Nav: Home

Scientists identify rare evolutionary intermediates to understand the origin of eukaryotes

September 10, 2019

A new study by Yale scientists provides a key insight into a milestone event in the early evolution of life on Earth - the origin of the cell nucleus and complex cells called eukaryotes.

While simple prokaryotic bacteria formed within the first billion years of the Earth, the origin of eurkaryotes, the first cells with nuclei, took much longer. Dating back to between 1.7 and 2.7 billion years ago, an ancient prokaryote was first transformed with a compartment, the nucleus, designed to keep their DNA material more protected from the environment (such as harmful UV damage). From this ancient event, relatively simple organisms, such as bacteria were transformed into more sophisticated ones that ultimately gave rise to all modern animals, plants and fungi.

The details of this key event have remained elusive for many years because not a single transitional fossil has been found to date.

Now, in a study led by Dr. Sergey Melnikov, from the Dieter Söll Laboratory in the Department of Molecular Biophysics and Biochemistry at Yale University, has finally found these missing fossils. To do so, they relied not on unearthing clay or rocks but peering deep inside current living cells, known as Archaea - the organisms that are believed to most closely resemble the ancient intermediates between bacteria and the more complex cells that we now know as eukaryotic cells.

These transitional forms are nothing like the traditional fossils we think of, such as dinosaur bones deposited in the ground or insects trapped in amber. Known as ribosomal proteins, these particular transitional forms are about 100-million times smaller than our bodies. Melnikov and his colleagues discovered that ribosomal proteins can be used as living "molecular fossils", whose ancient origin and structure may hold the key to understanding the origin of the cell nucleus.

"Simple lifeforms, such as bacteria, are analogous to a studio apartment: they have a single interior space which is not subdivided into separate rooms or compartments. By contrast, more complex organisms, such as fungi, animals, and plants, are made up of cells that are separated into multiple compartments," explained Melnikov. "These microscopic compartments are connected to one another via 'doors' and 'gates.' To pass through these doors and gates, the molecules that inhabit living cells must carry special ID badges, some of which are called nuclear localization signals, or NLSs."

Seeking to better understand when NLS-motifs might have emerged in ribosomal proteins, the Yale team assessed their conservation among ribosomal proteins from the three domains of life.

To date, NLS-motifs have been characterized in ten ribosomal proteins from several eukaryotic species. They compared all of the NLS-motifs found in eukaryotic ribosomal proteins (from 482 species) and tried to find a match in bacteria (2,951 species) and Archaea (402 species).

Suprisingly, they found four proteins - uL3, uL15, uL18, and uS12 - to have NLS-type motifs not only in the Eukarya but also in the Archaea. "Contrary to our expectations, we found that NLS-type motifs are conserved across all the archaeal branches, including the most ancient superphylum, called DPANN," said Melnikov.

But since Archaea don't have nuclei, the logical question which then arose was, why do they have these IDs? And what was the original biological function of these IDs in non-compartmentalized cells?"

"If you think about an equivalent to our discovery in the macroscopic world, it is similar to discoveries made during the last century of bird-like dinosaurs such as Caudipteryx zoui," said Melnikov. "These ancient flightless birds have illustrated that it took multiple millions of years for dinosaurs to develop wings. Yet, strikingly, for the first few million years their wings were not good enough to support flight."

Similarly, the study by Melnikov and colleagues suggests that, even though NLSs may not initially have emerged to allow cellular molecules to pass through microscopic doors and gates between cellular compartments, they could have emerged to fulfill a similar biological function - to help molecules get to their proper biological partners.

As Melnikov explains: "Our analysis shows that in complex cells the very same IDs that allow proteins to pass through the microscopic gates are also used to recognize biological partners of these proteins. In other words, in complex cells, the IDs fulfill two conceptually similar biological functions. In the Archaea, however, these IDs play just one of these functions - these IDs, or NLSs, help proteins to recognize their biological partners and distinguish them from the thousands of other molecules that float in a cell."

