Publication Information
Nühse et al., 2004
No external accession available
Abstract
Plant Cell. 2004 Sep;16(9):2394-405. doi: 10.1105/tpc.104.023150. Epub 2004 Aug
12.
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation
site database.
Nühse TS(1), Stensballe A, Jensen ON, Peck SC.
Author information:
(1)Sainsbury Laboratory, John Ines Centre, Norwich NR4 7UH, United Kingdom.
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.
DOI: 10.1105/tpc.104.023150
PMCID: PMC520941
PMID: 15308754 [Indexed for MEDLINE]
