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De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder. Am J Hum Genet 2017; 101:716-724. [PMID: 29100085 DOI: 10.1016/j.ajhg.2017.09.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 11/21/2022] Open
Abstract
DHX30 is a member of the family of DExH-box helicases, which use ATP hydrolysis to unwind RNA secondary structures. Here we identified six different de novo missense mutations in DHX30 in twelve unrelated individuals affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment and gait abnormalities. While four mutations are recurrent, two are unique with one affecting the codon of one recurrent mutation. All amino acid changes are located within highly conserved helicase motifs and were found to either impair ATPase activity or RNA recognition in different in vitro assays. Moreover, protein variants exhibit an increased propensity to trigger stress granule (SG) formation resulting in global translation inhibition. Thus, our findings highlight the prominent role of translation control in development and function of the central nervous system and also provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.
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52
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Hou CC, Wei CG, Lu CP, Gao XM, Yang WX, Zhu JQ. Prohibitin-mediated mitochondrial ubiquitination during spermiogenesis in Chinese mitten crab Eriocheir sinensis. Oncotarget 2017; 8:98782-98797. [PMID: 29228727 PMCID: PMC5716767 DOI: 10.18632/oncotarget.21961] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/23/2017] [Indexed: 12/21/2022] Open
Abstract
The sperm of Eriocheir sinensis has a cup-shaped nucleus that contains several mitochondria embedded at the opening of the cup. The acrosome vesicle also contains derivants of mitochondria. The mitochondria distribution pattern involves a decrease in the number and changes in the structure and transportation of these organelles. The decreased number of sperm mitochondria is achieved through autophagy or the ubiquitination pathway. Prohibitin (PHB), the mitochondria inner membrane protein, is an evolutionarily highly conserved protein, is closely associated with spermatogenesis and sperm quality control and is also a potential substrate of ubiquitination. However, whether PHB protein mediates the ubiquitination pathway of sperm mitochondria in crustacean animals remains poorly understood. In the present study, we revealed that PHB, a substrate of ubiquitin, participates in the ubiquitination and degradation of mitochondria during spermiogenesis in E. sinensis. To confirm this finding, we used shRNA interference to reduce PHB expression and an overexpression technique to increase PHB expression in vitro. The interference experiment showed that the reduced PHB expression directly affected the polyubiquitination level and mitochondria status, whereas PHB overexpression markedly increased the polyubiquitination level. In vitro experiments also showed that PHB and its ubiquitination decide the fate of mitochondria.
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Affiliation(s)
- Cong-Cong Hou
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Chao-Guang Wei
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Cheng-Peng Lu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xin-Ming Gao
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun-Quan Zhu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo 315211, China
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53
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Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B. DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Res 2017; 45:7237-7248. [PMID: 28486639 PMCID: PMC5499585 DOI: 10.1093/nar/gkx395] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/27/2017] [Indexed: 12/02/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions. To study this possibility, we used optical tweezers to determine and compare the structure and energetics of long, individual HmtSSB–DNA complexes assembled on preformed ssDNA and on ssDNA generated gradually during ‘in situ’ DNA synthesis. We show that HmtSSB binds to preformed ssDNA in two major modes, depending on salt and protein concentration. However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two binding modes was observed under all experimental conditions. Our results reveal a key role for the gradual generation of ssDNA in modulating the binding mode of a multimeric SSB protein and consequently, in generating the appropriate nucleoprotein structure for DNA synthetic reactions required for genome maintenance.
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Affiliation(s)
- José A Morin
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Fernando Cerrón
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain
| | - Javier Jarillo
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Elena Beltran-Heredia
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Grzegorz L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
| | - Laurie S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, 33520 Tampere, Finland.,Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Francisco J Cao
- Departamento Física Atómica, Molecular y Nuclear, Universidad Complutense, 28040 Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) and CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología', 28049 Madrid, Spain
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54
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Lee SR, Han J. Mitochondrial Mutations in Cardiac Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 982:81-111. [PMID: 28551783 DOI: 10.1007/978-3-319-55330-6_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mitochondria individually encapsulate their own genome, unlike other cellular organelles. Mitochondrial DNA (mtDNA) is a circular, double-stranded, 16,569-base paired DNA containing 37 genes: 13 proteins of the mitochondrial respiratory chain, two ribosomal RNAs (rRNAs; 12S and 16S), and 22 transfer RNAs (tRNAs). The mtDNA is more vulnerable to oxidative modifications compared to nuclear DNA because of its proximity to ROS-producing sites, limited presence of DNA damage repair systems, and continuous replication in the cell. mtDNA mutations can be inherited or sporadic. Simple mtDNA mutations are point mutations, which are frequently found in mitochondrial tRNA loci, causing mischarging of mitochondrial tRNAs or deletion, duplication, or reduction in mtDNA content. Because mtDNA has multiple copies and a specific replication mechanism in cells or tissues, it can be heterogenous, resulting in characteristic phenotypic presentations such as heteroplasmy, genetic drift, and threshold effects. Recent studies have increased the understanding of basic mitochondrial genetics, providing an insight into the correlations between mitochondrial mutations and cardiac manifestations including hypertrophic or dilated cardiomyopathy, arrhythmia, autonomic nervous system dysfunction, heart failure, or sudden cardiac death with a syndromic or non-syndromic phenotype. Clinical manifestations of mitochondrial mutations, which result from structural defects, functional impairment, or both, are increasingly detected but are not clear because of the complex interplay between the mitochondrial and nuclear genomes, even in homoplasmic mitochondrial populations. Additionally, various factors such as individual susceptibility, nutritional state, and exposure to chemicals can influence phenotypic presentation, even for the same mtDNA mutation.In this chapter, we summarize our current understanding of mtDNA mutations and their role in cardiac involvement. In addition, epigenetic modifications of mtDNA are briefly discussed for future elucidation of their critical role in cardiac involvement. Finally, current strategies for dealing with mitochondrial mutations in cardiac disorders are briefly stated.
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Affiliation(s)
- Sung Ryul Lee
- Department of Integrated Biomedical Science, Cardiovascular and Metabolic Disease Center, College of Medicine, Inje University, Busan, 47392, South Korea
| | - Jin Han
- National Research Laboratory for Mitochondrial Signaling, Cardiovascular and Metabolic Disease Center, Department of Physiology, College of Medicine, Inje University, Busan, 47392, South Korea.
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55
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Pawar T, Bjørås M, Klungland A, Eide L. Metabolism and DNA repair shape a specific modification pattern in mitochondrial DNA. Mitochondrion 2017; 40:16-28. [PMID: 28893634 DOI: 10.1016/j.mito.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial DNA (mtDNA) resides in the vicinity of energy-rich reactions. Thus, chemical modifications of mtDNA might mirror mitochondrial processes and could serve as biomarkers of metabolic processes in the mitochondria. This hypothesis was tested by assessing modifications at 17 different sites in the mtDNA as a function of cell type, oxidative stress and mitochondrial activity. Two mouse mutants with a metabolic phenotype were compared to wild-type (WT) mice: the ogg1-/- mouse that lacks the 8-oxoguanine DNA glycosylase (OGG1), and the alkbh7-/- mouse missing the ALKBH7 protein that has been implicated in fatty acid oxidation. It was found that cell type, oxidative stress and mitochondrial complex activity shaped distinct modification patterns in mtDNA, and that OGG1 and ALKBH7 independently modulated these modification patterns. The modifications included ribonucleotides, which also accumulated in mtDNA with age. Interestingly, this age-dependent accumulation most likely involves DNA repair, as mtDNA from ogg1-/- mice did not accumulate modifications with age. On the other hand, alkbh7-/- mtDNA accumulated more modifications with age than WT mtDNA. Our results show that mtDNA is dynamically modified with metabolic activity and imply a novel synergy between metabolism and mtDNA repair proteins.
