Structural clones of UAG decoding RNA

Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gyanxet.com. We observe that aside from the usual pyl-gene-cluster, pyl-carrying Methanosarcinaceae have a good number of conjugate-halves from pyl-tRNA (pylT) gene split at 37/38 spread over their genomes. On in silico ligation, the secondary structures of these pairs clone the clover-leaf of pylT of M. barkeri. Of these nineteen methanogens, four, namely, M. stadtmanae, M. kandleri, M. hungatei, and M. thermautotrophicus, have these pairs at levels at or higher than in the pyl-carrying ones. Screening these we arrive at four pairs, i.e., one from each of these four genomes. On ligation, these are close homologs of pylT gene of M. barkeri. The intervening sequences between the split pairs in these four cases are shown to nearly reproduce the known secondary structures at exon-intron boundaries.