Johns Hopkins University
To achieve size-regulation of nucleic acid based biomolecular condensates and sustained cycles of condensate formation-growth-dissolution by coupling condensation dynamics and chemical reaction dynamics
Biomolecular condensates are transient organelles that are ubiquitous across life, and which are widely used -for instance- to host intracellular chemistry. The ubiquity of transient compartmentalization hints at an evolutionarily earlier time when complex chemistry and compartmentalization coupled to evolve in tandem. This grant funds Rebecca Schulman, a Professor of Chemical and Biomolecular Engineering at Johns Hopkins University, Elisa Franco, a Professor of Mechanical and Aerospace Engineering at the University of California Los Angeles, and Deborah Fygenson, a Professor of Physics at the University of California Santa Barbara, to conduct a series of in vitro studies to improve our understanding of systems where chemical reactions are coupled to condensation dynamics. What are the elementary components of, and the fundamental principles governing, a plausibly-origin-of-life-relevant ‘dynamic soup’ whereby chemistry and compartmentalization couple to achieve biological function? Schulman, et. al. plan to explore this question by studying how chemical reactions affect condensate (or droplet) volume and the dynamics of droplet size change. They’ll then leverage that knowledge to achieve sustained cycles of condensate creation, growth, and dissolution over a range of spatial and temporal scales. Under project phase 1, the team will measure the phase behavior of various condensing nucleic acid (NA) polymers as a function of the concentration of several ‘effector’ molecules that are designed to modify the condensate state. The team seeks to determine the steady state properties of a condensing-molecule / effector system defined by a fixed concentration of effector molecules. Doing so will help them interpret the effects of rapid changes in, and non-uniform distributions of, effectors produced or consumed by various chemical reactions. Under phase 2, the team will explore whether it’s possible to achieve stabilized micron-scale condensates by coupling chemical reactions and condensation. The strategy relies on two key ideas. First, that the chemistry of interest should interfere with the tendency of droplet molecules to aggregate since this will inhibit the growth of an existing droplet. The PIs will exploit chemistry that produces growth inhibiting effectors (RNA polymers). Second, the growth inhibiting chemistry should become more effective with increased droplet size since this amounts to size-stabilizing negative feedback. The team will leverage in-droplet chemistry to synthesize the growth inhibiting RNA polymers and they expect that these polymers will be more effective in large droplets because it takes longer on average to diffuse out of large droplets than small droplets. Under phase 3, the researchers aim to build reaction-condensate systems that exhibit sustained cycles of droplet emergence, growth, and dissolution. The team will pursue two strategies. First, they’ll use a so-called ‘transcriptional oscillator’ positioned in the condensate environment (the surrounding dilute phase) to chemically synthesize a droplet-growth-inhibiting (RNA-based) effector. Second, they’ll implement a chemical feedback system featuring a growth inhibiting effector that does not inhibit growth until it diffuses out of a droplet and chemically reacts with certain molecules in the environmental. If successful, the project will provide insight into how cells exploit couplings between chemical and condensation dynamics to implement biological function, while also establishing a toolset that allows researchers to build information-bearing entities that exhibit sustained cycles of formation, growth, and dissolution.