Back to School: What Mitochondria Really Do

When you walk up the stairs, your breathing gets heavier. In your cells, that extra oxygen is used by mitochondria to generate more energy in the form of adenosine triphosphate (ATP).

Your biology classes might have led you to believe that the primary job of mitochondria is to be the “powerhouse of the cell.” And indeed, the organelle acts as a furnace that burns nutrients from food and oxygen to generate ATP.

But the role of mitochondria extends beyond energy generation. There is growing recognition in the scientific community that the organelles are central hubs for many cellular processes, including signaling, biosynthesis, hosting biochemical reactions, and even memory formation. And when they malfunction, often due to genetic mutations, there can be significant health consequences.

Yale School of Medicine (YSM) experts are exploring the diverse contributions of mitochondria, as well as how certain mutations affect their functioning, to understand why disease arises when things go awry. This research may reveal new treatment targets for conditions such as metabolic diseases, mood disorders, neurodevelopmental disorders, and neurodegenerative conditions.

“The idea that mitochondria are simply there to generate ATP is overplayed and ignores a lot of the other functions of mitochondria that are necessary for the cell,” says Matthew J. Merrins, PhD, Joseph F. Hoffman Professor of Cellular and Molecular Physiology.

And mitochondria have been linked to just about every single disease that’s out there, adds Richard Kibbey, MD, PhD, Ensign Professor of Medicine (Endocrinology and Metabolism), who directs YSM’s Program for Mitochondrial Biology and Intermediary Metabolism. “Being able to understand the organelle in all of its functions will help us be better scientists, pharmacologists, and physicians,” he says.

Over the last several decades, scientists have revealed that mitochondria are constantly in flux. “Mitochondria are so changeable—there can be such incredible structural and functional changes even within minutes,” says Elizabeth Jonas, MD, Harvey and Kate Cushing Professor of Medicine (Endocrinology). “Our understanding of this plastic nature of mitochondria has been the major breakthrough of the last 20 to 30 years.”

Beyond their role as a furnace, for example, mitochondria can transition into factories, in which they create the building blocks for lipids, proteins, and other essential materials. This factory function is especially important in the developing cells of infants, for cellular repair, and for generating signals. In the pancreas, for example, mitochondria can help produce signals that drive insulin secretion.

Merrins’ laboratory studies the specialized insulin-producing cells in the pancreas known as beta cells. “What’s really cool about beta cells is that they oscillate between these two functions, furnace and factory, over and over again,” he says.

In the furnace state, the mitochondria generate ATP. But when in factory mode, the organelles are highly energized. “When the energy state of the cell is really high, they don’t need to make more energy,” says Merrins. “They need to signal for the cell to accomplish other functions, and they need to build things.”

In collaboration with Kibbey, Merrins’ team has uncovered the mechanisms that transform mitochondria from furnaces to factories. For decades, Kibbey has been studying a rare genetic disorder known as hyperinsulinism/hyperammonemia (HI/HA) syndrome. The condition is caused by a mutation in which eating protein triggers beta cells to release too much insulin, resulting in a drop in blood sugar.

In the process of studying this mutation, the researchers identified important mitochondrial pathways, including a cycle in which the organelle ends up generating a compound called phosphoenolpyruvate. When the mitochondria send that compound out into the cell, an enzyme called pyruvate kinase breaks it down into pyruvate. “In doing so, it does something interesting and important,” says Kibbey. “Pyruvate kinase has the ability to raise the energy level of the cell to a higher level than the mitochondria can.”

This process of breaking down phosphoenolpyruvate into pyruvate uses up adenosine diphosphate (ADP), the precursor of ATP, in the cell. “When you deprive mitochondria of ADP, they become super energized because they’re no longer burning fuel and making ATP,” Kibbey explains. “The cell switches off the mitochondria from burning and turns them on to making things that we believe are essential for glucose sensing and a lot of other functions throughout the body.”

The identification of pyruvate kinase as an enzyme that can switch mitochondria from furnace to factory mode could have exciting clinical implications, the researchers say. In ongoing studies at YSM, pyruvate kinase enzyme activators appear promising for treating obesity.

