Molecular determinants of viral receptor-binding protein evolution; innovation, constraints, and evolvability

University Of California, San Diego, La Jolla CA

Investigators

Abstract

Project Summary For over a decade our group has studied the coevolution of interactions between bacteriophage λ and Escherichia coli as a model system to study species interactions as well as molecular interactions such as between λ’s receptor-binding protein (RBP) and outer membrane receptors. Using this model system, we have had success with studying many important subjects including the evolution of novelty, species, evolvability, and complexity. The next stage of this research is to more thoroughly understand the molecular drivers of RBP evolution, from understanding what types of mutations allow RBPs to gain new function, to what constrains their evolution and the properties that enhance their evolvability. Recently, we published a molecular model for how λ’s RBP evolves new function through a two-step process. The first is to gain mutations that destabilize protein quaternary structure that cause the protein to form a range of confirmations, creating new geometries of the RBP binding surface. Next, mutations in the RBP loops that create the binding surface evolve to further augment the chemical properties of the surface to facilitate interactions with new receptors. This model is in line with classic predictions that innovations evolve through non-genetic phenotypic heterogeneity (initial destabilizing mutations that create confirmational heterogeneity) and then canalization of new function (loop mutations). We propose to collect data on massive RBP genetic libraries to test this model and to further refine it. To do this, we will use high throughput RBP gene-editing and phenotyping assays that we have developed over the past decade. We will also assemble a library of 96 E. coli outer membrane proteins to test activity of the RBP variants on a diversity of receptors. For Aim 1, we will test the molecular model by determining which mutations cause RBP gain-of-function. Aim 2 builds on 1 by examining what protein characteristics constrain RBP gain-of-function evolution and these data will be used to test protein tradeoff theories. Aim 3’s goal is the opposite of Aim 2 and is designed to determine which protein features drive increased gain-of-function evolvability. Aim 3 data will be used to test theories on protein robustness and evolvability. Overall, our goals are to establish a molecular model for RBP gain of function that can be generalized to other viral systems with the goal of predicting viral host-shifts, and to test general evolutionary theories on how novel protein-protein interactions evolve, test which physical principals cause protein tradeoffs, and identify determinants of protein evolvability.