Tiny Tubes Reveal Clues to the Evolution of Complex Life
Cytoskeleton proteins are a vital part of eukaryotic cells. Researchers have now found similar proteins in Asgard archaea.
Torsten Wittmann/Science Source
Introduction
In 2010, biologists made a shocking discovery. Living in the mud of the North Sea were microorganisms whose genes looked a lot like ours. Genetic analysis revealed that humans, oak trees, blue whales — any living things whose cells have nuclei and mitochondria — are related to these microbes, which were named the Asgard archaea after the home of the Norse gods. Two billion years ago, it was an ancestor of an Asgard that diverged from its kin and eventually became us.
No one knows precisely how that happened, and for a long time, no one even knew what these long-lost cousins looked like. Asgard DNA could be fished out of the mud and studied, but the cells themselves were so rare and hard to grow in the lab that no one could scrutinize them under the microscope. There was an explosion of speculation among scientists about what they would be like. Would they be big? Small? Covered with tentacles, shaped like rods, perfectly spherical? Do their cells look like ours inside, or are they completely different?
Little by little, researchers have worked out ways to grow them and watch as they go about their lives. Now, some of the first reports about the biology of certain Asgards are revealing new, provocative details about the interior lives of these cells. The latest paper, from the labs of Martin Pilhofer at ETH Zurich and Christa Schleper at the University of Vienna, describes how a portion of their cytoskeleton — the set of cellular structures that give a cell its shape — is surprisingly similar to what can be found in more complex organisms such as ourselves.
In our cells, cytoskeletal proteins called tubulins snap onto each other to form soaring tubular arches and rails, capable of spanning entire cells, growing at one end while they fall apart at the other. These tubes, known as microtubules, form and bloom and decay in a dance that controls many aspects of eukaryotic life. They handle our chromosomes and help cells divide. They carry machines and act as tracks for motors. They push and pull cellular membranes, turning them into useful shapes.
Now, researchers have found that these proteins are in those mysterious cells. What are they doing there? And could they be part of what, so long ago, helped our ancestors strike out in new directions?
The latest findings on Asgard archaea come from the labs of Martin Pilhofer (left) at ETH Zurich and Christa Schleper at the University of Vienna.
Vera Hartmann; Courtesy of Schleper Lab
Intermediate Interest
The eukaryotic cell, in some ways, looks as though it came out of nowhere. Unlike bacteria and archaea, which are much older forms of life called prokaryotes, a eukaryotic cell has a double membrane of lipids around it. It also has mitochondria — remnants of formerly free-living bacteria — providing energy, a nucleus containing its genome, and a gaggle of membrane-bound bubbles, or organelles, transacting its business. It might have a propellor-like tail, or flagellum, or hairlike cilia. It is huge compared to the cells of prokaryotes. Its inner space is dense with filaments of tubulin and actin, another protein that plays a similar skeletal role. It is like a city, plumbed with subways and awash in traffic.
How the eukaryotic cell evolved has been hard to trace; there are no living intermediate states between prokaryote and eukaryote that could reveal its evolutionary trajectory. “We are missing a long time, a long branch of evolution, where intermediate forms did lots of other things,” said Bill Wickstead, a molecular biologist at the University of Nottingham. Eukaryotic innovations were apparently so successful that they outcompeted everything even remotely like them.
That is why the Asgards have provoked such intense interest from evolutionary biologists. From the very start, it was clear from their DNA that they might be, if not an intermediate state, then at least a relative of the original cell that began to transform itself and its descendants into something strange and new. There were versions of genes that had previously been seen only in eukaryotes, right there in the Asgards’ genome sequences, just waiting for biologists to see what they could do in this surprising new context. This is the kind of information that can imply what came first in the development of a eukaryotic cell: the mitochondrion, the nucleus, the membrane or the organelles, said Buzz Baum, a cell biologist at the MRC Laboratory of Molecular Biology Cambridge.
Samuel Velasco/Quanta Magazine; Source: Florian Wollweber/ETH Zurich
“It is lifting the veil on this deep mystery of life on Earth,” he said. “And you think — we might find out how this thing, 2 billion years ago, happened.”
Transition Elements
The cytoskeleton may have had an especially important role to play in this transition. “It must be one of the main steps that elaborated when the first eukaryotes arose on Earth,” said Iain Duggin, a microbiologist at the University of Technology Sydney in Australia. “Those cells are characterized by a much larger cell volume, much more complicated. To organize that, you need a sophisticated internal cytoskeleton. There’s a big gap in our knowledge of how those structures have formed.”
