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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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Wang Z, Sun Q, Sun N, Liang M, Tian Z. Mitochondrial Dysfunction and Altered Renal Metabolism in Dahl Salt-Sensitive Rats. Kidney Blood Press Res 2017; 42:587-597. [PMID: 28922660 DOI: 10.1159/000479846] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/26/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS The kidney plays a critical role in the control of blood pressure and its elevation in salt-induced hypertension. Mitochondrial dysfunction, especially in energy metabolism, has been associated with hypertension. Here, we aimed to investigate mitochondrial function and metabolic features in renal mitochondria of Dahl salt-sensitive (SS) rats to gain further insight into the relationship between mitochondrial metabolism and predisposition to hypertension. METHODS In this study, SS rats fed low-salt (LS) or high-salt (HS) diets were used to investigate mitochondrial function and metabolism including mitochondrial enzyme activities, pyridine nucleotides, metabolites, and oxidative stress by biochemical analysis and gas chromatography-mass spectrometer (GC-MS). RESULTS Significantly lower activity levels of fumarase, isocitrate dehydrogenase and succinyl-CoA synthetase were observed in renal mitochondria of SS rats compared with SS.13BN control rats fed LS diets. Intra-mitochondrial pyridine nucleotide content and mitochondrial metabolism were adversely affected in SS rats. In accordance with this, reduced ATP production, Δψm, and superoxide dismutase (SOD) activity were also observed in mitochondria of the renal medulla and cortex of SS rats. Moreover, ATP production was further impaired and oxidative stress was increased, confirming that the mitochondria of SS rats fed HS diets were dysfunctional compared to those of rats fed LS diets. CONCLUSIONS Our data demonstrated that the renal mitochondria of SS rats exhibited complicated metabolic alteration and dysfunction in low-salt diets, and high-salt diets aggravated these dysfunctions. Thus, these results may be associated with renal dysfunction, which, in turn, would help in understanding the development of salt-sensitive hypertension.
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Affiliation(s)
- Zhengjun Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Qiong Sun
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Na Sun
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Zhongmin Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
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Novel high throughput pooled shRNA screening identifies NQO1 as a potential drug target for host directed therapy for tuberculosis. Sci Rep 2016; 6:27566. [PMID: 27297123 PMCID: PMC4906352 DOI: 10.1038/srep27566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/20/2016] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED Chemical regulation of macrophage function is one key strategy for developing host-directed adjuvant therapies for tuberculosis (TB). A critical step to develop these therapies is the identification and characterization of specific macrophage molecules and pathways with a high potential to serve as drug targets. Using a barcoded lentivirus-based pooled short-hairpin RNA (shRNA) library combined with next generation sequencing, we identified 205 silenced host genes highly enriched in mycobacteria-resistant macrophages. Twenty-one of these "hits" belonged to the oxidoreductase functional category. NAD(P)H quinone oxidoreductase 1 (NQO1) was the top oxidoreductase "hit". NQO1 expression was increased after mycobacterial infection, and NQO1 knockdown increased macrophage differentiation, NF-κB activation, and the secretion of pro-inflammatory cytokines TNF-α and IL-1β in response to infection. This suggests that mycobacteria hijacks NQO1 to down-regulate pro-inflammatory and anti-bacterial functions. The competitive inhibitor of NQO1 dicoumarol synergized with rifampin to promote intracellular killing of mycobacteria. Thus, NQO1 is a new host target in mycobacterial infection that could potentially be exploited to increase antibiotic efficacy in vivo. Our findings also suggest that pooled shRNA libraries could be valuable tools for genome-wide screening in the search for novel druggable host targets for adjunctive TB therapies.
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Holzem KM, Vinnakota KC, Ravikumar VK, Madden EJ, Ewald GA, Dikranian K, Beard DA, Efimov IR. Mitochondrial structure and function are not different between nonfailing donor and end-stage failing human hearts. FASEB J 2016; 30:2698-707. [PMID: 27075244 DOI: 10.1096/fj.201500118r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/05/2016] [Indexed: 01/06/2023]
Abstract
During human heart failure, the balance of cardiac energy use switches from predominantly fatty acids (FAs) to glucose. We hypothesized that this substrate shift was the result of mitochondrial degeneration; therefore, we examined mitochondrial oxidation and ultrastructure in the failing human heart by using respirometry, transmission electron microscopy, and gene expression studies of demographically matched donor and failing human heart left ventricular (LV) tissues. Surprisingly, respiratory capacities for failing LV isolated mitochondria (n = 9) were not significantly diminished compared with donor LV isolated mitochondria (n = 7) for glycolysis (pyruvate + malate)- or FA (palmitoylcarnitine)-derived substrates, and mitochondrial densities, assessed via citrate synthase activity, were consistent between groups. Transmission electron microscopy images also showed no ultrastructural remodeling for failing vs. donor mitochondria; however, the fraction of lipid droplets (LDs) in direct contact with a mitochondrion was reduced, and the average distance between an LD and its nearest neighboring mitochondrion was increased. Analysis of FA processing gene expression between donor and failing LVs revealed 0.64-fold reduced transcript levels for the mitochondrial-LD tether, perilipin 5, in the failing myocardium (P = 0.003). Thus, reduced FA use in heart failure may result from improper delivery, potentially via decreased perilipin 5 expression and mitochondrial-LD tethering, and not from intrinsic mitochondrial dysfunction.-Holzem, K. M., Vinnakota, K. C., Ravikumar, V. K., Madden, E. J., Ewald, G. A., Dikranian, K., Beard, D. A., Efimov, I. R. Mitochondrial structure and function are not different between nonfailing donor and end-stage failing human hearts.
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Affiliation(s)
- Katherine M Holzem
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kalyan C Vinnakota
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vinod K Ravikumar
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Eli J Madden
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Gregory A Ewald
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Krikor Dikranian
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Igor R Efimov
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA; George Washington University, Washington, D.C., USA
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Chen X, Li J, Hou J, Xie Z, Yang F. Mammalian mitochondrial proteomics: insights into mitochondrial functions and mitochondria-related diseases. Expert Rev Proteomics 2014; 7:333-45. [DOI: 10.1586/epr.10.22] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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OXPHOS susceptibility to oxidative modifications: The role of heart mitochondrial subcellular location. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1106-13. [DOI: 10.1016/j.bbabio.2011.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 04/11/2011] [Accepted: 04/13/2011] [Indexed: 11/30/2022]
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Broedel O, Krause E, Stephanowitz H, Schuemann M, Eravci M, Weist S, Brunkau C, Wittke J, Eravci S, Baumgartner A. In-Gel 18O Labeling for Improved Identification of Proteins from 2-DE Gel Spots in Comparative Proteomic Experiments. J Proteome Res 2009; 8:3771-7. [DOI: 10.1021/pr8010765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oliver Broedel
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Eberhard Krause
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Heike Stephanowitz
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Michael Schuemann
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Murat Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Stephanie Weist
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Cindy Brunkau
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Janosch Wittke
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Selda Eravci
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
| | - Andreas Baumgartner
- Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany, A+M Proteome Science, Berlin, Germany, and Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
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Fenselau C, Yao X. 18O2-Labeling in Quantitative Proteomic Strategies: A Status Report. J Proteome Res 2009; 8:2140-3. [DOI: 10.1021/pr8009879] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Catherine Fenselau
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Xudong Yao
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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Ruiz-Romero C, Blanco FJ. Mitochondrial proteomics and its application in biomedical research. MOLECULAR BIOSYSTEMS 2009; 5:1130-42. [DOI: 10.1039/b906296n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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