51
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Huang JH, Hood DA. Age-associated mitochondrial dysfunction in skeletal muscle: Contributing factors and suggestions for long-term interventions. IUBMB Life 2009; 61:201-14. [DOI: 10.1002/iub.164] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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52
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Elstner M, Andreoli C, Klopstock T, Meitinger T, Prokisch H. The mitochondrial proteome database: MitoP2. Methods Enzymol 2009; 457:3-20. [PMID: 19426859 DOI: 10.1016/s0076-6879(09)05001-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Defining the mitochondrial proteome is a prerequisite for fully understanding the organelles function as well as mechanisms underlying mitochondrial pathology. The core functions of mitochondria include oxidative phosphorylation, amino acid metabolism, fatty acid oxidation, and ion homeostasis. In addition to these well-known functions, many crucial properties in cell signaling, cell differentiation and cell death are only now being elucidated, and with them the proteins involved. With the wealth of information arriving from single protein studies and sophisticated genome-wide approaches, MitoP2 was designed and is maintained to consolidate knowledge on mitochondrial proteins in one comprehensive database, thus making all pertinent data readily accessible (http://www.mitop2.de). Although the identification of the human mitochondrial proteome is ultimately the prime objective, integration of other species includes Saccharomyces cerevisiae, mouse, Arabidopsis thaliana, and Neurospora crassa so orthology between these species can be interrogated. Data from genome-wide studies can be individually retrieved and are also processed by a support vector machine (SVM) to generate a score that indicates the likelihood of a candidate protein having a mitochondrial location. Manually validated proteins constitute the reference set of the database that contains over 590 yeast, 920 human, and 1020 mouse entries, and that is used for benchmarking the SVM score. Multiple search options allow for the interrogation of the reference set, candidates, disease related proteins, chromosome locations as well as availability of mouse models. Taken together, MitoP2 is a valuable tool for basic scientists, geneticists, and clinicians who are investigating mitochondrial physiology and dysfunction.
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Affiliation(s)
- M Elstner
- Institute of Human Genetics, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
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53
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Chapter 3 Proteome Characterization of Mouse Brain Mitochondria Using Electrospray Ionization Tandem Mass Spectrometry. Methods Enzymol 2009; 457:49-62. [DOI: 10.1016/s0076-6879(09)05003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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54
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Hell K, Neupert W. Oxidative Protein Folding in Mitochondria. OXIDATIVE FOLDING OF PEPTIDES AND PROTEINS 2008. [DOI: 10.1039/9781847559265-00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Kai Hell
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München Butenandtstrasse 5 81377 München Germany
| | - Walter Neupert
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München Butenandtstrasse 5 81377 München Germany
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55
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Aiyar RS, Gagneur J, Steinmetz LM. Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods 2008; 46:248-55. [PMID: 18930150 PMCID: PMC2774125 DOI: 10.1016/j.ymeth.2008.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 10/03/2008] [Accepted: 10/08/2008] [Indexed: 11/24/2022] Open
Abstract
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 to this approach. Here we explain the application of integrative approaches to the identification of mitochondrial disease genes. We first examine various datasets that can be used to evaluate the involvement of each gene in mitochondrial function. The data integration methodology is then described, accompanied by examples of common implementations. Finally, we discuss how gene networks are constructed using integrative techniques and applied to candidate gene prioritization. Relevant public data resources are indicated. This report highlights the success and potential of data integration as well as its applicability to the search for mitochondrial disease genes.
