Origin of Complex Life

A new Nature study this week provided the strongest evidence yet of this in its description of a new archaeon – found near an arctic hydrothermal vent - with genetic properties of both archaea and eukarya.

“The most surprising moment was when we were a couple of weeks into the project and were were looking at the first datasets that we retrieved from the sequencing center,” senior author Uppsala University microbiologist Thijs Ettema told Bioscience Technology. “We started finding all these 'eukaryotic-type' genes among these archaeal sequences. We very soon realized that this was either a very big and significant find, or some kind of weird artefact. After doing a whole array of checks in order to make sure that we could rule out the latter, we were sure: we found an archaeon that shared several genes uniquely with eukaryotes. When later this archaeon, which we then named Lokiarchaeon, turned out to form a sistergroup with eukaryotes in the Tree of Life, we were ecstatic!”

Until recent years, it has been believed that life at base is comprised of three distinct branches, all of which hailed, individually, from an unknown single ancestor: arachael and bacterial cells, simple cells that lacked nuclei, and complex eukaryotic cells containing nuclei, cytoskeletons, organelles. That three-tree system was proposed by University of Illinois microbiologist Carl Woese, who added a third branch—the archaeal branch—to the tree in 1977.

But at about the same time, a 1967 paper by University of Massachusetts biologist Lynn Margulis began catching on. That unusual paper proposed that humans’ mitochondria, the critical energy packs of our cells, are actually bacteria that were once engulfed by other cells. Genetic analyses backing this up, in addition to other genetic data finding similarities between the life branches, led to doubt the three branches rose independently of each other.

The Uppsala team’s new discovery of Lokiarchaea, which possesses many unique eukaryotic and archaeal qualities, offers what Embley called in a companion commentary “spectacular” evidence that the above independent evolution may indeed not have occurred.

Instead, chaotic, complex eukaryotes like us may have emerged out of a two-billion-year old sea of serene, simple life forms due to the unusual engulfing of a bacteria by an archaea, forming a creature rife with new possibilities.

The new paper identifies “archaeal forms that are much more closely related to the hypothetical archaeal ancestor of eukaryotes than any other currently known group of archaea,” said Koonin. “These findings clinch the case for the origin of eukaryotes from within the archaeal diversity, and point to specific part of the archaeal evolutionary tree where eukaryotes belong.”

Equally importantly, Koonin continued, are the group’s findings that, “Lokiarchaeota combine a number of ‘eukaryotic-like’ features that previously have been found scattered among different archaeal genomes. In particular, they encode components of the actin cytoskeleton, the ESCRT-III system for membrane remodeling, and the ubiquitin system. Taken together, these findings give credence to the evolutionary scenario in which the eukaryotes evolved from an archaeon with a complex cellular organization that might have been capable of engulfing bacteria.”

Embley said that, in terms of clarifying the origins of our mitochondria, “the new Archaea appear to have the potential for endocytosis and/or phagocytosis (cellular incorporation and/or ingestion). This could allow them to take up material from the environment.  In some versions of endosymbiotic theory, the host for the mitochondrial endosymbiont uses phagocytosis to engulf the bacterium that became the endosymbiont, and eventually the mitochondrion.”

 On the other hand, he noted: “There is no genetic evidence in the new paper that the new Archaea contain any genes from the mitochondrial endosymbiont, so they do not appear to have mitochondria.” But the newly discovered creature’s actin-like proteins may simply indicate, he said, that eukaryotes evolved phagocytosis before acquiring mitochondria.

Did the team prove we are descended from Lokiarchaea-like creatures? “I think that the phylogenetic analyses are carefully done and use state-of-the-art methods,” Embley said. “It is really hard to correctly infer events that may have occurred some two billion years ago. But taken together, the combination of the tree, and the enhanced number of eukaryotic-like proteins, are rather convincing for a close relationship between Lokiarchaea and eukaryotes.  I am sure that the new data and analyses will be subjected to very close scrutiny by the community once it is published, and the robustness of the trees and the position of eukaryotes within them, will be carefully tested as part of that process.”