In the early 1960s, scientists discovered that there existed an organelle in the human cell that had its own DNA separate from the nucleus. This finding sparked a rat race among scientists across the globe to determine the source and purpose of this DNA. Soon, researchers discovered that the DNA in question was inherited from the mother and that many maternally inherited mutations resulted in mitochondrial mutations.
However, when Peter Mitchell was awarded the Nobel Prize in Chemistry in 1978 for discovering that ATP synthesis occurs within the mitochondria, the scientific community shifted its focus to viewing the mitochondria predominantly as the site of ATP production.
More to Mitochondria
Gerald Shadel, Professor of Pathology at the Yale School of Medicine, has always thought that there was much more to the organelle. “People have a simplified view of mitochondria, but mitochondria are very complicated and important,” he explained.
In the early 1990s, cytochrome C was found in mitochondria, which led to the discovery that the organelle assists in cell death. In the past five years, researchers have found that mitochondria are also involved in calcium regulation, nuclear signaling pathways, and metabolic pathways. Moreover, the Shadel lab, which focuses on mitochondria, has made several key discoveries suggesting that the organelles play a role in human aging.
The Shadel lab studies how mutations in mitochondrial DNA can cause disease and aging. Mitochondria have their own set of proteins and factors that regulate gene expression, and manipulation of these molecules aids in the study of their functions.
Research in the Shadel lab often begins with yeast, as the organism provides a simple genetic model that allows investigators to identify the factors in the nucleus that exert control over the mitochondria. Once something promising is discovered in yeast, researchers move on to human cells. Certain genes can be under- or over-expressed, and the resulting changes can then be analyzed.
If this data also proves auspicious, the experiments are taken a step further and carried out in mice. Finally, the results collected from this model system may then be extrapolated toward elucidating the biochemical pathways in human mitochondria.
The Shadel lab currently uses this approach to study three main projects: methylation in human mitochondrial transcription factor B1/2 (h-mtTFB1/2) causing premature deafness, the ataxia-telangiectasia mutated (ATM) pathway, and the target of rapamycin (TOR) pathway linked to the free radical theory of aging.
What Do Mitochondrial Transcription Factors Have to Do with Deafness?
While studying transcription, researchers in the Shadel lab first identified a specific transcription factor in yeast that was localized in mitochondria. Next, they identified two human homologs of this transcription factor, known as h-mtTFB1 and h-mtTFB2. When these homologs, which are also closely related to a family of enzymes, were cloned, the researchers found that the enzymatic activity of h-mtTFB1 was more important than the protein’s role as a transcription factor. For h-mtTFB2, however, the protein’s transcription factor role played a larger part than its enzymatic role.
The Shadel lab also discovered that when h-mtTFB2 is knocked out in E. coli, the bacteria become resistant to kasugamycin, an aminoglycoside antibiotic. This discovery was very interesting because kasugamycin resistance is associated with deafness. The investigators recognized that h-mtTFB2 methylates two adenines in human mitochondrial 12S RNA and acts as a RNA methyltransferase, and this methylation occurs at a specific loop that is conserved from E. coli to humans.
If a person maternally inherits a specific mutation slightly upstream from the h-mtTFB2 methylation, that person is more likely to become deaf with age. However, if the same person accidentally receives a dose of kasugamycin, he or she will become deaf immediately. The researchers found that people with the upstream mutation actually have more methylation at the h-mtTFB2 methylation site, and it is believed that this hypermethylation is most likely the cause of the deafness.
Yet, not everyone with the upstream mutation suffers premature deafness when exposed to kasugamycin. Another evolutionary factor protects families commonly affected by this mutation. The Shadel lab discovered that if a person has a mutation in the h-mtTFB1 gene, there is less methylation at the h-mtTFB2 methylation site. Conversely, if h-mtTFB1 is over-expressed, there is more methylation.
As a result, Shadel believes that the upstream mutation and the h-mtTFB1 mutation are counteracting each other. If a person has both mutations, then the methylation will be at a normal level and the person is not believed to have an increased risk of premature deafness. These opposing mutations are hypothesized to be an evolutionary development that protects families with the upstream mutation.
mtDNA’s Mysterious Multiplicity
Another fascinating aspect of mitochondria is that although cells have many copies of mitochondrial DNA (mtDNA), different cells have different amounts. Shadel is very interested in what controls the amount of DNA in each cell.