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Affiliation(s)
- Raeka S. Aiyar
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Julien Gagneur
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Lars M. Steinmetz
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
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56
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Magda D, Lecane P, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund KD, Hacia JG. mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft. BMC Genomics 2008; 9:521. [PMID: 18980691 PMCID: PMC2612029 DOI: 10.1186/1471-2164-9-521] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 11/03/2008] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA) levels have on the nuclear transcriptome have not been defined under physiological conditions. In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted rho0 counterparts grown in culture and as tumor xenografts in immune-deficient mice. RESULTS Cultured A549 rho0 cells were respiration-deficient and showed enhanced levels of transcripts relevant to metal homeostasis, initiation of the epithelial-mesenchymal transition, and glucuronidation pathways. Several well-established HIF-regulated transcripts showed increased or decreased abundance relative to the parental cell line. Furthermore, growth in culture versus xenograft has a significantly greater influence on expression profiles, including transcripts involved in mitochondrial structure and both aerobic and anaerobic energy metabolism. However, both in vitro and in vivo, mtDNA levels explained the majority of the variance observed in the expression of transcripts in glucuronidation, tRNA synthetase, and immune surveillance related pathways. mtDNA levels in A549 xenografts also affected the expression of genes, such as AMACR and PHYH, involved in peroxisomal lipid metabolic pathways. CONCLUSION We have identified mtDNA-dependent gene expression profiles that are shared in cultured cells and in xenografts. These profiles indicate that mtDNA-depleted cells could provide informative model systems for the testing the efficacy of select classes of therapeutics, such as anti-angiogenesis agents. Furthermore, mtDNA-depleted cells grown culture and in xenografts provide a powerful means to investigate possible relationships between mitochondrial activity and gene expression profiles in normal and pathological cells.
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Affiliation(s)
- Darren Magda
- Department of Biochemistry and Molecular Biology, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA.
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57
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MitoP2: an integrative tool for the analysis of the mitochondrial proteome. Mol Biotechnol 2008; 40:306-15. [PMID: 18780189 DOI: 10.1007/s12033-008-9100-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 08/21/2008] [Indexed: 12/21/2022]
Abstract
Mitochondria are crucial for normal cell metabolism and maintenance. Mitochondrial dysfunction has been implicated in a spectrum of human diseases, ranging from rare monogenic to common multifactorial disorders. Important for the understanding of organelle function is the assignment of its constituents, and although over 1,500 proteins are predicted to be involved in mammalian mitochondrial function, so far only about 900 are assigned to mitochondria with reasonable certainty. Continuing efforts are being taken to obtain a complete inventory of the mitochondrial proteome by single protein studies and high-throughput approaches. To be of best value for the scientific community this data needs to be structured, explored, and customized. For this purpose, the MitoP2 database ( http://www.mitop2.de ) was established and is maintained in order to incorporate such data. The central database contains manually evaluated yeast, mouse, and human reference proteins, which show convincing evidence of a mitochondrial location. In addition, entries from genome-wide approaches that suggest protein localization are integrated and serve to compile a combined score for each candidate, which provides a best estimate of mitochondrial localization. Furthermore, it integrates information on the orthology between species, including Saccharomyces cerevisiae, mouse, human, Arabidopsis thaliana, and Neurospora crassa, thus mutually enhancing evidence across species. In contrast to other known databases, MitoP2 takes into account the reliability by which the protein is estimated as being mitochondrially located, as described herein. Multiple search functions, as well as information on disease causing genes and available mouse models, makes MitoP2 a valuable tool for the genetic investigation of human mitochondrial pathology.