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Affiliation(s)
- Tina Pawar
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway; Department of clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
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56
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Paraskevaidi M, Martin-Hirsch PL, Kyrgiou M, Martin FL. Underlying role of mitochondrial mutagenesis in the pathogenesis of a disease and current approaches for translational research. Mutagenesis 2017; 32:335-342. [PMID: 27816931 DOI: 10.1093/mutage/gew058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/21/2016] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial diseases have been extensively investigated over the last three decades, but many questions regarding their underlying aetiologies remain unanswered. Mitochondrial dysfunction is not only responsible for a range of neurological and myopathy diseases but also considered pivotal in a broader spectrum of common diseases such as epilepsy, autism and bipolar disorder. These disorders are a challenge to diagnose and treat, as their aetiology might be multifactorial. In this review, the focus is placed on potential mechanisms capable of introducing defects in mitochondria resulting in disease. Special attention is given to the influence of xenobiotics on mitochondria; environmental factors inducing mutations or epigenetic changes in the mitochondrial genome can alter its expression and impair the whole cell's functionality. Specifically, we suggest that environmental agents can cause damage in mitochondrial DNA and consequently lead to mutagenesis. Moreover, we describe current approaches for handling mitochondrial diseases, as well as available prenatal diagnostic tests, towards eliminating these maternally inherited diseases. Undoubtedly, more research is required, as current therapeutic approaches mostly employ palliative therapies rather than targeting primary mechanisms or prophylactic approaches. Much effort is needed into further unravelling the relationship between xenobiotics and mitochondria, as the extent of influence in mitochondrial pathogenesis is increasingly recognised.
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Affiliation(s)
- Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Central Lancashire Teaching Hospitals NHS Foundation Trust, Preston PR5 6AW, UK and
| | - Maria Kyrgiou
- Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0NN, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
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57
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Kazak L, Chouchani ET, Stavrovskaya IG, Lu GZ, Jedrychowski MP, Egan DF, Kumari M, Kong X, Erickson BK, Szpyt J, Rosen ED, Murphy MP, Kristal BS, Gygi SP, Spiegelman BM. UCP1 deficiency causes brown fat respiratory chain depletion and sensitizes mitochondria to calcium overload-induced dysfunction. Proc Natl Acad Sci U S A 2017; 114:7981-7986. [PMID: 28630339 PMCID: PMC5544316 DOI: 10.1073/pnas.1705406114] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Brown adipose tissue (BAT) mitochondria exhibit high oxidative capacity and abundant expression of both electron transport chain components and uncoupling protein 1 (UCP1). UCP1 dissipates the mitochondrial proton motive force (Δp) generated by the respiratory chain and increases thermogenesis. Here we find that in mice genetically lacking UCP1, cold-induced activation of metabolism triggers innate immune signaling and markers of cell death in BAT. Moreover, global proteomic analysis reveals that this cascade induced by UCP1 deletion is associated with a dramatic reduction in electron transport chain abundance. UCP1-deficient BAT mitochondria exhibit reduced mitochondrial calcium buffering capacity and are highly sensitive to mitochondrial permeability transition induced by reactive oxygen species (ROS) and calcium overload. This dysfunction depends on ROS production by reverse electron transport through mitochondrial complex I, and can be rescued by inhibition of electron transfer through complex I or pharmacologic depletion of ROS levels. Our findings indicate that the interscapular BAT of Ucp1 knockout mice exhibits mitochondrial disruptions that extend well beyond the deletion of UCP1 itself. This finding should be carefully considered when using this mouse model to examine the role of UCP1 in physiology.
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Affiliation(s)
- Lawrence Kazak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Irina G Stavrovskaya
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215
| | - Gina Z Lu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | | | - Daniel F Egan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Manju Kumari
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Xingxing Kong
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Brian K Erickson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Evan D Rosen
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, MA 02215
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Bruce S Kristal
- Department of Neurosurgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215
- Division of Sleep Medicine, Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115;
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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58
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Being right on Q: shaping eukaryotic evolution. Biochem J 2017; 473:4103-4127. [PMID: 27834740 PMCID: PMC5103874 DOI: 10.1042/bcj20160647] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/18/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
Abstract
Reactive oxygen species (ROS) formation by mitochondria is an incompletely understood eukaryotic process. I proposed a kinetic model [BioEssays (2011) 33, 88–94] in which the ratio between electrons entering the respiratory chain via FADH2 or NADH (the F/N ratio) is a crucial determinant of ROS formation. During glucose breakdown, the ratio is low, while during fatty acid breakdown, the ratio is high (the longer the fatty acid, the higher is the ratio), leading to higher ROS levels. Thus, breakdown of (very-long-chain) fatty acids should occur without generating extra FADH2 in mitochondria. This explains peroxisome evolution. A potential ROS increase could also explain the absence of fatty acid oxidation in long-lived cells (neurons) as well as other eukaryotic adaptations, such as dynamic supercomplex formation. Effective combinations of metabolic pathways from the host and the endosymbiont (mitochondrion) allowed larger varieties of substrates (with different F/N ratios) to be oxidized, but high F/N ratios increase ROS formation. This might have led to carnitine shuttles, uncoupling proteins, and multiple antioxidant mechanisms, especially linked to fatty acid oxidation [BioEssays (2014) 36, 634–643]. Recent data regarding peroxisome evolution and their relationships with mitochondria, ROS formation by Complex I during ischaemia/reperfusion injury, and supercomplex formation adjustment to F/N ratios strongly support the model. I will further discuss the model in the light of experimental findings regarding mitochondrial ROS formation.
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59
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Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:8060949. [PMID: 28680532 PMCID: PMC5478868 DOI: 10.1155/2017/8060949] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/06/2017] [Accepted: 04/03/2017] [Indexed: 11/18/2022]
Abstract
Mitochondria preserve very complex and distinctively unique machinery to maintain and express the content of mitochondrial DNA (mtDNA). Similar to chromosomes, mtDNA is packaged into discrete mtDNA-protein complexes referred to as a nucleoid. In addition to its role as a mtDNA shield, over 50 nucleoid-associated proteins play roles in mtDNA maintenance and gene expression through either temporary or permanent association with mtDNA or other nucleoid-associated proteins. The number of mtDNA(s) contained within a single nucleoid is a fundamental question but remains a somewhat controversial issue. Disturbance in nucleoid components and mutations in mtDNA were identified as significant in various diseases, including carcinogenesis. Significant interest in the nucleoid structure and its regulation has been stimulated in relation to mitochondrial diseases, which encompass diseases in multicellular organisms and are associated with accumulation of numerous mutations in mtDNA. In this review, mitochondrial nucleoid structure, nucleoid-associated proteins, and their regulatory roles in mitochondrial metabolism are briefly addressed to provide an overview of the emerging research field involving mitochondrial biology.
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60
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Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY. Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. Cell Chem Biol 2017; 24:404-414. [PMID: 28238724 DOI: 10.1016/j.chembiol.2017.02.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/21/2016] [Accepted: 01/31/2017] [Indexed: 11/27/2022]
Abstract
A recurring challenge in cell biology is to define the molecular components of macromolecular complexes of interest. The predominant method, immunoprecipitation, recovers only strong interaction partners that survive cell lysis and repeated detergent washes. We explored peroxidase-catalyzed proximity biotinylation, APEX, as an alternative, focusing on the mitochondrial nucleoid, the dynamic macromolecular complex that houses the mitochondrial genome. Via 1-min live-cell biotinylation followed by quantitative, ratiometric mass spectrometry, we enriched 37 nucleoid proteins, seven of which had never previously been associated with the nucleoid. The specificity of our dataset was very high, and we validated three hits by follow-up studies. For one novel nucleoid-associated protein, FASTKD1, we discovered a role in downregulation of mitochondrial complex I via specific repression of ND3 mRNA. Our study demonstrates that APEX is a powerful tool for mapping macromolecular complexes in living cells, and can identify proteins and pathways that have been missed by traditional approaches.
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Affiliation(s)
- Shuo Han
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California at San Diego, La Jolla, CA 92093, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA.
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61
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Abstract
Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.
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Affiliation(s)
- A A Kolesnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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62
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Genin EC, Plutino M, Bannwarth S, Villa E, Cisneros-Barroso E, Roy M, Ortega-Vila B, Fragaki K, Lespinasse F, Pinero-Martos E, Augé G, Moore D, Burté F, Lacas-Gervais S, Kageyama Y, Itoh K, Yu-Wai-Man P, Sesaki H, Ricci JE, Vives-Bauza C, Paquis-Flucklinger V. CHCHD10 mutations promote loss of mitochondrial cristae junctions with impaired mitochondrial genome maintenance and inhibition of apoptosis. EMBO Mol Med 2016; 8:58-72. [PMID: 26666268 PMCID: PMC4718158 DOI: 10.15252/emmm.201505496] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
CHCHD10-related diseases include mitochondrial DNA instability disorder, frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS) clinical spectrum, late-onset spinal motor neuropathy (SMAJ), and Charcot-Marie-Tooth disease type 2 (CMT2). Here, we show that CHCHD10 resides with mitofilin, CHCHD3 and CHCHD6 within the "mitochondrial contact site and cristae organizing system" (MICOS) complex. CHCHD10 mutations lead to MICOS complex disassembly and loss of mitochondrial cristae with a decrease in nucleoid number and nucleoid disorganization. Repair of the mitochondrial genome after oxidative stress is impaired in CHCHD10 mutant fibroblasts and this likely explains the accumulation of deleted mtDNA molecules in patient muscle. CHCHD10 mutant fibroblasts are not defective in the delivery of mitochondria to lysosomes suggesting that impaired mitophagy does not contribute to mtDNA instability. Interestingly, the expression of CHCHD10 mutant alleles inhibits apoptosis by preventing cytochrome c release.
