A Study of Transfer RNA

A PLOS Computational Biology paper titled Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses and authored by Feng-Jie Sun and Gustavo Caetano-Anollés, reported findings the authors state implies the following relationships between Archaea, viruses, Eukarya and Bacteria:

Archaea was said to be the most ancient followed by viruses which were linked to Archaea. Following in order were Eukarya and Bacteria. Transfer RNA (tRNA) was the object of study. The linked paper had this to say:

Transfer RNA (tRNA) molecules are central to the entire translation process. They interact with the ribosomal RNA (rRNA) subunits as they are being ratcheted through the center of the ribosome [1],[2]. Their acceptor arms charge specific amino acids through the activity of cognate aminoacyl-tRNA synthetases, while triplets of bases on their ‘anticodon’ arms recognize complementary ‘codon’ sequences in messenger RNA. These and many other molecular interactions define the identities and functions of these tRNA adaptors and establish a genetic code that translates nucleic acid into protein information in the cell. The structural make-up of tRNA is therefore fundamental to our understanding of how the biosynthetic machinery was set up into place in an emerging protein and organismal world. tRNAs are clearly ancient molecules [3] and they have been used profusely to study the evolution of ancient life [4]–[8]. The identity and function of tRNAs are fundamentally delimited by the structure of the molecules, and structure is more conserved than sequence. In fact, we recently showed that tRNA structure carries deep phylogenetic signal and can be used directly to reconstruct evolutionary history [9]. However, understanding phylogenetic trees is challenging because tRNA evolution embeds a history of recruitment in which structures gain or co-opt new identities and functions or takeover established ones.

The authors utilized an established cladistic method, embedding structure into phylogenetic analysis, to explore phylogenetic signatures in tRNA. The phylogenetic analysis entailed treating molecular structural features as phylogenetic multi-state characters. The multi-state characters have transforming character states. The assumption of an evolutionary tendency towards molecular order was made in polarizing character state transformations.