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58
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Fang X, Wang W, Yang L, Chandrasekaran K, Kristian T, Balgley BM, Lee CS. Application of capillary isotachophoresis-based multidimensional separations coupled with electrospray ionization-tandem mass spectrometry for characterization of mouse brain mitochondrial proteome. Electrophoresis 2008; 29:2215-23. [PMID: 18425750 DOI: 10.1002/elps.200700609] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
By employing a capillary ITP (CITP)/CZE-based proteomic technology, a total of 1795 distinct mouse Swiss-Prot protein entries (or 1705 nonredundant proteins) are identified from synaptic mitochondria isolated from mouse brain. The ultrahigh resolving power of CITP/CZE is evidenced by the large number of distinct peptide identifications measured from each CITP fraction together with the low peptide fraction overlapping among identified peptides. The degree of peptide overlapping among CITP fractions is even lower than that achieved using combined CIEF/nano-RP LC separations for the analysis of the same mitochondrial sample. When evaluating the protein sequence coverage by the number of distinct peptides mapping to each mitochondrial protein identification, CITP/CZE similarly achieves superior performance with 1041 proteins (58%) having 3 or more distinct peptides, 233 (13%) having 2 distinct peptides, and 521 (29%) having a single distinct peptide. The reproducibility of protein identifications is found to be around 86% by comparing proteins identified from repeated runs of the same mitochondrial sample. The analysis of the mouse mitochondrial proteome by two CITP/CZE runs results in the detection of 2095 distinct mouse Swiss-Prot protein entries (or 1992 nonredundant proteins), corresponding to 59% coverage of the updated Maestro mitochondrial reference set. The collective analysis from combined CITP/CZE and CIEF-based proteomic studies yields the identification of 2191 distinct mitochondrial protein entries (or 2082 nonredundant proteins), corresponding to 76% coverage of the MitoP2-database reference set.
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Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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59
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Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK. A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008; 134:112-23. [PMID: 18614015 DOI: 10.1016/j.cell.2008.06.016] [Citation(s) in RCA: 1527] [Impact Index Per Article: 95.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/06/2008] [Accepted: 06/02/2008] [Indexed: 01/04/2023]
Abstract
Mitochondria are complex organelles whose dysfunction underlies a broad spectrum of human diseases. Identifying all of the proteins resident in this organelle and understanding how they integrate into pathways represent major challenges in cell biology. Toward this goal, we performed mass spectrometry, GFP tagging, and machine learning to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. We link poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. Using this approach, we predict 19 proteins to be important for the function of complex I (CI) of the electron transport chain. We validate a subset of these predictions using RNAi, including C8orf38, which we further show harbors an inherited mutation in a lethal, infantile CI deficiency. Our results have important implications for understanding CI function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria.
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Affiliation(s)
- David J Pagliarini
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
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60
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Moon S, Cho S, Kim H. Organization and evolution of mitochondrial gene clusters in human. Genomics 2008; 92:85-93. [PMID: 18559289 DOI: 10.1016/j.ygeno.2008.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/07/2008] [Accepted: 01/08/2008] [Indexed: 11/29/2022]
Abstract
Currently, the spatial patterns of mitochondrial genes and how the genomic localization of (pseudo)genes originated from mitochondrial DNA remain largely unexplained. The aim of this study was to elucidate the organization of mitochondrial (pseudo)genes given their evolutionary origin. We used a keyword finding method and a bootstrapping method to estimate parameter values that represent the distribution pattern of mitochondrial genes in the nuclear genome. Almost half of mitochondrial genes showing physical clusters were located in the pericentromeric and subtelomeric regions of the chromosome. Most interestingly, the size of these clusters ranged from 0.085 to 3.2 Mb (average+/-SD 1.3+/-0.73 Mb), which coincides with the size of the evolutionary pocket, or the average size of evolutionary breakpoint regions. Our findings imply that the localization of mitochondrial genes in the human genome is determined independent of adaptation.
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Affiliation(s)
- Sunjin Moon
- Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
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61
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Martinvalet D, Dykxhoorn DM, Ferrini R, Lieberman J. Granzyme A cleaves a mitochondrial complex I protein to initiate caspase-independent cell death. Cell 2008; 133:681-92. [PMID: 18485875 DOI: 10.1016/j.cell.2008.03.032] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 11/14/2007] [Accepted: 03/24/2008] [Indexed: 10/22/2022]
Abstract
The killer lymphocyte protease granzyme A (GzmA) triggers caspase-independent target cell death with morphological features of apoptosis. We previously showed that GzmA acts directly on mitochondria to generate reactive oxygen species (ROS) and disrupt the transmembrane potential (DeltaPsi(m)) but does not permeabilize the mitochondrial outer membrane. Mitochondrial damage is critical to GzmA-induced cell death since cells treated with superoxide scavengers are resistant to GzmA. Here we find that GzmA accesses the mitochondrial matrix to cleave the complex I protein NDUFS3, an iron-sulfur subunit of the NADH:ubiquinone oxidoreductase complex I, after Lys56 to interfere with NADH oxidation and generate superoxide anions. Target cells expressing a cleavage site mutant of NDUFS3 are resistant to GzmA-mediated cell death but remain sensitive to GzmB.
