Simulation of how E. coli-killer operates is a roadmap for targeted treatments

For the first time, researchers have simulated the mechanical process of how a virus, a type of bacteriophage, infiltrates and kills a bacterial cell—offering new insights that could improve treatment of stubborn bacterial infections, as well as other diseases.

Bacteriophages are a type of virus that infect and kill bacteria. And the T4 bacteriophage has a knack for killing E.coli, which causes roughly 265,000 cases of food poisoning in the U.S. annually.

A University of Michigan team led by Ameneh Maghsoodi, a postdoctoral researcher, and Noel Perkins, a professor of mechanical engineering, collaborated with the laboratory of Ioan Andricioaei, a professor at the University of California,  Irvine, to simulate the process T4 uses to inject its DNA into a target cell. Maghsoodi, who is now a postdoctoral fellow at Harvard University, and Perkins answered questions about the findings.

Why is understanding a process like this—T4’s infection of E.Coli—important?

Perkins: The injection process isn’t something we can observe or measure with current experimental methods. Understanding it would answer basic scientific questions, as well as queue up potential engineering advances for medicine.

Maghsoodi: What we learn from research like this can advance both science and engineering. How much energy is used in the injection process? What are the mechanisms that dissipate that energy? What force is needed to rupture the outer membrane of E.coli? What’s the timescale of the process?

How did you go about figuring out this process?

Perkins: We employed a multi-scale modeling approach, one that leverages atomistic-level detail for a small but critical fraction of phage T4 through our collaborator (Andricioaei). A second model approximates the remainder of T4 as an elastic continuum. Doing so leads to an intricate, but complete, model of T4 that can simulate the entire injection process including the interactions between, and changes to, the major components (protein subdomains) of T4.

How does your simulation describe the interaction between T4 and E.coli?

Maghsoodi: Phage T4 employes a fascinating nano-scale injection machine that attacks E.coli, rupturing the host cell membrane like a drill or hypodermic needle. The virus then injects its genomic DNA into the host. The host then makes and releases many copies of the virus and subsequently perishes. 

In other words, phage T4 hijacks E. coli into replicating the virus in completing the infection life-cycle.

We observed that the energy that drives the injection process derives from the initial (elastic) energy stored in a flexible sheath-like structure that is available when the tail tube is suddenly released from the grip of the baseplate. That sudden release causes the sheath to contract in a “contraction wave” that propagates from the bottom of the sheath where it attaches to the baseplate to the top of the sheath where it attaches to the neck. 

This results in a very large (i.e., nonlinear conformational) change of the sheath that contracts to a small fraction of its original length. As the sheath contracts, it drives the needle-like tail tube down and into the outer cell membrane of E.coli. It does this with the speed and force needed to pierce that outer membrane without otherwise damaging the host. The sheath’s energy that drives this process is also dissipated by several mechanisms and, importantly, the viscosity of the nano-scale fluid gap between the sheath and the tail tube and the internal damping of the sheath.

It’s the energetic competition between this energy source and these dissipation mechanisms that controls the time scale of the injection process. 

With all that detailed information about how the process works, what can we do with it?

Maghsodi: Knowing how T4’s injection machinery works can open the door to engineering nano-injection machines for successful DNA injection in future medical applications.

T4 creates just the right force and velocity at the injection point to avoid damaging the host membrane and organelles inside. Any engineered nanoscale design must replicate that feat in order to successfully deliver DNA to a host—a feat honed over millions of years of evolution!

Understanding that feat, in the quantitative way we have in this study, provides rich information for designing efficient nano-scale injection devices for future applications.

The paper is titled “How the Phage T4 Injection Machinery Works: Energetics, Forces, and Dynamic Pathway.” The research was supported by the National Science Foundation.