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

The Canonical Table of the Genetic Code as a periodic system of triplets

The Canonical Table of the Genetic Code (CTGC) is constructed theoretically on the basis of the similarity of PFs (PF) of proteins with the conformation of 4-arc chain graphs (Karasev, 2019). Of the 64 conformations of the graph, specified by the position of the connectivity edges, and the matrices of 6 variables (x₁ … x₆), x_i = (0, 1), 4 blocks of 16 elements each were formed. Then they were coded in the form of triplets based on the correspondence of pairs of variables to four letters of the code: 00 = C, 01 = U, 10 = G, 11 = A, and supplemented based on the known triplet-amino acid assignment. The resulting table is compared with the Periodic Table of Chemical Elements (PTCE). As in the PTCE, this CTGC has an initial element - a triplet that encodes graphs with zero number of connected edges. Within each block, vacancies are filled with connectivity edges in two alternative ways, both in rows and in the columns. As we move from the initial block 00 to the final block 11, there is a sequential filling of vacancies for variables x₃x₄: 00, 01, 10, 11. In general, the CTGC can be considered as a periodic system of triplets. Comparison with the previously described variety of tables of the genetic code made it possible to conclude that the CTGC more adequately reflects the properties of the genetic code. Prospects for the possible application of this table are being discussed.

Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies

Synonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.

Queuosine-modified tRNAs confer nutritional control of protein translation

Global protein translation as well as translation at the codon level can be regulated by tRNA modifications. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the diet and gut microbiota. We show here that nutritionally determined Q‐tRNA levels promote Dnmt2‐mediated methylation of tRNA Asp and control translational speed of Q‐decoded codons as well as at near‐cognate codons. Deregulation of translation upon queuine depletion results in unfolded proteins that trigger endoplasmic reticulum stress and activation of the unfolded protein response, both in cultured human cell lines and in germ‐free mice fed with a queuosine‐deficient diet. Taken together, our findings comprehensively resolve the role of this anticodon tRNA modification in the context of native protein translation and describe a novel mechanism that links nutritionally determined modification levels to effective polypeptide synthesis and cellular homeostasis.