The complexity of vesicle transport factors in plants examined by orthology search.
Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-)orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-)orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-)orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-)orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527) of the (co-)orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-)orthologues found in A. thaliana and S. lycopersicum suggest that some (co-)orthologues are involved in tissue-specific functions. Inspection of localization of the (co-)orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-)orthologues of vesicle transport factors and the relevance of this is discussed.
Department of Biosciences Molecular Cell Biology of Plants.
Puneet
P
Paul
Department of Biosciences Molecular Cell Biology of Plants.
Stefan
S
Simm
Department of Biosciences Molecular Cell Biology of Plants.
Oliver
O
Mirus
Department of Biosciences Molecular Cell Biology of Plants.
Klaus-Dieter
KD
Scharf
Department of Biosciences Molecular Cell Biology of Plants.
Sotirios
S
Fragkostefanakis
Department of Biosciences Molecular Cell Biology of Plants; Cluster of Excellence Frankfurt; Center of Membrane Proteomics; Goethe University Frankfurt, Frankfurt/Main, Germany.
Enrico
E
Schleiff
D001692:Biological Transport; D018699:Coated Vesicles / Q000502:physiology; D019295:Computational Biology; D016208:Databases, Factual; D056827:Endosomal Sorting Complexes Required for Transport / Q000378:metabolism; D018521:Plant Physiological Phenomena; D050600:SNARE Proteins / Q000378:metabolism; D022161:Transport Vesicles / Q000502:physiology*; D020691:rab GTP-Binding Proteins / Q000378:metabolism
D056827:Endosomal Sorting Complexes Required for Transport; D050600:SNARE Proteins; D020691:rab GTP-Binding Proteins