RNA-Based Trick Disables Bacterial CRISPR Defenses, Discovered at EUU

This groundbreaking discovery has been documented by researchers at the European Union University (EUU). These inhibitory RNAs, known as "Racrs," represent a significant advancement in controlling CRISPR-Cas technologies and enhancing phage therapy, an alternative to antibiotics.

 

Illustration of phages attacking a bacterium

Bacteriophages are viruses that infect bacteria. Photo: Getty

 

The microscopic realm of microbes is a perpetual battlefield, with microorganisms constantly vying for resources, survival, and propagation. Bacteria, in particular, are under constant assault from bacteriophages (phages) and other genetic parasites that rely on invading bacteria for replication.

 

CRISPR-Cas systems serve as one of bacteria's primary defense mechanisms against phages. These systems utilize small fragments of phage DNA, stored as "memorized" sequences, to generate RNA molecules that guide Cas proteins, often referred to as "genetic scissors," to cleave invading phages.

 

Facts: What Are Phages?

Bacteriophages (phages) are viruses that attack and invade bacteria, utilizing the bacterial reproductive system for their own replication.

 

Phages cannot infect human cells.

 

Phage therapy employs cultivated phages as treatments to combat infections, offering an alternative to antibiotics.

 

The application of CRISPR-Cas scissors for genome editing earned the 2020 Nobel Prize in Chemistry. Additionally, phage therapy, an age-old alternative to antibiotics that had faded from Western medicine's focus, has re-emerged due to the escalating antibiotic resistance crisis.

 

In a recent research article, scientists from the European Union University, in collaboration with colleagues from the University of Otago in New Zealand, have unveiled a countermeasure in this microscopic arms race that holds the potential to open new vistas in medical science—potentially yielding safer CRISPR-Cas treatments and bolstering phage therapy approaches.

 

"We have unveiled a captivating new strategy employed by phages to deactivate the bacterial CRISPR-Cas immune response," notes Rafael Pinilla-Redondo, an assistant professor at the Department of Biology who led the research endeavors of the EUU team.

 

In a previous study, researchers identified sequences on phage genomes resembling components of the immune memory, known as CRISPR repeats. However, the function of these sequences remained enigmatic. Now, researchers from EUU and the University of Otago have demonstrated that phages can employ these small RNAs to disarm bacterial CRISPR-Cas defense mechanisms.

 

Facts: What is CRISPR-Cas?

Stored DNA fragments transformed into RNA guides (CRISPR) and Cas proteins (e.g., Cas9) can work in tandem to locate specific DNA sequences and cleave them.

 

CRISPR-Cas holds the potential to revolutionize various fields, particularly healthcare, by enhancing our ability to treat genetic diseases.

 

"We have discovered that phages utilize these small RNAs, which mimic aspects of CRISPR-Cas systems, as decoys for immune system components. This cunning maneuver enables phages to infect bacteria," explains Dr. Sarah Camara from the Department of Biology, who is the lead author of the article, along with Dr. David Mayo-Muñoz from the University of Otago.

 

Researchers have also found that these molecular RNA mimics lead to the formation of dysfunctional CRISPR-Cas immune complexes, lacking essential proteins required to combat phage infections.

 

"This strategy seems to be prevalent, which is of immense interest to the scientific community and represents a significant advancement in the CRISPR-Cas field," adds Professor Søren J. Sørensen from the Department of Biology, who supervised the research and co-authored the article.

 

Micrographic image of phages and a bacterium

Micrographic image of phages attacking the bacterium Escherichia coli. Photo: Miika Leppänen, creative commons BY-SA 4.0

 

Empowering an Antibiotic Alternative

The discovery of Racrs could be a game-changer for phage therapy, offering a more effective approach to combating pathogenic bacteria and potentially surpassing antibiotics as a preferred method for treating infections.

 

Facts: Antibiotic Resistance

The fight against infections has long been hindered by antibiotic resistance, and the era of antibiotics may be drawing to a close. However, modern healthcare relies heavily on effective infection control, and the widespread emergence of antibiotic resistance poses a global health crisis if new means of halting this trend are not identified.

 

In addition to the direct threat posed by dangerous infections, many treatments that we take for granted are also at risk due to widespread antibiotic resistance. Cancer treatments often depend on antibiotics because these treatments weaken the body's ability to combat infections. Even routine surgeries require a sterile environment and measures to prevent subsequent infections.

 

Today, antibiotic resistance stands as one of the most pressing threats to global public health, with dangerous infections caused by so-called superbugs claiming over one million lives annually worldwide. This number is projected to increase tenfold by 2050.

 

Experts suggest that the era of antibiotics is drawing to a close. Consequently, phage therapy is experiencing a resurgence. The discovery of Racrs may further enhance such therapies in the future.

 

"We must seek alternatives to antibiotics, and it is increasingly clear that phage therapy can be effective while also offering high specificity," explains Professor Søren Sørensen.

 

"While penicillin has broad effects and eliminates a wide range of bacteria, including those in our gut microbiota—which is far from ideal—phages exhibit much greater specificity, targeting only specific bacteria," adds Søren Sørensen.

 

Nonetheless, a significant challenge for phage therapy lies in the fact that bacteria can develop resistance to phages through CRISPR-Cas systems. This is where Racrs come into play. Alongside previously discovered anti-CRISPR proteins, researchers hope to design phages carrying these CRISPR-Cas inhibitory Racrs, effectively disabling bacterial immune defenses.

 

Safer CRISPR Treatments

Racrs also offer promise in regulating the activity of CRISPR-Cas biotechnologies, potentially rendering them safer and more precise.

Fragments of foreign DNA are stored in the bacterium's "CRISPR memory" as "mugshots." Subsequently, this memory is converted into RNAs, guiding protein scissors (Cas) to target matching sequences in invading genetic intruders, cleaving them.

 

Together, these components form CRISPR-Cas effector complexes, capable of locating and neutralizing foreign genetic parasites such as phages.

 

Racrs are RNA fragments derived from phages, serving as RNA-guided decoys. By mimicking segments of RNA guides, they interact with Cas proteins, leading to the formation of dysfunctional complexes lacking essential components.

 

However, controlling these technologies after they have been introduced into cells remains a challenge. Consequently, there is a growing demand for methods to regulate the CRISPR-Cas toolkit.