Novel ribosomes

Can we hack nature's 3D printer to unlock new functions?

Synthetic biology is a 21st century field that involves engineering the genetic material of organisms to have new characteristics. Our vision is to alter the machinery of the ribosome to expand beyond "normal" protein translation it was evolved to do, and unlock entirely new modes of polymer synthesis.

Advances in synthetic biology methods now allow us to use the existing machinery of the ribosome as a starting point to engineer and evolve specialized constructs capable of new and improved synthetic function. We envision ribosomes specialized in four directions:

… towards specific products: We aim to engineer rRNA variants towards the overexpression of pharmacologically relevant and high-value proteins, particularly those with low recombinant expression. After identifying the mechanism of why these products are not expressed well, specific activity regions of the ribosome are engineered as needed.

… towards environments: we will explore rRNA motifs that increase resistance to oxidization or reduction, nutrient starvation, and reaction temperature. Adapting to challenging environments may be necessary to produce certain difficult proteins and contribute to efficient and sustainable production of biologicals. Ribosomes can be specialized by randomizing critical features and evolving them under new environmental conditions and by drawing inspiration from extremophile organisms thriving in these same environments to create a chimeric ribosome.

… towards non-canonical substrates: Elongated peptide backbones from β- and γ-amino acids, enabling synthesis of protease-resistant peptidomimetic drugs, as well as substrates with functionalized, bulky side chains would benefit from a dedicated ribosomal active site. As the catalytic center has evolved to accommodate α-substrates with side chains of modest size, this goal would require engineering of the active site rRNA or retro-evolving the ribosome.

… towards genetic code expansion: Expansion beyond the current 64 codons allow new substrates to be introduced site-specifically while preserving all canonical tRNA:codon pairs. By incorporating novel tRNAs that form not three, but four base pairs with the mRNA. Preliminary research shows that ribosomes can be evolved to better accept quadruplet tRNAs and reliably undergo a +1 frameshift.

The creation of custom specialized ribosomes is a transformative technology for enhanced protein production and creating novel bioactive drugs, and would interface well with existing efforts at the NIH/NCI in molecular medicine and protein technologies.