Abstract
Understanding the mechanistic basis of the disruption of tRNA genes, as manifested in the intron-containing and split tRNAs found in Archaea, will provide considerable insight into the evolution of the tRNA molecule. However, the evolutionary processes underlying these disruptions have not yet been identified. Previously, a composite genome of the deep-branching archaeon Caldiarchaeum subterraneum was reconstructed from a community genomic library prepared from a C. subterraneum–dominated microbial mat. Here, exploration of tRNA genes from the library reveals that there are at least three types of heterogeneity at the tRNAThr(GGU) gene locus in the Caldiarchaeum population. All three involve intronic gain and splitting of the tRNA gene. Of two fosmid clones found that encode tRNAThr(GGU), one (tRNAThr-I) contains a single intron, whereas another (tRNAThr-II) contains two introns. Notably, in the clone possessing tRNAThr-II, a 5′ fragment of the tRNAThr-I (tRNAThr-F) gene was observed 1.8-kb upstream of tRNAThr-II. The composite genome contains both tRNAThr-II and tRNAThr-F, although the loci are >500 kb apart. Given that the 1.8-kb sequence flanked by tRNAThr-F and tRNAThr-II is predicted to encode a DNA recombinase and occurs in six regions of the composite genome, it may be a transposable element. Furthermore, its dinucleotide composition is most similar to that of the pNOB8-type plasmid, which is known to integrate into archaeal tRNA genes. Based on these results, we propose that the gain of the tRNA intron and the scattering of the tRNA fragment occurred within a short time frame via the integration and recombination of a mobile genetic element.
Highlights
Transfer RNA is a small RNA molecule that plays a key role in protein biosynthesis
We reported a tRNAThr(GGU) gene containing two introns at nucleotide positions 24/25 and 45/46 (Figure 1A) in a composite genome of C. subterraneum that was reconstructed from a community genomic library prepared from a C. subterraneum– dominated microbial-mat community [21]
We did not identify the tRNAThr-I sequence in the composite genome of C. subterraneum following a homology search, we did find a sequence fragment identical to the 59 half of tRNAThr-I
Summary
Transfer RNA (tRNA) is a small RNA molecule that plays a key role in protein biosynthesis. In Archaea, a more unusual tRNA arrangement, the so-called ‘split tRNA’, has been reported. This is produced by the trans splicing of two or three pieces of RNA transcribed from different genes [8,9,10]. The intron-containing tRNA and the split tRNA share a common structural motif, called the ‘bulge–helix– bulge’, at the intron/leader–exon boundary. This motif is recognized by tRNA splicing endonucleases, suggesting that the intron-containing tRNA and the split tRNA are evolutionarily related [8,9,10,11,12,13]
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