In all the taxa and genomic systems, numerous trn genes (specifying tRNA) exhibit at specific conserved positions nucleotide triplets corresponding to stop codons (TAG/TAA). Similarly, relatively high frequencies of start codons (ATG/ATA) occur in fungi/metazoan mitochondrial-trn genes. The last nucleotide of these triplets is the first involved in the 5′-D- or 5′-T-stem, respectively. Their frequencies are tRNA species dependent. The products of these genes which bear one or two types of these codons are called ss-tRNAs (for stop/start). Metazoan mt-genomes are generally very compact, and many same strand overlapping sequences may simultaneously code for tRNAs and mRNAs. However, this study suggests that overlaps are not a direct mechanism to substantially reduce genome size. For protein-encoding genes, occulting possible overlaps, there are only alternative start codons and/or truncated stop codons, but the first putative in-frame standard initiation codon or complete stop codon is in the upstream or downstream overlapping ss-trn sequences, respectively. Even if, to date, experimental data are missing, stress signals might regulate producing extended or not proteins. Finally, possible implications of tRNA/mRNA hybrid molecules in the “RNA world” to “RNA/protein world” transition will be discussed.
Part of the book: Mitochondrial DNA