Kibbey and Merrins have found that the use of these activators in pancreatic tissue increased insulin secretion and amplified glucagon-like peptide-1 (GLP-1) receptor signaling—GLP-1 is a hormone produced in the body shortly after eating that helps regulate blood sugar. In animal models, these activators caused significant weight reduction; when combined with a GLP-1 receptor agonist, the rodents lost double the amount of weight than what was achieved by a GLP-1 agonist alone.

Furthermore, a common problem with GLP-1 medications, such as Ozempic, is that they lead to muscle loss. The researchers found that pyruvate kinase activators helped build more muscle mass and, when combined with GLP-1 agonists, prevented excess muscle loss.

Kibbey and Merrins, in collaboration with Ania Jastreboff, MD, PhD, professor of medicine (endocrinology) and director of the Yale Obesity Research Center (Y-Weight), have launched the Yale spinout company State 4 Therapeutics to further develop pyruvate kinase activators for the treatment of obesity. They hope to begin trials in humans within the next year or two.

“By identifying this regulator of mitochondria that switches them from ATP synthesis mode into signaling and synthetic function mode, we’ve really hit the heart of energy, control, and regulation in multiple tissues throughout the body,” says Kibbey. “We think targeting this will have a lot of therapeutic benefits. Re-engineering mitochondria to do something else by controlling their function is very exciting.”

A key part of generating ATP is the pumping of hydrogen ions from within the mitochondria to their inner membrane. But in some cases, this membrane leaks and the ions spill out. “It doesn’t sound like that would be a good function,” says Jonas. “But this leak is actually important because it adjusts metabolism.”

For example, after eating a large meal, you might take in more energy than your body can store. As a result, the inner mitochondrial membrane becomes leaky to get rid of excess energy and mitigate weight gain. On the other hand, if you eat too little, mitochondria close the leak and make energy more efficiently.

Closing the leak is also important for other crucial functions such as memory formation. Our brains do not exist in a static state; they continually undergo structural changes in response to new experiences. Some of these changes occur at the gaps between neurons, called synapses, where the cells transmit signals to one another.

In order to communicate, the first (pre-synaptic) neuron releases chemical messengers called neurotransmitters, which travel across the gap and bind to receptors on the second (post-synaptic) neuron. When we make memories, the number of these receptors grows, enabling more efficient communication among neurons. “This is really important for remembering things,” says Jonas.

Her team has discovered that this synaptic receptor growth wouldn’t be possible without mitochondria. When they shut off their hydrogen leaks, mitochondria in neurons are able to modify proteins that travel to the neuronal membrane and become receptors. These additional receptors help make our memory stronger, Jonas explains.

Abnormal leaking, on the other hand, may contribute to the onset of many diseases, says Jonas. In collaboration with In-Hyun Park, PhD, associate professor of genetics, and Hilary Blumberg, MD, John and Hope Furth Professor of Psychiatric Neuroscience, Jonas’ team studied cells from patients with bipolar disorder and discovered that their mitochondria leaked significantly more than cells from people without the disorder.

Manipulating the hydrogen leak may offer a way to treat disease. For instance, the laboratory of Gerald Shulman, MD, PhD, George R. Cowgill Professor of Medicine (Endocrinology), is designing drugs to treat fatty liver disease that cause mitochondria to leak in order to reduce fat in the liver.

Jonas is currently investigating how leaky membranes in mitochondria can contribute to a wide range of conditions including autism, Parkinson’s disease, kidney disease, and stroke. Her goal is to develop different drugs that alter the hydrogen ion leak in the membrane in both directions to help prevent and treat diseases that have too much leak and those that occur because the leak is too small.

Hongying Shen, PhD, associate professor of cellular and molecular physiology, is struck by the range of biochemical reactions that take place inside the mitochondria. Many of these processes are catabolic pathways, in which the organelles break down nutrients to produce ATP. “Mitochondria are an important reaction chamber that house a variety of different metabolic pathways,” she says. “There are many things happening within this small organelle.”

