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In this review the composition, structure and function of the complexes of the mammalian mitochondrial electron transport chain and the ATP synthase are highlighted in the context of the Chemiosmotic Hypothesis and our understanding of oxidative phosphorylation. Thus, a firm biochemical foundation is established for the diagnosis of human mitochondrial diseases. The significant insights achieved to date also lead to new questions about the biogenesis of these multisubunit complexes, their interactions, their regulation, and the integration of their activities with other mitochondrial and cellular functions.

The mitochondrion contains a circular DNA genome (mtDNA) that serves as the basis for its own genetic system. This system is semiautonomous because the coding capacity of mtDNA is limited to 13 subunits of the respiratory chain apparatus and the rRNAs and tRNAs necessary for their translation. The inheritance of mtDNA differs from that of nuclear DNA in that it segregates randomly during mitosis and meiosis and is transmitted exclusively through the female germ line. Nucleus-encoded enzymes and factors direct the transcription and replication of mtDNA within the mitochondrial matrix. Mitochondrial translation also relies upon nucleus-encoded ribosomal proteins, synthetases and translation factors. In recent years, molecular mechanisms for the bi-genomic control of mitochondrial biogenesis and function have been elucidated.

Oxidative phosphorylation defects are a common group of inborn errors of metabo lism. Patients may present to a variety of different physicians and at any age. Whilst some patients present with a characteristic phenotype that allows early diagnosis, in many the clinical features are suggestive rather than diagnostic. Neurological features are often prominent in all age groups, but the involvement may be diffuse or remarkable specific (for example optic atrophy alone). In other patients, involvement of other systems is more prominent and in some there is evidence of multiorgan failure. Clinical investigations such as imaging, cardiac studies, and endocrine investigations are often supportive of a diagnosis and form an important part of the clinical investigation. The clinical diagnosis of defects of oxidative phosphorylation is likely to remain a challenge with only the alert clinician identifying the difficult cases.

In muscle histopathological hallmarks for OXPHOS disorders are the so-called ragged-red fiber, the COX-negative or COX-deficient fiber, and the paracrystalline inclusions in mitochondria. Ragged-red fibers may be found in cases with mitochondrial DNA mutations. Up to now no morphological hallmarks were found for nuclear DNA mutations in genes coding for OXPHOS proteins. However, mutations in (nuclear) assembly genes for Complex IV may give rise to severe COX deficiency.

In the central nervous system, the peripheral nervous system, and in other organs, histopathological changes may be severe and specific for a particular OXPHOS disorder. However, direct indications to OXPHOS disorders are generally not present.

In this chapter the biochemical diagnosis of OXPHOS disorders is presented. The laboratory investigations in suspected patients are started with the examination of body fluids. The most important metabolite to be measured is lactate, that is frequendy found to be elevated in blood, urine and cerebrospinal fluid of patients with OXPHOS disorders. The next step in the diagnostic procedure consists of the examination of tissues. The biochemical diagnostic investigations are preferably performed in muscle tissue because in most patients the defect is expressed in muscle. Biopsy material is preferred above autopsy material. Biochemical examination of a fresh muscle sample is to be preferred because mitochondria are intact in fresh muscle thus allowing measurement of the overall oxidative capacity of the mitochondria. In a frozen muscle sample only enzyme activities of the OXPHOS complexes can be measured. In the latter case patients with a disturbance in the oxidative phosphorylation not localized in one of the OXPHOS complexes remain undiagnosed. Practical guidelines for the biochemical examinations of muscle are provided. In certain circumstances it is necessary to examine also fibroblasts. This is an absolute prerequisite in case prenatal diagnosis is requested. The interpre-tation of the biochemical investigations is discussed with special emphasis on the observed residual enzyme activities.

Mitochondrial OXPHOS is at the crosspoint of two quite different genetic systems, the nuclear genome, and the mitochondrial genome (mitochondrial DNA, mtDNA). The latter encodes a few essential components of the mitochondrial respiratory chain, and has unique molecular and genetic properties that account for some of the peculiar features of mitochondrial disorders. Although mitochondrial disorders have been known for more than thirty years, a major breakthrough in their understanding has come much later, with the discovery of an impressive, ever increasing number of mutations of mitochondrial DNA. Partial deletions or duplications of mtDNA, or maternally inherited point mutations, have been associated with well-defined clinical syndromes. Given the complexity of mitochondrial genetics and biochemistry, the clinical manifestations of mitochondrial disorders are extremely heterogeneous. They range from lesions of single tissues or structures, such as the optic nerve in Leber s hereditary optic neuropathy, or the cochlea in maternally-inherited nonsyndromic deafness, to more widespread lesions including myopathies, encephalomyopathies, cardiopathies, or complex multisystem syndromes. The recent advances in genetic studies provide both diagnostic tools and new pathogenetic insights in this rapidly expanding area of human pathology.

The ubiquitous nature of mitochondria, the dual genetic foundation of the OXPHOS system in mitochondrial and nuclear genome, and the peculiar rules of mitochondrial genetics all contribute to the extraordinary heterogeneity of clinical disorders associated with defects of oxidative phosphorylation (mitochondrial encephalomyopathies). Here, we review recent findings about nuclear gene defects in OXPHOS enzyme complex deficiency. This information should help in identifying patients with mitochondrial disease and defining a biochemical and molecular basis of the disorder found in each patient. This knowledge is indispensable for accurate genetic counseling and prenatal diagnosis, and is a prerequisite for the development of rational therapies, which are still, at present, woefully inadequate.

During the past century mitochondria have been recognized to play a central role in many cellular functions. Apart from producing cellular energy in the form of ATP (adenosine 5′-triphosphate) this organelle harbors essential parts of the urea cycle and is crucial for the breakdown of fatty acids, heat generation and the biosynthesis of heme, pyrimidines, amino acids, phospholipids and nucleotides. In addition to these ‘classical’ functions, mitochondria are also key players in cellular signaling through their involvement in apoptosis, generation of reactive nitrogen- and oxygen species (ROS/RNS), transduction of electrical signals and calcium homeostasis. This chapter summarizes current insights concerning the consequences of oxidative phosphorylation (OXPHOS) dysfunction at the cellular level. We will start with illustrating how mitochondrial and cellular metabolism is intertwined during ATP generation, calcium transport and ROS production. Moreover, the relation between mitochondrial morphology and function will be addressed. Next, we will summarize how OXPHOS deficiency and cellular functioning have been analyzed using pharmacological model systems and patient-derived cell lines. Also results of mathematical modeling, applied to integrate and understand the complex experimental data, will be treated. Finally, we will discuss possible adaptive mechanisms that counterbalance OXPHOS deficiency in the living cell.

Dysfunction of the mitochondrial respiratory chain has been associated with a wide range of human diseases ranging from diabetes to cardiomyopathy. Mutations in a number of nuclear as well as mitochondrial genes have been implicated in causing these diseases. Several animal models have now been created which reproduce some of the clinical pathology observed in human patients suffering from OXPHOS disorders. In this chapter we review some of these animal models of OXPHOS disorders and how they have led to a further understanding of both mitochondrial respiratory chain function and dysfunction.

No curative treatment of OXPHOS disorders is currently available, despite great progress in our understanding of the molecular bases of these diseases. We review available and experimental therapeutic approaches that fall into the following categories:

(a) Palliative therapy; (b) removal of noxious metabolites; (c) administration of artificial electron acceptors; (d) administration of metabolites and cofactors; (e) administration of oxygen radical scavengers and f-gene therapy.

Progress in each of these approaches provides some glimmer of hope for the future, although much work remains to be done.