title: Prediction of the plant beta-barrel proteome: a case study of the chloroplast outer envelope.
abstract: In the postgenomic era, the transformation of genetic information into biochemical meaning is required. We have analyzed the proteome of the chloroplast outer envelope membrane by an in silico and a proteomic approach. Based on its evolutionary relation to the outer membrane of Gram-negative bacteria, the outer envelope membrane should contain a large number of beta-barrel proteins. We therefore calculated the probability for the existence of beta-sheet, beta-barrel, and hairpin structures among all proteins of the Arabidopsis thaliana genome. According to the existence of these structures, a number of candidates were selected. This protein pool was analyzed by TargetP to discard sequences with signals that would direct the protein to other organelles different from chloroplasts. In addition, the pool was manually controlled for the presence of proteins known to function outside of the chloroplast envelope. The approach developed here can be used to predict the topology of beta-barrel proteins. For the proteomic approach, proteins of highly purified outer envelope membranes of chloroplasts from Pisum sativum were analyzed by ESI-MS/MS mass spectrometry. In addition to the known components, four new proteins of the outer envelope membranes were identified in this study.
authors.affiliation: Botanisches Institut der Ludwig-Maximilian Universität München, 80368 München, Germany. schleiff@botanik.biologie.uni-muenchen.de
authors.forename: Enrico
authors.initials: E
authors.lastname: Schleiff
authors.forename: Lutz Andreas
authors.initials: LA
authors.lastname: Eichacker
authors.forename: Kerstin
authors.initials: K
authors.lastname: Eckart
authors.forename: Thomas
authors.initials: T
authors.lastname: Becker
authors.forename: Oliver
authors.initials: O
authors.lastname: Mirus
authors.forename: Tanja
authors.initials: T
authors.lastname: Stahl
authors.forename: Jürgen
authors.initials: J
authors.lastname: Soll
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry / Q000502:physiology; D002736:Chloroplasts / Q000737:chemistry / Q000502:physiology*; D019295:Computational Biology; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D020543:Proteome
chemical_list: D020543:Proteome