Abstract

Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.

Highlights

  • Transfer RNA has an important function in protein translation

  • They consist of 15 ribosomal proteins, including L22, L2, L23, S10, S7, L1, L11, S9, S11, S13, S5, L6, S8, L5, and L14, and several other proteins including methionine Transfer RNA (tRNA) ligase, arginine tRNA ligase, elongation factor 1-alpha, phenylalanine tRNA ligase, and serine/threonine protein kinase

  • Our results support that the tRNA-ANNs might have not been evolved in the common ancestor of Archaea

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Summary

Introduction

Transfer RNA (tRNA) has an important function in protein translation In this process, tRNAs recognize codons in messenger RNAs (mRNAs) by base pairing between codon and anticodon. TRNAs recognize codons in messenger RNAs (mRNAs) by base pairing between codon and anticodon They transfer cognate amino acids onto nascent peptides. With necessary modification (cm U, 5-carboxymethyluridine) by Elp, tRNA-UNN (U34) could pair with codon NNG in addition to codon NNA, and functionally replace tRNACNN (Kurata et al, 2008; Grosjean et al, 2010; Novoa et al, 2012; Selvadurai et al, 2014). Some modifications affect the wobble ability of tRNAs, and reduce harmful pairing with irrelevant codons (Näsvall et al, 2007; Huang et al, 2008; Kurata et al, 2008; Grosjean et al, 2010; Novoa et al, 2012; Karlsborn et al, 2014; Selvadurai et al, 2014)

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