251
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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252
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Ngatia JN, Lan TM, Dinh TD, Zhang L, Ahmed AK, Xu YC. Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments? Ecol Evol 2019; 9:6821-6832. [PMID: 31380018 PMCID: PMC6662336 DOI: 10.1002/ece3.5250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/25/2022] Open
Abstract
The mammoths originated in warm and equatorial Africa and later colonized cold and high-latitude environments. Studies on nuclear genes suggest that woolly mammoth had evolved genetic variations involved in processes relevant to cold tolerance, including lipid metabolism and thermogenesis, and adaptation to extremely varied light and darkness cycles. The mitochondria is a major regulator of cellular energy metabolism, thus the mitogenome of mammoths may also exhibit adaptive evolution. However, little is yet known in this regard. In this study, we analyzed mitochondrial protein-coding genes (MPCGs) sequences of 75 broadly distributed woolly mammoths (Mammuthus primigenius) to test for signatures of positive selection. Results showed that a total of eleven amino acid sites in six genes, namely ND1, ND4, ND5, ND6, CYTB, and ATP6, displayed strong evidence of positive selection. Two sites were located in close proximity to proton-translocation channels in mitochondrial complex I. Biochemical and homology protein structure modeling analyses demonstrated that five amino acid substitutions in ND1, ND5, and ND6 might have influenced the performance of protein-protein interaction among subunits of complex I, and three substitutions in CYTB and ATP6 might have influenced the performance of metabolic regulatory chain. These findings suggest metabolic adaptations in the mitogenome of woolly mammoths in relation to extreme environments and provide a basis for further tests on the significance of the variations on other systems.
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Affiliation(s)
| | - Tian Ming Lan
- BGI‐ShenzhenShenzhenChina
- Laboratory of Genomics and Molecular Biomedicine, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National Genebank, BGI‐ShenzhenShenzhenChina
| | - Thi Dao Dinh
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | - Le Zhang
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | | | - Yan Chun Xu
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and UtilizationHarbinChina
- State Forestry and Grassland Administration Detecting Centre of WildlifeHarbinChina
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253
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Saura P, Frey DM, Gamiz-Hernandez AP, Kaila VRI. Electric field modulated redox-driven protonation and hydration energetics in energy converting enzymes. Chem Commun (Camb) 2019; 55:6078-6081. [PMID: 31066378 PMCID: PMC6932871 DOI: 10.1039/c9cc01135h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Biological energy conversion is catalysed by proton-coupled electron transfer (PCET) reactions that form the chemical basis of respiratory and photosynthetic enzymes. Despite recent advances in structural, biophysical, and computational experiments, the mechanistic principles of these reactions still remain elusive. Based on common functional features observed in redox enzymes, we study here generic mechanistic models for water-mediated long-range PCET reactions. We show how a redox reaction within a buried protein environment creates an electric field that induces hydration changes between the proton acceptor and donor groups, and in turn, lowers the reaction barrier and increases the thermodynamic driving forces for the water-mediated PCET process. We predict linear free energy relationships, and discuss the proposed mechanism in context of PCET in cytochrome c oxidase.
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Affiliation(s)
- Patricia Saura
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
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254
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Indrieri A, Carrella S, Romano A, Spaziano A, Marrocco E, Fernandez‐Vizarra E, Barbato S, Pizzo M, Ezhova Y, Golia FM, Ciampi L, Tammaro R, Henao‐Mejia J, Williams A, Flavell RA, De Leonibus E, Zeviani M, Surace EM, Banfi S, Franco B. miR-181a/b downregulation exerts a protective action on mitochondrial disease models. EMBO Mol Med 2019; 11:emmm.201708734. [PMID: 30979712 PMCID: PMC6505685 DOI: 10.15252/emmm.201708734] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial diseases (MDs) are a heterogeneous group of devastating and often fatal disorders due to defective oxidative phosphorylation. Despite the recent advances in mitochondrial medicine, effective therapies are still not available for these conditions. Here, we demonstrate that the microRNAs miR-181a and miR-181b (miR-181a/b) regulate key genes involved in mitochondrial biogenesis and function and that downregulation of these miRNAs enhances mitochondrial turnover in the retina through the coordinated activation of mitochondrial biogenesis and mitophagy. We thus tested the effect of miR-181a/b inactivation in different animal models of MDs, such as microphthalmia with linear skin lesions and Leber's hereditary optic neuropathy. We found that miR-181a/b downregulation strongly protects retinal neurons from cell death and significantly ameliorates the disease phenotype in all tested models. Altogether, our results demonstrate that miR-181a/b regulate mitochondrial homeostasis and that these miRNAs may be effective gene-independent therapeutic targets for MDs characterized by neuronal degeneration.