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Affiliation(s)
- Denis Martinvalet
- Immune Disease Institute and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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62
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Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 2008; 8:1564-75. [PMID: 18348319 DOI: 10.1002/pmic.200700851] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mitochondria play essential roles in cardiac pathophysiology and the murine model has been extensively used to investigate cardiovascular diseases. In the present study, we characterized murine cardiac mitochondria using an LC/MS/MS approach. We extracted and purified cardiac mitochondria; validated their functionality to ensure the final preparation contains necessary components to sustain their normal function; and subjected these validated organelles to LC/MS/MS-based protein identification. A total of 940 distinct proteins were identified from murine cardiac mitochondria, among which, 480 proteins were not previously identified by major proteomic profiling studies. The 940 proteins consist of functional clusters known to support oxidative phosphorylation, metabolism, and biogenesis. In addition, there are several other clusters, including proteolysis, protein folding, and reduction/oxidation signaling, which ostensibly represent previously under-appreciated tasks of cardiac mitochondria. Moreover, many identified proteins were found to occupy other subcellular locations, including cytoplasm, ER, and golgi, in addition to their presence in the mitochondria. These results provide a comprehensive picture of the murine cardiac mitochondrial proteome and underscore tissue- and species-specification. Moreover, the use of functionally intact mitochondria insures that the proteomic observations in this organelle are relevant to its normal biology and facilitates decoding the interplay between mitochondria and other organelles.
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Affiliation(s)
- Jun Zhang
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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63
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Dinur-Mills M, Tal M, Pines O. Dual targeted mitochondrial proteins are characterized by lower MTS parameters and total net charge. PLoS One 2008; 3:e2161. [PMID: 18478128 PMCID: PMC2367453 DOI: 10.1371/journal.pone.0002161] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 03/20/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In eukaryotic cells, identical proteins can be located in different subcellular compartments (termed dual-targeted proteins). METHODOLOGY/PRINCIPAL FINDINGS We divided a reference set of mitochondrial proteins (published single gene studies) into two groups: i) Dual targeted mitochondrial proteins and ii) Exclusive mitochondrial proteins. Mitochondrial proteins were considered dual-targeted if they were also found or predicted to be localized to the cytosol, the nucleus, the endoplasmic reticulum (ER) or the peroxisome. We found that dual localized mitochondrial proteins have i) A weaker mitochondrial targeting sequence (MitoProtII score, hydrophobic moment and number of basic residues) and ii) a lower whole-protein net charge, when compared to exclusive mitochondrial proteins. We have also generated an annotation list of dual-targeted proteins within the predicted yeast mitochondrial proteome. This considerably large group of dual-localized proteins comprises approximately one quarter of the predicted mitochondrial proteome. We supported this prediction by experimental verification of a subgroup of the predicted dual targeted proteins. CONCLUSIONS/SIGNIFICANCE Taken together, these results establish dual targeting as a widely abundant phenomenon that should affect our concepts of gene expression and protein function. Possible relationships between the MTS/mature sequence traits and protein dual targeting are discussed.
