Origin of Most Primitive mRNAs and Genetic Codes via Interactions between Primitive tRNA Ribozymes

Koji Ohnishi[1] (ohnishi@sc.niigata-u.ac.jp)
Shouken Hokari[1]
Hiroshi Shutou[1]
Madoka Ohshima[1] (madoka@bio.sc.niigata-u.ac.jp)
Naotaka Furuichi[2] (huruichi@agr.niigata-u.ac.jp)
Masaki Goda[3] (mgoda@cc.niigata-u.ac.jp)

[1]Department of Biology, Faculty of Science, Niigata University, Igarashi-2, Niigata 950-2181, Japan
[2]Faculty of Agriculture, Niigata University, Igarashi-2, Niigata 950-2181, Japan
[3]Faculty of Engineering, Niigata University, Igarashi-2, Niigata 950-2181, Japan


Abstract

The origin and early evolution of genetic codon system and early mRNAs were analyzed from a viewpoint of primordial gene theory and the poly-tRNA theory. A hypothetical 25-amino acid (aa)-primordial peptide was deduced from internal aa-sequence homology of adenylate kinases. Theoretical models were made which can reasonably explain how primitive tRNA(s) could have had converted to be earliest mRNAs via interactions between presumptive anticodons and (poly-)tRNA ribozyme. Transfer-RNA gene clusters in the trrnD- and rrnB-operons of Bacillus subtilis seemed to be relics of early peptide-synthesizing RNA machine. Detailed analyses revealed that the poly-tRNA regions in these operons are true relics of RNA-machine for making a 16-aa trrnD-peptide and a 21-aa rrnB-peptide, whose aa sequences are in the order of aa specificities of tRNAs in the tRNA gene clusters of the trrnD-operon and rrnB-operon, respectively. The primordial gene-encoded peptide deduced from adenylate kinases were found to be a genuine homologue of the rrnB-peptide. Various protein superfamilies were found to have evolved from either of these two types of primitive peptides. Earlist mRNAs were concluded to have evolved from tRNAGly(trrnD-mRNA) or tRNAHis (rrnB-mRNA) , where trrnD- and rrnB-mRNAs are hypothetical primitive mRNAs complementary to the tandem arrangement of 16 or 21 anticodons of tRNAs in the trrnD-operon and rrnB-operon, respectively. The poly-tRNA model is considered to be an excellent theory, because it can reasonably explain origins of both genetic codes and earliest mRNAs, and because the hypothesis can be statistically evaluated by base-identity levels in proper alignments. The genetic codon system is a typical mature semeiotic system within a cell, and the genesis of the geneic codon system was discussed from an aspect of de Saussure's semeiology. Arbitrary correspondence between (anti)codon and aa would be most plausibly a result of semeiotic culture system of intracellular tRNA-riboorganismic society.

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Japanese Society for Bioinformatics