Evolution of Elongation Factor‐Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences

Abstract

Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral gene transfer and/or ancestral co-occurrence followed by differential loss of either of the two factors. Our current understanding of the EF-1α/EFL evolution in the eukaryotic group Rhizaria, composed of Foraminifera, Radiolaria, Filosa, and Endomyxa, remains insufficient, as no information on EF-1α/EFL gene is available for any members of Radiolaria. In this study, EFL genes were experimentally isolated from four polycystine radiolarians (i.e. Dictyocoryne, Eucyrtidium, Collozoum, and Sphaerozoum), as well as retrieved from publicly accessible expressed sequence tag data of two acantharean radiolarians (i.e. Astrolonche and Phyllostaurus) and the endomyxan Gromia. The EFL homologs from radiolarians, foraminiferans, and Gromia formed a robust clade in both maximum-likelihood and Bayesian phylogenetic analyses, suggesting that EFL genes were vertically inherited from their common ancestor. We propose an updated model for EF-1α/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study.

An evolutionary ratchet leading to loss of elongation factors in eukaryotes

“…Phylogenetic analysis of the EFL sequences detected in this study gives a tree that is overall similar to other published EFL phylogenies (for example [13,14,16,20]), although with fewer taxa as we only considered organisms with large scale EST and whole genome data available (Additional file 2: Figure S1A). Even with additional sequences from PCR amplification and sequencing of individual genes, phylogenetic analysis of EFL does not shed much light on the origin and deep evolutionary history of EFL; the deepest branches in the phylogenetic tree lack strong statistical support in ML and/or Bayesian analyses, and the EFL tree can not be rooted reliably due to long branch attraction of divergent sequences to the outgroup [20].…”

The evolution of paralogous enzymes MAT and MATX within the Euglenida and beyond

“…A similar disproportion of losses is present in the tree of eukaryotes. If we compare the MAT/MATX history to the case of EF-1α/EFL, the discrepancy is not as significant in the EF-1α/EFL case; the occurrence of EFL is more fragmented not only in euglenids but also in other eukaryotic groups [15-17,23]. To our knowledge, it is impossible to evaluate the significance of the observed disproportion between the number of losses of one paralogue compared to the other, so we must conclude that in this respect our observations do not contradict the deep paralogy scenario.…”

“…Like MAT/MATX, the EF-1α/EFL paralogues have a patchy distribution across the tree of eukaryotes and rarely occur together in the same organism. EFL has been localized so far in eight groups of unrelated organisms: dinoflagellates, haptophytes, cercozoans, green algae, choanoflagellates, fungi, diatoms, and radiolarians [11-17]. …”

A Complex Distribution of Elongation Family GTPases EF1A and EFL in Basal Alveolate Lineages

“…Nodes with Bayesian posterior probabilities ≥0.95 and ML bootstrap support ≥50% are given with thick lines. The “RFG” clade stands for Radiolaria, Foraminifera, and Gromia —a tentative group introduced in Ishitani et al (2012). PPC, periplastid compartment.

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“…Distinguishing between the two is difficult because the great diversity of taxa involved and ancient time scales of the events, which both contribute to insufficient resolution in the phylogenies to unequivocally document cases of HGT or lineage sorting (Cocquyt et al 2009; Kamikawa et al 2010). EFL has now been found in lineages from all major eukaryotic supergroups, and its overall distribution has become even more complex (Ruiz-Trillo et al 2006; Cocquyt et al 2009; Gile, Faktorová, et al 2009; Sakaguchi et al 2009; Cavalier-Smith and Chao 2012; Henk and Fisher 2012; Ishitani et al 2012; Kamikawa et al 2013). But more interestingly, deeper analyses into some EFL-containing lineages have shown that the distribution patterns between closely related lineages may also be complex; this is particularly well documented in green algae and euglenozoa, where very unusual distribution patterns conflict with known phylogenetic relationships (Gile, Faktorová, et al 2009; Gile, Novis, et al 2009).…”