TRNA gene diversity in the three domains of life.

Kosuke Fujishima,Akio Kanai

doi:10.3389/fgene.2014.00142

Abstract

Transfer RNA (tRNA) is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs) are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs) possess long variable arms that are specific to eukaryotic class II tRNASer and tRNALeu but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus, this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.

Highlights

Transfer RNA is a short non-coding RNA of approximately 70–100 bases
While it is still unclear how Transfer RNA (tRNA) molecules originated, evolutionary biologists continue to question how these chains of ribonucleotides became involved in the context of protein synthesis, and how they influenced the evolution of these biological systems
We focused on the co-evolution of tRNA and their splicing endonucleases, and discussed how subfunctionalization of the enzyme could shape tRNA gene arrangement by allowing the tRNA gene to accept introns at various positions as well as allowing gene fragmentation and permutation

Summary

Introduction

Transfer RNA (tRNA) is a short non-coding RNA of approximately 70–100 bases. The principal function of tRNA is its involvement in translation machinery. Some type of disrupted tRNA genes such as split tRNA are considered as potential analogs of early tRNA, creating a hot debate in the field of tRNA evolution (Randau and Söll, 2008; Di Giulio, 2012). While it is still unclear how tRNA molecules originated, evolutionary biologists continue to question how these chains of ribonucleotides became involved in the context of protein synthesis, and how they influenced the evolution of these biological systems. We will recapitulate the characteristics of modern tRNA gene diversity, summarize the coevolutionary scenario of tRNA and their processing enzymes, and provide different models for the origin and evolution of early tRNA

Objectives

Findings

Conclusion