NSF-DBT: Exploiting codon usage bias to maximize the productivity of recombinant Komagataella pastoris

Tufts University, Medford MA

Investigators

Abstract

Pichia pastoris is a food-safe yeast. It is widely used as a model organism for basic biological research and in a variety of biomanufacturing applications. Nevertheless, how to maximize the productivity of this microbe is not well understood. This project will focus on understanding how this yeast allocates its resources for protein synthesis. The results can be used to maximize productivity. The outcomes could enable significant advances in food, biomedical, and scientific applications of this yeast. Optimizing transcription and translation initiation rates to enhance recombinant protein biosynthesis have been well-studied. Controlling translation elongation has not. Using specific codon usage patterns to regulate translation elongation will be evaluated. The relative supply-demand constraints of individual codons will be assessed. This will inform coding schemes that co-maximize expression and host fitness/robustness, advancing the idea of “host-aware” synthetic biology. Outcomes will show how codon choice in heterologous genes can be exploited to simultaneously enhance expression level and minimize competition with native essential genes, which in turn enhances cellular fitness and volumetric productivity. This work leverages the expertise of the Nair lab (in systems & synthetic microbiology) with that of Adlakha lab (in engineering fungal secretion systems) and Rode lab (in chemical biology). The Nair lab will focus on optimizing production of cytosolic proteins, the Adlakha lab will focus on secreted proteins, and the Rode lab will optimize immobilization of secreted proteins for cell-free biocatalysis. Work will proceed in parallel in India and the US. Exchange visits for trainees are planned to further strengthen collaboration and co-mentoring. This project involves a collaboration between researchers from the United State and India. It is jointly supported by the US National Science Foundation and the Department of Biotechnology of the Government of India (NSF-DBT). This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.