**3.4. Some known structures in the living world bearing a start or stop codon at least in part of a stem-loop structure**

In the living world, many nucleic sequences with secondary structures playing a physiological role involving stop and/or start codons have been discovered. Some representative examples are briefly presented here. (1) The tropism switching of the bacteriophage BPP-1 is mediated by a phage-encoded diversity-generating retroelement, which introduces nt substitutions in a gene that specifies a host cell-binding protein (*Mtd*) [37]. The nt substitutions are introduced in a variable repeat located at the 3′-end of this gene. Two nts after this region, the UAG stop codon is present, and its last nt is situated at the 5′ beginning of the 5′-stem of a hairpin. Both the UAG codon and hairpin are required for phage tropism switching. (2) Programmed translational bypassing is a process, whereby ribosomes "ignore" a substantial interval of mRNA sequence. In a bacteriophage T4 gene, bypassing requires translational blockage at a "takeoff codon" immediately upstream of the UAG stop codon, and both codons are in the 5′-stem of a hairpin; moreover, this region is mobile [38]. (3) The operon *flgFG* of the bacterium *Campylobacter jejuni* can encode two genes (*flgF* and *flgG*). Its expression in *E. coli* produces a fusion protein probably due to ribosomal frameshifting (translational hopping) [39]. The putative hop region contains, among others, a hairpin beginning by the last nt of the UAA stop codon of the first mRNA. The AUG start codon of the second gene is in the loop of the following hairpin. (4) In Eubacteria, riboswitches are regulatory segments of DNA or mRNA that can bind a small molecule (the effector), which repress or activate their cognate genes at transcriptional and/or translational levels. In the riboflavin and *cob* operons, conformational changes can form a stem loop which sequesters the translational start site, consisting of the Shine-Dalgarno (SD) sequence plus start codon thus preventing gene translation [40]. (5) Bacterial transfer-messenger RNAs (tmRNAs) have dual TLS and mRNA-like properties. They rescue stalled ribosomes on mRNAs lacking proper translational stop signal; the tRNA-like structure acts first as an alanine-tRNA, and then the short mRNA reading frame is translated and the product is released [41]. This *trans*-translation terminates at the stop codon terminating the tmRNA reading frame. This stop can be in a little loop or totally or partially integrated in the stem of a hairpin-like structure. In eukaryotes, structurally reduced tmRNAs (no mRNA-like domain) rarely occur in chloroplasts [42] and in mt-genomes (in Jakobids, presumably close to the most ancient living eukaryotes with bacterial-like mt-genome) [41]. Moreover, tmRNA TLSs function even without any canonical initiation factors. These examples show that start or stop codons located in hairpin may have various functions, as we suggest for TAR10 and ATR49.
