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Body and mind

Researchers map the immune response of bacteria

The discovery of the molecular mechanism behind the immune response of bacteria may become important in combating antibiotic resistance.

Like all other organisms on Earth, bacteria have an immune response they primarily use to protect themselves from viruses that infect bacteria, called phages.

One part of the bacterial immune response sounds familiar to many people because it is a variant of the CRISPR-Cas system that researchers use to cut and paste genetic material.

Researchers have closely studied a variant of the CRISPR-Cas system and mapped the structure of the molecular actors that defend the bacteria.

The discovery may be important for understanding the development of antibiotic resistance and the evolutionary origin of our own immune response.

“We have discovered one of the mechanisms behind the immune response of bacteria to viruses. The interesting thing is that we can see that the basis of the mechanisms that bacteria use are conserved in eukaryotic cells, which are part of the human body,” explains a researcher behind the new study, Guillermo Montoya, Professor, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen.

The study has been published in Nature Communications.

How bacteria cleave the genes of invading phages into fragments

The bacterial immune response mapped by Guillermo Montoya and his colleagues involves a type III-B CRISPR-Cas system, a cyclic oligoadenylate molecule cOA4 and the genetic scissors Csx1.

Half of the bacteria containing type III CRISPR-Cas use this immune response to defend themselves from invading phages.

When a phage invades a bacterium, the phage tries to insert its own genetic material in the form of RNA into the genome of the bacterium, so that the bacterium begins to produce new phages at the expense of its own potential survival.

In response, a type III-B CRISPR-Cas system activates cOA4, and this binds to Csx1. Then, when they are interconnected, this complex begins to cleave nearby RNA into small fragments, thereby stopping any further cellular activity, thus rendering the phage unable to infect the bacteria.

“The CRISPR-Cas system identifies the infectious material and generates cOA4, which activates Csx1, which destroys all RNAs inactivating the infection,” explains Guillermo Montoya.

Mapping the structure of the protein complex using advanced technologies

Researchers from the University of Copenhagen have mapped the structure of how cOA4 activates Csx1.

They used X-ray crystallography, which involves sending X-rays through the protein complex to determine its structure. They also used cryoelectron microscopy, in which an electron microscope takes hundreds of blurry images of the protein complex and then consolidates them into one high-resolution image.

That way they could determine the structure of the protein complex in its activated and deactivated forms.

Providing new knowledge on the human immune response

Understanding this part of the immune response of bacteria that involves CRIPSR-Cas, cOA4 and Csx1 has several different interesting applications.

First, researchers have now determined that the same principle that applies to the immune response of bacteria – activating molecular scissors to cleave viral RNA – is conserved in evolution, since both bacteria and animals, including humans, possess this kind of protection against viruses.

This means that researchers can now more clearly determine how our own immune system evolved.

“However, note that eukaryotic cells do not have the CRISPR-Cas system but another system for activating specific enzymes that cleave invading DNA into fragments. But the concept is the same,” says Guillermo Montoya.

An interesting genetic tool in the laboratory?

Second, the discovery presents various molecular biological opportunities.

For example, researchers often want to see what happens if they remove all the RNA from a cell. RNA is the basis for forming proteins, so removing all the RNA removes the proteins.

The discovery of the Csx1-cOA4 complex gives researchers a very precise tool for eliminating RNA. They can now not only remove all RNA and thus all proteins in a cell but also do this at a specific time in a cell cycle, for example.

Previous techniques for removing RNA have not been good enough to eliminate all the RNA, but the new discovery potentially enables researchers to do this in the laboratory.

“We can use this system as a regulatory mechanism that switches on if we add cOA4 to Csx1. The protein complex will then cleave all the RNA into fragments and eliminate the possibility of producing proteins. We call this RNA silencing, an important tool for examining cellular function and in genetic experiments,” explains Guillermo Montoya.

Enhancing knowledge on antibiotic resistance

The discovery may also be used to improve understanding of how bacteria develop antibiotic resistance.

A lot of genetic material is cleaved when phages try to infect bacteria, and much of this is moved around inside the bacteria. These situations in which DNA from phages and bacteria are mixed together often enable antibiotic-resistance genes to gain a foothold in the bacteria and make them immune to the treatments people use to try to eliminate them.

“Part of the genetic material that phages transmit to bacteria contains the genetic code for antibiotic resistance. Knowing what happens in the process of genetic material becoming part of a bacterium is important. Maybe one day we can use this knowledge to inhibit the development of antibiotic resistance,” says Guillermo Montoya.

Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas” has been published in Nature Communications. Guillermo Montoya is employed at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen. In 2018, the Novo Nordisk Foundation awarded a Distinguished Investigator grant to Guillermo Montoya.

Guillermo Montoya
Research director, professor
The Montoya Group works to illuminate the molecular details of cellular processes. This knowledge is the basis for the understanding of diseases and the possible development of treatments. The group works in the interface between biology, physics and chemistry and uses molecular biology, X-ray crystallography and cryo-electron microscopy to dissect the working mechanisms of the macromolecules that constitute the cell’s machinery. Although these machines underlie all biological processes, there is a lack of knowledge of their function at the atomic level. “Our approach is to use advanced methodology to understand basic cellular mechanisms at an atomic level. We investigate the structural details and function of macromolecules involved in cell cycle progression and genome integrity. Deciphering the working mechanisms of these important processes provides the basis for understanding disease.” says Guillermo Montoya A recent leap in methodological development has overcome some of the barriers that avoided the study of large macromolecular complexes and allows for a degree of accuracy that has not been possible before. The Montoya group is part of this revolution and since 2017 the group has contributed to set up a state-of-the-art cryo-electron microscopy system that have accelerated their research.