Non-Standard Genetic Codes Define New Concepts for Protein Engineering

Abstract

The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.

An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons

“…Therefore, it is possible that the observed bias against the usage of UAG, UAA, and UGA codons is at least partly due to limited abundance of hypothetical cognate aminoacyl-tRNAs. However, efficient accommodation of any of UAG, UAA, or UGA codons as sense ones requires not only the existence of (sufficiently abundant) cognate aminoacyl-tRNAs but also specific modifications in the eukaryotic release factor 1, eRF1 [23]. This protein is responsible for recognizing all three termination codons in an mRNA during translation and liberating the nascent polypeptide chain from the tRNA that has brought the last (C-terminal) amino acid residue [24].…”

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks

“…Codon reassignments can take three routes–sense-to-stop, stop-to-sense and sense-to-sense replacements–with modifications of aaRS/tRNA pairs an efficient route towards creating any alternative code [49]. …”

The “periodic table” of the genetic code: A new way to look at the code and the decoding process

“…The genetic code is nearly universal, meaning that in almost all living organisms, the identity of the amino acid encoded by a given triplet codon is the same. 4,5 With 4 bases (A, G, U, and C), there are 64 possible triplet codons; 61 sense (encoding amino acids) and 3 nonsense (UAA, UAG, and UGA, socalled stop codons that direct termination of translation). In most organisms, there are 20 common amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids being encoded by more than one codon.…”

“…In most organisms, there are 20 common amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids being encoded by more than one codon. Only two amino acids (Met and Trp) are encoded by just a single codon in most of the organisms (although exceptions to this rule do exist 4,5 ). Phe, Tyr, His, Gln, Asn, Lys, Asp, Glu, and Cys are each encoded by 2 distinct codons, which in each case are identical at positions 1 and 2 but different in position 3 (for example, Phe is encoded by UUU and UUC) (Fig.…”