Mitochondria are compartments — so-called “organelles” — in our cells that provide the chemical energy supply we need to move, think and live. Chloroplasts are organelles in plants and algae that capture sunlight and carry out photosynthesis. At first glance, they might look worlds apart. But an international team of researchers, led by the University of Bergen, used data science and computational biology to show that the same “rules” shaped how both organelles — and more — evolved throughout life’s history.
Both types of organelle were once independent organisms, with their own complete genomes. Billions of years ago, these organisms were captured and imprisoned by other cells — the ancestors of modern species. Since then, the organelles have lost most of their genomes, with only a handful of genes remaining in modern-day mitochondrial and chloroplast DNA. These remaining genes are essential for life and important in many devastating diseases, but why they remain in organelle DNA — when so many others have been lost — has been debated for decades.
For a fresh perspective on this question, the scientists took a data approach. They collected data on the entire DNA organelle that was sequenced throughout life. They then used modeling, biochemistry, and structural biology to represent a wide range of different hypotheses about gene retention as a set of numbers associated with each gene. Using data science and statistics tools, they asked which ideas could best explain the patterns of retained genes 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 at Bergen and co-first author on the paper. “Many of these genes encode subunits of larger cellular machines that are assembled like a puzzle. Genes for the pieces in the middle of the puzzle are most likely to remain in organelle DNA.”
The team believes this is because maintaining local control over the production of such central subunits helps the organelle respond quickly to change — a version of the so-called “CoRR” model. They also found support for other existing, discussed and new ideas. For example, if a gene product is hydrophobic — and difficult to import into the organelle from the outside — the data show that it is often retained there. Genes that are themselves encoded using stronger-binding chemical groups are also more often retained — perhaps because they are more robust in the organelle’s harsh environment.
“These different hypotheses have usually been thought of as competing in the past,” says Iain Johnston, professor at Bergen and leader of the team. “But in fact no single mechanism can explain all the observations – a combination is needed. A strength of this unbiased, data-driven approach is that it can show that many ideas are partially correct, but none exclusively so – perhaps explaining the long debate on these issues.”
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 make up 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.
“That was an amazing 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 striking.”
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 hereditary diseases; the team uses modeling, statistics and experiments to investigate how these mutations are dealt with in humans, plants and more.
Materials provided by the University of Bergen. Note: Content may be edited for style and length.
