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Arf family comprises one of the group within the Ras superfamily GTPases with diverse functions in eukaryotic cell, e.g. the regulation of vesicular trafficking, cytoskeleton dynamics or cilium-associated functions. So far, only 8 ancestral eukaryote Arf family members (Arf, Arl1, Arl2, Arl3, Arl5, Arl8, Arfrp1 and Sar1) and several presumed animal-specific members are recognised. The phylogeny within Arf family is largely unknown despite the fact, that the understanding of Arf family evolution could shed light on some aspect of the eukaryogenesis as the closest known prokaryote relatives of eukaryotes, Asgard phylum members, harbour a very large complement of the Arf family proteins. We decided to take advantage of the growing amount of eukaryote lineages with sequenced representatives and improve our knowledge about the distribution and evolution of the Arf family. We carefully selected 114 eukaryotic species that cover the diversity of eukaryotes and searched their genome and/or transcriptome sequences in order to detect all Arf family proteins. Using BLAST, we identified more than 2000 gene sequences. Each gene was manually inspected and respective protein prediction was corrected whenever necessary. We identified 16 groups of putative eukaryotic ancestral Arf family paralogues, namely Arf1, Arf6, Arl1, Arl2, Arl3, Arl5, Arl6, Arl8, Arl13, Arl16, Arl17, Arl18, Arfrp1, Sar1, Sar1-like and SR? (all SR? sequences were excluded from further analyses due to high divergence). Three of them (Arl17, Arl18 and Sar1-like) were identified for the first time. Arf6, Arl13 and Arl16 known mostly from opisthokonts were shown to have broad eukaryotic distribution and ancestral origin predates the divergence of all major eukaryotic lineages. In order to unravel the phylogenetic relationships between identified ancestral paralogues, we employed ScrollSaw method developed for the inferring of the evolution of another Ras superfamily GTPases, Rab family.
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