Prediction of the plant β‐barrel proteome: A case study of the chloroplast outer envelope

Schleiff, Enrico; Eichacker, Lutz A.; Eckart, Kerstin; Becker, Thomas; Mirus, Oliver; Stahl, Tanja; Soll, Jürgen

doi:10.1110/ps.0237503

Cited by 107 publications

(148 citation statements)

References 51 publications

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“…The distal C-terminal sequence of nOmp85 (Fig. 1A, distal (D)) contains conserved regions and contributes the last eight membrane-inserted ␤-strands (6,17,18). The C-terminal domain, however, facilitates the transport of sucrose or NaCl (18).…”

Section: Methodsmentioning

confidence: 99%

“…Section 1734 solely to indicate this fact. □ S The on-line version of this article (available at http://www.jbc.org) contains supplemental 6 The abbreviations and trivial names used are: PTB, polypeptide-transporting ␤-barrel channels; Omp85, outer membrane protein of 85 kDa; Sam, sorting and assembly machinery; Tob, component for topogenesis of mitochondrial outer membrane ␤-barrel proteins; Toc, translocon on the outer envelope of chloroplast; pS, picosiemens; Mops, 4-morpholinepropanesulfonic acid. …”

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confidence: 99%

“…One class of these proteins is composed of polypeptide-transporting ␤-barrel (PTB) 6 channels, whose topology was determined by modeling (5)(6)(7). PTBs of recent interest are, e.g.…”

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Functional and Phylogenetic Properties of the Pore-forming β-Barrel Transporters of the Omp85 Family

Bredemeier

Schlegel

Ertel

et al. 2007

Journal of Biological Chemistry

101

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␤-Barrel-shaped channels of the Omp85 family are involved in the translocation or assembly of proteins of bacterial, mitochondrial, and plastidic outer membranes. We have compared these proteins to understand the evolutionary development of the translocators. We have demonstrated that the proteins from proteobacteria and mitochondria have a pore diameter that is at least five times smaller than found for the Omp85 in cyanobacteria and plastids. This finding can explain why Omp85 from cyanobacteria (but not the homologous protein from proteobacteria) was remodeled to become the protein translocation pore after endosymbiosis. Further, the pore-forming region of the Omp85 proteins is restricted to the C terminus. Based on a phylogenetic analysis we have shown that the pore-forming domain displays a different evolutionary relationship than the N-terminal domain. In line with this, the affinity of the N-terminal domain to the C-terminal region of the Omp85 from plastids and cyanobacteria differs, even though the N-terminal domain is involved in gating of the pore in both groups. We have further shown that the N-terminal domain of nOmp85 takes part in homo-oligomerization. Thereby, the differences in the phylogeny of the two domains are explained by different functional constraints acting on the regions. The poreforming domain, however, is further divided into two functional regions, where the distal C terminus itself forms a dimeric pore. Based on functional and phylogenetic analysis, we suggest an evolutionary scenario that explains the origin of the contemporary translocon.Polypeptide transport and assembly of proteins into or across the outer membrane of endosymbiotic organelles or Gram-negative bacteria depend on ␤-barrel-shaped channels (1-4). One class of these proteins is composed of polypeptide-transporting ␤-barrel (PTB) 6 channels, whose topology was determined by modeling (5-7). PTBs of recent interest are, e.g. outer membrane proteins (which secrete adhesins such as hemagglutinin) (8, 9) and bacterial (1, 7, 10 -12), mitochondrial (Tob55/Sam50) (5, 13, 14), and chloroplast outer membrane proteins (Toc75) (15) of the Omp85 family. The PTBs are partitioned into two functional categories, namely in translocation of precursor proteins across the membrane and in the assembly of outer membrane proteins (3). Furthermore, comparison between chloroplastic, mitochondrial, and bacterial Omp85 protein sequences revealed a high similarity of these PTBs (14,16,17).The PTB Toc75 forms a complex with Toc34, Toc64, and Toc159 (3). A precursor protein-binding site at Toc75 (15, 18), together with the action of Toc159 (19), facilitates the translocation of precursor proteins across the membrane. In contrast, the Omp85 proteins from Neisseria meningitidis, Escherichia coli, and mitochondria are involved in the assembly of outer membrane proteins (1,5,7,(11)(12)(13)(14). As found for Toc75, the mitochondrial PTB is a component of a larger complex with Mas37 (20, 13) and Tob38/Sam35 (21,22).Recently, it was demonstrated that t...

