Biology subjects

Gerbino, K. R.

Publications and source records attributed to Gerbino, K. R..

3 recordsLinked to original sources

bioRxiv2024

Bacteriophage {Phi}21s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity

How viruses evolve to expand their host range is a major question with implications for predicting the next pandemic. Gain-of-function experiments have revealed that host-range expansions can occur through relatively few mutations in viral receptor-binding proteins, and the search for molecular mechanisms that explain such expansions are underway. Previous research on expansions of receptor use in bacteriophage {lambda} has shown that mutations that destabilize {lambda}s receptor-binding protein cause the receptor-binding protein to fold into new conformations that can utilize novel receptors but have weakened thermostability. These observations led us to hypothesize that other viruses may take similar paths to expand their host range. Here, we find support for our hypothesis by studying another virus, bacteriophage 21 ({Phi}21), which evolves to use two new host receptors within two weeks of laboratory evolution. By measuring the thermodynamic stability of {Phi}21 and its descendants, we show that, as {Phi}21 evolves to use new receptors and expands its host range, it becomes less stable and produces viral particles that are genetically identical but vary in their thermostabilities. Next, we show that this non-genetic heterogeneity between particles is directly associated with receptor use innovation, as phage particles with more derived receptor use capabilities are more unstable and decay faster. Lastly, by manipulating the expression of protein chaperones during {Phi}21 infection, we demonstrate that heterogeneity in thermostability and receptor use breadth of phage particles is directly related to the folding of phage proteins into different conformers. Altogether, our results provide support for the hypothesis that viruses can evolve new receptor-use tropisms through mutations that destabilize the receptor-binding protein and produce multiple protein conformers.

evolutionary biology↗

bioRxiv2023

Rapid bacteria-phage coevolution drives the emergence of multi-scale networks

Interactions between species have catalyzed the evolution of multiscale ecological networks-including both nested and modular elements that regulate the function of diverse communities. One common assumption is that such complex pattern formation requires long evolutionary timescales, spatial isolation, or other exogenous processes. Here we show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure. In just 21 days of laboratory coevolution, Escherichia coli and bacteriophage {Phi}21 coevolve and diversify to form elaborate cross-infection networks. By measuring [~]10,000 phage-bacteria infections and testing the genetic basis of interactions, we identify the mechanisms that create each component of the multiscale pattern. Initially, nested patterns form through an arms race where hosts successively lose the original receptor (LamB) and phages evolve to use a second (OmpC) and then a third (OmpF) receptor. Next, modules form when the cost of losing the third receptor, OmpF, increases and bacteria evolve resistance mutations that modify the OmpF receptors extramembrane loops. In turn, phages evolve adaptations that facilitate specialized interactions with different OmpF variants. Nestedness reemerges within modules as bacteria evolve increased resistance and phages enhance infectivity against module-specific receptor variants. Our results demonstrate how multiscale networks evolve in parasite-host systems, illustrating Darwins idea that simple adaptive processes can generate entangled banks of ecological interactions.

evolutionary biology↗

bioRxiv2022

Comparison of bacterial suppression by phage cocktails, dual-receptor generalists, and coevolutionarily trained phages

The evolution and spread of antibiotic resistant bacteria have renewed interest in phage therapy, the use of bacterial viruses (phages) to combat bacterial infections. The delivery of phages in cocktails where constituent phages target different modalities (e.g., receptors) may improve treatment outcomes by making it more difficult for bacteria to evolve resistance. However, the multipartite nature of cocktails may lead to unintended evolutionary and ecological outcomes. Here, we compare a 2-phage cocktail with a largely unconsidered group of phages: generalists that can infect through multiple, independent receptors. We find that both generalists and cocktails that target the same receptors suppress bacteria similarly for ~2 d. Yet a "trained" generalist phage, which previously adapted to its host via 28 d of coevolution, demonstrated superior suppression. To understand why the trained generalist was more effective, we measured the resistance of bacteria against each of our phages. We find that, when bacteria were assailed by 2 phages in the cocktail, they evolved mutations in manXYZ, a host inner-membrane transporter that {lambda} uses to move its DNA across the periplasmic space and into the cell for infection. This provided crossresistance against the cocktail and untrained generalist. However, these mutations were ineffective at blocking the trained generalist because, through coevolutionary training, it evolved to bypass manXYZ resistance. The trained generalists past experiences in training make it exceedingly difficult for bacteria to evolve resistance, further demonstrating the utility of coevolutionary phage training for improving the therapeutic properties of phages.

evolutionary biology↗