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PMID: 10715320 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins.

The Plant cell ·Vol. 12 ·No. 3 ·2000-03-00 ·Pages 319-41

Peltier JB, Friso G, Kalume DE, Roepstorff P, Nilsson F, Adamska I, van Wijk KJ

Abstract

The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching. After correcting to eliminate possible isoforms and post-translational modifications, we estimated that there are at least 200 to 230 different lumenal and peripheral proteins. Sixty-one proteins were identified; for 33 of these proteins, a clear function or functional domain could be identified, whereas for 10 proteins, no function could be assigned. For 18 proteins, no expressed sequence tag or full-length gene could be identified in the databases, despite experimental determination of a significant amount of amino acid sequence. Nine previously unidentified proteins with lumenal transit peptides are presented along with their full-length genes; seven of these proteins possess the twin arginine motif that is characteristic for substrates of the TAT pathway. Logoplots were used to provide a detailed analysis of the lumenal targeting signals, and all nuclear-encoded proteins identified on the two-dimensional gels were used to test predictions for chloroplast localization and transit peptides made by the software programs ChloroP, PSORT, and SignalP. A combination of these three programs was found to provide a useful tool for evaluating chloroplast localization and transit peptides and also could reveal possible alternative processing sites and dual targeting. The potential of proteomics for plant biology and homology-based searching with mass spectrometry data is discussed.

MeSH Terms
Amino Acid Sequence Chloroplasts/genetics,metabolism Databases, Factual Electron Transport Electrophoresis, Gel, Two-Dimensional Expressed Sequence Tags Gas Chromatography-Mass Spectrometry/methods Gene Expression Regulation, Plant Immunoblotting Molecular Sequence Data Peas/chemistry,genetics Photosynthetic Reaction Center Complex Proteins/analysis,genetics,isolation & purification Plant Proteins/analysis,genetics,isolation & purification Reproducibility of Results Sequence Analysis, Protein Software Thylakoids/metabolism
Chemicals
Photosynthetic Reaction Center Complex Proteins Plant Proteins
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Peltier J B
Department of Biochemistry, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden.
Friso G
Kalume D E
Roepstorff P
Nilsson F
Adamska I
van Wijk K J
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.12.3.319
Published
2000-03-00
Pages
319-41
Language
English
Region
England
NLM ID
9208688
PMCID
PMC139834
Subset
IM
Corrections
CommentIn
PMID: 10715314
External Links
PubMed source DOI: 10.1105/tpc.12.3.319 PMC Full Text View journal details
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