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Affiliation(s)
- Emmanuelle C Genin
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Morgane Plutino
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Sylvie Bannwarth
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France Department of Medical Genetics, National Centre for Mitochondrial Diseases, Nice Teaching Hospital, Nice Cedex 2, France
| | - Elodie Villa
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Eugenia Cisneros-Barroso
- Research Health Institute of Palma (IdISPa), Research Unit, Son Espases University Hospital, Palma de Mallorca, Spain
| | - Madhuparna Roy
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bernardo Ortega-Vila
- Research Health Institute of Palma (IdISPa), Research Unit, Son Espases University Hospital, Palma de Mallorca, Spain
| | - Konstantina Fragaki
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France Department of Medical Genetics, National Centre for Mitochondrial Diseases, Nice Teaching Hospital, Nice Cedex 2, France
| | - Françoise Lespinasse
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Estefania Pinero-Martos
- Research Health Institute of Palma (IdISPa), Research Unit, Son Espases University Hospital, Palma de Mallorca, Spain
| | - Gaëlle Augé
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France Department of Medical Genetics, National Centre for Mitochondrial Diseases, Nice Teaching Hospital, Nice Cedex 2, France
| | - David Moore
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, International Centre for Life Newcastle University, Newcastle upon Tyne, UK Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Florence Burté
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, International Centre for Life Newcastle University, Newcastle upon Tyne, UK Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Sandra Lacas-Gervais
- Joint Center for Applied Electron Microscopy, Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Yusuke Kageyama
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick Yu-Wai-Man
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, International Centre for Life Newcastle University, Newcastle upon Tyne, UK Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jean-Ehrland Ricci
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, Nice Cedex 2, France
| | - Cristofol Vives-Bauza
- Research Health Institute of Palma (IdISPa), Research Unit, Son Espases University Hospital, Palma de Mallorca, Spain
| | - Véronique Paquis-Flucklinger
- IRCAN, UMR CNRS 7284/INSERM U1081/UNS, School of Medicine, Nice Sophia-Antipolis University, Nice Cedex 2, France Department of Medical Genetics, National Centre for Mitochondrial Diseases, Nice Teaching Hospital, Nice Cedex 2, France
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63
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Abstract
Isolation of mitochondria from cultured cells and animal tissues for analysis of nucleic acids and bona fide mitochondrial nucleic acid binding proteins and enzymes is complicated by contamination with cellular nucleic acids and their adherent proteins. Protocols presented here allow for quick isolation of mitochondria from a small number of cells and for preparation of highly purified mitochondria from a larger number of cells using nuclease treatment and high salt washing of mitochondria to reduce contamination. We further describe a method for the isolation of mitochondrial DNA-protein complexes known as nucleoids from these highly purified mitochondria using a combination of glycerol gradient sedimentation followed by isopycnic centrifugation in a non-ionic iodixanol gradient.
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64
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He YH, Chen XQ, Yan DJ, Xiao FH, Lin R, Liao XP, Liu YW, Pu SY, Yu Q, Sun HP, Jiang JJ, Cai WW, Kong QP. Familial longevity study reveals a significant association of mitochondrial DNA copy number between centenarians and their offspring. Neurobiol Aging 2016; 47:218.e11-218.e18. [PMID: 27600867 DOI: 10.1016/j.neurobiolaging.2016.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 07/19/2016] [Accepted: 07/29/2016] [Indexed: 12/29/2022]
Abstract
Reduced mitochondrial function is an important cause of aging and age-related diseases. We previously revealed a relatively higher level of mitochondrial DNA (mtDNA) content in centenarians. However, it is still unknown whether such an mtDNA content pattern of centenarians could be passed on to their offspring and how it was regulated. To address these issues, we recruited 60 longevity families consisting of 206 family members (cohort 1) and explored their mtDNA copy number. The results showed that the first generation of the offspring (F1 offspring) had a higher level of mtDNA copy number than their spouses (p < 0.05) independent of a gender effect. In addition, we found a positive association of mtDNA copy number in centenarians with that in F1 offspring (r = 0.54, p = 0.0008) but not with that in F1 spouses. These results were replicated in another independent cohort consisting of 153 subjects (cohort 2). RNA sequencing analysis suggests that the single-stranded DNA-binding protein 4 was significantly associated with mtDNA copy number and was highly expressed in centenarians as well as F1 offspring versus the F1 spouses, thus likely regulates the mtDNA copy number in the long-lived family members. In conclusion, our results suggest that the pattern of high mtDNA copy number is likely inheritable, which may act as a favorable factor to familial longevity through assuring adequate energy supply.
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Affiliation(s)
- Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Dong-Jing Yan
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Lin
- Department of Biology, Hainan Medical College, Haikou, China
| | - Xiao-Ping Liao
- Department of Neurology, The Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Yao-Wen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Yan Pu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Peng Sun
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, China
| | - Jian-Jun Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Wang-Wei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, China.
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China.
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65
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Jourdain AA, Boehm E, Maundrell K, Martinou JC. Mitochondrial RNA granules: Compartmentalizing mitochondrial gene expression. J Cell Biol 2016; 212:611-4. [PMID: 26953349 PMCID: PMC4792075 DOI: 10.1083/jcb.201507125] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/11/2016] [Indexed: 11/25/2022] Open
Abstract
In mitochondria, DNA replication, gene expression, and RNA degradation machineries coexist within a common nondelimited space, raising the question of how functional compartmentalization of gene expression is achieved. Here, we discuss the recently characterized “mitochondrial RNA granules,” mitochondrial subdomains with an emerging role in the regulation of gene expression.
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Affiliation(s)
- Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
| | - Erik Boehm
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
| | - Kinsey Maundrell
- Department of Cell Biology, University of Geneva, 1211 Genève, Switzerland
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66
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Uittenbogaard M, Chiaramello A. Novel subcellular localization of the DNA helicase Twinkle at the kinetochore complex during mitosis in neuronal-like progenitor cells. Histochem Cell Biol 2015; 145:275-86. [PMID: 26678504 DOI: 10.1007/s00418-015-1388-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2015] [Indexed: 11/28/2022]
Abstract
During mitosis, the kinetochore, a multi-protein structure located on the centromeric DNA, is responsible for proper segregation of the replicated genome. More specifically, the outer kinetochore complex component Ndc80/Hec1 plays a critical role in regulating microtubule attachment to the spindle for accurate sister chromatid segregation. In addition, DNA helicases play a key contribution for precise and complete disjunction of sister chromatids held together through double-stranded DNA catenations until anaphase. In this study, we focused our attention on the nuclear-encoded DNA helicase Twinkle, which functions as an essential helicase for replication of mitochondrial DNA. It regulates the copy number of the mitochondrial genome, while maintaining its integrity, two processes essential for mitochondrial biogenesis and bioenergetic functions. Although the majority of the Twinkle protein is imported into mitochondria, a small fraction remains cytosolic with an unknown function. In this study, we report a novel expression pattern of Twinkle during chromosomal segregation at distinct mitotic phases. By immunofluorescence microscopy, we found that Twinkle protein colocalizes with the outer kinetochore protein HEC1 as early as prophase until late anaphase in neuronal-like progenitor cells. Thus, our collective results have revealed an unexpected cell cycle-regulated expression pattern of the DNA helicase Twinkle, known for its role in mtDNA replication. Therefore, its recruitment to the kinetochore suggests an evolutionary conserved function for both mitochondrial and nuclear genomic inheritance.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA
| | - Anne Chiaramello
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA.
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67
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Brown TA, Tkachuk AN, Clayton DA. Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA. PLoS One 2015; 10:e0142436. [PMID: 26545237 PMCID: PMC4636309 DOI: 10.1371/journal.pone.0142436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.
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Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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68
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Kang JW, Kim SJ, Cho HI, Lee SM. DAMPs activating innate immune responses in sepsis. Ageing Res Rev 2015; 24:54-65. [PMID: 25816752 DOI: 10.1016/j.arr.2015.03.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
Sepsis refers to the deleterious and non-resolving systemic inflammatory response of the host to microbial infection and is the leading cause of death in intensive care units. The pathogenesis of sepsis is highly complex. It is principally attributable to dysregulation of the innate immune system. Damage-associated molecular patterns (DAMPs) are actively secreted by innate immune cells and/or released passively by injured or damaged cells in response to infection or injury. In the present review, we highlight emerging evidence that supports the notion that extracellular DAMPs act as crucial proinflammatory danger signals. Furthermore, we discuss the potential of a wide array of DAMPs as therapeutic targets in sepsis.
