Evolution: new mechanisms reveal the proximity between eukaryotes and archaea

Within the realm of living organisms, between bacteria and eukaryotes, are the archaea. Unicellular and with no nucleus like bacteria, they are on the other hand much closer to eukaryotes, made up of cells with nuclei, from an evolutionary point of view. So much so, in fact, that scientists have speculated that eukaryotes evolved from archaea. Numerous studies have investigated these links by comparing molecules or genetic sequences in different organisms. In their publication, the team led by Emmanuelle Schmitt, CNRS Research Director at BIOC, took a different approach, studying the mechanisms by which the genetic code is translated into proteins which are essential to the organism's functioning.

At the heart of this translation lies the ribosome, the molecular machine which decodes genetic information on strands of messenger RNA to produce proteins. Ribosomes are present in all cells of all living organisms, making them ideal for scrutinizing evolution and relationships. Some archaea are closer to eukaryotes than others. In particular, the ribosome of the archaea Saccharolobus solfataricus is made up, among other things, of three proteins also present in eukaryotes. 

Observing the link between messenger RNA and ribosome

There are different ways in which messenger RNAs and ribosomes connect. The messenger RNAs translated by this archaea are of two types, distinguished by where the sequence to be translated begins. In the first type of messenger RNA, as in bacteria, this point is preceded by another “leader” sequence. But the other type of messenger RNA in this archaea has no such sequence. “How can these so-called leaderless messenger RNAs be translated by the ribosome? And what is the reason for the presence of these three additional proteins? These two questions motivated us to carry out this study”, explains Emmanuelle Schmitt.

To answer these questions, the scientists cultivated Saccharolobus solfataricus in the laboratory, extracted and purified the ribosomes so that they remained intact and active. Mixed with RNA of both types, these “translation machines” were observed, among other things, by cryo-electron microscopy, thanks to the CIMEX platform at École polytechnique. The numerous images taken allow us to reconstruct the ribosome in three dimensions, as it binds to the messenger RNAs.

Scientists have witnessed the coexistence of two binding mechanisms. Messenger RNAs with a leader sequence can bind it robustly to one end of the ribosome, as in bacteria. On the other hand, to bind leaderless RNAs, this end can be blocked by a protein (called eS26) that these archaea have in common with eukaryotes. “We believe that it is the concentration of this protein that enables the switch from one binding mode to another, and thus regulates translation”, explains the researcher. This second messenger RNA binding mechanism could be a very preliminary version of the one observed in eukaryotes. The presence of these two processes, one close to that of bacteria, the other close to that of eukaryotes, confirms that these latter could have evolved from archaea..

In the presence of a messenger RNA with a leader sequence (in red, left), the latter binds to one end of the archaeal ribosome (in brown). The eS26 protein ( in blue, right) can wrap around this ribosome end to neutralize it, enabling binding to leaderless messenger RNAs. 

Scientific publication:

Bourgeois, G., Coureux, PD., Lazennec-Schurdevin, C. et al. Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity. Nat Commun 16, 348 (2025). https://doi.org/10.1038/s41467-024-55718-5

*BIOC: a joint research unit CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France

*LCM: a joint research unit CNRS, École Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France