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PMID: 15308754 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database.

The Plant cell ·Vol. 16 ·No. 9 ·2004-09-00 ·Pages 2394-405

Nühse TS, Stensballe A, Jensen ON, Peck SC

Abstract

Functional genomic technologies are generating vast amounts of data describing the presence of transcripts or proteins in plant cells. Together with classical genetics, these approaches broaden our understanding of the gene products required for specific responses. Looking to the future, the focus of research must shift to the dynamic aspects of biology: molecular mechanisms of function and regulation. Phosphorylation is a key regulatory factor in all aspects of plant biology; but it is difficult, if not impossible, for most researchers to identify in vivo phosphorylation sites within their proteins of interest. We have developed a large-scale strategy for the isolation of phosphopeptides and identification by mass spectrometry (Nühse et al., 2003b). Here, we describe the identification of more than 300 phosphorylation sites from Arabidopsis thaliana plasma membrane proteins. These data will be a valuable resource for many fields of plant biology and overcome a major impediment to the elucidation of signal transduction pathways. We present an analysis of the characteristics of phosphorylation sites, their conservation among orthologs and paralogs, and the existence of putative motifs surrounding the sites. These analyses yield general principles for predicting other phosphorylation sites in plants and provide indications of specificity determinants for responsible kinases. In addition, more than 50 sites were mapped on receptor-like kinases and revealed an unexpected complexity of regulation. Finally, the data also provide empirical evidence on the topology of transmembrane proteins. This information indicates that prediction programs incorrectly identified the cytosolic portion of the protein in 25% of the transmembrane proteins found in this study. All data are deposited in a new searchable database for plant phosphorylation sites maintained by PlantsP (http://plantsp.sdsc.edu) that will be updated as the project expands to encompass additional tissues and organelles.

MeSH Terms
Amino Acid Motifs/genetics Amino Acid Sequence Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Binding Sites/genetics Cytosol/metabolism Databases, Protein Gene Expression Regulation, Plant/genetics Membrane Proteins/genetics,metabolism Molecular Sequence Data Phosphoproteins/genetics,metabolism Phosphorylation Phosphotransferases/metabolism Phylogeny Protein Conformation Protein Structure, Tertiary/genetics Proteome/genetics,metabolism Proteomics/methods Sequence Homology, Amino Acid Species Specificity
Chemicals
Arabidopsis Proteins Membrane Proteins Phosphoproteins Proteome Phosphotransferases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Nühse Thomas S
Sainsbury Laboratory, John Ines Centre, Norwich NR4 7UH, United Kingdom.
Stensballe Allan
Jensen Ole N
Peck Scott C
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.104.023150
Published
2004-09-00
Epub
2004-00-12
Pages
2394-405
Language
English
Region
England
NLM ID
9208688
PMCID
PMC520941
Subset
IM
Databases
GENBANK
AF150630, AF200525, AF200526, AF200528, AF200529, AF200533, AK098978, AV408250, BE577626, BE609663, BE660209, BF634138, BG273410, BG465505, BJ553825, BQ104792, BQ139762, BQ471177, BQ510147, BQ578769, BQ591881, BQ802778, BQ869850, BT009438, BU879114, CA924192, CB676883, CD005820, CD837398, D48636
External Links
PubMed source DOI: 10.1105/tpc.104.023150 PMC Full Text View journal details
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