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Affiliation(s)
- Maya Dinur-Mills
- Department of Molecular Biology, Hebrew University Medical School, Jerusalem, Israel
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64
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Zischka H, Kinkl N, Braun RJ, Ueffing M. Purification of Saccharomyces cerevisiae mitochondria by zone electrophoresis in a free flow device. Methods Mol Biol 2008; 432:51-64. [PMID: 18370010 DOI: 10.1007/978-1-59745-028-7_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This chapter describes the isolation of yeast mitochondria by differential centrifugation followed by mitochondrial purification through zone electrophoresis (ZE) using a free flow device (FFE). Starting from a yeast colony, cultures are grown under respiratory conditions to logarithmic phase. Cells are collected, their cell walls enzymatically disintegrated and the resulting spheroplasts are homogenized. Mitochondria are pre-fractionated from this homogenate by differential centrifugation. With the focus on further purification, pre-fractionated mitochondria are subjected to ZE-FFE. In ZE-FFE, mitochondria are transported with the buffer flow through the separation chamber and purified from contaminants by specific deflection through a perpendicularly oriented electric field. The purified mitochondria can be collected by centrifugation and used for further experiments and analysis such as sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), immunoblotting, 2-DE or electron microscopy.
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Affiliation(s)
- Hans Zischka
- GSF-National Research Center for Environment and Health, Institute of Toxicology, Munich-Neuherberg, Germany
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65
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Perocchi F, Mancera E, Steinmetz LM. Systematic screens for human disease genes, from yeast to human and back. MOLECULAR BIOSYSTEMS 2007; 4:18-29. [PMID: 18075670 DOI: 10.1039/b709494a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Systematic screens for human disease genes have emerged in recent years, due to the wealth of information provided by genome sequences and large scale datasets. Here we review how integration of genomic data in yeast and human is helping to elucidate the genetic basis of mitochondrial diseases. The identification of nearly all yeast mitochondrial proteins and many of their functional interactions provides insight into the role of mitochondria in cellular processes. This information enables prioritization of the candidate genes underlying mitochondrial disorders. In an iterative fashion, the link between predicted human candidate genes and their disease phenotypes can be experimentally tested back in yeast.
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Affiliation(s)
- Fabiana Perocchi
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
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66
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Groebe K, Krause F, Kunstmann B, Unterluggauer H, Reifschneider NH, Scheckhuber CQ, Sastri C, Stegmann W, Wozny W, Schwall GP, Poznanović S, Dencher NA, Jansen-Dürr P, Osiewacz HD, Schrattenholz A. Differential proteomic profiling of mitochondria from Podospora anserina, rat and human reveals distinct patterns of age-related oxidative changes. Exp Gerontol 2007; 42:887-98. [PMID: 17689904 DOI: 10.1016/j.exger.2007.07.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 06/18/2007] [Accepted: 07/06/2007] [Indexed: 01/07/2023]
Abstract
According to the 'free radical theory of ageing', the generation and accumulation of reactive oxygen species are key events during ageing of biological systems. Mitochondria are a major source of ROS and prominent targets for ROS-induced damage. Whereas mitochondrial DNA and membranes were shown to be oxidatively modified with ageing, mitochondrial protein oxidation is not well understood. The purpose of this study was an unbiased investigation of age-related changes in mitochondrial proteins and the molecular pathways by which ROS-induced protein oxidation may disturb cellular homeostasis. In a differential comparison of mitochondrial proteins from young and senescent strains of the fungal ageing model Podospora anserina, from brains of young (5 months) vs. older rats (17 and 31 months), and human cells, with normal and chemically accelerated in vitro ageing, we found certain redundant posttranslationally modified isoforms of subunits of ATP synthase affected across all three species. These appear to represent general susceptible hot spot targets for oxidative chemical changes of proteins accumulating during ageing, and potentially initiating various age-related pathologies and processes. This type of modification is discussed using the example of SAM-dependent O-methyltransferase from P. anserina (PaMTH1), which surprisingly was found to be enriched in mitochondrial preparations of senescent cultures.
