Engineering Biomolecular Condensates for Metabolic Pathway Control

Abstract

Biomolecular condensates—membrane-less organelles formed through liquid-liquid phase separation—play pivotal roles in cellular biochemistry by organizing processes like ribosome biogenesis, gene expression, and metabolism without membrane boundaries. Their native significance, combined with their relative ease of engineering due to their membrane-less nature, positions these structures as prime targets for synthetic biology, offering novel ways to compartmentalize and amplify cellular functions. Particularly in metabolic pathway control, where reaction dynamics are concentration-sensitive, biomolecular condensates present a unique opportunity for regulation. With varied outcomes currently reported in literature, a comprehensive framework to harness these assemblies for metabolic engineering remains elusive.

This thesis advances the integration of biomolecular condensates into metabolic engineering, exploring their potential to optimize pathway efficiencies. Following a review of current methodologies, the development of an optogenetic tool for inducing protein condensates in vivo is discussed. Subsequent sections detail the customization of condensates for targeted protein recruitment in Saccharomyces cerevisiae and assess their impact on metabolic processes through rigorous modeling. Experimental investigations reveal how engineered condensates influence metabolic pathway outputs in S. cerevisiae, highlighting the conditions under which they enhance performance.

In conclusion, this thesis provides a comprehensive examination of biomolecular condensates’ potential in re-engineering metabolic pathways for improved performance. By combining theoretical insights with practical methodologies, it contributes significantly to the field of metabolic engineering and more broadly to biomolecular condensate engineering, offering a new paradigm for the design and optimization of biological systems. Future work will likely explore the scalability of these approaches, their application across various biological pathways, and the integration of computational tools to further refine the design and functionality of biomolecular condensates for synthetic biology purposes.