Publication Information
Meyer et al., 2012
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Abstract
Plant Physiol. 2012 May;159(1):517-28. doi: 10.1104/pp.111.191700. Epub 2012 Mar
22.
Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and
soybean.
Meyer LJ(1), Gao J, Xu D, Thelen JJ.
Author information:
(1)Department of Biochemistry, Christopher S. Bond Life Sciences Center,
Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211,
USA.
To characterize protein phosphorylation in developing seed, a large-scale, mass
spectrometry-based phosphoproteomic study was performed on whole seeds at five
sequential stages of development in soybean (Glycine max), rapeseed (Brassica
napus), and Arabidopsis (Arabidopsis thaliana). Phosphopeptides were enriched
from 0.5 mg of total peptides using a combined strategy of immobilized metal
affinity and metal oxide affinity chromatography. Enriched phosphopeptides were
analyzed by Orbitrap tandem mass spectrometry and mass spectra mined against
cognate genome or cDNA databases in both forward and randomized orientations,
the latter to calculate false discovery rate. We identified a total of 2,001
phosphopeptides containing 1,026 unambiguous phosphorylation sites from 956
proteins, with an average false discovery rate of 0.78% for the entire study.
The entire data set was uploaded into the Plant Protein Phosphorylation Database
(www.p3db.org), including all meta-data and annotated spectra. The Plant Protein
Phosphorylation Database is a portal for all plant phosphorylation data and
allows for homology-based querying of experimentally determined phosphosites.
Comparisons with other large-scale phosphoproteomic studies determined that 652
of the phosphoproteins are novel to this study. The unique proteins fall into
several Gene Ontology categories, some of which are overrepresented in our study
as well as other large-scale phosphoproteomic studies, including metabolic
process and RNA binding; other categories are only overrepresented in our study,
like embryonic development. This investigation shows the importance of analyzing
multiple plants and plant organs to comprehensively map the complete plant
phosphoproteome.
DOI: 10.1104/pp.111.191700
PMCID: PMC3375983
PMID: 22440515 [Indexed for MEDLINE]