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Affiliation(s)
- Jung-Woo Kang
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - So-Jin Kim
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - Hong-Ik Cho
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - Sun-Mee Lee
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea.
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69
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Ban-Ishihara R, Tomohiro-Takamiya S, Tani M, Baudier J, Ishihara N, Kuge O. COX assembly factor ccdc56 regulates mitochondrial morphology by affecting mitochondrial recruitment of Drp1. FEBS Lett 2015; 589:3126-32. [PMID: 26358295 DOI: 10.1016/j.febslet.2015.08.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/31/2015] [Accepted: 08/31/2015] [Indexed: 11/21/2022]
Abstract
Mitochondria are dynamic organelles that alter their morphology in response to cellular signaling and differentiation through balanced fusion and fission. In this study, we found that the mitochondrial inner membrane ATPase ATAD3A interacted with ccdc56/MITRAC12/COA3, a subunit of the cytochrome oxidase (COX)-assembly complex. Overproduction of ccdc56 in HeLa cells resulted in fragmented mitochondrial morphology, while mitochondria were highly elongated in ccdc56-repressed cells by the defective recruitment of the fission factor Drp1. We also found that mild and chronic inhibition of COX led to mitochondrial elongation, as seen in ccdc56-repressed cells. These results indicate that ccdc56 positively regulates mitochondrial fission via regulation of COX activity and the mitochondrial recruitment of Drp1, and thus, suggest a novel relationship between COX assembly and mitochondrial morphology.
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Affiliation(s)
- Reiko Ban-Ishihara
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, Kurume 839-0864, Japan
| | | | - Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | | | - Naotada Ishihara
- Department of Protein Biochemistry, Institute of Life Science, Kurume University, Kurume 839-0864, Japan.
| | - Osamu Kuge
- Department of Chemistry, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan.
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70
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Akhmedov AT, Marín-García J. Mitochondrial DNA maintenance: an appraisal. Mol Cell Biochem 2015; 409:283-305. [DOI: 10.1007/s11010-015-2532-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 12/13/2022]
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71
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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72
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Mic60/Mitofilin determines MICOS assembly essential for mitochondrial dynamics and mtDNA nucleoid organization. Cell Death Differ 2015; 23:380-92. [PMID: 26250910 DOI: 10.1038/cdd.2015.102] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/14/2015] [Accepted: 06/22/2015] [Indexed: 01/23/2023] Open
Abstract
The MICOS complex (mitochondrial contact site and cristae organizing system) is essential for mitochondrial inner membrane organization and mitochondrial membrane contacts, however, the molecular regulation of MICOS assembly and the physiological functions of MICOS in mammals remain obscure. Here, we report that Mic60/Mitofilin has a critical role in the MICOS assembly, which determines the mitochondrial morphology and mitochondrial DNA (mtDNA) organization. The downregulation of Mic60/Mitofilin or Mic19/CHCHD3 results in instability of other MICOS components, disassembly of MICOS complex and disorganized mitochondrial cristae. We show that there exists direct interaction between Mic60/Mitofilin and Mic19/CHCHD3, which is crucial for their stabilization in mammals. Importantly, we identified that the mitochondrial i-AAA protease Yme1L regulates Mic60/Mitofilin homeostasis. Impaired MICOS assembly causes the formation of 'giant mitochondria' because of dysregulated mitochondrial fusion and fission. Also, mtDNA nucleoids are disorganized and clustered in these giant mitochondria in which mtDNA transcription is attenuated because of remarkable downregulation of some key mtDNA nucleoid-associated proteins. Together, these findings demonstrate that Mic60/Mitofilin homeostasis regulated by Yme1L is central to the MICOS assembly, which is required for maintenance of mitochondrial morphology and organization of mtDNA nucleoids.
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73
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Lemire BD. Glutathione metabolism links FOXRED1 to NADH:ubiquinone oxidoreductase (complex I) deficiency: A hypothesis. Mitochondrion 2015; 24:105-12. [PMID: 26235939 DOI: 10.1016/j.mito.2015.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/10/2015] [Accepted: 07/29/2015] [Indexed: 01/02/2023]
Abstract
FOXRED1 mutations result in complex I (NADH:ubiquinone oxidoreductase) deficiencies and Leigh syndrome (subacute necrotizing encephalomyelopathy). FOXRED1 is a mitochondrial flavoprotein related to N-methyl amino acid dehydrogenases. How is FOXRED1 required for the biogenesis of complex I? I present a hypothesis that suggests FOXRED1 catalytic activity as a sarcosine oxidase protects the developing fetus from oxidative stress during pregnancy. Loss of FOXRED1, coupled with protein, choline and/or folate-deficient diets results in the depletion of glutathione, the dysregulation of nitric oxide metabolism and the peroxynitrite-mediated inactivation of complex I.
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Affiliation(s)
- Bernard D Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G2H7, Canada.
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74
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Piechota J, Bereza M, Sokołowska A, Suszyński K, Lech K, Jańska H. Unraveling the functions of type II-prohibitins in Arabidopsis mitochondria. PLANT MOLECULAR BIOLOGY 2015; 88:249-267. [PMID: 25896400 DOI: 10.1007/s11103-015-0320-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
In yeast and mammals, prohibitins (PHBs) are considered as structural proteins that form a scaffold-like structure for interacting with a set of proteins involved in various processes occurring in the mitochondria. The role of PHB in plant mitochondria is poorly understood. In the study, the model organism Arabidopsis thaliana was used to identify the possible roles of type-II PHBs (homologs of yeast Phb2p) in plant mitochondria. The obtained results suggest that the plant PHB complex participates in the assembly of multisubunit complexes; namely, respiratory complex I and enzymatic complexes carrying lipoic acid as a cofactor (pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and glycine decarboxylase). PHBs physically interact with subunits of these complexes. Knockout of two Arabidopsis type-II prohibitins (AtPHB2 and AtPHB6) results in a decreased abundance of these complexes along with a reduction in mitochondrial acyl carrier proteins. Also, the absence of AtPHB2 and AtPHB6 influences the expression of the mitochondrial genome and leads to the activation of alternative respiratory pathways, namely alternative oxidase and external NADH-dependent alternative dehydrogenases.
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Affiliation(s)
- Janusz Piechota
- Department of Biotechnology, University of Wroclaw, F. Juliot-Curie 14a, 50-383, Wroclaw, Poland,
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75
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Bavelloni A, Piazzi M, Raffini M, Faenza I, Blalock WL. Prohibitin 2: At a communications crossroads. IUBMB Life 2015; 67:239-54. [PMID: 25904163 DOI: 10.1002/iub.1366] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023]
Abstract
Prohibitins (PHBs) are a highly conserved class of proteins first discovered as inhibitors of cellular proliferation. Since then PHBs have been found to have a significant role in transcription, nuclear signaling, mitochondrial structural integrity, cell division, and cellular membrane metabolism, placing these proteins among the key regulators of pathologies such as cancer, neuromuscular degeneration, and other metabolic diseases. The human genome encodes two PHB proteins, prohibitin 1 (PHB1) and prohibitin 2 (PHB2), which function not only as a heterodimeric complex, but also independently. While many previous reviews have focused on the better characterized prohibitin, PHB1, this review focuses on PHB2 and new data concerning its cellular functions both in complex with PHB1 and independent of PHB1.
