoproteomes, requiring relatively low amounts of starting material, no labeling, no fractionation, and no excessive analysis time. Following optimization of the different experimental steps on Arabidopsis thaliana samples, we transferred our workflow to maize, a major monocot crop, to study signaling upon drought stress. In addition, we included normalization to protein abundance to identify true phosphorylation changes. Overall, we identified a set of new phosphosites in both Arabidopsis thaliana and maize, some of which are differentially phosphorylated upon drought. All data are available via ProteomeXchange with identifier PXD003634, but to provide easy access to our model plant and crop data sets, we created an online database, Plant PTM Viewer (bioinformatics.psb.ugent.be/webtools/ptm\_viewer/), where all phosphosites identified in our study can be consulted.},
  author       = {Vu, Lam Dai and Stes, Elisabeth and Van Bel, Michiel and Nelissen, Hilde and Maddelein, Davy and Inz{\'e}, Dirk and Coppens, Frederik and Martens, Lennart and Gevaert, Kris and De Smet, Ive},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {phosphoproteomics,maize,Arabidopsis,drought stress,database,ABIOTIC STRESS,QUANTITATIVE PHOSPHOPROTEOMICS,ARABIDOPSIS-THALIANA,PROTEIN-PHOSPHORYLATION,AFFINITY-CHROMATOGRAPHY,SIGNALING PATHWAYS,DEFENSE-MECHANISMS,SEEDLING LEAVES,OSMOTIC-STRESS,ABSCISIC-ACID},
  language     = {eng},
  number       = {12},
  pages        = {4304--4317},
  title        = {Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.6b00348},
  volume       = {15},
  year         = {2016},
}

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