However, this study suggests that overlaps are not a direct mechanism tosubstantially reduce genome size. For protein-encoding genes, occulting possibleoverlaps, there are only alternative start codons and/or truncated stop codons,but the first putative complete in-frame stop codon or standard initiationcodon are in the downstream or upstream overlapping ss-trn sequences respectively. Even if, to date, experimental data aremissing, choice to produce extended or not proteins might be a regulatory responseto stress signals. Finally, possible implications of tRNA/mRNA hybrid moleculesin the “RNA world” to “RNA/protein world” transition will be discussed.1.IntroductionTransfer RNAs are key partners in the ribosome-translationmachinery.
Generally, they are composedof c.70-90 nucleotides (nts). Moreover, they are themost abundant nucleic acid species, constituting up to 10% of all cellular RNAs(Barciszewska et al.
, 2016) 1. Therewith,e.g.
, the number of tRNA molecules is, e.g., about 2 105 in Escherichia coli and 3 106 in ayeast cell (Li and Mason, 2014) 2. By dint of their anticodon, theyread genetic information on mRNAs and deliver codon specified amino acidsattached to their distal 3′-extremityfor peptide bond synthesis on the ribosome.
In this sense, tRNA is a keymolecule which makes itpossible to pass from a covalent bond between a RNA and an amino acid (fossiltrace of the RNA world to the RNA/protein world transition) to peptide bonds(RNA/protein world). Genesspecifying tRNAs (noted trn) arepresent in prokaryotes and nuclear genomes, and in most of those of organelles (chloroplasts and mitochondria). Usually, tRNAs have a characteristic canonical cloverleaf secondary structuremade up of the aminoacyl acceptor-stem and theD(as it contains dihydrouridine)-, anticodon- and T(for thesequence T?C where ? is pseudouridine)-arms, the hairpins or “arms”consisting of a stem (helicoidal region in 3D) ending in a loop (Figure 1). The lengths of each arm, as well as the loop “diameter” vary from the tRNA type andfrom species to species. Furthermore, deduced trnsequences and even sequenced mature tRNAs exhibit reduced D- or T-arms or evenlacking at least one of them and in the extreme situation such as in nematodes Enoplea mitochondrial (mt)-trn genes are totally armless (Wendeet al, 2013) 3. However, around 90% of the mt-tRNAs foldinto the canonical cloverleaf structure (Bernt et al.
, 2013) 4. In all the geneticsystems, the tRNAs can carry a myriad of idiosyncraticpost-transcriptional chemical modifications(http://modomics.genesilico.pl/; http://www.genesilico.
pl/rnapathwaysdb/),the total number of modified nts is nearly120 (Barciszewska et al., 2016) 1. Moreover, tRNAs madefunctional by postprocessing addition ofthe 3′-terminal CCA sequence. Modifications can also be necessaryto ensure correct folding (Berntet al., 2013) . The tRNAfolds into an L-shaped 3D structure in which two helical domains(acceptor/T and D/anticodon) are perpendicularlyarranged.
This particular juxtaposition of the two functional centers, the anticodonand the acceptor terminus is essential for tRNA function. The two domains arelinked together by connector regions, one between the acceptor- and D-stems(connector 1) and the second between the anticodon- and T-stems (connector 2 whichcan has a variable length from 0 to 21 nts is alsonamed variable region hereafter V-R) (Lang et al., 2012) .