1672681586 Spanish scientists are bringing proteins millions of years old back

Spanish scientists are bringing proteins millions of years old back to life and using them to correct albinism in human cells

The microbiologist Francis Mojica, in the Salinas de Santa Pola (Alicante), in 2017.The microbiologist Francis Mojica, in the Salinas de Santa Pola (Alicante), in 2017.Raúl Belinchón.

For years, scientists from around the world have searched for microbes in Antarctica’s ice, in the deepest trenches of the oceans, and in the Earth’s most hostile volcanic environments. His goal is to find new proteins that can be used to improve current gene editing techniques. This could open the door to a new era of science and medicine in which a variety of diseases can be cured with amazing ease by correcting the genome of patients. A study led by Spanish scientists is published today that is unique of its kind because they did not search in space but in time for these new molecules: they revived proteins from extinct organisms that lived billions of years ago to have.

Researchers have focused on recreating Cas9 enzymes, the molecules that work like scissors and are able to cut the DNA of any living thing at a specific point, and that form the basis of the CRISPR gene-editing system. Since its development in 2012, the technique has revolutionized biomedical research as it makes it possible to rewrite the textbook of any organism and is now beginning to find its first applications in the treatment of some human diseases. But this editing system is not perfect. It can introduce potentially dangerous errors into the genome. Hence the need to look for new tools for genetic editing.

CRISPR is the immune system of many bacteria and archaea. It allows them to embed virus genetic sequences into their own genome to preserve their robotic portrait. When the virus reappears, CRISPR identifies it and Cas9 kills it by cutting its genome. One of the biggest questions in this area is the origin of this bacterial immune system, which is much older than that of humans.

In search of an answer, a team composed of some of Spain’s leading gene-editing experts used a technique that reconstructs the genomes of extinct organisms. The technique is known as Ancestral Sequence Reconstruction. It uses powerful computers to compare the complete genomes of modern-day creatures – each made up of billions of letters of DNA – and estimate what the genomes of their common ancestors would look like. In this way, researchers have undertaken an amazing journey through time to obtain Cas proteins present in extinct microbes. The oldest they have reached date back to 2,600 million years ago. They’ve also made stops to rescue extinct proteins from microorganisms that lived 1,000 million, 200 million, 137 million, and 37 million years ago.

Researchers have used these ancient proteins to create new CRISPR systems and injected them into human cells. The results, published in Nature Microbiology, show that all proteins, despite being so primitive, are capable of editing the DNA of modern human cells.

Researchers have seen something like fast-forward evolution in the lab. The oldest protein of all can only cut single strands of DNA, perhaps the simplest and most primitive – human DNA is made up of double strands. But the rest of the newer Cas molecules are already becoming increasingly effective at cutting human DNA and even correcting two genes, TYR and OCA2, that cause albinism.

In the early 90s of the last century, the biologist Francis Mojica gave his name to CRISPR as part of his studies on microbes that lived in the hostile environment of the salt pans of Santa Pola (Alicante), a task for which he was assigned to the Nobel Pool . The researcher also analyzed other sequences called PAM, which are fundamental because they allow the microbe to distinguish between a virus’s genome and its own. Without PAMs, a bacterium could kill itself. What the study shows is that the oldest Cas was cut without the need for PAM. Mojica, co-author of the current work, emphasizes its importance in understanding the origin and evolution of CRISPR. “Thanks to this reconstruction, we see how the immune system of microbes became less harmful to its carriers and increasingly specific to each virus,” he points out. Additionally, “this work is important because it opens up a huge toolbox for designing better CRISPR systems,” he says.

Raúl Pérez-Jiménez, a researcher at the NanoGUNE Basque Center for Cooperative Research in Nanoscience and co-author of the study, explains the potential of the study. “These are the oldest Cas proteins that have ever been obtained. We believe they are like a diamond in the rough. Now we will examine how we can make them as efficient as the current ones or even better,” he points out.

The fact that early proteins were more generalists could be an advantage that allows them to do things that current CRISPRs are not capable of, such as: B. the simultaneous cutting of double- and single-stranded DNA and RNA sequences. “You are like a Swiss army knife. You have scissors, corkscrew, needle, screwdriver. They’re probably not the best tools in their class, but they have them all,” explains Pérez-Jiménez.

The researcher and his partner Borja Alonso Lerma patented these new molecules, which were purchased by Integra Therapeutics, a company co-founded by Marc Güell, a scientist at the Pompeu Fabra University in Barcelona and also a co-author of the study is , and who is searching for new formulas to edit genetics to treat various diseases. The company’s Scientific Advisory Board is headed by the charismatic George Church, one of the world’s leading experts in this field.

Miguel Ángel Moreno Pelayo, head of genetics at the Ramón y Cajal Hospital in Madrid and co-author of the paper, emphasizes that the reconstruction of ancient proteins opens up the possibility of developing new forms of synthetic CRISPR “that do not exist in nature”. Among other things, his team is developing these types of molecules to try to correct genetic defects in patients with amyotrophic lateral sclerosis. “We are facing a new paradigm,” summarizes the scientist.

Also co-responsible for the study is Lluís Montoliu, a researcher at the National Center for Biotechnology in Madrid, who highlights another advantage of the primitive Cas proteins. The gene-editing potential of the CRISPR system was discovered in S. pyogenes bacteria. These microbes can cause infections, so many people have antibodies that can trigger immune responses to the CRISPR extracted from them. The primitive Cass, on the other hand, are very different from all current versions, so they are not recognized by the immune system, a great advantage to avoid rejection in future medical applications, argues Montoliu.

The researcher proposes a final reflection on the results of the study. Why haven’t eukaryotes, the large group of multicellular organisms that includes us humans, evolved a CRISPR-based immune system? “Because it’s dangerous,” explains the scientist. “The most primitive CRISPR systems already allowed cutting of DNA, but they were very unselective, which probably resulted in killing the organism they were trying to protect. In the world of bacteria, the individual doesn’t matter, what matters is the population, and this system allowed them to evolve and perfect an immune system, even at the cost of killing many along the way,” he concludes.

Miguel Ángel Moreno Mateos, gene editing expert at the Andalusian Center for Developmental Biology, celebrates the new study. “Especially fascinating is the resurrection of [proteínas] Ancient Cas9 and the analysis of its activity billions of years later,” he points out. “These resurrected Cas9s offer new opportunities with considerable potential in biotechnology, although further studies and analysis are needed to make this a reality,” he adds.

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