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Affiliation(s)
- Alberto Bavelloni
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Manuela Piazzi
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - Mirco Raffini
- Laboratory RAMSES, Rizzoli Orthopedic Institute, Bologna, Italy
| | - Irene Faenza
- Department of Biomedical Sciences, University of Bologna, Bologna, Italy
| | - William L Blalock
- Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy.,National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy
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76
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Distribution of mitochondrial DNA nucleoids inside the linear tubules vs. bulk parts of mitochondrial network as visualized by 4Pi microscopy. J Bioenerg Biomembr 2015; 47:255-63. [PMID: 25833036 DOI: 10.1007/s10863-015-9610-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
Mitochondrial nucleoids are confined sites of mitochondrial DNA existing in complex clusters with the DNA-compacting mitochondrial (mt) transcription factor A (TFAM) and other accessory proteins and gene expression machinery proteins, such as a mt single-stranded-DNA-binding protein (mtSSB). To visualize nucleoid distribution within the mt reticular network, we have employed three-dimensional (3D) double-color 4Pi microscopy. The mt network was visualized in hepatocellular carcinoma HepG2 cells via mt-matrix-addressed GFP, while 3D immunocytochemistry of mtSSB was performed. Optimization of iso-surface computation threshold for nucleoid 4Pi images to 30 led to an average nucleoid diameter of 219 ± 110 and 224 ± 100 nm in glucose- and galactose-cultivated HepG2 cells (the latter with obligatory oxidative phosphorylation). We have positioned mtDNA nucleoids within the mt reticulum network and refined our model for nucleoid redistribution within the fragmented network--clustering of up to ten nucleoids in 2 μm diameter mitochondrial spheroids of a fragmented mt network, arising from an original 10 μm mt tubule of a 400 nm diameter. However, the theoretically fragmented bulk parts were observed most frequently as being reintegrated into the continuous mt network in 4Pi images. Since the predicted nucleoid counts within the bulk parts corresponded to the model, we conclude that fragmentation/reintegration cycles are not accompanied by mtDNA degradation or that mtDNA degradation is equally balanced by mtDNA replication.
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77
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Lemire BD. A structural model for FOXRED1, an FAD-dependent oxidoreductase necessary for NADH: Ubiquinone oxidoreductase (complex I) assembly. Mitochondrion 2015; 22:9-16. [PMID: 25765152 DOI: 10.1016/j.mito.2015.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 01/06/2023]
Abstract
The biogenesis of mitochondrial respiratory chain components is complex. Mammalian complex I (NADH:ubiquinone oxidoreductase) contains 44 different subunits, an FMN and seven iron-sulfur centers. Its assembly involves at least twelve additional proteins, called assembly factors. One of these is FOXRED1, a 486-amino acid FAD-dependent oxidoreductase. FOXRED1 is a member of the d-amino acid oxidase (DAO) family. A structural model of FOXRED1 reveals a large substrate-binding cavity and a putative oxygen-binding site. These features strongly suggest that FOXRED1 is catalytically active as an oxidoreductase. A metabolic role for FOXRED1 in the biogenesis of complex I should be considered.
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Affiliation(s)
- Bernard D Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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78
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Mitochondria in health, aging and diseases: the epigenetic perspective. Biogerontology 2015; 16:569-85. [DOI: 10.1007/s10522-015-9562-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/19/2015] [Indexed: 01/15/2023]
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79
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Rajala N, Hensen F, Wessels HJCT, Ives D, Gloerich J, Spelbrink JN. Whole cell formaldehyde cross-linking simplifies purification of mitochondrial nucleoids and associated proteins involved in mitochondrial gene expression. PLoS One 2015; 10:e0116726. [PMID: 25695250 PMCID: PMC4335056 DOI: 10.1371/journal.pone.0116726] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/13/2014] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial DNA/protein complexes (nucleoids) appear as discrete entities inside the mitochondrial network when observed by live-cell imaging and immunofluorescence. This somewhat trivial observation in recent years has spurred research towards isolation of these complexes and the identification of nucleoid-associated proteins. Here we show that whole cell formaldehyde crosslinking combined with affinity purification and tandem mass-spectrometry provides a simple and reproducible method to identify potential nucleoid associated proteins. The method avoids spurious mitochondrial isolation and subsequent multifarious nucleoid enrichment protocols and can be implemented to allow for label-free quantification (LFQ) by mass-spectrometry. Using expression of a Flag-tagged Twinkle helicase and appropriate controls we show that this method identifies many previously identified nucleoid associated proteins. Using LFQ to compare HEK293 cells with and without mtDNA, but both expressing Twinkle-FLAG, identifies many proteins that are reduced or absent in the absence of mtDNA. This set not only includes established mtDNA maintenance proteins but also many proteins involved in mitochondrial RNA metabolism and translation and therefore represents what can be considered an mtDNA gene expression proteome. Our data provides a very valuable resource for both basic mitochondrial researchers as well as clinical geneticists working to identify novel disease genes on the basis of exome sequence data.
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Affiliation(s)
- Nina Rajala
- Mitochondrial DNA Maintenance Group, BioMediTech, FI-33014 University of Tampere, Tampere, Finland
| | - Fenna Hensen
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Hans J. C. T. Wessels
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Proteomics Centre, Department of Laboratory Medicine, Laboratory of Genetic Endocrine and Metabolic Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Daniel Ives
- MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Jolein Gloerich
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Proteomics Centre, Department of Laboratory Medicine, Laboratory of Genetic Endocrine and Metabolic Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Johannes N. Spelbrink
- Mitochondrial DNA Maintenance Group, BioMediTech, FI-33014 University of Tampere, Tampere, Finland
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- * E-mail:
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Antonicka H, Shoubridge EA. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. Cell Rep 2015; 10:920-932. [PMID: 25683715 DOI: 10.1016/j.celrep.2015.01.030] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 12/10/2014] [Accepted: 01/09/2015] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic RNA granules play a central role in mRNA metabolism, but the importance of mitochondrial RNA granules remains relatively unexplored. We characterized their proteome and found that they contain a large toolbox of proteins dedicated to RNA metabolism. Investigation of four uncharacterized putative RNA-binding proteins-two RNA helicases, DHX30 and DDX28, and two proteins of the Fas-activated serine-threonine kinase (FASTKD) family, FASTKD2 and FASTKD5-demonstrated that both helicases and FASTKD2 are required for mitochondrial ribosome biogenesis. RNA-sequencing (RNA-seq) analysis showed that DDX28 and FASTKD2 bound the 16S rRNA. FASTKD5 is required for maturing precursor mRNAs that are not flanked by tRNAs and that therefore cannot be processed by the canonical mRNA maturation pathway. Silencing FASTKD5 rendered mature COX I mRNA almost undetectable, which severely reduced the synthesis of COX I, resulting in a complex IV assembly defect. These data demonstrate that mitochondrial RNA granules are centers for posttranscriptional RNA processing and the biogenesis of mitochondrial ribosomes.
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Affiliation(s)
- Hana Antonicka
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada
| | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada.
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81
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Mitochondrial heat shock protein machinery hsp70/hsp40 is indispensable for proper mitochondrial DNA maintenance and replication. mBio 2015; 6:mBio.02425-14. [PMID: 25670781 PMCID: PMC4337576 DOI: 10.1128/mbio.02425-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial chaperones have multiple functions that are essential for proper functioning of mitochondria. In the human-pathogenic protist Trypanosoma brucei, we demonstrate a novel function of the highly conserved machinery composed of mitochondrial heat shock proteins 70 and 40 (mtHsp70/mtHsp40) and the ATP exchange factor Mge1. The mitochondrial DNA of T. brucei, also known as kinetoplast DNA (kDNA), is represented by a single catenated network composed of thousands of minicircles and dozens of maxicircles packed into an electron-dense kDNA disk. The chaperones mtHsp70 and mtHsp40 and their cofactor Mge1 are uniformly distributed throughout the single mitochondrial network and are all essential for the parasite. Following RNA interference (RNAi)-mediated depletion of each of these proteins, the kDNA network shrinks and eventually disappears. Ultrastructural analysis of cells depleted for mtHsp70 or mtHsp40 revealed that the otherwise compact kDNA network becomes severely compromised, a consequence of decreased maxicircle and minicircle copy numbers. Moreover, we show that the replication of minicircles is impaired, although the lack of these proteins has a bigger impact on the less abundant maxicircles. We provide additional evidence that these chaperones are indispensable for the maintenance and replication of kDNA, in addition to their already known functions in Fe-S cluster synthesis and protein import. Impairment or loss of mitochondrial DNA is associated with mitochondrial dysfunction and a wide range of neural, muscular, and other diseases. We present the first evidence showing that the entire mtHsp70/mtHsp40 machinery plays an important role in mitochondrial DNA replication and maintenance, a function likely retained from prokaryotes. These abundant, ubiquitous, and multifunctional chaperones share phenotypes with enzymes engaged in the initial stages of replication of the mitochondrial DNA in T. brucei.
