Jumbo phages' protective shield offers clues for fighting antibiotic resistance

Scientists are learning more about how an intriguing type of virus protects itself. Revealing its strategies could boost the fight against antibiotic resistance.

Phages are viruses that attack bacteria by injecting their DNA, then usurping bacterial machinery to reproduce. Eventually, they make so many copies of themselves that the bacteria burst.

By looking at this process in a unique type of virus called a jumbo phage, scientists hope to learn how to make new antibiotics that can address the growing crisis of resistance.

The jumbo phage has more than four times the DNA of an average phage. It uses this genetic material to create a restricted space inside bacteria where it can copy its DNA while surrounded by a protective shield made of protein.

Researchers at UC San Francisco have discovered that the shield works via a set of "secret handshakes." They allow only a specific set of useful proteins to pass through.

The handshakes all involve a large, central protein. It has a shape that lets it use different parts of itself to screen and recognize different proteins and grant them passage.

"This isn't what we expected to see at all," said Joseph Bondy-Denomy, PhD, associate professor of microbiology and immunology at UC San Francisco and senior author of the study, which appears Feb. 5 in Nature.

"It's a surprisingly complicated thing for a phage to be doing," he said.

Secret handshakes

Jumbo phages belong to a group of viruses called bacteriophages, or phages for short, which were discovered more than a century ago. Initially, phages were seen as a way to treat bacterial infections, because they are harmless to humans and can kill specific bacteria while leaving others alone. 

Interest died away once antibiotic drugs were developed, but the urgency to find new ways of fighting antibiotic-resistant bacteria is sparking it once again.

Scientists first began working on jumbo phages in the early 1980s but it wasn't until 2017 that researchers at UCSF and UC San Diego worked together to identify the flexible protein that makes up the shield. 

In 2020, Bondy-Denomy led a study showing that the protein shield protects the phage's DNA from attacks by the bacteria's defenses.

He and Claire Kokontis, BS, a graduate student, suspected this shield may give jumbo phages distinct advantages over regular phages when it comes to using these viruses against infections.

The researchers wanted to learn how the shield recognizes the useful proteins and gives them passage into the protected area. 

The secret, they discovered, was a group of proteins made by the phage that interact in an unexpected way. 

At the center was a phage protein Kokontis called Importer1, or Imp1. For proteins to be imported into the protected space, they had to interact with Imp1. 

The researchers also found an additional set of importer proteins that assist Imp1 in bringing outside proteins through the shield. 

The interaction between Imp1 and a protein outside the shield needs to be just right before the protein gets the go-ahead to enter the protected area. 

"It's like a secret handshake between two friends," said Bondy-Denomy. "The ones that have the right handshake get the OK, and the others are tossed out."

To see exactly what those handshakes looked like, Kokontis mapped the surface of the Imp1 "hand" at the molecular level. 

The map revealed that each phage protein that is allowed into the protected area has its own unique way of interacting with the Imp1 hand – one protein touches a thumb, another a finger, another a different finger. 

This variety of combinations allows the group of importer proteins to recognize an array of handshakes. 

A new way of making antibiotics

The researchers did their work using Pseudomonas bacteria, which they chose because it is notorious for its resistance to most antibiotics. 

What they learned will help scientists improve on an old approach that was left behind once antibiotics had become standard. Called phage therapy, it involves fighting one infection with another. First a human gets infected by bacteria. Then the human uses a phage to kill the bacteria. 

But bacteria are quick to evolve new defenses. Once they have devised a way to get past the phage's protective shield, they will kill the phages.

Understanding exactly how the shield's secret handshakes work will help scientists engineer phages that can withstand these evolutionary changes. 

Bondy-Denomy's lab has already developed a CRISPR-based method to make the necessary genetic changes to this specific family of phage. 

Scientists can also employ that knowledge to engineer jumbo phages that produce drugs or fight cancers caused by bacterial infections.

We're just at the starting point of realizing all this potential. By getting a handle on the basic science of how these phages work, we're laying the groundwork to adapt them for fighting disease."

Claire Kokontis, BS, graduate student