Plant Physiology 135:723-734 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties1,[w]
Qi Sun,
Olof Emanuelsson2 and
Klaas J. van Wijk*
Computational Biology Service Unit, Cornell Theory Center (Q.S.) and Department of Plant Biology (K.J.v.W.), Cornell University, Ithaca, New York; and Stockholm Bioinformatics Center, Stockholm University, SE–10691 Stockholm, Sweden (O.E.)
Carefully curated proteomes of the inner envelope membrane, the thylakoid membrane, and the thylakoid lumen of chloroplasts from Arabidopsis were assembled based on published, well-documented localizations. These curated proteomes were evaluated for distribution of physical-chemical parameters, with the goal of extracting parameters for improved subcellular prediction and subsequent identification of additional (low abundant) components of each membrane system. The assembly of rigorously curated subcellular proteomes is in itself also important as a parts list for plant and systems biology. Transmembrane and subcellular prediction strategies were evaluated using the curated data sets. The three curated proteomes differ strongly in average isoelectric point and protein size, as well as transmembrane distribution. Removal of the cleavable, N-terminal transit peptide sequences greatly affected isoelectric point and size distribution. Unexpectedly, the Cys content was much lower for the thylakoid proteomes than for the inner envelope. This likely relates to the role of the thylakoid membrane in light-driven electron transport and helps to avoid unwanted oxidation-reduction reactions. A rule of thumb for discriminating between the predicted integral inner envelope membrane and integral thylakoid membrane proteins is suggested. Using a combination of predictors and experimentally derived parameters, four plastid subproteomes were predicted from the fully annotated Arabidopsis genome. These predicted subproteomes were analyzed for their properties and compared to the curated proteomes. The sensitivity and accuracy of the prediction strategies are discussed. Data can be extracted from the new plastid proteome database (http://ppdb.tc.cornell.edu).
1 This work was supported by the National Science Foundation (MCB no. 0090942) and NYSTAR (grant to K.J.v.W.). All large-scale data collection at Cornell was conducted using the resources of the Cornell Theory Center, which receives funding from Cornell University, New York State, federal agencies, foundations, and corporate partners.
2 Present address: Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520.
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.040717.
* Corresponding author; email kv35{at}cornell.edu; fax 607–255–7979.
Received February 13, 2004;
returned for revision March 25, 2004;
accepted April 14, 2004.
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