Evolution from Possible Primitive tRNA-Viroids to Early Poly-tRNA-Derived mRNAs: A New Approach from the Poly-tRNA Theory

Koji Ohnishi[1],[2],[3] (ohnishi@sc.niigata-u.ac.jp)
Madoka Ohshima[2] (ume0403@docomo.ne.jp)
Naotaka Furuichi[3] (nfuru@agrews.agr.niigata-u.ac.jp)

[1] Department of Biology, Faculty of Science, Niigata University, Ikarashi-2, Niigata 950-2181, Japan
[2] Graduate School of Sciences, Niigata University, Ikarashi-2, Niigata 950-2181, Japan
[3] Center for Interdisciplinary Research, Niigata University, Ikarashi-2, Niigata 950-2181, Japan


Abstract

Poly-tRNA theory have revealed that the tRNA gene-clusters in the Bacillus subtilis trrnD- and rrnB-operons are relics of early peptide-synthesizing RNA apparatus. The trrnD-type and rrnB-type poly-tRNA models were re-analyzed by using recent databases. The results elucidated that the 16 amino acid (aa)-trrnD- and the 21 aa-rrnB-peptides (whose aa sequences are in the order of aa specificities of tRNAs in the respective tRNA cluster) are really relics of earliest peptides encoded by most primitive mRNAs, trrnD-mRNA and rrnB-mRNA, which are homologous to tRNAGly and tRNAHis, respectively. Genes encoding various protein superfamilies (including pgtB protein, glycyl-tRNA synthetase alpha, C-type lectin, F1-ATP-synthase gamma, etc) were concluded to have derived from tRNAGly-tRNACys-tRNALeu region (including trrnD-mRNA region) in the trrnD-poly-tRNA. Genes for another group of protein superfamilies (including adenylate kinase, glyceraldehyde-3-phosphate dehydrogenase, helix-turn-helix DNA-binding domains, etc.) were found to have derived rrnB-mRNA, which is most plausibly homologous to a region containing the tRNAHis of the rrnB-poly-tRNA. Thus Proto-tRNA(Gly) reconstructed from tRNAGly and other tRNAs strongly suggested that proto-tRNA was most plausibly a viroid-like possibly self-cleavable replicable ribozyme possessing a possible hammerhead-like structure.

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Japanese Society for Bioinformatics