Timeline of early eukaryotic evolution

Bioinformaticians at Utrecht University have reconstructed the evolutionary events leading to the creation of eukaryotic cells, the precursors to virtually all life you can see with the naked eye. By analysing duplicates of thousands of genes, the researchers discovered that the evolutionary timeline from simple bacterial cells to complex eukaryotic cells progressed differently than had previously been presumed. The researchers published their findings together with colleagues from Barcelona 26 October in Nature Ecology & Evolution.

One of the most important and puzzling events in the evolution of life was the origin of the first complex eukaryotic cells. Almost all of the life we can see without a microscope, such as algae, plants, animals and fungi, are made up of complex cells known as ‘eukaryotes’. But for roughly the first half of the history of life on Earth, the only forms of life were the relatively simple cells of bacteria. “Eukaryotic cells are larger, contain more DNA and are made up of compartments that each have their own task”, explains first author Julian Vosseberg from Utrecht University. “In that sense, you could compare bacterial cells with a tent, while eukaryotic cells are more like houses with several rooms.”

How and when organisms traded the tent for a house is still a mystery, as there are no intermediate forms. One important moment in evolution was the origin of mitochondria, one of the components of eukaryotic cells, which function as the ‘power plant’ of the cell. These were once free-living bacteria, but over the course of evolution they were absorbed by the ancestors of today’s eukaryotic cells. As gene duplication was probably a driving force behind the increase in complexity at the cellular level, the researchers attempted to reconstruct the evolutionary events based on these genetic changes.

Our genes were formed over aeons of evolution, but they still hold echos of a distant past

Reconstruction

“We can use the DNA of contemporary species to reconstruct evolutionary events. Our genes were formed over aeons of evolution. They have changed dramatically over that time, but they still hold echos of a distant past.” Vosseberg adds. “We have a vast quantity of genetic material available, from a variety of organisms, and we can use computers to reconstruct the evolution of thousands of genes, including ancient gene duplications. These reconstructions enabled us to uncover the timing of important intermediate steps.”

As last author Berend Snel from Utrecht University, explains, scientists did not have a timeline of these events. “But now we’ve managed to reconstruct a rough timeline.” To create it, the researchers adapted an existing method to create a new protocol, which has resulted in new insights. These indicate that a lot of complex cellular machinery had evolved even before the symbiosis with mitochondria. “The symbiosis wasn’t an event that served as the catalyst for everything else. We observed a peak in gene duplications much earlier in time, indicating that cell complexity had already increased before that moment”, says Snel. 

“Our study suggests that the ancestral host that acquired the mitochondrial endosymbiont had already developed some complexity in terms of a dynamic cytoskeleton and membrane trafficking”, says Toni Gabaldón, from the Biomedical Research Institute and the Barcelona Supercomputing Centre at Barcelona. “This might have favoured the establishment of symbiotic associations with other microorganisms, including the mitochondrial ancestor, which eventually became integrated.”

“The discussion of the development of the eukaryotic cell often deals with whether acquiring the mitochondria was the crucial first step, or the last step in the process”, Vosseberg adds. “Our study has now shown that we can differentiate more intermediate stages. The interaction with what became the mitochondria was neither prologue nor finale, but rather an important plot twist in-between.”

Publication

Timing the origin of eukaryotic cellular complexity with ancient duplications. Nature Ecology & Evolution. 26 October 2020. Julian Vosseberg*, Jolien J. E. van Hooff*, Marina Marcet-Houben, Anne van Vlimmeren*, Leny M. van Wijk*, Toni Gabaldón, Berend Snel*. DOI 10.1038/s41559-020-01320-z

*Authors affiliated with Utrecht University.