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Mitochondrial OXPHOS defects are responsible for a large group of human diseases and have been associated with degenerative disorders and aging. The accurate in vivo and in organello biochemical assessment of the OXPHOS system is necessary for the diagnosis and investigation of such conditions. Here I describe a set of accurate polarographic and spectrophotometric assays that use relatively small...
Levels of phosphorylated adenosine nucleotides, including the universal energy carrier adenosine 5 ' -triphosphate (ATP) and its metabolites adenosine 5 ' -diphosphate (ADP) and adenosine 5 ' -monophosphate (AMP), define the energy state in living cells and are dependent mainly on mitochondrial function. In this article, we describe a method based on the luciferase-luciferin...
Mitochondrial diseases are a clinically heterogeneous group of disorders related to dysfunction of various components of oxidative metabolism. Common manifestations of these diseases include encephalopathy, skeletal myopathy, and cardiomyopathy, but essentially any tissue can be affected. To understand better the pathogenesis of mitochondrial disease and to potentially evaluate novel therapies, several...
The biogenesis and maintenance of mitochondria relies on a sizable number of proteins. Many of these proteins are organized into complexes, which are located in the mitochondrial inner membrane. Blue Native polyacrylamide gel electrophoresis (BN-PAGE) is a method for the isolation of intact protein complexes. Although it was initially used to study mitochondrial respiratory chain enzymes, it can also...
Mitochondria play a central role in programmed cell death through the release of cytochrome c and other proapoptotic factors. Fluorescence microscopy is used to visualize cytochrome c translocation and loss of mitochondrial membrane potential. Flow cytometry can also be used to measure mitochondrial membrane potential. Cytochrome c content in cytosol and mitochondria can be determined by immunoblotting...
There is currently great interest in the development of methods to analyze intracellular redox state and the cellular damages generated by oxidative stress. General methods for analyzing reactive oxygen species and glutathione level are presented together with more recently developed protocols to analyze the consequences of oxidative stress on the oxidation of macromolecules. Finally, techniques to...
We describe cell-free strategies for analysis of the biogenesis of membrane proteins. Special emphasis is placed on the unique challenges presented by tail-anchor proteins for the analysis of: targeting specificity, binding to membranes such as endoplasmic reticulum, mitochondria and pure lipid membranes, protein topology in the membrane and the dependence of various steps on additional proteins....
The mammalian mitochondrial (mt) genome codes for only 13 proteins, which are essential components in the process of oxidative phosphorylation of ADP into ATP. Synthesis of these proteins relies on a proper mt translation machinery. While 22 tRNAs and 2 rRNAs are also coded by the mt genome, all other factors including the set of aminoacyl-tRNA synthetases (aaRSs) are encoded in the nucleus and imported...
The use of live cell microscopy has made a number of contributions to the study of apoptosis. Many of the tools and techniques are available that allow us to image the key events that occur during cell death including mitochondrial outer membrane permeabilization, mitochondrial transmembrane potential changes, translocation of Bcl-2 family members, caspase activation, phosphatidylserine flip and plasma...
Following most cell death signals, pro-apoptotic Bcl-2 members as Bax and Bak are activated and oligomerize into the mitochondria outer membrane, triggering its permeabilization and release into the cytosol of soluble apoptogenic factors such as cytochrome c involved in caspase activation. Thus, in many studies focused on apoptosis, cytochrome c release within cells is frequently examined to assess...
Endogenous fluorophores provide a simple, but elegant means to investigate the relationship between agonist-evoked Ca 2+ signals and the activation of mitochondrial metabolism. In this article, we discuss the methods and strategies to measure cellular pyridine nucleotide and flavoprotein fluorescence alone or in combination with Ca 2+ -sensitive indicators. These methods were developed...
Among the many unsolved problems of calcium signalling, the role of calcium elevations in apoptotic and necrotic cell death has been a focus of research in recent years. Evidence has been presented that calcium oscillations can effectively trigger apoptosis under certain conditions and that dysregulation of calcium signalling is a common cause of cell death. These effects are regularly mediated through...
Mitochondrial DNA (mtDNA) mutations contribute to the pathology of a number of age-related disorders, including Parkinson disease [A. Bender et al., Nat. Genet. 38 (2006) 515,Y. Kraytsberg et al., Nat. Genet. 38 (2006) 518], muscle-wasting [J. Wanagat, Z. Cao, P. Pathare, J.M. Aiken, FASEB J. 15 (2001) 322], and the metastatic potential of cancers [K. Ishikawa et al., Science 320 (2008) 661]. The...
Determining the genetic factors in a disease is crucial to elucidating its molecular basis. This task is challenging due to a lack of information on gene function. The integration of large-scale functional genomics data has proven to be an effective strategy to prioritize candidate disease genes. Mitochondrial disorders are a prevalent and heterogeneous class of diseases that are particularly amenable...
Mitochondria have their own DNA (mtDNA) and hence biogenesis of mitochondria requires a coordination of nuclear and mtDNA, both of which encode for mitochondria proteins. Our understanding of the molecular control of mitochondria biogenesis has increased in recent years, providing key signatures of the process. To determine whether or not a tissue or an organ of human or animal origin is undergoing...
Defects in mitochondrial oxidative phosphorylation (OXPHOS) are a frequent cause of severe inherited metabolic disorders and also contribute to aging. The OXPHOS system constitutes five multi-subunit complexes embedded in the mitochondrial inner membrane. Correct function of this system requires proper assembly of the ∼80 proteins in the complexes, as well as numerous assembly factors. Blue native...
Saccharomyces cerevisiae has played an important role as a model system to understand the biochemistry and molecular biology of mammalian cells. The genetic tools available and the short life span have also made S. cerevisiae a powerful system to study aging. The yeast chronological life span (CLS) is a measure of the survival of a non-dividing population of cells, and thus can model aging of mammalian...
Oxidative phosphorylation (OXPHOS) deficiency results in a number of human diseases, affecting at least one in 5000 of the general population. Altering the function of genes by mutations are central to our understanding their function. Prior to the development of gene targeting, this approach was limited to rare spontaneous mutations that resulted in a phenotype. Since its discovery, targeted mutagenesis...
The main source of mitochondrial DNA (mtDNA) damage is reactive oxygen species (ROS) generated during normal cellular metabolism. The main mtDNA lesions generated by ROS are base modifications, such as the ubiquitous 8-oxoguanine (8-oxoG) lesion; however, base loss and strand breaks may also occur. Many human diseases are associated with mtDNA mutations and thus maintaining mtDNA integrity is critical...
Mitochondria are difficult targets for microscopy because of their small size and highly compartmentalized, membranous interior. Super-resolution fluorescence microscopy methods have recently been developed that exceed the historical limits of optical imaging. Here we outline considerations and techniques in preparing to image the relative location of mitochondrial proteins using photoactivated localization...
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