For years, scientists from around the world have been searching for microbes in the ice Antarctica, in the deepest ocean trenches and in the most hostile volcanic environments on the planet. The goal is to track down new proteins that can be used to improve gene-editing techniques. This may open the door to a new era of science and medicine, in which many diseases can be treated by correcting the defective genomes of patients with surprising ease.
Today, a study was published by a group of Spanish scientists who didn’t just look for new molecules in space – they looked for them in time. The team managed to revive proteins from organisms that have been extinct for billions of years.
The researchers focused on recreating Cas9 enzymes – molecules that act like scissors, capable of cutting the DNA of any organism. This is the basis of the CRISPR gene editing system.
CRISPR is the immune system of many bacteria and archaea. It allows them to embed the genetic sequences of the virus into their genome so that if the virus appears again, CRISPR can identify it, while Cas9 enzymes can cut into its genome.
Since its development in 2012, the CRISPR gene-editing system has revolutionized biomedical research, making it possible to rewrite the instruction book for any organism. Now, it has begun to be used to treat some diseases in humans. However, this gene-editing system is not perfect: it can lead to potentially dangerous errors in the genome. The search for safer alternatives continues.
The outstanding question in the field of genetics is how the bacterial immune system – much older than that of mankind – came into existence. In search of an answer, a team made up of some of Spain’s leading gene-editing experts has used technology to reconstruct the genomes of extinct creatures. This technique is known as ancestral sequence reconstruction. It uses powerful computers to compare the entire genomes of organisms — each made up of billions of letters of DNA — and assess what the genomes of their common ancestors would have looked like.
So far, researchers have made impressive progress recovering Cas proteins from extinct microbes. The oldest one they discovered is 2.6 billion years old. They also rescued extinct protozoans from microorganisms that lived between 37 million and 1 billion years ago.
The researchers created new CRISPR systems using these ancient proteins, and injected them into human cells. The results — published in the journal Nature Microbiology — show that despite being very primitive, all of these ancient proteins are capable of modifying modern DNA. human cells.
In the early 1990s, biologist Francis Mujica was studying microbes that lived in the hostile environment of the salt flats of Santa Pola, in the Valencian Community of Spain. He also analyzed a DNA sequence known as PAM, which allows microbes to distinguish between their genomes and those of viruses. Without PAMs, bacteria can easily kill themselves. But the new study—which Mojica co-authored—suggests that some of the oldest CAS enzymes are able to precisely cut DNA without the need for PAM.
Mojica highlights the importance of this discovery for understanding the origin and evolution of CRISPR:
“Thanks to this recovery, we can see how the immune system has become less harmful to its carriers of microbes and more specific to each virus.”
Additionally, “this work is important, as it opens up a huge toolbox for creating better CRISPR systems.”
Raul Perez Jimenez – a co-author of the study and a researcher at the Basque Center for Collaborative Research in Nanoscience – also sees a lot of potential in the research.
These are the oldest Cas proteins ever obtained. Now, we’re going to examine how we can make them as effective as the current ones, or even better! “
Earlier proteins may be able to do things that current CRISPR cannot, such as cut both a double-stranded RNA sequence and a single-stranded DNA sequence at the same time.
“They’re like Swiss Army knives. They have scissors, wrenches, needles, screwdrivers… maybe not the best tools, but they have it all,” Perez Jimenez notes.
Reconstructing ancient proteins opens up the possibility of designing new forms of synthetic CRISPR “not found in nature,” says Miguel Angel Moreno Pelayo — chair of genetics at Ramón y Cajal Hospital in Madrid and another co-author on the work. Among other projects, he is working on He and his team are developing a method to correct genetic defects in patients with ALS.
Co-author Lluís Montoliu – a researcher at the National Center for Biotechnology in Madrid – emphasizes another feature of primitive Cas proteins. Unlike modern proteins, they are not detected by the human immune system, which means they are less likely to be rejected by patients’ immune systems when used in future medical applications.
Miguel Angel Moreno Mateos, an expert in gene editing at the Andalusian Center for Developmental Biology, celebrates the new study:
“It’s especially surprising that old Cas9 is being revived [proteins] And analyze their activity after billions of years. Revived Cas9s offer new possibilities with great potential in biotechnology.” Although, he warns, “further study and analysis needs to be done for this to become a reality.”