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Open Access Research article

Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes

Ryoma Kamikawa12*, Matthew W Brown3, Yuki Nishimura4, Yoshihiko Sako5, Aaron A Heiss6, Naoji Yubuki7, Ryan Gawryluk3, Alastair GB Simpson6, Andrew J Roger3, Tetsuo Hashimoto48 and Yuji Inagaki48

Author Affiliations

1 Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan

2 Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan

3 Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada

4 Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan

5 Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Kyoto 606-8502, Japan

6 Department of Biology, Dalhousie University, Halifax NS, Canada

7 Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada

8 Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577, Japan

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BMC Evolutionary Biology 2013, 13:131  doi:10.1186/1471-2148-13-131

Published: 26 June 2013

Abstract

Background

Elongation factor-1α (EF-1α) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a ‘differential loss’ hypothesis that assumes that EF-1α and EFL were present in the most recent common ancestor of eukaryotes followed by independent differential losses of one of the two factors in the descendant lineages. To date, however, just one diatom and one fungus have been found to have both EF-1α and EFL (dual-EF-containing species).

Results

In this study, we characterized 35 new EF-1α/EFL sequences from phylogenetically diverse eukaryotes. In so doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groups including the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested vertical inheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1α genes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to the co-occurring EFL genes.

Conclusions

According to the known EF-1α/EFL distribution, the differential loss process should have occurred independently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predict that dual-EF-containing species retain the divergent EF-1α homologues only for a sub-set of the original functions. As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1α function took place in multiple branches in the tree of eukaryotes.

Keywords:
Diatoms; Differential Gene Loss; EF-1α; EFL; Functional Remodeling; Goniomonas; Pythium; Spizellomyces; Thecamonas