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Section: Methodsmentioning

confidence: 99%

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Functional and Phylogenetic Properties of the Pore-forming β-Barrel Transporters of the Omp85 Family

Bredemeier

Schlegel

Ertel

et al. 2007

Journal of Biological Chemistry

101

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“…Relatively small sub-proteomes of the chloroplast have been experimentally identified (Kieselbach et al, 1998;Nakabayashi et al, 1999;Peltier et al, 2000;Ferro et al, 2002;Gomez et al, 2002;Peltier et al, 2002;Schubert et al, 2002;Balmer et al, 2003;Ferro et al, 2003;Schleiff et al, 2003), but a saturating organelle-wide proteomic screen has not yet been performed. Thus, large-scale detection of chloroplast proteins can be attempted only in silico.…”

Section: Introductionmentioning

confidence: 99%

An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

Richly¹,

Leister²

2004

Gene

166

146

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Proteins that form part of the chloroplast proteome can be identified by computational prediction of the N-terminal presequences (chloroplast transit peptides, cTPs) of their cytoplasmic precursor proteins. The accuracy of four different cTP predictors has been evaluated on a test set of 4500 proteins whose subcellular localization is known, and was found to be substantially lower than previously reported. A combination of cTP prediction programs was superior to any one of the predictors alone. This combination was employed to estimate the size and composition of the chloroplast proteomes of Arabidopsis and rice, and about 2,100 (Arabidopsis thaliana) and 4800 (Oryza sativa) different chloroplast proteins with a cTP are predicted to be encoded by their nuclear genomes. A subset of around 900 chloroplast proteins, predominantly derived from the cyanobacterial endosymbiont and with functions mostly related to metabolism, energy and transcription, is shared by the two species. This points to the existence of both conserved nucleus-encoded chloroplast proteins that are predominantly of prokaryotic origin, and a large fraction of taxon-specific chloroplast-targeted proteins, in flowering plants. D

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“…outer membrane ͉ PhoE ͉ protein import ͉ TOB complex ͉ TOM complex M itochondria and chloroplasts contain ␤-barrel proteins in their outer membranes (1)(2)(3). The only other biological membrane known to harbor ␤-barrel proteins is the outer membrane of Gram-negative bacteria (4).…”

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confidence: 99%

Signals in bacterial β-barrel proteins are functional in eukaryotic cells for targeting to and assembly in mitochondria

Walther

Papić

Bos

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

109

127

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The outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts harbor ␤-barrel proteins. The signals that allow precursors of such proteins to be targeted to mitochondria were not characterized so far. To better understand the mechanism by which ␤-barrel precursor proteins are recognized and sorted within eukaryotic cells, we expressed the bacterial ␤-barrel proteins PhoE, OmpA, Omp85, and OmpC in Saccharomyces cerevisiae and demonstrated that they were imported into mitochondria. A detailed investigation of the import pathway of PhoE revealed that it is shared with mitochondrial ␤-barrel proteins. PhoE interacts initially with surface import receptors, and its further sorting depends on components of the TOB/SAM complex. The bacterial Omp85 and PhoE integrated into the mitochondrial outer membrane as nativelike oligomers. For the latter protein this assembly depended on the C-terminal Phe residue, which is important also for the correct assembly of PhoE into the bacterial outer membrane. Collectively, it appears that mitochondrial ␤-barrel proteins have not evolved eukaryotic-specific signals to ensure their import into mitochondria. Furthermore, the signal for assembly of ␤-barrel proteins into the bacterial outer membrane is functional in mitochondria.outer membrane ͉ PhoE ͉ protein import ͉ TOB complex ͉ TOM complex

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Prediction of the plant β‐barrel proteome: A case study of the chloroplast outer envelope

Cited by 107 publications

References 51 publications

Functional and Phylogenetic Properties of the Pore-forming β-Barrel Transporters of the Omp85 Family

Functional and Phylogenetic Properties of the Pore-forming β-Barrel Transporters of the Omp85 Family

An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice

Signals in bacterial β-barrel proteins are functional in eukaryotic cells for targeting to and assembly in mitochondria

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