Bogenhagen's lab >> Mitochondria

Why Are We So Interested in Mitochondria?

The mitochondrion is most widely recognized as the main source of cellular ATP, as the cell’s powerhouse. It is much more than this. It is intimately involved in the life and death of the cell, capable of integrating pro- and anti-apoptotic signals and committing the cell to apoptosis. It is a critical integrating center for control of carbon, nitrogen and oxygen metabolism and in Ca, Fe and Cu storage. As such, it is thought to contain on the order of 1000 proteins, although it is clear that the mitochondrial proteome can vary widely in different tissues and under different conditions of development or disease. Thus, there is no single reference proteome applicable to all human mitochondria.

A unique aspect of mitochondrial biology is that this is the only organelle apart from the nucleus that is known to contain DNA. The presence of this compact circular mtDNA genome, which encodes only 13 proteins, requires the importation of a full set of nuclear-encoded proteins to replicate and transcribe mtDNA and to translate mRNAs and assemble their protein products into functional respiratory complexes. While the DNA polymerase, transcription machinery and ribosomal proteins are distinct from their nuclear or cytoplasmic counterparts, some processes, including RNA processing and DNA repair, can involve products of individual genes that are differentially targeted to more than one cell compartment. This genetic dichotomy requires a delicate coordination of nuclear and mitochondrial gene expression that is still poorly understood and can become unbalanced in disease states.

Mitochondrial Dysfunction in Disease

Mitochondria are involved in a strikingly diverse range of disease processes. Primary genetic disorders fall into two broad classes: those with deficiencies in either nuclear or mitochondrial genes. As early as 1988, Sholte (Sholte, 1988) reported over 60 human diseases with defects in nuclear genes encoding mitochondrial functions. There are currently 129 nuclear gene defects associated with mitochondrial disorders. Coincidentally, 1988 was also the beginning of the era of discovery of the role of mtDNA mutations in human disease, with the characterization of MERRF, myoclonus epilepsy with ragged red fibers. Subsequent research has now discovered over 30 mutations in mtDNA that impair respiratory chain activity and give rise to diseases with a wide range of clinical presentations (DiMauro and Schon, 2003). Many mtDNA-encoded disorders may be considered orphan diseases that have received little study since they are individually rather rare genetic disorders. However, the aggregate incidence of mtDNA-encoded disease is estimated at 10 to 15 per 100,000 in the population, comparable to the incidence of Huntington’s disease.

Mitochondrial dysfunction is not limited to these rare disorders. It is increasingly recognized as a contributor to common diseases with multifactorial pathogenesis. Some examples are given below, concluding with the default condition of aging, which has a clear relationship to oxidative stress of mitochondrial origin.

Many progressive neurological diseases result from the execution of neurons by mitochondrial apoptosis. Friedrich’s ataxia results from a genetic defect in the frataxin gene, which is involved in mitochondrial iron transport (Babcock et al., 1997); human deafness dystonia results from a defect in a small component of the mitochondrial protein import machinery (Koehler et al., 1999); one well-characterized cause of amyotrophic lateral sclerosis is deficiency in Cu-Zn superoxide dismutase, which is located in the mitochondrial intermembrane space as well as the cytoplasm (Deng et al., 1993). The discovery that several environmental toxins cause Parkinsonism by inhibiting respiratory complex I and promoting the generation of reactive oxygen species has made this complex a focus for research on the basis of Parkinson’s disease (Dawson and Dawson, 2003). More recently, the mitochondrial protein encoded by PINK1 has provided a direct link between mitochondria and Parkinson’s disease (Valente et al., 2004). Alzheimer’s disease is also linked to mitochondrial toxicity through the mitochondrial protein ABAD, a target of amyloid (Lustbader et al., 2004) . The Bogenhagen laboratory is conducting a study of the effects of chronic oxidative stress generated by complex I inhibitors on the expression of nuclear genes encoding proteins that function in mitochondria.

The central role of mitochondria in metabolism of carbohydrates and fatty acids gives this organelle an important function in diabetes (Maechler and Wollheim, 2001). A mouse knockout of an abundant mitochondrial transcription factor has provided a model for b-cell ablation in juvenile diabetes (Silva et al., 2000). Mutations in mtDNA and in PPAR g, a master regulator of mitochondrial biogenesis, are correlated with type II diabetes. Insulin release depends on mitochondrial function as influenced by the expression of the membrane transporter UCP2 (Petersen et al., 2003; Zhang et al., 2001). The activity of thiazolidinediones as antidiabetic agents appears to depend on their ability to serve as ligands for PPAR g and its co-activator, PGC-1, in their control of expression of nuclear genes for mitochondrial gene products (Mootha et al., 2003; Puigserver and Spiegelman, 2003). There is a great potential for future studies to exploit mitochondrial biology to regulate carbohydrate and fatty acid metabolism in diabetics.