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Affiliation(s)
- Alessia Indrieri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly
| | - Sabrina Carrella
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Precision MedicineUniversity of Campania “L. Vanvitelli”Caserta CEItaly
| | - Alessia Romano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elena Marrocco
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Sara Barbato
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Yulia Ezhova
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Ludovica Ciampi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Jorge Henao‐Mejia
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA,Institute for ImmunologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Adam Williams
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA,Department of Genetics and Genomic SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
| | - Richard A Flavell
- Department of ImmunobiologyYale University School of MedicineNew HavenCTUSA,Howard Hughes Medical InstituteChevy ChaseMDUSA
| | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Institute of Cellular Biology and Neurobiology “ABT”CNRRomaItaly
| | - Massimo Zeviani
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Enrico M Surace
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly,Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly,Present address:
Medical GeneticsDepartment of Translational Medical ScienceUniversity of Naples “Federico II”NaplesItaly
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy .,Medical Genetics, Department of Precision Medicine, University of Campania "L. Vanvitelli", Caserta CE, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy .,Medical Genetics, Department of Translational Medical Science, University of Naples "Federico II", Naples, Italy
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255
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Meyer EH, Welchen E, Carrie C. Assembly of the Complexes of the Oxidative Phosphorylation System in Land Plant Mitochondria. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:23-50. [PMID: 30822116 DOI: 10.1146/annurev-arplant-050718-100412] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants-compared with those described in fungal and animal models-we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.
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Affiliation(s)
- Etienne H Meyer
- Organelle Biology and Biotechnology Research Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Current affiliation: Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany;
| | - Elina Welchen
- Cátedra de Biología Celular y Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Chris Carrie
- Plant Sciences Research Group, Department Biologie I, Ludwig-Maximilians-Universität, 82152 Planegg-Martinsried, Germany
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256
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Haapanen O, Djurabekova A, Sharma V. Role of Second Quinone Binding Site in Proton Pumping by Respiratory Complex I. Front Chem 2019; 7:221. [PMID: 31024903 PMCID: PMC6465577 DOI: 10.3389/fchem.2019.00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Respiratory complex I performs the reduction of quinone (Q) to quinol (QH2) and pumps protons across the membrane. Structural data on complex I have provided spectacular insights into the electron and proton transfer paths, as well as into the long (~30 Å) and unique substrate binding channel. However, due to missing structural information on Q binding modes, it remains unclear how Q reduction drives long range (~20 nm) redox-coupled proton pumping in complex I. Here we applied multiscale computational approaches to study the dynamics and redox chemistry of Q and QH2. Based on tens of microseconds of atomistic molecular dynamics (MD) simulations of bacterial and mitochondrial complex I, we find that the dynamics of Q is remarkably rapid and it diffuses from the N2 binding site to another stable site near the entrance of the Q channel in microseconds. Analysis of simulation trajectories also reveal the presence of yet another Q binding site 25–30 Å from the N2 center, which is in remarkable agreement with the electron density observed in recent cryo electron microscopy structure of complex I from Yarrowia lipolytica. Quantum chemical computations on the two Q binding sites closer to the entrance of the Q tunnel reveal redox-coupled protonation reactions that may be important in driving the proton pump of complex I.
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Affiliation(s)
- Outi Haapanen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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257
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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258
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Saura P, Kaila VRI. Energetics and Dynamics of Proton-Coupled Electron Transfer in the NADH/FMN Site of Respiratory Complex I. J Am Chem Soc 2019; 141:5710-5719. [PMID: 30873834 PMCID: PMC6890364 DOI: 10.1021/jacs.8b11059] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complex I functions as an initial electron acceptor in aerobic respiratory chains that reduces quinone and pumps protons across a biological membrane. This remarkable charge transfer process extends ca. 300 Å and it is initiated by a poorly understood proton-coupled electron transfer (PCET) reaction between nicotinamide adenine dinucleotide (NADH) and a protein-bound flavin (FMN) cofactor. We combine here large-scale density functional theory calculations and quantum/classical models with atomistic molecular dynamics simulations to probe the energetics and dynamics of the NADH-driven PCET reaction in complex I. We find that the reaction takes place by concerted hydrogen atom (H•) transfer that couples to an electron transfer (eT) between the aromatic ring systems of the cofactors and further triggers reduction of the nearby FeS centers. In bacterial, Escherichia coli-like complex I isoforms, reduction of the N1a FeS center increases the binding affinity of the oxidized NAD+ that prevents the nucleotide from leaving prematurely. This electrostatic trapping could provide a protective gating mechanism against reactive oxygen species formation. We also find that proton transfer from the transient FMNH• to a nearby conserved glutamate (Glu97) residue favors eT from N1a onward along the FeS chain and modulates the binding of a new NADH molecule. The PCET in complex I isoforms with low-potential N1a centers is also discussed. On the basis of our combined results, we propose a putative mechanistic model for the NADH-driven proton/electron-transfer reaction in complex I.
