Cargando…

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 protein...

Descripción completa

Detalles Bibliográficos
Autores principales: Paul, Puneet, Simm, Stefan, Mirus, Oliver, Scharf, Klaus-Dieter, Fragkostefanakis, Sotirios, Schleiff, Enrico
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028247/
https://www.ncbi.nlm.nih.gov/pubmed/24844592
http://dx.doi.org/10.1371/journal.pone.0097745
_version_ 1782317051804647424
author Paul, Puneet
Simm, Stefan
Mirus, Oliver
Scharf, Klaus-Dieter
Fragkostefanakis, Sotirios
Schleiff, Enrico
author_facet Paul, Puneet
Simm, Stefan
Mirus, Oliver
Scharf, Klaus-Dieter
Fragkostefanakis, Sotirios
Schleiff, Enrico
author_sort Paul, Puneet
collection PubMed
description 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.
format Online
Article
Text
id pubmed-4028247
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-40282472014-05-21 The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search Paul, Puneet Simm, Stefan Mirus, Oliver Scharf, Klaus-Dieter Fragkostefanakis, Sotirios Schleiff, Enrico PLoS One Research Article 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. Public Library of Science 2014-05-20 /pmc/articles/PMC4028247/ /pubmed/24844592 http://dx.doi.org/10.1371/journal.pone.0097745 Text en © 2014 Paul et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Paul, Puneet
Simm, Stefan
Mirus, Oliver
Scharf, Klaus-Dieter
Fragkostefanakis, Sotirios
Schleiff, Enrico
The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title_full The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title_fullStr The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title_full_unstemmed The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title_short The Complexity of Vesicle Transport Factors in Plants Examined by Orthology Search
title_sort complexity of vesicle transport factors in plants examined by orthology search
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028247/
https://www.ncbi.nlm.nih.gov/pubmed/24844592
http://dx.doi.org/10.1371/journal.pone.0097745
work_keys_str_mv AT paulpuneet thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT simmstefan thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT mirusoliver thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT scharfklausdieter thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT fragkostefanakissotirios thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT schleiffenrico thecomplexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT paulpuneet complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT simmstefan complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT mirusoliver complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT scharfklausdieter complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT fragkostefanakissotirios complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch
AT schleiffenrico complexityofvesicletransportfactorsinplantsexaminedbyorthologysearch