(543a) Synthetic Genomes and Genetic Codes for Virus Resistance, Biocontainment, and Therapy

From viruses to human cells, life's most fundamental process—the translation of genetic information into proteins—relies on an ancient and remarkably conserved language: the genetic code. This universal language orchestrates the precise interactions between messenger RNA, transfer RNAs (tRNAs), and the ribosome to convert nucleic acid-encoded instructions into proteins using just 20 standard amino acids. While evolution has generated an astounding biological diversity over billions of years, the genetic code remained near-perfectly conserved across all domains of life – until very recently.

With this project, we demonstrate how rational genome design and genetic code engineering have enabled us to generate organisms that achieve three key innovations: (i) broad resistance to natural viruses, (ii) prevention of genetic information flow between engineered organisms and natural species, and (iii) the capability to biosynthesize entirely new classes of genetically encoded polymers.

As genetic code engineering for the three goals above requires the reassignment of multiple of the 64 codons nature uses to encode proteins, we are constructing a computationally redesigned 57-codon Escherichia coli genome. In this synthetic genome, seven codons have been liberated for subsequent reassignment by computationally replacing them with synonymous alternatives in all protein-coding genes. We will describe the construction of this chemically synthesized genome, new discoveries about the genetic code, and a novel technology (SynOMICS; Nyerges, A et al., BioRxiv, 2024) that expedites the generation and troubleshooting of synthetic genomes with radically altered genetic codes in any species of microbe, plant, or animal.

In parallel with genome construction, we developed a genetic-code-based firewall that—using reprogrammed viral tRNAs—reassigns two of the six serine codons to leucine during translation and combines this technology with noncanonical amino acid-based biocontainment. This amino-acid-swapped, engineered genetic code renders cells completely resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to tightly biocontain this virus-resistant host through dependence on an amino acid not found in nature (Nyerges, A et al., Nature, 2023).

Beyond enabling new therapeutics, biocatalysts, and biomaterials with properties unattainable with existing biology, these advances provide secure biosystems and foundational methods for engineering life beyond the constraints of natural biology.