title: Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination.
abstract: The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a "stop" codon? We provide evidence, based on ribosomal profiling and "stop" codon depletion shortly before coding sequence ends, that mRNA 3' ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution.
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
authors.forename: Estienne Carl
authors.initials: EC
authors.lastname: Swart
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Serra
authors.affiliation: Department of Biology, University of Pisa, Pisa 56126, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Petroni
authors.affiliation: Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland. Electronic address: mariusz.nowacki@izb.unibe.ch.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Nowacki
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000818:Animals; D020369:Bradyrhizobium / Q000235:genetics; D016798:Ciliophora / Q000235:genetics; D018388:Codon, Terminator; D001517:Coleoptera / Q000235:genetics; D005815:Genetic Code; D012343:RNA, Transfer; D061806:Transcription Termination, Genetic
chemical_list: D000596:Amino Acids; D018388:Codon, Terminator; D012343:RNA, Transfer