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67
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Habib SJ, Neupert W, Rapaport D. Analysis and prediction of mitochondrial targeting signals. Methods Cell Biol 2007; 80:761-81. [PMID: 17445721 DOI: 10.1016/s0091-679x(06)80035-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shukry J Habib
- Institut für Physiologische Chemie, Universität München, D-81377 Munich, Germany
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68
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Athanasiou A, Smith PA, Vakilpour S, Kumaran NM, Turner AE, Bagiokou D, Layfield R, Ray DE, Westwell AD, Alexander SPH, Kendall DA, Lobo DN, Watson SA, Lophatanon A, Muir KA, Guo DA, Bates TE. Vanilloid receptor agonists and antagonists are mitochondrial inhibitors: how vanilloids cause non-vanilloid receptor mediated cell death. Biochem Biophys Res Commun 2007; 354:50-5. [PMID: 17214968 DOI: 10.1016/j.bbrc.2006.12.179] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 12/12/2006] [Indexed: 12/12/2022]
Abstract
Time-lapse photomicroscopy of human H460 lung cancer cells demonstrated of the transient receptor potential V1 (TRPV1) channel agonists, (E)-capsaicin and resiniferatoxin, and the TRPV1 antagonists, capsazepine, and SB366791, were able to bring about morphological changes characteristic of apoptosis and/or necrosis. Immunoblot analysis identified immunoreactivity for the transient receptor potential V1 (TRPV1) channel in rat brain samples, but not in rat heart mitochondria or in H460 cells. In isolated rat heart mitochondria, all four ligands caused concentration-dependent decreases in oxygen consumption and mitochondrial membrane potential. (E)-Capsaicin and capsazepine evoked concentration-dependent increases and decreases, respectively, in mitochondrial hydrogen peroxide production, whilst resiniferatoxin and SB366791 were without significant effect. These data support the hypothesis that (E)-capsaicin, resiniferatoxin, capsazepine, and SB366791 are all mitochondrial inhibitors, able to activate apoptosis and/or necrosis via non-receptor mediated mechanisms, and also support the use of TRPV1 ligands as anti-cancer agents.
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Affiliation(s)
- Andriani Athanasiou
- School of Biomedical Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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69
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Boldogh IR, Pon LA. Purification and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae. Methods Cell Biol 2007; 80:45-64. [PMID: 17445688 DOI: 10.1016/s0091-679x(06)80002-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Istvan R Boldogh
- Department of Anatomy and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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70
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Hu ZZ, Valencia JC, Huang H, Chi A, Shabanowitz J, Hearing VJ, Appella E, Wu C. Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2007; 259:147-160. [PMID: 17375895 PMCID: PMC1828028 DOI: 10.1016/j.ijms.2006.09.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Complete and accurate profiling of cellular organelle proteomes, while challenging, is important for the understanding of detailed cellular processes at the organelle level. Mass spectrometry technologies coupled with bioinformatics analysis provide an effective approach for protein identification and functional interpretation of organelle proteomes. In this study, we have compiled human organelle reference datasets from large-scale proteomic studies and protein databases for 7 lysosome-related organelles (LROs), as well as the endoplasmic reticulum and mitochondria, for comparative organelle proteome analysis. Heterogeneous sources of human organelle proteins and rodent homologs are mapped to human UniProtKB protein entries based on ID and/or peptide mappings, followed by functional annotation and categorization using the iProXpress proteomic expression analysis system. Cataloging organelle proteomes allows close examination of both shared and unique proteins among various LROs and reveals their functional relevance. The proteomic comparisons show that LROs are a closely related family of organelles. The shared proteins indicate the dynamic and hybrid nature of LROs, while the unique transmembrane proteins may represent additional candidate marker proteins for LROs. This comparative analysis, therefore, provides a basis for hypothesis formulation and experimental validation of organelle proteins and their functional roles.