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Affiliation(s)
- Patricia Saura
- Department of Chemistry , Technical University of Munich (TUM) , Lichtenbergstrasse 4 , Garching D-85747 , Germany
| | - Ville R I Kaila
- Department of Chemistry , Technical University of Munich (TUM) , Lichtenbergstrasse 4 , Garching D-85747 , Germany
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259
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ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. Mol Cell 2019; 71:567-580.e4. [PMID: 30118679 DOI: 10.1016/j.molcel.2018.06.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/08/2018] [Accepted: 06/25/2018] [Indexed: 01/28/2023]
Abstract
The electron transport chain (ETC) is an important participant in cellular energy conversion, but its biogenesis presents the cell with numerous challenges. To address these complexities, the cell utilizes ETC assembly factors, which include the LYR protein family. Each member of this family interacts with the mitochondrial acyl carrier protein (ACP), the scaffold protein upon which the mitochondrial fatty acid synthesis (mtFAS) pathway builds fatty acyl chains from acetyl-CoA. We demonstrate that the acylated form of ACP is an acetyl-CoA-dependent allosteric activator of the LYR protein family used to stimulate ETC biogenesis. By tuning ETC assembly to the abundance of acetyl-CoA, which is the major fuel of the TCA cycle and ETC, this system could provide an elegant mechanism for coordinating the assembly of ETC complexes with one another and with substrate availability.
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260
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Liu L, Qi L, Knifley T, Piecoro DW, Rychahou P, Liu J, Mitov MI, Martin J, Wang C, Wu J, Weiss HL, Butterfield DA, Evers BM, O'Connor KL, Chen M. S100A4 alters metabolism and promotes invasion of lung cancer cells by up-regulating mitochondrial complex I protein NDUFS2. J Biol Chem 2019; 294:7516-7527. [PMID: 30885944 DOI: 10.1074/jbc.ra118.004365] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
It is generally accepted that alterations in metabolism are critical for the metastatic process; however, the mechanisms by which these metabolic changes are controlled by the major drivers of the metastatic process remain elusive. Here, we found that S100 calcium-binding protein A4 (S100A4), a major metastasis-promoting protein, confers metabolic plasticity to drive tumor invasion and metastasis of non-small cell lung cancer cells. Investigating how S100A4 regulates metabolism, we found that S100A4 depletion decreases oxygen consumption rates, mitochondrial activity, and ATP production and also shifts cell metabolism to higher glycolytic activity. We further identified that the 49-kDa mitochondrial complex I subunit NADH dehydrogenase (ubiquinone) Fe-S protein 2 (NDUFS2) is regulated in an S100A4-dependent manner and that S100A4 and NDUFS2 exhibit co-occurrence at significant levels in various cancer types as determined by database-driven analysis of genomes in clinical samples using cBioPortal for Cancer Genomics. Importantly, we noted that S100A4 or NDUFS2 silencing inhibits mitochondrial complex I activity, reduces cellular ATP level, decreases invasive capacity in three-dimensional growth, and dramatically decreases metastasis rates as well as tumor growth in vivo Finally, we provide evidence that cells depleted in S100A4 or NDUFS2 shift their metabolism toward glycolysis by up-regulating hexokinase expression and that suppressing S100A4 signaling sensitizes lung cancer cells to glycolysis inhibition. Our findings uncover a novel S100A4 function and highlight its importance in controlling NDUFS2 expression to regulate the plasticity of mitochondrial metabolism and thereby promote the invasive and metastatic capacity in lung cancer.
