Both types of organelles were once independent organisms with their own complete genomes. Billions of years ago, these organisms were trapped and trapped in other cells – the ancestors of modern species. Since then, organelles have lost most of their genomes, leaving only a handful of genes in modern mitochondrial and chloroplast DNA. These remaining genes are essential for life and important in many devastating diseases, but for decades it remains unclear why they remain in organelle DNA while many others are lost. It’s been discussed.

To gain a new perspective on this question, scientists have adopted a data-driven approach. They collected data on all sequenced organelle DNA over a lifetime. Modeling, biochemistry and structural biology were then used to express various hypotheses about gene retention as a set of numbers associated with each gene. Using data science and statistical tools, they asked which ideas could best explain the patterns of genes retained in the data they collected. We tested the results with unseen data to confirm its power.

“Some clear patterns emerged from the modeling,” explains Kostas Giannakis, a postdoctoral researcher in Bergen and co-first author of the paper. “Many of these genes encode subunits of larger cellular machinery that are assembled like a jigsaw. Genes in the middle part of the jigsaw are most likely to remain in organelle DNA.”

The team believes that maintaining local control over the production of such central subunits helps organelles respond quickly to changes. This is a version of the so-called “CoRR” model. They also found support for other existing, discussed, and new ideas. For example, data show that if a gene product is hydrophobic and less likely to be externally taken up by an organelle, it is more likely to be retained there. Genes encoded using stronger linking chemistries are also more frequently retained. probably because they are more robust in the harsh environment of organelles.

“These different hypotheses have typically been considered competing in the past,” says Yin Johnston, a professor at the University of Bergen and leader of the team. “But in practice no single mechanism can explain all observations. A combination is needed. The strength of this unbiased, data-driven approach is that many ideas are partially correct. What can be shown is, but not entirely, perhaps a lengthy discussion on these topics.”

Surprisingly, the team also found that models trained to describe mitochondrial genes also predicted retention of chloroplast genes, and vice versa. They also found that the same genetic features that shape the DNA of mitochondria and chloroplasts appear to play a role in the evolution of other endosymbionts.

“It was an amazing moment,” says Johnston. “We and others had the idea that similar pressures might apply to the evolution of different organelles. But to see this universal, quantitative link, Data from one organelle accurately predicted patterns in another, and more recently, in endosymbionts — very impressive.”

The study is part of a broader project funded by the European Research Council, in which the team is currently working on the parallel question of how to maintain organelle genes carried by different organisms. Mutations in mitochondrial DNA can lead to devastating genetic diseases. The team is using modeling, statistics and experiments to investigate how these mutations are handled in humans, plants and more.

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