Study shows how CRISPR RNAs help the immune system to identify and combat viruses

What tasks must be completed today, and which are the most vital? In their daily lives, people must continuously make priorities. Bacteria are no exception: while using CRISPR to battle viruses, they must prioritize as well. However, the method by which this priority is accomplished is unknown.

Chunyu Liao, lead author of the study, in the HIRI lab. Image Credit: Mario Schmitt / Helmholtz Institute for RNA-based Infection Research.

In collaboration with researchers from the universities of Würzburg, Freiburg, and Leipzig, scientists from the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, a joint project of the Helmholtz Centre for Infection Research (HZI) in Braunschweig and Julius-Maximilians-Universität (JMU) Würzburg, have now outlined an underlying mechanism for the first time. The results of their research were reported in the journal Nature Microbiology.

To prevent themselves from infecting viruses, most bacteria employ CRISPR-Cas systems. The defensive mechanisms capture fragments of viral DNA and place them between repeated, fixed patterns. These segments, which are made up of alternating repetitions and viral DNA snippets, eventually create CRISPR ribonucleic acids (RNA).

CRISPR RNAs assist the immune system in recognizing and combating viruses. Grabbing a fragment of viral DNA gives instant protection. Protection can be handed down across generations by preserving the bits inside the bacterial DNA.

Preventing system overload—but how?

The process of storage, however, is not without risk: Exploring with that many viruses at once would overload the CRISPR-Cas systems with tens or perhaps hundreds of snippets. As a consequence, the systems have created a method of prioritizing the most recent protection snippets.

As a reason, they give better protection against the viruses that the cell has recently encountered. While the phenomena have been observed, the mechanism that causes it has remained unknown.

The study team revealed that the leader RNA optimizes immune defense using the CRISPR-Cas9 system from bacterium Streptococcus pyogenes as a model. This sequence is responsible for taking up viral snippets and is placed next to the section of repetitions and viral DNA.

It wraps with the first two repetitions enclosing the newest snippet during transcription, favoring the generation of the initial CRISPR RNA over subsequent CRISPR RNAs. As a result, the system begins to seek for the infection.

The mechanism is specific to many CRISPR systems involving the Cas9 protein commonly used for genome editing, although other mechanisms likely exist for prioritizing anti-viral defense.”

Chunyu Liao, Study Lead Author and Former Postdoc, Helmholtz Institute for RNA-based Infection Research

New CRISPR element, new possibilities

Chase Beisel is a JMU professor and the director of HIRI’s Synthetic RNA Biology Department added, “This outcome was fully unexpected. The leader RNA was only thought to direct where new viral snippets were integrated.”

The structure formed between this sequence and the first two repeats is a new element in CRISPR biology. It reveals another mechanism by which RNA can contribute to immune defense. Our research assigns a whole new role to the leader sequence, which has not previously been associated with CRISPR RNA production.”

Chunyu Liao, Study Lead Author and Former Postdoc, Helmholtz Institute for RNA-based Infection Research

“The 2020 Nobel Prize in Chemistry was awarded, among other things, for the discovery of how CRISPR systems involving Cas9 produce CRISPR RNAs. Our study offers new insights into this process: It shows why the location of these snippets is as important as their sequence,” Beisel Concluded.

This newly found process might be utilized to build multiplexed CRISPR technologies for the diagnosis and treatment of diseases caused by a range of mutations in the genome, in addition to offering insights into the arms race among bacteria and viruses.