Catalog of mitochondria across life’s family tree unearths new roles for the cell’s powerhouse

A research consortium has generated the broadest look yet at the proteins that make up mitochondria, capturing the organelle’s diversity across multiple branches on the tree of complex life. With major contributions from Broad Institute scientists as well as its Proteomics Platform, the consortium generated and analyzed the mitochondrial proteomes of one plant and five single-celled pathogens that affect millions of people globally every year. Their results reveal unexpected new functions of the organelle, clues to its origin and role in the evolution of complex-celled organisms known as eukaryotes, and potential new drug targets for neglected tropical diseases.

The MitoCarta Tree of Life project was led by scientists at the Broad Institute, Mass General Brigham, Harvard Medical School (HMS), Harvard T.H. Chan School of Public Health, and Boston University Henry M. Goldman School of Dental Medicine. Their findings appear in nine scientific papers and a commentary article in Cell and related journals.

“With this consortium, we’ve repurposed everything we’ve learned over the last 15 years characterizing the mammalian mitoproteome to rapidly and diligently build out these inventories, creating a foundational resource for a new field of comparative mitochondrial biology,” said project leader Vamsi Mootha, an institute member at the Broad, professor of systems biology at HMS, investigator in the Department of Molecular Biology at Mass General Brigham, and Howard Hughes Medical Institute (HHMI) Investigator.

Mitochondrial marvels

It’s been two billion years since an ancient host cell engulfed a bacterium that later became the mitochondrion, the “powerhouse” 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 over time, the organelle’s composition and function shifted to suit the needs of each organism.

In 2008, a Broad-led team announced MitoCarta, the first comprehensive inventory of the mammalian mitochondria’s 1,100 proteins, which later was used to discover genes underlying illnesses such as metabolic disease and neurodegeneration. Yet, the researchers knew they could learn even more about the organelle by comparing it across different forms of life and exploring not only its origins, but also how it might be targeted in pathogens to treat infections.

In 2022, with support from the HHMI Emerging Pathogens Initiative, Mootha and his colleagues built a consortium of seven labs consisting of 25 researchers to produce mitoproteomes of organisms spanning the tree of life, focusing on the model plant Arabidopsis and five parasites that cause human disease.

The researchers worked with Broad Institute’s newest advanced mass spectrometry technologies to help determine which nuclear genes encode proteins that end up in each organism’s mitochondria. “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,” said Namrata Udeshi, senior director of proteomics at the Broad, where she is an institute scientist, and one of the principal investigators in the consortium.

In work led by team member and Harvard MD-PhD student Michael Chen, the researchers compared the data on these six organisms along with the existing human and yeast inventories. They discovered many mitochondrial proteins in multiple pathogens that are missing from human mitochondria, representing potential targets for new drugs to treat tropical diseases.

The researchers also used the new data to explore a longstanding scientific mystery about whether mitochondria originated early or late in eukaryotic evolution. Using the new data to retrain a machine-learning based tool and predict the mitoproteomes for hundreds of untested species, the scientists reconstructed the timeline of when various organelles first appeared. Their analysis supports the notion that mitochondria appeared relatively late, after the ancestral eukaryote already had developed other complex parts.

The other papers focused on analyses of individual organisms. In one study, the team catalogued the mitochondrial machinery of Giardia, which causes a diarrheal disease, contains a mere 59 proteins, and lacks energy-producing capabilities, making it more of a “remnant” mitochondrion that further challenges the narrow view of the organelle as simply a powerhouse.

For another study, they developed new methods to study the mitochondria of Babesia, a tick-borne pathogen behind a malaria-like illness that's spreading in New England due to climate change. Importantly, those methods may also work for related pathogens, such as those that cause malaria and toxoplasmosis.

In their analysis of the mitoproteome of Acanthamoeba, an organism that can cause blindness in contact lens wearers, they observed the most complicated energy-producing machinery of any organism. Team member Jon Stefely, now at the Morgridge Institute for Research, led experiments that showed its mitochondria are capable of switching between aerobic and anaerobic respiration based on oxygen conditions, possibly reflecting an ancient adaptation to the fluctuating oxygen in its primordial environment.

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

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

“This project is one step in the larger scientific effort to use the existing diversity on Earth as a stepping stone toward answering one of the deepest questions: How did complex life evolve on our planet?” said team member Sarah Calvo, a senior computational scientist at the Broad.

In addition, more than half of the proteins in these catalogs have unknown functions, so future studies may one day reveal even more clues to 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 HMS, Manoj Duraisingh of Harvard T.H. Chan School of Public Health, and John Samuelson, Ruslan Afasizhev, and Inna Afasizheva of Boston University Henry M. Goldman School of Dental Medicine.