But there are many metabolic pathways beyond energy production that have yet to be understood. While mitochondrial dysfunction has been implicated in a broad range of human diseases, not all of these diseases are driven by a deficit in energy. Shen’s laboratory focuses on identifying the metabolic pathways that occur within mitochondria to better understand how their dysfunction contributes to different conditions.

Mitochondria have a permeable outer membrane and a highly folded, impermeable inner membrane. Her team is especially interested in the inner membrane, which is home to proteins known as transporters. Transporters help move key metabolites across the impermeable membrane and drive metabolism. “We believe that if we focus on these transporters, we can have a holistic understanding into all of the things that happen inside the mitochondria,” Shen says.

Shen’s research identified the transporter for glutathione, an important antioxidant inside the cell, as well as the mechanism through which mitochondria control glutathione’s abundance. “Many human diseases, including neurodegenerative disorders, have been linked to oxidative stress,” Shen says. Oxidative stress occurs when the body has too many harmful molecules called free radicals and not enough defenses, or antioxidants, to control them. “There are many clinical trials trying to restore glutathione levels in order to combat that stress, but the outcomes have been limited. We are eager to probe this mechanism in the context of neurodegeneration.”

Shen’s team has also characterized the transporter for and mechanisms regulating cofactor coenzyme A (CoA), another key molecule for energy metabolism that is derived from Vitamin B. “This gives us a new view of how this cofactor might be limited under certain pathological conditions and could be a target for therapeutics,” says Shen, “We are really excited to pursue this as well.”

Genetic mutations can alter mitochondria, which have their own set of DNA. The laboratory of Nicole Lake, PhD, assistant professor of genetics, studies mitochondrial DNA to better understand which genetic variants contribute to disease. Lake’s laboratory develops novel tools that help scientists predict which genetic changes impact mitochondrial function. Using these tools, her team is creating a map of mitochondrial DNA to help pinpoint which parts are most important for health. “We’re especially interested in this part of our DNA because it’s relatively understudied, but we know it’s super important for human health and survival,” Lake says.

Her research has found that increasing mutations in mitochondrial DNA are associated with greater risk of disease and mortality. These mutations, for example, were linked to various kinds of cancer, especially blood-related cancers. “Everyone carries mitochondrial mutations. In fact, we get more of them as we age,” says Lake.

In future research, she plans to use her laboratory’s tools to measure the impact of damaging mutations and predict individuals’ risk of developing disease. “We’re developing more powerful tools to really dive deep into the mechanism of how these genetic changes actually change cell function, cause symptoms in different tissues, and underlie disease.”

Pietro De Camilli, MD, John Klingenstein Professor of Neuroscience, is interested in how cells deliver lipids to the mitochondria to maintain its outer plasma membrane. His research has shed light on how a mutation in a gene known as VPS13D can cause conditions such as ataxia with spasticity, a progressive neurodegenerative disorder that disrupts muscle coordination, as well as other childhood movement disorders.

To build the mitochondrial membrane, the cell needs to transport lipids—which are primarily synthesized in its endoplasmic reticulum—to the organelle. In collaboration with Karin Reinisch, PhD, David W. Wallace Professor of Cell Biology, De Camilli’s team discovered a special type of transport proteins that carry lipids from the endoplasmic reticulum to other destinations. VPS13D, they found, is one such protein that carries lipids to mitochondria.

“If you don’t have VPS13D—let’s say you have a mutation that completely abolishes these proteins­—there is no life,” De Camilli says. “This is a fundamental protein that’s important for delivering lipids to mitochondria.”

Mutations that partially hinder VPS13D also have consequences for health. De Camilli’s team found that these kinds of mutations cause the mitochondrial membrane to be chronically leaky, and as a result, mitochondrial DNA leaks into the cell. Our cells detect this DNA as a threat and try to attack the perceived invader, which can lead to cell death.

“Mutations in these proteins are responsible for neurological disease,” De Camilli says. “These findings provide a foundation for understanding the mechanism of these diseases and eventually, could lead to treatments.”

In collaboration with Shen, De Camilli plans to further explore the impact of these mutations beyond hindering lipid delivery. “We are just at the beginning of understanding how this deficiency globally affects mitochondrial function,” he says.