Researchers determine a novel antiviral technique to combat bacteria

Bacteria use a wide range of defense strategies to combat viral infection, and some of these systems have resulted in game-changing technologies like CRISPR-based gene editing. Researchers think that there will be many more antiviral weapons discovered in the microbial world.

A team headed by scientists from MIT’s Broad Institute and Harvard’s McGovern Institute for Brain Research found and characterized one of these previously unknown microbial defense systems.

They discovered that certain proteins in bacteria and archaea (commonly referred to as prokaryotes) detect viruses in surprisingly direct ways, recognizing crucial components of the viruses and causing the single-celled organisms to attempt suicide to stop the infection within a microbial community.

The research is the first to demonstrate that organisms in all three domains of life—bacteria, archaea, and eukaryotes (which involve plants and animals)—use classification techniques of conserved viral proteins to safeguard against pathogens.

The research was published in the journal Science.

This work demonstrates a remarkable unity in how pattern recognition occurs across very different organisms. It’s been very exciting to integrate genetics, bioinformatics, biochemistry, and structural biology approaches in one study to understand this fascinating molecular system.”

Feng Zhang, Study Senior Author and Core Institute Member, Broad Institute, Massachusetts Institute of Technology

Zhang was also a James and Patricia Poitras Professor of Neuroscience at MIT, a professor of brain and cognitive sciences and biological engineering at MIT, and an investigator at MIT’s McGovern Institute and the Howard Hughes Medical Institute.

Microbial armory

In a previous study, the scientists scanned data on the DNA sequences of hundreds of thousands of bacteria and archaea, discovering thousands of genes with microbial defense signatures. They focused on a few of these genes that encode enzymes from the STAND ATPase family of proteins, which are implicated in the innate immune response in eukaryotes.

STAND ATPase proteins in humans and plants fight infection by recognizing patterns in the pathogen or the cell’s reaction to infection. The scientists wanted to see if the proteins in prokaryotes work in the same manner to protect against infection.

The researchers selected a few STAND ATPase genes from the previous study, presented them to bacterial cells, and then confronted those cells with bacteriophage viruses. The cells survived after a dramatic defensive response.

The researchers then wanted to know which part of the bacteriophage causes that response, so they produced viral genes to the bacteria one at a time. The portal, a component of the virus’s capsid shell that includes viral DNA, and the terminase, a molecular motor that aids in virus assembly by urging viral DNA into the capsid, both elicited an immune response. To defend the cell, each of these viral proteins activated a distinct STAND ATPase.

The discovery was startling and unprecedented. Most known bacterial defense systems detect viral DNA or RNA or cellular stress caused by infection. Instead, these bacterial proteins were directly sensing key components of the virus.

The researchers then demonstrated that bacterial STAND ATPase proteins could recognize different phage portal and terminase proteins.

“Surprisingly, bacteria have these highly versatile sensors that can recognize all sorts of different phage threats that they might encounter,” said co-first author Linyi Gao, a junior fellow in the Harvard Society of Fellows and a former graduate student in the Zhang lab.

The proteins also function as DNA endonuclease enzymes, which can cut up a bacterium’s own DNA and destroy the cell, limiting the virus’s distribution. Correspondingly, STAND ATPases in humans are known to react to bacterial infections by inducing programmed cell death in tumor cells.

“It’s quite exciting to see a connection in prokaryotes to a system that’s also inside of us,” said co-first author Jonathan Strecker, a postdoctoral researcher in the Zhang lab.

Structural analysis

The scientists used cryo-electron microscopy to investigate the molecular structure of the microbial STAND ATPases when bound to the viral proteins to get a better understanding of how they find the viral proteins.

“By analyzing the structure, we were able to precisely answer a lot of the questions about how these things actually work,” said co-first author Max Wilkinson, a postdoctoral researcher in the Zhang lab.

The team discovered that the virus’s portal or terminase protein fits into a pocket in the STAND ATPase protein, for each STAND ATPase protein comprehending one viral protein. The STAND ATPase proteins then form tetramers, which yield together key components of the bacterial proteins called effector domains. This stimulates the endonuclease function of the proteins, cutting up cellular DNA and fighting the cell.

The tetramers bound viral proteins from other bacteriophages just as firmly, indicating that the STAND ATPases detect the three-dimensional shape of the viral proteins rather than their sequence. This explains how a single STAND ATPase can recognize dozens of distinct viral proteins.

“Regardless of sequence, they all fit like a hand in a glove,” said Wilkinson.

STAND ATPases in humans and plants also perform by establishing multi-unit complexes that activate specific cell functions.

“That’s the most exciting part of this work. To see this across the domains of life is unprecedented,” said Strecker.