AI reveals ancient microbes' role in shaping our immune system
What's the story
A groundbreaking study conducted by the University of Texas (UT) has revealed that ancient microbes, which originated billions of years ago, played a crucial role in shaping our immune systems. The research suggests that without these single-celled ancestors, complex organisms like humans might not have been as capable of combating viruses. These ancestral microbes were widespread on Earth before multicellular life evolved.
Microbial lineage
Discovery and study of ancient microbes' living descendants
The living descendants of these ancient microbes were only discovered in 2015, via traces of their DNA found deep in the ocean between Greenland and Norway. These lifeforms belong to a superphylum of archaea known as Asgard. In 2020, scientists successfully cultivated these organisms in a laboratory setting for the first time. Despite their bacterial appearance under a microscope, the archaea cells are evolutionarily closer to eukaryotic life forms than they are to simpler microbial relatives.
Evolutionary split
Asgard archaea's role in evolution of complex life
Genomic studies suggest that Asgard archaea and our eukaryotic ancestors diverged around two billion years ago. This separation marked the beginning of all complex life on Earth, including plants, animals, protists, fungi, and most algae. Some scientists theorize that Asgard ancestors developed a nucleus from a virus, that established a protective compartment referred to as a viral factory. Mitochondria might have originated from engulfing a bacterial ancestor.
Immune systems
Ancient immune defenses in Asgard genomes
The UT researchers utilized an artificial intelligence (AI) program to analyze an expanded set of Asgard genomes and identify ancient immune defenses. The analysis revealed that in comparison to bacteria, Asgard archaea have evolved a diverse range of defense systems, some of which are also innate in eukaryotes. Around 2% of the defense systems in the analyzed genomes from Asgard archaea were linked to an immune protein called viperin, which combats several viral infections by seemingly 'silencing' viral reproduction.
Protein lineage
Viperin: A common ancestor of eukaryotic and Asgard immune systems
Viperin is present in the immune systems of all complex life on Earth, suggesting it was present in the last common ancestor of archaea and eukaryotes. The new findings indicate that eukaryotic viperins and Asgard viperins are "sister proteins and share a common ancestor." Brett Baker, an integrative biologist from UT explains, "Now it's saying that even some of the defense systems in eukaryotes came from Asgards."
Defense mechanism
Asgard archaea defense genes linked to argonautes
Besides viperin, nearly 8% of the Asgard archaea defense genes analyzed were associated with argonautes—immune proteins that cut DNA to stop viral spread. Argonautes serve as "programmable immune systems" across all life domains, from archaea and bacteria to eukaryotes. To test how these proteins perform in living cells, scientists took the genetic instructions for viperins from the Asgard archaea genomes and cloned them in E. coli bacteria. When a virus was introduced, the bacterial cells showed some signs of protection.