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Affiliation(s)
- Zhang-Zhi Hu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
| | - Julio C. Valencia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Hongzhan Huang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
| | - An Chi
- Department of Chemistry, University of Virginia, Charlottesville, VA
| | | | - Vincent J. Hearing
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Address Correspondence to: Dr. Ettore Appella, Laboratory of Cell Biology, Building 37, Room 2140, National Institutes of Health, Bethesda, MD 20892, , Dr. Cathy H. Wu, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street, NW, Suite 1200, Washington, DC 20007,
| | - Cathy Wu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
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Abstract
It is widely recognized that much of the information for determining the final subcellular localization of proteins is found in their amino acid sequences. Thus the prediction of protein localization sites is of both theoretical and practical interest. In most cases, the prediction has been attempted in two ways: one is based on the knowledge of experimentally characterized targeting signals, while the other utilizes the statistical differences of general sequence characteristics, such as amino acid composition, between localization sites. Both approaches have limitations, and it is recommended to check the results of various prediction methods based on different principles as well as training data. Recently, increased proteomic analyses of localization sites have provided new data to assess the current status of predictive methods. In this chapter we discuss these issues and close with an example illustrating the use of the WoLF PSORT web server for localization prediction.
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Affiliation(s)
- Kenta Nakai
- Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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72
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Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM. Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet 2006; 2:e170. [PMID: 17054397 PMCID: PMC1617129 DOI: 10.1371/journal.pgen.0020170] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Accepted: 08/28/2006] [Indexed: 10/25/2022] Open
Abstract
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders.
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Affiliation(s)
| | - Lars J Jensen
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julien Gagneur
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Uwe Ahting
- Institute of Human Genetics, Technical University, Munich, and GSF National Research Center for Environment and Health, Neuherberg, Germany
| | | | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technical University, Munich, and GSF National Research Center for Environment and Health, Neuherberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Heidelberg, Germany
- * To whom correspondence should be addressed. E-mail:
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73
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Millar AH, Whelan J, Small I. Recent surprises in protein targeting to mitochondria and plastids. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:610-5. [PMID: 17008120 DOI: 10.1016/j.pbi.2006.09.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 09/15/2006] [Indexed: 05/12/2023]
Abstract
The functions of mitochondria and chloroplasts rely on thousands of proteins, mostly imported from the cytosol through specialized import channels. Neither the detailed import mechanisms nor the identities of all targeted proteins are known. Recent surprises include unexpected results concerning import receptors, unexpectedly frequent dual-targeting of proteins, and the discovery of novel routes of protein trafficking. Such findings make it more difficult to predict which proteins really are targeted to organelles. By combining experimental and bioinformatics data, we estimate the size of the mitochondrial and plastid proteomes to be approximately 2000 and 2700 proteins, respectively. Advances in cell and organelle fractionation coupled with modern proteomics techniques are probably the best route to understanding organellar protein composition.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Molecular and Chemical Sciences Building (M316), University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Western Australia, Australia
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74
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Pierleoni A, Martelli PL, Fariselli P, Casadio R. eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res 2006; 35:D208-12. [PMID: 17108361 PMCID: PMC1669738 DOI: 10.1093/nar/gkl775] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic Subcellular Localization DataBase collects the annotations of subcellular localization of eukaryotic proteomes. So far five proteomes have been processed and stored: Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae and Arabidopsis thaliana. For each sequence, the database lists localization obtained adopting three different approaches: (i) experimentally determined (when available); (ii) homology-based (when possible); and (iii) predicted. The latter is computed with a suite of machine learning based methods, developed in house. All the data are available at our website and can be searched by sequence, by protein code and/or by protein description. Furthermore, a more complex search can be performed combining different search fields and keys. All the data contained in the database can be freely downloaded in flat file format. The database is available at .
