DOI: 10.1104/pp.104.040717. Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties

Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties

10.1104/pp.104.040717

Crossref journal-article

Oxford University Press (OUP)

Plant Physiology (286)

Abstract

Abstract 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).

Bibliography

Sun, Q., Emanuelsson, O., & van Wijk, K. J. (2004). Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties Â . Plant Physiology, 135(2), 723â734.

Authors 3

Qi Sun (first)
Olof Emanuelsson (additional)
Klaas J. van Wijk (additional)

References 48 Referenced 62

Dates

Type	When
Created	21 years, 2 months ago (June 18, 2004, 6:33 p.m.)
Deposited	4 years, 2 months ago (June 27, 2021, 7:24 a.m.)
Indexed	1 year, 2 months ago (June 6, 2024, 6:37 p.m.)
Issued	21 years, 3 months ago (June 1, 2004)
Published	21 years, 3 months ago (June 1, 2004)
Published Online	21 years, 2 months ago (June 18, 2004)
Published Print	21 years, 3 months ago (June 1, 2004)

Funders 0

None

BibTeX

@article{Sun_2004, title={Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties }, volume={135}, ISSN={0032-0889}, url={http://dx.doi.org/10.1104/pp.104.040717}, DOI={10.1104/pp.104.040717}, number={2}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Sun, Qi and Emanuelsson, Olof and van Wijk, Klaas J.}, year={2004}, month=jun, pages={723–734} }

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