Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption

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 tRNA ^Thr(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 tRNA ^Thr(GGU), one (tRNA ^Thr-I) contains a single intron, whereas another (tRNA ^Thr-II) contains two introns. Notably, in the clone possessing tRNA ^Thr-II, a 5′ fragment of the tRNA ^Thr-I (tRNA ^Thr-F) gene was observed 1.8-kb upstream of tRNA ^Thr-II. The composite genome contains both tRNA ^Thr-II and tRNA ^Thr-F, although the loci are >500 kb apart. Given that the 1.8-kb sequence flanked by tRNA ^Thr-F and tRNA ^Thr-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.