Received: 14 March 2024 Revised: 19 April 2024 Accepted: 23 April 2024 DOI: 10.1002/bies.202400058 REVIEW Prospects & Overviews mRNA context and translation factors determine decoding in alternative nuclear genetic codes Ali Salman Nikita Biziaev Ekaterina Shuvalova Elena Alkalaeva Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia Correspondence Elena Alkalaeva, Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, 119991 Moscow, Russia. Email: alkalaeva@eimb.ru Funding information Russian Science Foundation, Grant/Award Number: 23-24-00498 Abstract The genetic code is a set of instructions that determine how the information in our genetic material is translated into amino acids. In general, it is universal for all organ- isms, from viruses and bacteria to humans. However, in the last few decades, exceptions to this rule have been identified both in pro- and eukaryotes. In this review, we discuss the 16 described alternative eukaryotic nuclear genetic codes and observe theories of their appearance in evolution. We consider possible molecular mechanisms that allow codon reassignment. Most reassignments in nuclear genetic codes are observed for stop codons. Moreover, in several organisms, stop codons can simultaneously encode amino acids and serve as termination signals. In this case, the meaning of the codon is determined by the additional factors besides the triplets. A comprehensive review of various non-standard coding events in the nuclear genomes provides a new insight into the translation mechanism in eukaryotes. KEYWORDS genetic code, codon reassignment, stop codon, eRF1, suppressor tRNA INTRODUCTION Genetic code determines how the unique triplets of nucleotides in DNA and RNA code for amino acid residues in translated proteins. It con- sists of 64 codons, 61 of which encode amino acids, and 3 encode stop codons (UAA, UAG, and UGA). [ 1,2] The genetic code, once believed to be universal and immutable, is now known to have many exceptions and is not quite universal. [ 3] Genome research has shown many instances in prokaryotes, eukaryotes, and viruses of the universal genetic code deviation. [ 4–6] In eukaryotes, it could vary in the mitochondrial and nuclear genomes. [ 4,6–8] Nuclear genetic code is more stable than the mitochondrial, however, at the moment, 15 alternative nuclear genetic codes have been determined (Table 1). Most reassignments of nuclear genetic codes are observed for stop codons. In the known variant nuclear genetic codes, commonly one or two stop codons are reas- signed to sense codons, but recently some organisms were revealed to use all three stop codons as sense. [ 9–15] Three independent mod- els are proposed to explain genetic code evolution: codon capture model, tRNA loss driven codon reassignment model, and ambiguous intermediate model. [ 4,6] In this review, we describe all known alternative nuclear genetic codes. Also, we discuss the evolutional and functional mechanisms of the occurrence of these codes. In this context, we describe additional proteins responsible for some alternative codes formation. Finally, we review the possible benefits and harm of their appearance. THE CONCEPT OF THE UNIVERSAL GENETIC CODE AND ITS ALTERATIONS The genetic code is the rule that attributes the nucleotide triplet in the mRNA to the amino acid in the protein. This process is realized by the aminoacyl-tRNA synthetases during tRNA aminoacylation and is continued by the ribosome during translation. Defined by the end of the 60s of the 20th century, the so-called the Standard genetic code turned out to be practically universal. Of the 64 possible triplet codons, BioEssays. 2024;46:2400058. © 2024 Wiley Periodicals LLC. 1 of 14 wileyonlinelibrary.com/journal/bies https://doi.org/10.1002/bies.202400058