But what led to the evolution of these IDs among cellular proteins in the first place?

As Melnikov explains, "When life first emerged on the face of our planet, the earliest life forms were likely made of a very limited number of molecules. Therefore, it was relatively easy for these molecules to find one specific partner among all the other molecules in a living cell. However, as cells grew in size and complexity, it is possible, even probable, that the old rules of specific interactions between cellular molecules had to be redefined, and this is how the IDs were introduced into the structure of cellular proteins - to help these proteins identify their molecular partners more easily in the complex environment of a complex cell. Coming back to the analogy with bird-like dinosaurs, our study illustrates the remarkable similarity between how evolution happens in the macroscopic world and how evolution happens in the world that Darwin never saw - the microscopic world of invisible molecules that inhabit living cells."
-end-
The study was published in the advanced online edition of Molecular Biology and Evolution.

Molecular Biology and Evolution (Oxford University Press)

Related Bacteria Articles:

Bacteria must be 'stressed out' to divide
Bacterial cell division is controlled by both enzymatic activity and mechanical forces, which work together to control its timing and location, a new study from EPFL finds.
How bees live with bacteria
More than 90 percent of all bee species are not organized in colonies, but fight their way through life alone.
The bacteria building your baby
Australian researchers have laid to rest a longstanding controversy: is the womb sterile?
Detecting bacteria in space
A new genomic approach provides a glimpse into the diverse bacterial ecosystem on the International Space Station.
Hopping bacteria
Scientists have long known that key models of bacterial movement in real-world conditions are flawed.
Bacteria uses viral weapon against other bacteria
Bacterial cells use both a virus -- traditionally thought to be an enemy -- and a prehistoric viral protein to kill other bacteria that competes with it for food according to an international team of researchers who believe this has potential implications for future infectious disease treatment.
Drug diversity in bacteria
Bacteria produce a cocktail of various bioactive natural products in order to survive in hostile environments with competing (micro)organisms.
Bacteria walk (a bit) like we do
EPFL biophysicists have been able to directly study the way bacteria move on surfaces, revealing a molecular machinery reminiscent of motor reflexes.
Using bacteria to create a water filter that kills bacteria
Engineers have created a bacteria-filtering membrane using graphene oxide and bacterial nanocellulose.
Probiotics are not always 'good bacteria'
Researchers from the Cockrell School of Engineering were able to shed light on a part of the human body - the digestive system -- where many questions remain unanswered.
More Bacteria News and Bacteria Current Events

Top Science Podcasts

We have hand picked the top science podcasts of 2019.
Now Playing: TED Radio Hour

In & Out Of Love
We think of love as a mysterious, unknowable force. Something that happens to us. But what if we could control it? This hour, TED speakers on whether we can decide to fall in — and out of — love. Guests include writer Mandy Len Catron, biological anthropologist Helen Fisher, musician Dessa, One Love CEO Katie Hood, and psychologist Guy Winch.
Now Playing: Science for the People

#541 Wayfinding
These days when we want to know where we are or how to get where we want to go, most of us will pull out a smart phone with a built-in GPS and map app. Some of us old timers might still use an old school paper map from time to time. But we didn't always used to lean so heavily on maps and technology, and in some remote places of the world some people still navigate and wayfind their way without the aid of these tools... and in some cases do better without them. This week, host Rachelle Saunders...
Now Playing: Radiolab

Dolly Parton's America: Neon Moss
Today on Radiolab, we're bringing you the fourth episode of Jad's special series, Dolly Parton's America. In this episode, Jad goes back up the mountain to visit Dolly's actual Tennessee mountain home, where she tells stories about her first trips out of the holler. Back on the mountaintop, standing under the rain by the Little Pigeon River, the trip triggers memories of Jad's first visit to his father's childhood home, and opens the gateway to dizzying stories of music and migration. Support Radiolab today at Radiolab.org/donate.