title: Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction.
abstract: Experimental proteome analysis was combined with a genome-wide prediction screen to characterize the protein content of the thylakoid lumen of Arabidopsis chloroplasts. Soluble thylakoid proteins were separated by two-dimensional electrophoresis and identified by mass spectrometry. The identities of 81 proteins were established, and N termini were sequenced to validate localization prediction. Gene annotation of the identified proteins was corrected by experimental data, and an interesting case of alternative splicing was discovered. Expression of a surprising number of paralogs was detected. Expression of five isomerases of different classes suggests strong (un)folding activity in the thylakoid lumen. These isomerases possibly are connected to a network of peripheral and lumenal proteins involved in antioxidative response, including peroxiredoxins, m-type thioredoxins, and a lumenal ascorbate peroxidase. Characteristics of the experimentally identified lumenal proteins and their orthologs were used for a genome-wide prediction of the lumenal proteome. Lumenal proteins with a typical twin-arginine translocation motif were predicted with good accuracy and sensitivity and included additional isomerases and proteases. Thus, prime functions of the lumenal proteome include assistance in the folding and proteolysis of thylakoid proteins as well as protection against oxidative stress. Many of the predicted lumenal proteins must be present at concentrations at least 10,000-fold lower than proteins of the photosynthetic apparatus.
authors.affiliation: Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
authors.forename: Jean-Benoît
authors.initials: JB
authors.lastname: Peltier
authors.forename: Olof
authors.initials: O
authors.lastname: Emanuelsson
authors.forename: Dário E
authors.initials: DE
authors.lastname: Kalume
authors.forename: Jimmy
authors.initials: J
authors.lastname: Ytterberg
authors.forename: Giulia
authors.initials: G
authors.lastname: Friso
authors.forename: Andrea
authors.initials: A
authors.lastname: Rudella
authors.forename: David A
authors.initials: DA
authors.lastname: Liberles
authors.forename: Linda
authors.initials: L
authors.lastname: Söderberg
authors.forename: Peter
authors.initials: P
authors.lastname: Roepstorff
authors.forename: Gunnar
authors.initials: G
authors.lastname: von Heijne
authors.forename: Klaas J
authors.initials: KJ
authors.lastname: van Wijk
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D060387:Ascorbate Peroxidases; D015180:Electrophoresis, Gel, Two-Dimensional; D010450:Endopeptidases / Q000235:genetics / Q000378:metabolism; D020224:Expressed Sequence Tags; D015870:Gene Expression / Q000235:genetics; D018745:Genome, Plant; D007526:Isoelectric Point; D007535:Isomerases / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010544:Peroxidases / Q000235:genetics / Q000378:metabolism; D054464:Peroxiredoxins; D045322:Photosynthetic Reaction Center Complex Proteins / Q000235:genetics / Q000378:metabolism; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013879:Thioredoxins / Q000235:genetics / Q000378:metabolism; D020524:Thylakoids / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D045322:Photosynthetic Reaction Center Complex Proteins; D020033:Protein Isoforms; D020543:Proteome; D013879:Thioredoxins; D010544:Peroxidases; D060387:Ascorbate Peroxidases; D054464:Peroxiredoxins; D010450:Endopeptidases; D007535:Isomerases