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82
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Týč J, Klingbeil MM, Lukeš J. Mitochondrial heat shock protein machinery hsp70/hsp40 is indispensable for proper mitochondrial DNA maintenance and replication. mBio 2015. [PMID: 25670781 DOI: 10.1128/mbio.02425-02414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
UNLABELLED Mitochondrial chaperones have multiple functions that are essential for proper functioning of mitochondria. In the human-pathogenic protist Trypanosoma brucei, we demonstrate a novel function of the highly conserved machinery composed of mitochondrial heat shock proteins 70 and 40 (mtHsp70/mtHsp40) and the ATP exchange factor Mge1. The mitochondrial DNA of T. brucei, also known as kinetoplast DNA (kDNA), is represented by a single catenated network composed of thousands of minicircles and dozens of maxicircles packed into an electron-dense kDNA disk. The chaperones mtHsp70 and mtHsp40 and their cofactor Mge1 are uniformly distributed throughout the single mitochondrial network and are all essential for the parasite. Following RNA interference (RNAi)-mediated depletion of each of these proteins, the kDNA network shrinks and eventually disappears. Ultrastructural analysis of cells depleted for mtHsp70 or mtHsp40 revealed that the otherwise compact kDNA network becomes severely compromised, a consequence of decreased maxicircle and minicircle copy numbers. Moreover, we show that the replication of minicircles is impaired, although the lack of these proteins has a bigger impact on the less abundant maxicircles. We provide additional evidence that these chaperones are indispensable for the maintenance and replication of kDNA, in addition to their already known functions in Fe-S cluster synthesis and protein import. IMPORTANCE Impairment or loss of mitochondrial DNA is associated with mitochondrial dysfunction and a wide range of neural, muscular, and other diseases. We present the first evidence showing that the entire mtHsp70/mtHsp40 machinery plays an important role in mitochondrial DNA replication and maintenance, a function likely retained from prokaryotes. These abundant, ubiquitous, and multifunctional chaperones share phenotypes with enzymes engaged in the initial stages of replication of the mitochondrial DNA in T. brucei.
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Affiliation(s)
- Jiří Týč
- Faculty of Sciences, University of South Bohemia and Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Michele M Klingbeil
- Department of Microbiology, Morrill Science Center, University of Massachusetts, Amherst, Massachusetts, USA
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83
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Shutt TE, Bestwick M, Shadel GS. The core human mitochondrial transcription initiation complex: It only takes two to tango. Transcription 2014; 2:55-59. [PMID: 21468229 DOI: 10.4161/trns.2.2.14296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 11/24/2010] [Accepted: 11/29/2010] [Indexed: 11/19/2022] Open
Abstract
We recently demonstrated that the core transcription initiation complex in human mitochondria is a two-component system (POLRMT and h-mtTFB2). Human mtTFA/TFAM, previously proposed to be a requisite initiation complex member, is dispensable for promoter-specific initiation in vitro. We propose that it instead regulates relative promoter activity and/or overall nucleoid transcription and replication potential.
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Affiliation(s)
- Timothy E Shutt
- Department of Pathology Yale University School of Medicine; New Haven, CT USA
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84
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Gatsi R, Schulze B, Rodríguez-Palero MJ, Hernando-Rodríguez B, Baumeister R, Artal-Sanz M. Prohibitin-mediated lifespan and mitochondrial stress implicate SGK-1, insulin/IGF and mTORC2 in C. elegans. PLoS One 2014; 9:e107671. [PMID: 25265021 PMCID: PMC4180437 DOI: 10.1371/journal.pone.0107671] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/13/2014] [Indexed: 12/29/2022] Open
Abstract
Lifespan regulation by mitochondrial proteins has been well described, however, the mechanism of this regulation is not fully understood. Amongst the mitochondrial proteins profoundly affecting ageing are prohibitins (PHB-1 and PHB-2). Paradoxically, in C. elegans prohibitin depletion shortens the lifespan of wild type animals while dramatically extending that of metabolically compromised animals, such as daf-2-insulin-receptor mutants. Here we show that amongst the three kinases known to act downstream of daf-2, only loss of function of sgk-1 recapitulates the ageing phenotype observed in daf-2 mutants upon prohibitin depletion. Interestingly, signalling through SGK-1 receives input from an additional pathway, parallel to DAF-2, for the prohibitin-mediated lifespan phenotype. We investigated the effect of prohibitin depletion on the mitochondrial unfolded protein response (UPRmt). Remarkably, the lifespan extension upon prohibitin elimination, of both daf-2 and sgk-1 mutants, is accompanied by suppression of the UPRmt induced by lack of prohibitin. On the contrary, gain of function of SGK-1 results in further shortening of lifespan and a further increase of the UPRmt in prohibitin depleted animals. Moreover, SGK-1 interacts with RICT-1 for the regulation of the UPRmt in a parallel pathway to DAF-2. Interestingly, prohibitin depletion in rict-1 loss of function mutant animals also causes lifespan extension. Finally, we reveal an unprecedented role for mTORC2-SGK-1 in the regulation of mitochodrial homeostasis. Together, these results give further insight into the mechanism of lifespan regulation by mitochondrial function and reveal a cross-talk of mitochondria with two key pathways, Insulin/IGF and mTORC2, for the regulation of ageing and stress response.
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Affiliation(s)
- Roxani Gatsi
- CABD, Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Bettina Schulze
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - María Jesús Rodríguez-Palero
- CABD, Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Blanca Hernando-Rodríguez
- CABD, Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Ralf Baumeister
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Center for Biochemistry and Molecular Cell Research, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Marta Artal-Sanz
- CABD, Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- Laboratory for Bioinformatics and Molecular Genetics, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
- * E-mail:
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85
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Strand JM, Skinnes R, Scheffler K, Rootvelt T, Woldseth B, Bjørås M, Eide L. Genome instability in Maple Syrup Urine Disease correlates with impaired mitochondrial biogenesis. Metabolism 2014; 63:1063-70. [PMID: 24928662 DOI: 10.1016/j.metabol.2014.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/09/2014] [Accepted: 05/04/2014] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The mitochondrial branched-chain ketoacid dehydrogenase (BCKD) catalyzes the degradation of branched-chain amino acids (BCAA), which have been shown to induce oxidative stress. Maple Syrup Urine Disease (MSUD) is caused by impaired activity of BCKD, suggesting that oxidative stress and resulting DNA damage could contribute to pathology. We evaluated the potential effect of BCKD deficiency on genome integrity and mitochondrial function as a downstream target. METHODS Primary fibroblasts from MSUD patients and controls were either cultivated under normal conditions or exposed to metabolic or oxidative stress. DNA was analyzed for damage and mitochondrial function was evaluated by gene expression analyses, functional assays and immunofluorescent methods. RESULTS Patient fibroblasts accumulated damage in mitochondrial DNA (mtDNA) and nuclear DNA, with a corresponding reduction in mitochondrial transcription, mtDNA copy number and pyruvate dehydrogenase. We found no evidence of increased level of reactive oxygen species (ROS) in patient fibroblasts under normal conditions, suggesting that the genotoxic effect is ascribed to accumulating metabolites. CONCLUSIONS Impaired BCKD activity as in MSUD, results in accumulation of DNA damage and corresponding mitochondrial dysfunction.
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Affiliation(s)
- Janne M Strand
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Ragnhild Skinnes
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Katja Scheffler
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Terje Rootvelt
- Women and Children's Division, Oslo University Hospital, Oslo, Norway
| | - Berit Woldseth
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Microbiology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.
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86
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Hensen F, Cansiz S, Gerhold JM, Spelbrink JN. To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins. Biochimie 2014; 100:219-26. [DOI: 10.1016/j.biochi.2013.09.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023]
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87
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Muftuoglu M, Mori MP, de Souza-Pinto NC. Formation and repair of oxidative damage in the mitochondrial DNA. Mitochondrion 2014; 17:164-81. [PMID: 24704805 DOI: 10.1016/j.mito.2014.03.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
The mitochondrial DNA (mtDNA) encodes for only 13 polypeptides, components of 4 of the 5 oxidative phosphorylation complexes. But despite this apparently small numeric contribution, all 13 subunits are essential for the proper functioning of the oxidative phosphorylation circuit. Thus, accumulation of lesions, mutations and deletions/insertions in the mtDNA could have severe functional consequences, including mitochondrial diseases, aging and age-related diseases. The DNA is a chemically unstable molecule, which can be easily oxidized, alkylated, deaminated and suffer other types of chemical modifications, throughout evolution the organisms that survived were those who developed efficient DNA repair processes. In the last two decades, it has become clear that mitochondria have DNA repair pathways, which operate, at least for some types of lesions, as efficiently as the nuclear DNA repair pathways. The mtDNA is localized in a particularly oxidizing environment, making it prone to accumulate oxidatively generated DNA modifications (ODMs). In this article, we: i) review the major types of ODMs formed in mtDNA and the known repair pathways that remove them; ii) discuss the possible involvement of other repair pathways, just recently characterized in mitochondria, in the repair of these modifications; and iii) address the role of DNA repair in mitochondrial function and a possible cross-talk with other pathways that may potentially participate in mitochondrial genomic stability, such as mitochondrial dynamics and nuclear-mitochondrial signaling. Oxidative stress and ODMs have been increasingly implicated in disease and aging, and thus we discuss how variations in DNA repair efficiency may contribute to the etiology of such conditions or even modulate their clinical outcomes.
