Visualisation of argonaute
Visualisation of argonaute

Study reveals unified origin of life’s antiviral defenses

All life on Earth deals with viral infections on a daily basis, so defense mechanisms against viruses are crucial for survival. In humans, our immune system fulfills this function. But where does this defense mechanism come from, and can it be traced back to a single ancestor? Dr. Pedro Leão, a new researcher at RIBES, combined protein lineage research with AI-powered protein structure prediction, showing that some proteins involved in our immune system evolved from an ancient common ancestor.

Antiviral systems

Immune systems are integral to survival against viral infections. To find a common ancestor of these defense mechanisms, researchers are examining antiviral systems shared by all life forms, from prokaryotes (such as bacteria and archaea) to eukaryotes (animals, plants, and humans). Recently, there has been a growing discussion about a potential bacterial origin of innate immune mechanisms. However, little is known about the role of these defense mechanisms in archaea.

Link between Prokaryotes and Eukaryotes

In this new study, led by dr. Pedro Leão, a new researcher at RIBES together with groups from UT Austin (University of Texas, Austin), the researchers examined defense systems in Asgard archaea, which is the closest relative between prokaryotes and eukaryotes. The study aims to shed light on the origins of proteins involved in the immune system. The researchers combined protein sequence phylogeny, a well-established technique for examining the evolutionary heritage of proteins, with AI-powered protein structure prediction. For this, they focused on two proteins shared by all forms of life: viperins and argonautes. Dr. Pedro Leão: “It was already well established that Asgard archaea contribute to the Eukaryotic cellular complexity we see today. We believe the same applies for their defense mechanisms.”

Common ancestor of antiviral mechanisms

The research demonstrated that Asgard viperins (asVip) are sister proteins to eukaryotic viperins, suggesting that eukaryotic and Asgard viperins evolved from a common ancestor. Moreover, they found that asVip proteins are functional and capable of protecting cells against viral infections.

Regarding argonautes, by positioning Asgard proteins in a sequence and structural context, they uncovered compelling evidence linking eukaryotic and prokaryotic argonautes to ancient Asgard versions of this protein, showing a remarkably high degree of conservation.

Infographic of the mechanisms of viperins and argonautes
Mechanism of viperins and argonautes

AI-powered predictions

These computational predictions have been recently validated by two independent research groups. Leão: “This underscores the effectiveness of combining classic protein phylogeny with protein structure homology in the quest to elucidate the functions and origins of proteins found across the tree of life.”

This work is important to bring archaea to the debate about the origin of immune mechanisms we see today in Eukaryotes. In fact, by shedding light into the participation of Asgard archaea in the origin of immune system mechanisms a new concept of Ancestral Immunity was recently introduced

Dr. Leão’s newly established group at the Microbiology department at RIBES intends to leverage the protein structure prediction to find new defense systems in archaea that can be linked to eukaryotic immune system proteins. The aim of the research is not only to help elucidate the evolutionary history of immunity but find proteins with potential interest into biomedicine and therapeutics.

Leão: “Today in the world of computational biology the biggest challenge is to select the best data to move forward in your research. Protein structure prediction with AI can be a powerful ally in facilitating this filtering process, helping us to save time and money on the selection of the best candidates for experimental validation of computational predictions.”