Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves

Abstract

The discovery of separate 5′ and 3′ halves of transfer RNA (tRNA) molecules—so-called split tRNA—in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was encoded on 1 or 2 genes. We performed a comprehensive phylogenetic analysis of tRNAs in 45 archaeal species to explore the relationship between the three types of tRNAs (nonintronic, intronic and split). We classified 1953 mature tRNA sequences into 22 clusters. All split tRNAs have shown phylogenetic relationships with other tRNAs possessing the same anticodon. We also mimicked split tRNA by artificially separating the tRNA sequences of 7 primitive archaeal species at the anticodon and analyzed the sequence similarity and diversity of the 5′ and 3′ tRNA halves. Network analysis revealed specific characteristics of and topological differences between the 5′ and 3′ tRNA halves: the 5′ half sequences were categorized into 6 distinct groups with a sequence similarity of >80%, while the 3′ half sequences were categorized into 9 groups with a higher sequence similarity of >88%, suggesting different evolutionary backgrounds of the 2 halves. Furthermore, the combinations of 5′ and 3′ halves corresponded with the variation of amino acids in the codon table. We found not only universally conserved combinations of 5′–3′ tRNA halves in tRNAiMet, tRNAThr, tRNAIle, tRNAGly, tRNAGln, tRNAGlu, tRNAAsp, tRNALys, tRNAArg and tRNALeu but also phylum-specific combinations in tRNAPro, tRNAAla, and tRNATrp. Our results support the idea that tRNA emerged through the combination of separate genes and explain the sequence diversity that arose during archaeal tRNA evolution.

Permuted tRNA genes of Cyanidioschyzon merolae, the origin of the tRNA molecule and the root of the Eukarya domain

“…There is a great deal of evidence in favour of this view of tRNA origin (Di Giulio, 1992, 1995, 2006a, b, 2008Tanaka and Kikuchi, 2001;Nagaswamy and Fox, 2003;Widmann et al, 2005;Fujishima et al, 2008). One of the strongest pieces of evidence concerns the position of introns in tRNA genes.…”

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea

“…In our previous research, we found a leader sequence of N. equitans split tRNA Lys and an intron from P. aerophilum tRNA Arg 's possessing similar sequences with 50% identity that were both intervened at an identical nucleotide position, representing a unique example connecting the 2 types of tRNA genes (13). In the current study, a total 3 nucleotide positions were intervened by the leader sequences of C. maquilingensis split tRNAs, such as positions 25/26 and 37/38 in tRNA Gly , 29/30 in tRNA Ala , and 25/26 in tRNA Glu .…”

“…The discovery of these tRNA genes raised the question of whether ancestral tRNA was encoded on a single gene or on separate genes. Our previous study has shown clear phylogenetic relationships among these 3 types of archaeal tRNAs (13). Because N. equitans is a parasite with indications of a massive genome reduction (14), whether its tRNAs represent the ancient form of tRNA or a later product of genome reduction is still unclear.…”

“…Because N. equitans is a parasite with indications of a massive genome reduction (14), whether its tRNAs represent the ancient form of tRNA or a later product of genome reduction is still unclear. Therefore, we have been conducting comprehensive prediction and analysis of tRNA sequences in various species on the basis of our original software, SPLITS (8,9,13,15,16). We have especially focused on the hyperthermoacidophilic archaeon Caldivirga maquilingensis, which belongs to the deep branching archaeal order Thermoproteales and was isolated from an acidic hot spring in the Philippines (17), because it is the only species that lacks 6 tRNA genes for a full complement of the codon table.…”

The origin of genes could be polyphyletic

“…It has indeed been proven that the origin of tRNA genes is polyphyletic (Di Giulio, 2006a). In particular, the existence in Nanoarchaeum equitans of half-genes codifying for the 5′ and 3′ halves of tRNA (Randau et al, 2005), for which there are strong arguments supporting their ancestrality (Di Giulio, 2006a, b;Fujishima et al, 2008), and the assembly of these half-genes to make the complete tRNA molecule (Di Giulio, 1992, 1995, 1999, 2006a pave the way for the logical proof that tRNA genes were assembled in the main phyletic lines and, therefore, their origin was nonmonophyletic (Di Giulio, 2006a, 2008. However, if the origin of genes was polyphyletic, how can it be explained that, as said above, the same proteins from organisms in all three domains of life can form multiple alignments that apparently define these proteins as homologous, thus substantiating their monophyletic origin?…”