ArticlePlant physiology2004
Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties.
Article in Plant physiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 71 citations in OpenAlex.
- Genome-Wide Identification of theInternational journal of molecular sciences · 2026Article
- The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.The Plant cell · 2021Article
- Marginal protein stability drives subcellular proteome isoelectric point.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The Plastid and Mitochondrial Peptidase Network inThe Plant cell · 2017Review
- Suppressors of the Chloroplast Protein Import MutantThe Plant cell · 2017Article
- Towards understanding the evolution and functional diversification of DNA-containing plant organelles.F1000Research · 2016Review
- Article
- Metabolic studies in plant organs: don't forget dilution by growth.Frontiers in plant science · 2014Article
- Direct interaction between a precursor mature domain and transport component Tha4 during twin arginine transport of chloroplasts.Plant physiology · 2013Article
- The role of organelle genomes in plant adaptation: time to get to work!Plant signaling & behavior · 2011Review
- Article
- Evidence for the adaptation of protein pH-dependence to subcellular pH.BMC biology · 2009Article
- PPDB, the Plant Proteomics Database at Cornell.Nucleic acids research · 2009Article
- Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis.Plant physiology · 2008Article
- Article
- Chloroplast biogenesis: control of plastid development, protein import, division and inheritance.The arabidopsis book · 2008Article
- Chloroplast envelope membranes: a dynamic interface between plastids and the cytosol.Photosynthesis research · 2007Review
- POGs/PlantRBP: a resource for comparative genomics in plants.Nucleic acids research · 2007Article
- PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization.Genomics, proteomics & bioinformatics · 2006Article
- Synthesis of the sulfur amino acids: cysteine and methionine.Photosynthesis research · 2005Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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).
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