Open Access Research article

Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism

Johan-Owen De Craene1, Raymond Ripp2, Odile Lecompte2, Julie D Thompson2, Olivier Poch2* and Sylvie Friant1*

Author Affiliations

1 Department of Molecular and Cellular Genetics, UMR7156 CNRS/Université de Strasbourg, 21 rue Descartes, 67084, Strasbourg, France

2 Integrative Bioinformatics and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMC (CNRS/INSERM/UdS), 1 rue Laurent Fries, 67404, Illkirch, France

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BMC Genomics 2012, 13:297  doi:10.1186/1471-2164-13-297

Published: 2 July 2012

Additional files

Additional file 1:

Figure S1. Phylogeny of the proteins with a GAT domain. The sequence of most proteins with a GAT domain were analyzed, excluding sequences CAF91904 and CAF95287 from Tetraodon nigroviridis, NP_973770 and NP_850834 from Arabidopsis thaliana and EDM05672 from Rattus norvegicus due to bad predictions. The phylogenetic tree was calculated using SeaView by parsimony with 500 bootstrapped replications [57]. The tree display was performed by iTOL and the tree re-rooted at the base of the TOM branch [58]. (*) denotes wrongly attributed taxa for NP_00112339 (TOMl1 X. tropicalis) in GGA and NP_572571 (GGA D. melanogaster) in Fungi GGA.

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Additional file 2:

Figure S2. Aligment of the VHS domains of GGA and TOM proteins. (A) The sequences of the VHS domain of Metazoa, Fungi, Plantae and Prostists GGA were aligned and the secondary structure of human GGA1 is shown above the sequence alignment (PDB ID code 1JWF). (B) The sequences of the VHS domain of Metazoa TOM were aligned and the secondary structure of human TOM1 is shown above the sequence alignment (PDB ID code 1ELK). Arrows indicate features specific to the TOM family. ESPript website was used for displaying purposes [60].

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Additional file 3:

Figure S3. List of Opisthokonta specific proteins identified by the 4 way comparative genomic analysis. Among the 320 proteins specific to H. sapiens and S. cerevisiae that were found by comparative genomic analysis, 245 proteins were confirmed and kept for further GO Term Enrichment analysis and 75 proteins were rejected. To identify the biological processes in which these 245 confirmed proteins were involved, we used the S. cerevisiae Gene Ontology (GO) annotation database and we also manually searched the SGD (Saccharomyces Genome Database) database. We highlighted the proteins involved in membrane trafficking (in red), in cytokinesis (in yellow), in metabolism (in chartreuse green), in trafficking and cytokinesis (in orange), in trafficking and metabolism (in khaki green), in metabolism and cytokinesis (in light green) and in the three processes in black. The proteins that did not belong to any of these catagories were highlighted in grey for the proteins involved in other biological processes and not highlighted proteins are of unknown function.

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Additional file 4:

Figure S4. GO Term Enrichment of Opisthokonta proteins. The complete analysis of the yeast S. cerevisiae GO Term Enrichment analysis for cellular processes is shown. The categories with a P-value inferior to 10-3 and comprising more than 3 proteins were retained. Biological processes involved in metabolism are highlighted in green, trafficking in red and cytokinesis in yellow.

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Additional file 5:

Figure S5. GO Term Enrichment of yeast-plant and yeast-protist proteins.The complete analysis of the yeast S. cerevisiae GO Term Enrichment analysis for cellular processes is shown, only categories with a P-value inferior to 10-3 and comprising more than 3 proteins were retained. (A) Proteins common to S. cerevisiae and A. thaliana are all involved in metabolism (mainly in amino-acids and some vitamins biosynthesis pathways) and highlighted in green. (B) Proteins common to S. cerevisiae and E. histolytica are involved in the chitin metabolism. Chitin is a major component of the yeast cell wall and of the Entamoeba cyst wall. (PDF 426 kb)

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