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Affiliation(s)
- Meltem Muftuoglu
- Department of Molecular Biology and Genetics, Acibadem University, Atasehir, 34752 Istanbul, Turkey
| | - Mateus P Mori
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil
| | - Nadja C de Souza-Pinto
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil.
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88
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Bogenhagen DF, Martin DW, Koller A. Initial steps in RNA processing and ribosome assembly occur at mitochondrial DNA nucleoids. Cell Metab 2014; 19:618-29. [PMID: 24703694 DOI: 10.1016/j.cmet.2014.03.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/17/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) resides in compact nucleoids, where it is replicated and transcribed into long primary transcripts processed to generate rRNAs, tRNAs, and mRNAs encoding 13 proteins. This situation differs from bacteria and eukaryotic nucleoli, which have dedicated rRNA transcription units. The assembly of rRNAs into mitoribosomes has received little study. We show that mitochondrial RNA processing enzymes involved in tRNA excision, ribonuclease P (RNase P) and ELAC2, as well as a subset of nascent mitochondrial ribosomal proteins (MRPs) associate with nucleoids to initiate RNA processing and ribosome assembly. SILAC pulse-chase labeling experiments show that nascent MRPs recruited to the nucleoid fraction were highly labeled after the pulse in a transcription-dependent manner and decreased in labeling intensity during the chase. These results provide insight into the landscape of binding events required for mitochondrial ribosome assembly and firmly establish the mtDNA nucleoid as a control center for mitochondrial biogenesis.
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Affiliation(s)
- Daniel F Bogenhagen
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
| | - Dwight W Martin
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794-8160, USA; Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
| | - Antonius Koller
- Proteomics Center, Stony Brook University, Stony Brook, NY 11794-8691, USA
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89
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Schiavi A, Ventura N. The interplay between mitochondria and autophagy and its role in the aging process. Exp Gerontol 2014; 56:147-53. [PMID: 24607515 DOI: 10.1016/j.exger.2014.02.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 01/07/2023]
Abstract
Mitochondria are highly dynamic organelles which play a central role in cellular homeostasis. Mitochondrial dysfunction leads to life-threatening disorders and accelerates the aging process. Surprisingly, on the other hand, a mild reduction of mitochondria functionality can have pro-longevity effects in organisms spanning from yeast to mammals. Autophagy is a fundamental cellular housekeeping process that needs to be finely regulated for proper cell and organism survival, as underlined by the fact that both its over- and its defective activation have been associated with diseases and accelerated aging. A reciprocal interplay exists between mitochondria and autophagy, which is needed to constantly adjust cellular energy metabolism in different pathophysiological conditions. Here we review general features of mitochondrial function and autophagy with particular focus on their crosstalk and its possible implication in the aging process.
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Affiliation(s)
- Alfonso Schiavi
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany; University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Natascia Ventura
- Institute for Clinical Chemistry and Laboratory Diagnostic, Heinrich Heine University, Medical Faculty, Düsseldorf, Germany; IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany; University of Rome "Tor Vergata", 00133 Rome, Italy.
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90
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91
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Biasi F, Leonarduzzi G, Oteiza PI, Poli G. Inflammatory bowel disease: mechanisms, redox considerations, and therapeutic targets. Antioxid Redox Signal 2013; 19:1711-47. [PMID: 23305298 PMCID: PMC3809610 DOI: 10.1089/ars.2012.4530] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oxidative stress is thought to play a key role in the development of intestinal damage in inflammatory bowel disease (IBD), because of its primary involvement in intestinal cells' aberrant immune and inflammatory responses to dietary antigens and to the commensal bacteria. During the active disease phase, activated leukocytes generate not only a wide spectrum of pro-inflammatory cytokines, but also excess oxidative reactions, which markedly alter the redox equilibrium within the gut mucosa, and maintain inflammation by inducing redox-sensitive signaling pathways and transcription factors. Moreover, several inflammatory molecules generate further oxidation products, leading to a self-sustaining and auto-amplifying vicious circle, which eventually impairs the gut barrier. The current treatment of IBD consists of long-term conventional anti-inflammatory therapy and often leads to drug refractoriness or intolerance, limiting patients' quality of life. Immune modulators or anti-tumor necrosis factor α antibodies have recently been used, but all carry the risk of significant side effects and a poor treatment response. Recent developments in molecular medicine point to the possibility of treating the oxidative stress associated with IBD, by designing a proper supplementation of specific lipids to induce local production of anti-inflammatory derivatives, as well as by developing biological therapies that target selective molecules (i.e., nuclear factor-κB, NADPH oxidase, prohibitins, or inflammasomes) involved in redox signaling. The clinical significance of oxidative stress in IBD is now becoming clear, and may soon lead to important new therapeutic options to lessen intestinal damage in this disease.
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Affiliation(s)
- Fiorella Biasi
- 1 Department of Clinical and Biological Sciences, University of Turin , San Luigi Gonzaga Hospital, Orbassano, Italy
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92
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Kang T, Lu W, Xu W, Anderson L, Bacanamwo M, Thompson W, Chen YE, Liu D. MicroRNA-27 (miR-27) targets prohibitin and impairs adipocyte differentiation and mitochondrial function in human adipose-derived stem cells. J Biol Chem 2013; 288:34394-402. [PMID: 24133204 DOI: 10.1074/jbc.m113.514372] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prohibitin (PHB) has been reported to play a crucial role in adipocyte differentiation and mitochondrial function. However, the regulative mechanism of PHB during adipogenesis remains unclear. In this study, we determined that the levels of both microRNA (miR)-27a and miR-27b were down-regulated following adipogenic induction of human adipose-derived stem cells, whereas the mRNA level of PHB was up-regulated. Overexpression of miR-27a or miR-27b inhibited PHB expression and adipocyte differentiation. Using PHB 3'-UTR luciferase reporter assay, we observed that miR-27a and miR-27b directly targeted PHB in human adipose-derived stem cells. A compensation of PHB partially restored the adipogenesis inhibited by miR-27. Moreover, we demonstrated the novel finding that ectopic expression of miR-27a or miR-27b impaired mitochondrial biogenesis, structure integrity, and complex I activity accompanied by excessive reactive oxygen species production. Our data suggest that miR-27 is an anti-adipogenic microRNA partly by targeting PHB and impairing mitochondrial function. Pharmacological modulation of miR-27 function may provide a new therapeutic strategy for the treatment of obesity.
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Affiliation(s)
- Ting Kang
- From the Cardiovascular Research Institute
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93
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Szczesny B, Olah G, Walker DK, Volpi E, Rasmussen BB, Szabo C, Mitra S. Deficiency in repair of the mitochondrial genome sensitizes proliferating myoblasts to oxidative damage. PLoS One 2013; 8:e75201. [PMID: 24066171 PMCID: PMC3774773 DOI: 10.1371/journal.pone.0075201] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species (ROS), generated as a by-product of mitochondrial oxidative phosphorylation, are particularly damaging to the genome of skeletal muscle because of their high oxygen consumption. Proliferating myoblasts play a key role during muscle regeneration by undergoing myogenic differentiation to fuse and restore damaged muscle. This process is severely impaired during aging and in muscular dystrophies. In this study, we investigated the role of oxidatively damaged DNA and its repair in the mitochondrial genome of proliferating skeletal muscle progenitor myoblasts cells and their terminally differentiated product, myotubes. Using the C2C12 cell line as a well-established model for skeletal muscle differentiation, we show that myoblasts are highly sensitive to ROS-mediated DNA damage, particularly in the mitochondrial genome, due to deficiency in 5’ end processing at the DNA strand breaks. Ectopic expression of the mitochondrial-specific 5’ exonuclease, EXOG, a key DNA base excision/single strand break repair (BER/SSBR) enzyme, in myoblasts but not in myotubes, improves the cell’s resistance to oxidative challenge. We linked loss of myoblast viability by activation of apoptosis with deficiency in the repair of the mitochondrial genome. Moreover, the process of myoblast differentiation increases mitochondrial biogenesis and the level of total glutathione. We speculate that our data may provide a mechanistic explanation for depletion of proliferating muscle precursor cells during the development of sarcopenia, and skeletal muscle dystrophies.
