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J Mol Evol (2009) 69:497504 DOI 10.1007/s00239-009-9294-6
Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios
Junichi Sugahara Kosuke Fujishima
Keisuke Morita Masaru Tomita Akio Kanai
Received: 30 June 2009 / Accepted: 2 October 2009 / Published online: 14 October 2009 Springer Science+Business Media, LLC 2009
Abstract The following unusual tRNAs have recently been discovered in the genomes of Archaea and primitive Eukaryota: multiple-intron-containing tRNAs, which have more than one intron; split tRNAs, which are produced from two pieces of RNA transcribed from separate genes; tri-split tRNAs, which are produced from three separate genes; and permuted tRNA, in which the 50 and 30 halves are encoded with permuted orientations within a single gene. All these disrupted tRNA genes can form mature contiguous tRNA, which is aminoacylated after processing by cis or trans splicing. The discovery of such tRNA disruptions has raised the question of when and why these complex tRNA processing pathways emerged during the evolution of life. Many previous reports have noted that tRNA genes contain a single intron in the anticodon loop region, a feature common throughout all three domains of life, suggesting an ancient trait of the last universal common ancestor. In this context, these unique tRNA disruptions recently found only in Archaea and primitive Eukaryota provide new insight into the origin and evolution of tRNA genes, encouraging further research in this eld. In this paper, we summarize the phylogeny, structure,
and processing machinery of all known types of disrupted tRNAs and discuss possible evolutionary scenarios for these tRNA genes.
Keywords tRNA Intron-containing tRNA Split tRNA
Permuted tRNA Evolution Archaea
Cyanidioschyzon merolae
Introduction
In 1958, Francis Crick proposed the central dogma of molecular biology, which explains the transfer of sequence information among DNA, RNA, and protein (Crick 1958). From this doctrine, Crick predicted the existence of an adaptor molecule that converts the genetic code in messenger RNA (mRNA) into the amino acid sequences of proteins and suggested that the adaptor could be an RNA molecule, because only base pairing is suitable for the specic recognition of small nucleotide sequences. Soon thereafter, Cricks prediction was conrmed chemically when a small noncoding RNA, currently known as transfer RNA (tRNA), was identied (Hoagland et al. 1958). tRNAs, comprising one of the classic noncoding RNA families, are...