Molecular mechanisms underlying functional evolution of bioluminescent proteins from haloalkane dehalogenases

The National Institute of General Medical Sciences awarded The University of Chicago $150,104 on March 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate the molecular mechanisms underlying the repeated functional evolution of bioluminescent proteins derived from haloalkane dehalogenases.

The research examines how a new catalytic mechanism—monooxygenase-catalyzed light production—repeatedly evolved in distantly related taxa by recruiting homologous haloalkane dehalogenases with ancestral hydrolase activity. Specifically, the work focuses on bioluminescent proteins in octocorals and brittle stars, using computational phylogenetic methods to reconstruct genetic trajectories and understand the repeated transition from hydrolase to monooxygenase activities. The recipient will collaborate with Dr. Joseph Thornton at the University of Chicago. Understanding these molecular mechanisms has potential applications for bioengineering bioluminescent proteins used as biological tools in gene expression reporting, protein-protein interaction monitoring, and optogenetics.

The award period runs from March 1, 2026, through February 28, 2029, with place of performance in Illinois.

Abstract

Research in evolutionary biochemistry has provided insights into how new enzyme functions evolve through changes in substrate specificity. However, much less is known about how new catalytic mechanisms evolve. What molecular mechanisms and processes shape the emergence of new catalytic mechanisms? To what extent is this evolution repeatable? And how might evolutionary history shape the evolution of new catalytic mechanisms? Addressing these questions provides a mechanistic understanding how extant enzymes catalyze diverse chemical reactions, functioning as molecular machines to produce the diversity of life. This research is often challenging because diverse catalytic mechanisms are usually found across protein superfamilies, beyond the phylogenetic horizon of what can be reconstructed. Here, i propose to work with DR. Joseph thornton at the university of chicago to investigate the repeated evolution of a new catalytic mechanism, monooxygenase-catalyzed light production, in the bioluminescent proteins of octocorals (cnidaria) and brittle STARS (echinodermata). This is an especially powerful system, since these bioluminescent proteins repeatedly evolved in distantly related taxa, each time by recruiting homologous haloalkane dehalogenases with ancestral hydrolase activity. A mechanistic understanding of how these bioluminescent proteins repeatedly evolved may provide fundamental information useful for bioengineering these proteins, which already serve as invaluable biological tools for reporting gene expression, monitoring protein-protein interactions, and activating molecules in optogenetics. In this project, i will investigate the molecular mechanisms underlying the repeated functional transition between hydrolase to monooxygenase activities. First, i will use computational phylogenetic methods to reconstruct the genetic trajectories to evolving monooxygenase activity for each taxon. Then, i will then use experimental methods to functionally identify causal mutations between protein sequence and function. Finally, i will perform manipulative experiments to test the effects of functional mutations at deeper nodes within each lineage and across lineages. Altogether, these findings will illuminate the molecular mechanisms and factors underlying the repeated evolution of monooxygenase-catalyzed light production from haloalkane dehalogenases. More broadly, this research will provide insight into how historical contingency and lineage specific evolutionary processes shaped the emergence of new catalytic mechanisms. The research training plan proposed here will prepare me for my future career as an independent principal investigator by strengthening my expertise in experimental evolutionary biology and computational molecular phylogenetics. This training will allow me to develop a robust framework in molecular evolution, supporting my integrative and interdisciplinary research program that combines organismal evolutionary biology with biochemistry to understand the evolution of novel phenotypes across biological scales.