Specifically, his lab is studying the ataxia-telangiectasia mutated (ATM) pathway, a signaling pathway that is conserved from yeast to humans and is involved in regulating the mtDNA copy number in cells.
Previously, scientists believed that the ATM pathway plays a role in DNA damage because when damage occurs, the pathway turns on several genes that halt replication and initiate repair. Yet while the ATM pathway in the nucleus is only activated in the event of DNA damage, it is always active in mitochondria.
This pathway is of interest to the mitochondria’s role in aging because it is involved with ataxia-telangiectasia, a neurodegenerative disease. Ataxia refers to the degeneration of the cerebellum, which brings about uncontrolled movements, and telangiectasia refers to dilated blood vessels, causing spider veins. In addition to suffering neural degeneration, those with ataxia-telangiectasia are predisposed to cancer, premature aging, sterility, and diabetes.
The Shadel lab studied the disease in mice by knocking down the ATM gene. They found that certain mutations in the ATM pathway decrease production of mitochondrial DNA. Additionally, this mutation causes nuclear genomic instability, which could explain some symptoms of ataxia-telangiectasia, including as predisposition to cancer and sterility.
Symptoms such as premature aging and predisposition to diabetes, which are typically associated with other mitochondrial diseases, are not explained by this nuclear instability. The neurodegenerative part of ataxia-telangiectasia might still be explained by mitochondria though, as they are important in neural pathways.
Research in the Shadel lab is currently focusing on the ATM pathway in an attempt to understand the ataxia-telangiectasia symptoms that are unexplained by its nuclear effects. If the source of these symptoms can be better understood, then treatment and prevention of the disease may be improved.
Protection Against Free Radicals: the TOR Pathway
Another pathway of great interest to the Shadel lab is the target of rapamycin (TOR) pathway, which senses the availability of nutrients and controls metabolism.
For several decades, it has been known that mitochondria play a large role in metabolic pathways. For example, the Citric Acid Cycle and oxidative phosphorlyation, two processes that produce energy rich molecules in cellular respiration, occur within the organelle. In oxidative phosphorylation, an electron transport chain passes electrons along through redox reactions toward the final electron acceptor of oxygen. The energy released during the redox reactions is used to produce the energy rich molecule ATP. It is also known that electrons can prematurely exit the electron transport chain and interact with oxygen. This results in very reactive oxygen molecules called free radicals that are dangerous to tissues. According to the free radical theory of aging, the buildup of these molecules causes damage to cells, aging the organism.
The TOR gene decreases the production of free radical oxygen molecules and thus, according to the radical theory of aging, extends lifespan. Before, scientists believed that if more respiration occurred in the cell, there would be more oxidative species degrading the cell. Yet the Shadel lab has shown that the TOR pathway is more active during periods of greater oxidative respiration, keeping the level of oxidative species low. By this mechanism, it is believed that the TOR pathway protects the cell from these dangerous molecules. Already studied in worms and flies, the TOR pathway is now being investigated in mice.
Promise of the “Underestimated” Organelle
“The role of mitochondria is grossly underestimated,” said Shadel. “It is an area that hasn’t been looked at carefully. The way in which mitochondria has a role in aging is underappreciated.”
Although the idea that mitochondria play a role in aging was first postulated in the 1950s, the experimental evidence to support it has been weak until recently. The work of the Shadel lab has shown that mitochondrial transcription factors affect premature aging, that the aging symptoms of ataxia-telangiectasia might be a result of a mitochondrial signaling pathway, and that mitochondrial genes control free radicals, one of the leading causes of aging.
Drugs on the current market typically target nuclear or cytoplasmic receptors. None, however, specifically target the mitochondria. Antioxidants, for instance, are believed to target the mitochondria, but these vitamins and drugs are not very specific and only moderately successful.
With the incoming knowledge of mitochondria generated by the Shadel lab comes the potential to control mitochondrial function and manipulate age-related pathology.