Mitochondrial research has contributed to two paradigm shifts in oncology. The first was the pioneering research by Warburg showing that cancer cells often rely heavily on glycolytic metabolism, even in the presence of an adequate oxygen supply (Warburg, 1956). The molecular genetic basis of this phenomenon remains an intriguing subject for current research (Cuezva et al., 2002; Dang and Semenza, 1999) and is not likely to be understood fully until the fields of metabolic control analysis and mitochondrial proteomics are united in a true systems biology synthesis of the biochemical derangements in cancer cells. Given the diversity of tumor types, this is a daunting task that may uncover different patterns of dysfunction in different tumors. It is clear that altered protein kinase cascades must ultimately be controlled by ATP levels and that the ability of certain tumor cells to sustain either chronic hypoxia or chronically elevated oxidative stress are factors that help define the hallmarks of cancer (Hanrahan and Weinberg, 2000). It is particularly interesting that tumors have been described in which primary mutations in mitochondrial housekeeping genes such as fumarate hydratase and succinate dehydrogenase play a primary role (Eng et al., 2003). Finally, recent studies have shown that tumors, due to their clonal origin, frequently bear homoplasmic mtDNA mutations that may contribute to tumor promotion.

The second paradigm shift in oncology provided by mitochondrial research is the appreciation that the ability of cancer cells to avoid apoptosis contributes to their limitless replicative potential and limits the efficacy of cancer chemotherapy (Thompson, 1995). Understanding the interactions of pro- and anti-apoptotic factors requires further studies of gene expression, quantitative proteomics and fundamental protein and membrane biochemistry in diverse cancer lineages. Within the next decade, basic research in these areas may answer the major challenge in this field to provide an understanding of the control of mitochondrial apoptosis in sufficient detail to permit therapy to target tumor cells selectively.

The past few decades have witnessed significant progress in development of chemotherapeutic agents for cancer and viral diseases. In the case of conventional cancer chemotherapy, the goal of selectively killing tumor cells has been difficult to attain due to collateral toxicity to normal cells. Cancer chemotherapeutic agents delivered to damage nuclear DNA may directly damage mtDNA as well, even in “resting tissues” where nuclear DNA replication is inactive but mtDNA replication continues. Mitochondria are poorly equipped to repair this sort of collateral damage. The degree to which impaired mitochondrial function contributes to health problems, including secondary tumors, in long-term cancer survivors is poorly understood (Bhatia and Sklar, 2002). Nucleoside analogues used as either anticancer or antiviral agents can also have significant mitochondrial toxicity. The best known examples include the inhibition of DNA polymerase g by AZT and dideoxynucleosides used to target the related HIV reverse transcriptase and the fatal hepatotoxicity of fialuridine observed when this agent was tested for activity against hepatitis B virus (Lewis and Dalakas, 1995). Instances of mitochondrial toxicity are not limited to pathways that impinge on nucleic acid metabolism. There is growing evidence that the myopathy and rhabdomyolysis associated with the popular cholesterol-lowering statins (Thompson et al., 2003) may involve interference with mitochondrial ubiquinone biosynthesis. These examples have illustrated how potential mitochondrial toxicity must be considered in drug discovery efforts.

If an individual escapes inborn metabolic disease, neurodegenerative disorders, diabetes and cancer he or she may still succumb to the final consequence of mitochondrial dysfunction, aging. The inexorable decline of mitochondrial function with age contributes to the aging-related conditions of neurodegeneration, type II diabetes and adult cancer discussed above. Just as oxidative stress underlies some of these defined diseases, it is thought to contribute to generalized aging (Harman, 1981). Mutations if C. elegans and D. melanogaster that reduce mitochondrial oxidative stress have been shown to prolong lifespan in these organisms (Hekimi and Guarente, 2003). Moreover, mammals maintained on calorie-restricted diets have a reduced metabolic rate that is thought to contribute to significantly increased longevity. Numerous studies have documented an increase in point mutations and deletions in mtDNA with advancing age. Trifunovic et al. (Trifunovic et al., 2004) have recently showed that mice engineered to express an error prone mitochondrial DNA polymerase can serve as an excellent model for premature ageing.

Aging is now seen as a developmentally-programmed process, as reflected in the new NIH initial review group “Biology of Development and Aging.” The incompletely understood role of mitochondrial biology in aging requires fundamental research. For example, the degree to which the continued turnover of mitochondria and of mtDNA in terminally-differentiated cells may contribute to age-related neurodegeneration and sarcopenia is unknown. The increased incidence of mtDNA mutations, particularly deletions, with age is now well documented, but the contribution of nuclear background to these processes is not yet appreciated. Similarly, the observation that certain mtDNA haplotypes correlate with increased lifespan has not been explained in molecular terms (Zhang et al., 2003). In this field, as in others, it is critically important to evaluate the interactions between mtDNA polymorphisms and the nuclear genetic background. Thus, this is an area in which high-throughput gene expression studies and SNP analysis may be particularly instructive.

Some unanswered questions:  

1. Given the complete human genome sequence, what is the complete roster of genes that provide mitochondrial proteins in different cell types as a function of development and disease states?

2. How does the cell maintain an adequate number of mitochondria so that it does not overpack the cytoplasm with mitochondria or deplete its supply of organelles?

3. What are the key mechanisms that regulate mitochondrial biogenesis? How do extra-mitochondrial proteins cooperate as an “interactomes” to maintain properly-balanced mitochondrial functions

4. What are the key enzyme substrates and products, e.g. nucleotides, reactive oxygen species, that can be monitored to diagnose mitochondrial dysfunction and how can their metabolic flux be controlled to limit disease?

5. What is the capacity of cells to repair damage to mitochondria and especially mtDNA? Can we intervene to enhance repair or to alter the rate of turnover of mitochondria?

Literature Cited