Animal and plant cell structures evolved in the same way

The same mitochondria - structures called cellular organelles - that provide the chemical energy we need to move, think and live; and chloroplasts, which in plants and algae capture sunlight and carry out photosynthesis; They evolved in the same way throughout the history of life, and not differently, as has always been assumed.

A team from the University of Bergen, Norway, using data science and computational biology showed that the same rules shaped the characteristic organelles of the animal world and those of plants and determined their evolution. The two types of organelles were once independent organisms, with their own complete genomes.

Billions of years ago these organisms were trapped by other cells and lost most of their genomes. The remaining genomes are essential for life and are involved in devastating diseases. The reason why they remain in the DNA of organelles has always been a mystery to scientists.

Now Norwegian scientists are taking a data-driven approach, bringing together DNA from different organelles sequenced throughout life. They used modeling, biochemistry and structural biology to simulate different hypotheses about gene retention. Using data and statistical tools, they asked what ideas could best explain the gene patterns retained in the data they compiled – testing the results with unseen data to check their power.

"Some clear patterns emerged from the modeling," explains Kostas Giannakis, a postdoctoral researcher in Bergen and first author of the paper. “Many of these genes encode subunits of larger cellular machines, which are put together like a puzzle.”

The team believes this is because maintaining local control over the production of such core subunits helps the organelle respond quickly to change — a version of the so-called "CoRR" model. They also found support for other existing, debated, and new ideas. For example, if a gene product is hydrophobic -- and difficult to import into the organelle from outside -- the data shows that it is often retained there. Genes that are encoded using stronger binding chemical groups are also retained more often - perhaps because they are more robust in the organelle's harsh environment.

"These different hypotheses were generally considered to be competing in the past," says Iain Johnston, a Bergen professor and team leader. "But in fact, no mechanism can explain all observations - it takes a combination. A strength of this unbiased, data-driven approach is that it can show that many ideas are partially right, but none exclusively - perhaps explaining the long debate on these topics."

To their surprise, the team also found that their models trained to describe mitochondrial genes also predicted the retention of chloroplast genes and vice versa. They also found that the same genetic traits that shape mitochondrial and chloroplast DNA also appear to play a role in the evolution of other endosymbionts—organisms that were more recently captured by other hosts, from algae to insects.

“It was an expressive moment,” says Johnston. "We -- and others -- had this idea that similar pressures might apply to the evolution of different organelles. But to see this universal quantitative link -- data from one organelle accurately predicting patterns in another and in more recent endosymbionts -- was really impressive." ."

The research is part of a wider project funded by the European Research Council, and the team is now working on a parallel question – how different organisms maintain the organelle genes they retain. Mutations in mitochondrial DNA can cause devastating inherited diseases; the team is using modeling, statistics and experiments to explore how these mutations are handled in humans, plants and more.

The full article can be read here.