Scientists Map Mitochondria Across the Tree of Life

A research consortium led by scientists at the Broad Institute has produced the broadest catalog yet of the proteins that make up mitochondria, tracing the energy-producing organelle across six branches on the tree of complex life. The findings appear in nine scientific papers and a commentary published in Cell and related journals, according to a report by phys.org.

The results point to unexpected functions of the organelle, new clues to its role in the evolution of complex-celled organisms known as eukaryotes, and possible new drug targets for neglected tropical diseases.

A census of the powerhouse

The consortium, called MitoCarta Tree of Life, generated and analyzed the mitochondrial proteomes of one plant, the model organism Arabidopsis, and five single-celled pathogens that affect millions of people around the world every year. The effort drew on major contributions from the Broad Institute's Proteomics Platform, which used advanced mass spectrometry technology to determine which nuclear genes encode proteins that end up in each organism's mitochondria.

Project leader Vamsi Mootha, an institute member at the Broad, professor of systems biology at Harvard Medical School, and Howard Hughes Medical Institute investigator, said the consortium repurposed fifteen years of work characterizing the mammalian mitoproteome to build the new inventories. He described the result as a "foundational resource" for the new field of comparative mitochondrial biology.

In work led by Harvard MD-Ph.D. student Michael Chen, the researchers compared the new data with existing human and yeast inventories. They found many mitochondrial proteins in multiple pathogens that are missing from human mitochondria, which could serve as targets for new drugs to treat tropical diseases.

Namrata Udeshi, senior director of proteomics at the Broad and one of the consortium's principal investigators, said, "The speed and scale of this project would not have been possible without the platform's expertise in state-of-the-art, next-generation proteomic technology."

Surprises hiding in the organelle

The individual studies turned up sharp differences between organisms. The team cataloged the mitochondrial machinery of Giardia, which causes a diarrheal disease in humans. Its mitochondrion contains a mere 59 proteins and lacks energy-producing capabilities, making it more of a remnant mitochondrion that challenges the narrow view of the organelle as simply a cellular powerhouse.

Another study developed new methods to examine the mitochondria of Babesia, a tick-borne pathogen behind a malaria-like illness that is spreading in New England as the climate warms. The researchers said those methods may also work for related pathogens, including the ones that cause malaria and toxoplasmosis.

In their analysis of Acanthamoeba, an organism that can cause blindness in contact lens wearers, the team observed the most complicated energy-producing machinery of any organism studied. Team member Jon Stefely led experiments showing that its mitochondria can switch between aerobic and anaerobic respiration based on oxygen conditions, possibly reflecting an ancient adaptation to the fluctuating oxygen levels of its primordial environment.

An analysis of Leishmania and Trypanosoma revealed massive mitochondrial proteomes that are 50 percent larger than that of humans and contain proteins unique to those classes of parasites.

The team also studied the weed Arabidopsis, which uses energy not only from chloroplasts but also from mitochondria. While earlier work had helped define the plant mitochondrial proteome, this new inventory appears to be the most comprehensive and accurate, and was generated using an approach that the researchers said can likely work for other plants.

Rewriting the origin story

About two billion years have passed since an ancient host cell engulfed a bacterium that later became the mitochondrion, the producer of chemical energy for eukaryotic cells. Most of the bacterial DNA ended up in the host cell's nuclear genome, with a fraction remaining as a tiny mitochondrial genome. As single-celled and multicellular organisms evolved, the organelle's composition and function shifted to suit each organism's needs.

The researchers used the new data to explore a longstanding scientific question about whether mitochondria originated early or late in eukaryotic evolution. After retraining a machine learning tool on the data, the team predicted the mitoproteomes of hundreds of untested species and reconstructed a timeline of when various organelles first appeared. Their analysis supports the idea that mitochondria appeared relatively late, after the ancestral eukaryote had already developed other complex parts.

The project has deep roots. In 2008, a Broad-led team announced MitoCarta, the first comprehensive inventory of the 1,100 proteins in mammalian mitochondria. That catalog was later used to discover genes underlying illnesses such as metabolic disease and neurodegeneration.

In 2022, Mootha and his colleagues built a consortium of seven labs with 25 researchers to extend that work across the tree of life, focusing on Arabidopsis and the parasites that cause human disease.

Team member Sarah Calvo, a senior computational scientist at the Broad, said the project uses the existing diversity on Earth as a "stepping stone" toward answering how complex life evolved on this planet.

More than half of the proteins in these catalogs have unknown functions, so future studies may reveal further clues about what makes human life, and that of all complex organisms on Earth, possible. The data produced in these studies is freely available at mitocarta.org.

Other researchers who led the effort include Luke Chao of Mass General Brigham and Harvard Medical School, Manoj Duraisingh of the Harvard T.H. Chan School of Public Health, and John Samuelson, Ruslan Afasizhev, and Inna Afasizheva of the Boston University Henry M. Goldman School of Dental Medicine. The research was reported in the journal Cell and covered by phys.org.