title: Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life.
abstract: A search has been performed on 2878 tRNA sequences from 60 different genomes in order to detect the existence of closely related 'alloacceptor' tRNAs accepting dissimilar amino acids that could be paralogs generated by gene duplications. This has led to the identification of extremely conserved tRNA(Phe)-tRNA(Tyr) pairs displaying as high as 94% identity between them, and also other potentially paralogous tRNA pairs in archaeal species. These paralogous pairs are enriched for amino acid pairs belonging to the same amino acid biosynthetic family, thus providing evidence for the coevolution of genetic code and amino acid biosynthesis. Overall, the genetic distances between alloacceptor tRNAs yield estimates of how closely clustered in sequence space are the tRNAs in a genome. Among 34 Bacteria, 18 Archaea and 8 Eukarya, Methanopyrus kandleri and Aeropyrum pernix have yielded the lowest alloacceptor distances and largest number of paralogous pairs. Based on a cluster-dispersion model of tRNA evolution, such tight alloacceptor clustering is a measure of primitiveness of tRNA genotypes, and places last universal common ancestor (LUCA) between the branches leading to these two archaea in the tRNA phylogenetic tree.
authors.affiliation: Department of Biochemistry and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Xue
authors.forename: Ka-Lok
authors.initials: KL
authors.lastname: Tong
authors.forename: Christian
authors.initials: C
authors.lastname: Marck
authors.forename: Henri
authors.initials: H
authors.lastname: Grosjean
authors.forename: J Tze-Fei
authors.initials: JT
authors.lastname: Wong
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D000818:Animals; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000596:Amino Acids; D012343:RNA, Transfer