Abstract
Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis.
Highlights
Chromerids are single-celled photosynthetic apicomonads associated with corals [1,2,3,4,5].Phylogenetic analyses have shown that these algae are closely related to Apicomplexa, confirming the hypothesis that apicomplexan parasites originate from a photosynthetic alga [1,6,7,8]
This study identified sequences of Aminoacyl-tRNA synthetases (AaRSs) in chromerids, along with their putative protein localization and evolutionary origins
Five AaRSs were predicted to be targeted to all three compartments by an ambiguous targeting sequence that likely leads to the dual-targeting of these enzymes in C. velia; whereas, only two such AaRSs were predicted in V. brassicaformis
Summary
Chromerids are single-celled photosynthetic apicomonads associated with corals [1,2,3,4,5]. Chromera velia and Vitrella brassicaformis, representing two distinct lineages, have been formally described so far [1,2] They do not form sister species and they are considerably different in morphology, ultrastructure, pigmentation, organellar genomes, respiratory chains, and life cycles [1,2,5,8,9,10,11,12]. Phylogenetic analyses [1,9,15,18] and the use of non-canonical coding for tryptophan in C. velia [1,15] suggest that chromerid plastids share a common ancestry with the apicomplexan relic plastid [10] This relationship is evident in the similar arrangement of heme biosynthesis in chromerids and apicomplexans: δ-aminolevulinic acid (ALA) is synthesized in the mitochondrion (C4 pathway) and it is exported to the plastid [19,20]. No Aminoacyl-tRNA synthetases are plastid or mitochondrially encoded, they are all encoded by nuclear genes, and translated in the cytosol, with posttranslational targeting to the translationally active organelles
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