Contemporary DNA reveals how life became much more complex two billion years ago

Studying the DNA of organisms that live today can increase our understanding of how life evolved billions of years ago. For his PhD research, Julian Vosseberg delved into the DNA of contemporary organisms to find out how complex cells like those of plants, fungi and animals once evolved from simple, bacteria-like cells. His results offer new insights into key steps in the timeline of early complex life, such as the emergence of the cell nucleus.

Life on Earth originated about four billion years ago. For the first two billion years, life consisted of small, relatively simple single-celled organisms. The cells of these bacteria-like organisms, called prokaryotes, contained relatively little DNA and had no cell nucleus in which that DNA was stored.

About two billion years ago, more complex cells emerged. Those cells, eukaryotic cells, were larger, contained more DNA and had a cell nucleus. In addition, the complex cells contained organelles, subunits within the cell with a specific function. Mitochondria, the energy factories within eukaryotic cells, are an example of such organelles.

The evolution of genes

How these complex cells arose from their simple ancestors is a question that is not that easy to answer. Vosseberg: "There are still prokaryotes living today: bacteria and archaea. And almost all organism we can see with the naked eye, such as animals, plants and fungi, are eukaryotes. But there are no creatures living today that have cells that fall somewhere between the simple and complex form. Nor are there well-defined fossils that show such intermediate forms."

To gain insight into what happened two billion years ago, Vosseberg therefore looked into the DNA of organisms still living today. Vosseberg: "The DNA of contemporary species is the result of millions of years of evolution. Nowadays, we have a lot of information about the DNA of all kinds of organisms, both prokaryotes and eukaryotes. With that information, we can reconstruct the evolution of thousands of genes, regions in DNA that are ultimately translated into proteins. This provides us with a picture of what the DNA of the common ancestor of all eukaryotes was like, and allows us to infer intermediate forms between pro- and eukaryotes."

Gene duplications and introns

One of the things Vosseberg did was searching for duplicate copies of genes. Vosseberg: "The more complex cells attained more DNA because genes were duplicated. As a result, two copies of the same gene were now present in the cell. Mutations of the DNA in such copied genes led to new proteins that enabled new functions. That contributed to the fact that all kinds of organelles were able to form in the cell."

At the same time, Vosseberg looked at introns, pieces of DNA in a gene that are not directly involved in making a protein. Vosseberg: "I looked at whether introns were present before the duplication of a gene. That helped me create a timeline."

Mitochondria

The aforementioned mitochondria, energy factories within eukaryotic cells, play an important role in the question of how the complex cell came about. Mitochondria were once free-living bacteria. At some point in time, they were taken up by the ancestors of eukaryotic cells.

The DNA of contemporary species is the result of millions of years of evolution.

Vosseberg: "It is often assumed that the acquisition of mitochondria was the first, crucial step or the last step in the evolution of complex cells. Our research shows that there was a peak in gene duplications before mitochondria were integrated. This indicates that there already was an increase in cell complexity earlier in time. The acquisition of mitochondria therefore seems to have been an intermediate step."

Cell nucleus

Vosseberg's work also provided insights into the evolution of the cell nucleus. Vosseberg: "Prokaryotes usually do not have introns, eukaryotes do. The spread of introns is linked to the origin of the cell nucleus."

Here is how that works: to make protein from DNA, DNA is first transcribed to RNA, which in turn is translated to protein. The introns must be removed from the RNA before it is translated into protein, or else non-working proteins would be produced. The cell nucleus makes sure that there is time and space within the cell to do that properly. Vosseberg: "Our analyses show that introns were already widespread in early ancestors of eukaryotes. This suggests that the cell nucleus emerged early in the evolution of complex cells, even before most other features of eukaryotic cells emerged."

To make sense of the evolution of complex processes in cells in plants and animals, it turns out to be essential to also investigate the origin of eukaryotes.

Research continues

Despite the new insights by Vosseberg, who received his PhD in late January, much remains to be discovered about exactly how complex life on Earth originated. Berend Snel, Professor of Bioinformatics and PhD supervisor of Vosseberg, therefore indicates that research into this question will continue in his group. Snel: "To make sense of the evolution of complex processes in cells in plants and animals, it turns out to be essential to also investigate the origin of eukaryotes. And besides that, it is also quite simply a very fun and important research question."