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Affiliation(s)
- Bartosz Szczesny
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
| | - Gabor Olah
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dillon K. Walker
- Department of Nutrition and Metabolism, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Elena Volpi
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Blake B. Rasmussen
- Department of Nutrition and Metabolism, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sankar Mitra
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Lee KW, Okot-Kotber C, LaComb JF, Bogenhagen DF. Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid. J Biol Chem 2013; 288:31386-99. [PMID: 24036117 DOI: 10.1074/jbc.m113.515692] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified RNMTL1, MRM1, and MRM2 (FtsJ2) as members of the RNA methyltransferase family that may be responsible for the three known 2'-O-ribose modifications of the 16 S rRNA core of the large mitochondrial ribosome subunit. These proteins are confined to foci located in the vicinity of mtDNA nucleoids. They show distinct patterns of association with mtDNA nucleoids and/or mitochondrial ribosomes in cell fractionation studies. We focused on the role of the least studied protein in this set, RNMTL1, to show that this protein interacts with the large ribosomal subunit as well as with a series of non-ribosomal proteins that may be involved in coupling of the rate of rRNA transcription and ribosome assembly in mitochondria. siRNA-directed silencing of RNMTL1 resulted in a significant inhibition of translation on mitochondrial ribosomes. Our results are consistent with a role for RNMTL1 in methylation of G(1370) of human 16 S rRNA.
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Affiliation(s)
- Ken-Wing Lee
- From the Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
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95
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Guha M, Avadhani NG. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion 2013; 13:577-91. [PMID: 24004957 DOI: 10.1016/j.mito.2013.08.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/20/2013] [Accepted: 08/27/2013] [Indexed: 12/25/2022]
Abstract
Mitochondria play a central role not only in energy production but also in the integration of metabolic pathways as well as signals for apoptosis and autophagy. It is becoming increasingly apparent that mitochondria in mammalian cells play critical roles in the initiation and propagation of various signaling cascades. In particular, mitochondrial metabolic and respiratory states and status on mitochondrial genetic instability are communicated to the nucleus as an adaptive response through retrograde signaling. Each mammalian cell contains multiple copies of the mitochondrial genome (mtDNA). A reduction in mtDNA copy number has been reported in various human pathological conditions such as diabetes, obesity, neurodegenerative disorders, aging and cancer. Reduction in mtDNA copy number disrupts mitochondrial membrane potential (Δψm) resulting in dysfunctional mitochondria. Dysfunctional mitochondria trigger retrograde signaling and communicate their changing metabolic and functional state to the nucleus as an adaptive response resulting in an altered nuclear gene expression profile and altered cell physiology and morphology. In this review, we provide an overview of the various modes of mitochondrial retrograde signaling focusing particularly on the Ca(2+)/Calcineurin mediated retrograde signaling. We discuss the contribution of the key factors of the pathway such as Calcineurin, IGF1 receptor, Akt kinase and HnRNPA2 in the propagation of signaling and their role in modulating genetic and epigenetic changes favoring cellular reprogramming towards tumorigenesis.
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Affiliation(s)
- Manti Guha
- Department of Animal Biology and the Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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96
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Sobek S, Dalla Rosa I, Pommier Y, Bornholz B, Kalfalah F, Zhang H, Wiesner RJ, von Kleist-Retzow JC, Hillebrand F, Schaal H, Mielke C, Christensen MO, Boege F. Negative regulation of mitochondrial transcription by mitochondrial topoisomerase I. Nucleic Acids Res 2013; 41:9848-57. [PMID: 23982517 PMCID: PMC3834834 DOI: 10.1093/nar/gkt768] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial topoisomerase I is a genetically distinct mitochondria-dedicated enzyme with a crucial but so far unknown role in the homeostasis of mitochondrial DNA metabolism. Here, we present data suggesting a negative regulatory function in mitochondrial transcription or transcript stability. Deficiency or depletion of mitochondrial topoisomerase I increased mitochondrial transcripts, whereas overexpression lowered mitochondrial transcripts, depleted respiratory complexes I, III and IV, decreased cell respiration and raised superoxide levels. Acute depletion of mitochondrial topoisomerase I triggered neither a nuclear mito-biogenic stress response nor compensatory topoisomerase IIβ upregulation, suggesting the concomitant increase in mitochondrial transcripts was due to release of a local inhibitory effect. Mitochondrial topoisomerase I was co-immunoprecipitated with mitochondrial RNA polymerase. It selectively accumulated and rapidly exchanged at a subset of nucleoids distinguished by the presence of newly synthesized RNA and/or mitochondrial RNA polymerase. The inactive Y559F-mutant behaved similarly without affecting mitochondrial transcripts. In conclusion, mitochondrial topoisomerase I dampens mitochondrial transcription and thereby alters respiratory capacity. The mechanism involves selective association of the active enzyme with transcriptionally active nucleoids and a direct interaction with mitochondrial RNA polymerase. The inhibitory role of topoisomerase I in mitochondrial transcription is strikingly different from the stimulatory role of topoisomerase I in nuclear transcription.
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Affiliation(s)
- Stefan Sobek
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, University of Köln, D-50931 Köln, Germany, Center for Molecular Medicine Cologne, University of Köln, D-50931 Köln, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases, University of Köln, D-50931 Köln, Germany, Department of Pediatrics, Med. Faculty, University of Köln, D-50931 Köln, Germany and Center for Microbiology and Virology, Institute of Virology, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany
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97
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Warda M, Kim HK, Kim N, Ko KS, Rhee BD, Han J. A matter of life, death and diseases: mitochondria from a proteomic perspective. Expert Rev Proteomics 2013; 10:97-111. [PMID: 23414362 DOI: 10.1586/epr.12.69] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mitochondria are highly ordered, integrated organelles that energize cellular activities and contribute to programmed death by initiating disciplined apoptotic cascades. This review seeks to clarify our understanding of mitochondrial structural-functional integrity beyond the resolved nuclear genome by unraveling the dynamic mitochondrial proteome and elucidating proteome/genome interplay. The roles of mechanochemical coupling between mitoskeleton and cytoskeleton and crosstalk with other organelles in orchestrating cellular outcomes are explained. The authors also review the modulation of mitochondrial-related oxidative stress on apoptosis and cancer development and the context is applied to interpret pathogenetic events in neurodegenerative disorders and cardiovascular diseases. The accumulated proteomics evidence is used to describe the integral role that mitochondria play and how they influence other intracellular organelles. Possible mitochondrial-targeted therapeutic interventions are also discussed.
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Affiliation(s)
- Mohamad Warda
- Biochemistry, Molecular Biology and Chemistry of Nutrition Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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98
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Kasashima K, Nagao Y, Endo H. Dynamic regulation of mitochondrial genome maintenance in germ cells. Reprod Med Biol 2013; 13:11-20. [PMID: 24482608 PMCID: PMC3890057 DOI: 10.1007/s12522-013-0162-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/04/2013] [Indexed: 12/11/2022] Open
Abstract
Mitochondria play a crucial role in the development and function of germ cells. Mitochondria contain a maternally inherited genome that should be transmitted to offspring without reactive oxygen species‐induced damage during germ line development. Germ cells are also involved in the mitochondrial DNA (mtDNA) bottleneck; thus, the appropriate regulation of mtDNA in these cells is very important for this characteristic transmission. In this review, we focused on unique regulation of the mitochondrial genome in animal germ cells; paternal elimination and the mtDNA bottleneck in females. We also summarized the mitochondrial nucleoid factors involved in various mtDNA regulation pathways. Among them, mitochondrial transcription factor A (TFAM), which has pleiotropic and essential roles in mtDNA maintenance, appears to have putative roles in germ cell regulation.
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Affiliation(s)
- Katsumi Kasashima
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yasumitsu Nagao
- Center for Experimental Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498 Japan
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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99
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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100
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A New Method of the Visualization of the Double-Stranded Mitochondrial and Nuclear DNA. PLoS One 2013; 8:e66864. [PMID: 23825578 PMCID: PMC3688954 DOI: 10.1371/journal.pone.0066864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/12/2013] [Indexed: 11/19/2022] Open
Abstract
The study describes the method of a sensitive detection of double-stranded DNA molecules in situ. It is based on the oxidative attack on the deoxyribose moiety by copper(I) in the presence of oxygen. We have shown previously that the oxidative attack leads to the formation of frequent gaps in DNA. Here we have demonstrated that the gaps can be utilized as the origins for an efficient synthesis of complementary labeled strands by DNA polymerase I and that such enzymatic detection of the double-stranded DNA is a sensitive approach enabling in-situ detection of both the nuclear and mitochondrial genomes in formaldehyde-fixed human cells.
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