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Affiliation(s)
| | | | | | - Rita Casadio
- To whom correspondence should be addressed. Tel: +39 0512094005; Fax: +39 051242576;
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75
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Vo TD, Palsson BO. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. Am J Physiol Cell Physiol 2006; 292:C164-77. [PMID: 16885397 DOI: 10.1152/ajpcell.00193.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The emerging field of systems biology seeks to develop novel approaches to integrate heterogeneous data sources for effective analysis of complex living systems. Systemic studies of mitochondria have generated a large number of proteomic data sets in numerous species, including yeast, plant, mouse, rat, and human. Beyond component identification, mitochondrial proteomics is recognized as a powerful tool for diagnosing and characterizing complex diseases associated with these organelles. Various proteomic techniques for isolation and purification of proteins have been developed; each tailored to preserve protein properties relevant to study of a particular disease type. Examples of such techniques include immunocapture, which minimizes loss of posttranslational modification, 4-iodobutyltriphenylphosphonium labeling, which quantifies protein redox states, and surface-enhanced laser desorption ionization-time-of-flight mass spectrometry, which allows sequence-specific binding. With the rapidly increasing number of discovered molecular components, computational models are also being developed to facilitate the organization and analysis of such data. Computational models of mitochondria have been accomplished with top-down and bottom-up approaches and have been steadily improved in size and scope. Results from top-down methods tend to be more qualitative but are unbiased by prior knowledge about the system. Bottom-up methods often require the incorporation of a large amount of existing data but provide more rigorous and quantitative information, which can be used as hypotheses for subsequent experimental studies. Successes and limitations of the studies reviewed here provide opportunities and challenges that must be addressed to facilitate the application of systems biology to larger systems.
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Affiliation(s)
- Thuy D Vo
- Department of Bioengineering, University of California-San Diego, MC 0412, La Jolla, CA 92093, USA
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76
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Gabaldón T. Computational approaches for the prediction of protein function in the mitochondrion. Am J Physiol Cell Physiol 2006; 291:C1121-8. [PMID: 16870830 DOI: 10.1152/ajpcell.00225.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding a complex biological system, such as the mitochondrion, requires the identification of the complete repertoire of proteins targeted to the organelle, the characterization of these, and finally, the elucidation of the functional and physical interactions that occur within the mitochondrion. In the last decade, significant developments have contributed to increase our understanding of the mitochondrion, and among these, computational research has played a significant role. Not only general bioinformatics tools have been applied in the context of the mitochondrion, but also some computational techniques have been specifically developed to address problems that arose from within the mitochondrial research field. In this review the contribution of bioinformatics to mitochondrial biology is addressed through a survey of current computational methods that can be applied to predict which proteins will be localized to the mitochondrion and to unravel their functional interactions.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.
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77
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Gillardon F. Differential mitochondrial protein expression profiling in neurodegenerative diseases. Electrophoresis 2006; 27:2814-8. [PMID: 16739226 DOI: 10.1002/elps.200500911] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alterations in mitochondrial structure or function have been described in a variety of human diseases for nearly half a century. The complete sequence of the human mitochondrial genome has been published in 1981. The mitochondrial proteome database however, is still incomplete. Here I give a short review on recent advances to determine the complete set of mitochondrial proteins. The main emphasis is put on gel-based proteomic approaches to identify differentially expressed mitochondrial proteins in neurodegenerative diseases.
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Affiliation(s)
- Frank Gillardon
- Boehringer Ingelheim Pharma, CNS Research, Biberach, Germany.
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78
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Stuart JA, Brown MF. Mitochondrial DNA maintenance and bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:79-89. [PMID: 16473322 DOI: 10.1016/j.bbabio.2006.01.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 01/03/2006] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Oxidative phosphorylation requires assembly of the protein products of both mitochondrial and of nuclear genomes into functional respiratory complexes. Cellular respiration can be compromised when mitochondrial DNA (mtDNA) sequences are corrupted. Oxidative damage resulting from reactive oxygen species (ROS) produced during respiration is probably a major source of mitochondrial genomic instability leading to respiratory dysfunction. Here, we review mechanisms of mitochondrial ROS production, mtDNA damage and its relationship to mitochondrial dysfunction. We focus particular attention on the roles of mtDNA repair enzymes and processes by which the integrity of the mitochondrial genome is maintained and dysfunction prevented.
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Affiliation(s)
- Jeffrey A Stuart
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1.
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