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Submitted on June 10, 2005
Plant Biology, Cornell University, Ithaca, NY 14853
Corresponding Author: kv35{at}cornell.edu
This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of A. thaliana. 241 proteins (88% with predicted cTP), mostly assembled in oligomeric complexes, were identified by mass spectrometry with emphasis on distinguishing between paralogues. This is critical since different paralogues in a gene family often have different subcellular localizations and/or different expression patterns and functions. The native protein masses were determined for all identified proteins. Comparison with the few well-characterized stroma complexes from A. thaliana confirmed the accuracy of the native mass determination and, by extension, the usefulness of the native mass data for future in-depth protein interaction studies. Resolved protein interactions are discussed and compared with an extensive collection of native mass data of orthologues in other plants and bacteria. Relative protein expression levels were estimated from spot intensities and also provided estimates of relative concentrations of individual proteins. No such quantification has been reported so far. Surprisingly, proteins dedicated to chloroplast protein synthesis, biogenesis and fate represented nearly 10% of the total stroma protein mass. OPPP, glycolysis, Calvin cycle represented together about 75%, nitrogen assimilation 5-7% and all other pathways such as biosynthesis of e.g. fatty acids, amino acids, nucleotides, tetrapyrroles, vitamins B1 and B2, each less than 1% of total protein mass. Several proteins with diverse functions outside primary carbon metabolism, such the isomerase Roc4, lipoxygenase 2 (Lox2) involved in JA biosynthesis and a carbonic anhydrase (CA1), were surprisingly abundant, in the range of 0.75-1.5% of the total stromal mass. Native images with associated information are available via the Plastid Proteome Database, PPDB, at http://ppdb.tc.cornell.edu.
Revised on October 3, 2005
Accepted on October 4, 2005
The oligomeric stromal proteome of A. thaliana chloroplasts
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