A complex distribution of elongation family GTPases EF1A and EFL in basal alveolate lineages

. 2014 Sep ; 6 (9) : 2361-7.

Jazyk angličtina Země Anglie, Velká Británie Médium print

Typ dokumentu dopisy, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid25179686

Grantová podpora
MOP-42517 Canadian Institutes of Health Research - Canada

Translation elongation factor-1 alpha (EF1A) and the related GTPase EF-like (EFL) are two proteins with a complex mutually exclusive distribution across the tree of eukaryotes. Recent surveys revealed that the distribution of the two GTPases in even closely related taxa is frequently at odds with their phylogenetic relationships. Here, we investigate the distribution of EF1A and EFL in the alveolate supergroup. Alveolates comprise three major lineages: ciliates and apicomplexans encode EF1A, whereas dinoflagellates encode EFL. We searched transcriptome databases for seven early-diverging alveolate taxa that do not belong to any of these groups: colpodellids, chromerids, and colponemids. Current data suggest all seven are expected to encode EF1A, but we find three genera encode EFL: Colpodella, Voromonas, and the photosynthetic Chromera. Comparing this distribution with the phylogeny of alveolates suggests that EF1A and EFL evolution in alveolates cannot be explained by a simple horizontal gene transfer event or lineage sorting.

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Cavalier-Smith T, Chao EE. Oxnerella micra sp. n. (Oxnerellidae fam. n.), a tiny naked centrohelid, and the diversity and evolution of heliozoa. Protist. 2012;163:574–601. PubMed

Cocquyt E, et al. Gain and loss of elongation factor genes in green algae. BMC Evol Biol. 2009;9:39. PubMed PMC

Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. PubMed PMC

Gile GH, Faktorová D, et al. Distribution and phylogeny of EFL and EF-1alpha in Euglenozoa suggest ancestral co-occurrence followed by differential loss. PLoS One. 2009;4:e5162. PubMed PMC

Gile GH, Keeling PJ. Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes. Mol Biol Evol. 2008;25:1967–1977. PubMed

Gile GH, Novis PM, Cragg DS, Zuccarello GC, Keeling PJ. The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework. J Eukaryot Microbiol. 2009;56:367–372. PubMed

Gile GH, Patron NJ, Keeling PJ. EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates. Protist. 2006;157:435–444. PubMed

Gile GH, Slamovits CH. Transcriptomic analysis reveals evidence for a cryptic plastid in the colpodellid Voromonas pontica, a close relative of chromerids and apicomplexan parasites. PLoS One. 2014;9:e96258. PubMed PMC

Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95–98.

Henk DA, Fisher MC. The gut fungus Basidiobolus ranarum has a large genome and different copy numbers of putatively functionally redundant elongation factor genes. PLoS One. 2012;7:e31268. PubMed PMC

Ishitani Y, et al. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences. J Eukaryot Microbiol. 2012;59:367–373. PubMed

Janouškovec J, et al. Colponemids represent multiple ancient alveolate lineages. Curr Biol. 2013;23:2546–2552. PubMed

Janouškovec J, Horák A, Obornik M, Lukeš J, Keeling PJ. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci U S A. 2010;107:10949–10954. PubMed PMC

Kamikawa R, et al. Cercozoa comprises both EF-1alpha-containing and EFL-containing members. Eur J Protistol. 2011;47:24–28. PubMed

Kamikawa R, et al. Parallel re-modeling of EF-1alpha function: divergent EF-1alpha genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol Biol. 2013;13:131. PubMed PMC

Kamikawa R, Inagaki Y, Sako Y. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene. Proc Natl Acad Sci U S A. 2008;105:6965–6969. PubMed PMC

Kamikawa R, Sakaguchi M, Matsumoto T, Hashimoto T, Inagaki Y. Rooting for the root of elongation factor-like protein phylogeny. Mol Phylogenet Evol. 2010;56:1082–1088. PubMed

Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006;6:29. PubMed PMC

Keeling PJ, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12:e1001889. PubMed PMC

Keeling PJ, Inagaki Y. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. Proc Natl Acad Sci U S A. 2004;101:15380–15385. PubMed PMC

Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol. 1989;29:170–179. PubMed

Kuvardina ON, et al. The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans. J Eukaryot Microbiol. 2002;49:498–504. PubMed

Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:2286–2288. PubMed

Leander BS, Kuvardina ON, Aleshin VV, Mylnikov AP, Keeling PJ. Molecular phylogeny and surface morphology of Colpodella edax (Alveolata): insights into the phagotrophic ancestry of apicomplexans. J Eukaryot Microbiol. 2003;50:334–340. PubMed

Moore RB, et al. A photosynthetic alveolate closely related to apicomplexan parasites. Nature. 2008;451:959–963. PubMed

Moreira D, Le Guyader H, Philippe H. Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes. Mol Biol Evol. 1999;16:234–245. PubMed

Noble GP, Rogers MB, Keeling PJ. Complex distribution of EFL and EF-1alpha proteins in the green algal lineage. BMC Evol Biol. 2007;7:82. PubMed PMC

Obornik M, et al. Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef. Protist. 2012;163:306–323. PubMed

Page RDM. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996;12:357–358. PubMed

Ruiz-Trillo I, Lane CE, Archibald JM, Roger AJ. Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J Eukaryot Microbiol. 2006;53:379–384. PubMed

Sakaguchi M, Takishita K, Matsumoto T, Hashimoto T, Inagaki Y. Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads. Gene. 2009;441:126–131. PubMed

Schmidt HA. Testing tree topologies. In: Lemey P, Salemi M, Vandamme AM, editors. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. Cambridge: Cambridge University Press; 2009. pp. 381–404.

Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002;51:492–508. PubMed

Shimodaira H, Hasegawa M. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999;16:1114–1116.

Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001;17:1246–1247. PubMed

Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–2690. PubMed

Strimmer K, Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond B Biol Sci. 2002;269:137–142. PubMed PMC

Tikhonenkov DV, et al. Description of Colponema vietnamica sp. n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes. PLoS One. 2014;9:e95467. PubMed PMC

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