The protein translocation systems in plants - composition and variability on the example of Solanum lycopersicum

• Published in: BMC genomics 2013-03, Vol.14 (1), p.189-189, Article 189
• Main Authors: Paul, Puneet, Simm, Stefan, Blaumeiser, Andreas, Scharf, Klaus-Dieter, Fragkostefanakis, Sotirios, Mirus, Oliver, Schleiff, Enrico
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis thaliana; Chloroplasts; Computational Biology; Conserved Sequence - genetics; Data mining; Deoxyribonucleic acid; DNA; Evolution, Molecular; Flowers & plants; Gene Expression Regulation, Plant; Genome, Plant; Lycopersicon esculentum; Lycopersicon esculentum - genetics; Lycopersicon esculentum - physiology; Metabolic Networks and Pathways - genetics; Mitochondria; Phylogeny; Physcomitrella patens; Protein Transport - genetics; Proteins; Saccharomyces cerevisiae; Solanum; Species Specificity; Yeast
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-14-189

Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, mitochondria and chloroplasts have been established based on the analysis of model organisms. Today, these results have to be transferred to other plant species. We bioinformatically determined the inventory of putative translocation factors in tomato (Solanum lycopersicum) by orthologue search and domain architecture analyses. In addition, we investigated the diversity of such systems by comparing our findings to the model organisms Saccharomyces cerevisiae, Arabidopsis thaliana and 12 other plant species. The literature search end up in a total of 130 translocation components in yeast and A. thaliana, which are either experimentally confirmed or homologous to experimentally confirmed factors. From our bioinformatic analysis (PGAP and OrthoMCL), we identified (co-)orthologues in plants, which in combination yielded 148 and 143 orthologues in A. thaliana and S. lycopersicum, respectively. Interestingly, we traced 82% overlap in findings from both approaches though we did not find any orthologues for 27% of the factors by either procedure. In turn, 29% of the factors displayed the presence of more than one (co-)orthologue in tomato. Moreover, our analysis revealed that the genomic composition of the translocation machineries in the bryophyte Physcomitrella patens resemble more to higher plants than to single celled green algae. The monocots (Z. mays and O. sativa) follow more or less a similar conservation pattern for encoding the translocon components. In contrast, a diverse pattern was observed in different eudicots. The orthologue search shows in most cases a clear conservation of components of the translocation pathways/machineries. Only the Get-dependent integration of tail-anchored proteins seems to be distinct. Further, the complexity of the translocation pathway in terms of existing orthologues seems to vary among plant species. This might be the consequence of palaeoploidisation during evolution in plants; lineage specific whole genome duplications in Arabidopsis thaliana and triplications in Solanum lycopersicum.