In 2022, biologists began to see some tantalizing clues. Pilhofer and the postdoctoral researcher Florian Wollweber, working with Schleper and a team of collaborators, revealed the presence of a protein very much like eukaryotic actin in an Asgard, called Candidatus Lokiarchaeum ossiferum. They could see these proteins joining together to make filaments in the cells.
Genetic work, too, flagged genes similar to tubulin, an intriguing finding. “I might make the argument,” Wickstead said, “that tubulin is the [cytoskeletal protein] that eukaryotes absolutely can’t live without because of its role in division.” Microtubules, he explained, are what guide our chromosomes into two separate cells each time a cell divides. “There’s no eukaryote that has managed to escape that.”
No one knew, though, if the proteins these Lokiarchaea made from these tubulin genes actually made structures, and whether they were similar to what eukaryotes have. One paper, published in 2022, found that tubules in another type of Asgard did not look particularly similar. But that same year, Wollweber spotted something unusual in a microscope image.
It was a slender, elegantly curving structure. “It looked like a small tube,” he said, “a tube that went across the entire cell.” Wollweber looked through other images of the Asgards and realized that although these shapes were rare, they were present in a small fraction of cells. It was hard to tell what they were made of from the images, which were grayscale, like transmissions from the surface of another planet. But he had a few ideas about how to find out.
Assembly Line
Tubulin functions a bit like Tinkertoys, the building toy with modular parts. In eukaryotes, two versions of the protein, alpha and beta tubulin, snap together. Then they stack on top of each other to make long rods, which then assemble into tubes — usually 13 rods make a tube, although the number can vary depending on the specific type of cell. These microtubules exist in a delicate equilibrium, stacking on new tubulin units for a while, then reaching a crisis and falling apart. They grow and shrink as needed, forming an ever-changing skeleton.
Wollweber and his colleagues wanted to see if the Lokiarchaea’s tubulin-like proteins behaved like the eukaryotic versions. They focused on two proteins in particular, which they dubbed AtubA and AtubB. By growing them in insect cells, they were able to harvest large amounts of both. Then they put them together in test tubes and waited to see what happened. It took some time to find the right ingredients and conditions, but to their delight, they eventually saw tubules forming. “We saw they assembled quite fast,” Pilhofer said.
A closer look at the tubules revealed something wondrous and strange. The proteins fit together in the same way as in eukaryotes, although the structures were made up of five rods, rather than 13, making a miniature tubule. They, too, grew and fell apart, as eukaryotic tubules do. “Even though they form a smaller tube, which might make sense in such a small cell, the interaction is actually the same,” Wollweber said. They had found the source of the tubes in the images.
To other researchers not involved in the project, the images in the paper and the revelations about the tubules’ structure are thought-provoking. “They are forming these filaments that look a lot like microtubules, but also forming clusters of microtubules, pushing out, making protuberances,” Wickstead said. This dynamic matches one theory of how eukaryotic cilia and flagella evolved, he added. “It was really striking to me.”
Baum is intrigued by the smaller rod number, pointing out that different numbers can imply different uses for the structure. “That’s cool,” he said. “It raises all kinds of questions and gives you a path from Asgards to eukaryotes.”
Chief among these questions is what the tubulins are doing. Tubules may assemble readily enough in the lab, but they seem to be very rare in living Lokiarchaea. Wollweber had to examine more than 50 cells to find just a handful. This suggests that whatever they are being used for is not happening often in these cultured cells. What’s more, cell division — for which microtubules are crucial in eukaryotes — has yet to be observed consistently in these organisms. The Lokiarchaea grow very slowly, and they require an oxygen-free environment and the presence of symbiotic bacteria, a situation which can be tricky to maintain. It would take months of carefully nurturing them, taking regular images, to see the gears of cell division set in motion.
Perhaps another Asgard with similar tubulin genes but a quicker life cycle will turn up, said Tom Pollard, a professor of molecular, cellular and developmental biology at Yale University who studies cell division. “Somebody just has to find the right organism,” he said, “and tag the tubulin and watch what happens.”
Once scientists can watch Asgard cells dividing, they will be able to see whether microtubules have the central role in that process that they have in eukaryotes. Baum points out that there may be surprises there. Some prokaryotes have unrelated cytoskeletal proteins — maybe the tubulins don’t get involved. “We have no idea that works in any archaea, actually,” he said.
“That’s why the cytoskeleton is interesting,” Baum continued. Organisms need to organize things, move DNA, move proteins and bend membranes, and various forms of life have come up with their own solutions to this. The discovery of tubules in Asgards may help us understand how the cytoskeleton helped to shape not only these primitive microorganisms but also their descendants over eons.