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Affiliation(s)
- Lili Liu
- From the Markey Cancer Center and
| | - Lei Qi
- From the Markey Cancer Center and
| | | | | | | | - Jinpeng Liu
- From the Markey Cancer Center and.,Biostatistics
| | | | | | - Chi Wang
- From the Markey Cancer Center and.,Biostatistics
| | - Jianrong Wu
- From the Markey Cancer Center and.,Biostatistics
| | | | | | | | - Kathleen L O'Connor
- From the Markey Cancer Center and .,Molecular and Cellular Biochemistry, and
| | - Min Chen
- From the Markey Cancer Center and .,Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky 40536
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261
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VanHecke GC, Abeywardana MY, Ahn YH. Proteomic Identification of Protein Glutathionylation in Cardiomyocytes. J Proteome Res 2019; 18:1806-1818. [PMID: 30831029 DOI: 10.1021/acs.jproteome.8b00986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reactive oxygen species (ROS) are important signaling molecules, but their overproduction is associated with many cardiovascular diseases, including cardiomyopathy. ROS induce various oxidative modifications, among which glutathionylation is one of the significant protein oxidations that occur under oxidative stress. Despite previous efforts, direct and site-specific identification of glutathionylated proteins in cardiomyocytes has been limited. In this report, we used a clickable glutathione approach in a HL-1 mouse cardiomyocyte cell line under exposure to hydrogen peroxide, finding 1763 glutathionylated peptides with specific Cys modification sites, which include many muscle-specific proteins. Bioinformatic and cluster analyses found 125 glutathionylated proteins, whose mutations or dysfunctions are associated with cardiomyopathy, many of which include sarcomeric structural and contractile proteins, chaperone, and other signaling or regulatory proteins. We further provide functional implication of glutathionylation for several identified proteins, including CSRP3/MLP and complex I, II, and III, by analyzing glutathionylated sites in their structures. Our report establishes a chemoselective method for direct identification of glutathionylated proteins and provides potential target proteins whose glutathionylation may contribute to muscle diseases.
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Affiliation(s)
- Garrett C VanHecke
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | | | - Young-Hoon Ahn
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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262
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Thomas LW, Stephen JM, Esposito C, Hoer S, Antrobus R, Ahmed A, Al-Habib H, Ashcroft M. CHCHD4 confers metabolic vulnerabilities to tumour cells through its control of the mitochondrial respiratory chain. Cancer Metab 2019; 7:2. [PMID: 30886710 PMCID: PMC6404347 DOI: 10.1186/s40170-019-0194-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/05/2019] [Indexed: 12/15/2022] Open
Abstract
Background Tumour cells rely on glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) to survive. Thus, mitochondrial OXPHOS has become an increasingly attractive area for therapeutic exploitation in cancer. However, mitochondria are required for intracellular oxygenation and normal physiological processes, and it remains unclear which mitochondrial molecular mechanisms might provide therapeutic benefit. Previously, we discovered that coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4) is critical for regulating intracellular oxygenation and required for the cellular response to hypoxia (low oxygenation) in tumour cells through molecular mechanisms that we do not yet fully understand. Overexpression of CHCHD4 in human cancers correlates with increased tumour progression and poor patient survival. Results Here, we show that elevated CHCHD4 expression provides a proliferative and metabolic advantage to tumour cells in normoxia and hypoxia. Using stable isotope labelling with amino acids in cell culture (SILAC) and analysis of the whole mitochondrial proteome, we show that CHCHD4 dynamically affects the expression of a broad range of mitochondrial respiratory chain subunits from complex I-V, including multiple subunits of complex I (CI) required for complex assembly that are essential for cell survival. We found that loss of CHCHD4 protects tumour cells from respiratory chain inhibition at CI, while elevated CHCHD4 expression in tumour cells leads to significantly increased sensitivity to CI inhibition, in part through the production of mitochondrial reactive oxygen species (ROS). Conclusions Our study highlights an important role for CHCHD4 in regulating tumour cell metabolism and reveals that CHCHD4 confers metabolic vulnerabilities to tumour cells through its control of the mitochondrial respiratory chain and CI biology.
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Affiliation(s)
- Luke W. Thomas
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Jenna M. Stephen
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Cinzia Esposito
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
- Present address: Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Simon Hoer
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY UK
| | - Afshan Ahmed
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
- Present address: AstraZeneca Ltd., Cambridge, UK
| | - Hasan Al-Habib
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH UK
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263
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Matos I, Machado MP, Schartl M, Coelho MM. Allele-specific expression variation at different ploidy levels in Squalius alburnoides. Sci Rep 2019; 9:3688. [PMID: 30842567 PMCID: PMC6403402 DOI: 10.1038/s41598-019-40210-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/07/2019] [Indexed: 11/09/2022] Open
Abstract
Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.
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Affiliation(s)
- Isa Matos
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany
| | - Miguel P Machado
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany.,Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Manfred Schartl
- University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany. .,Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA.
| | - Maria Manuela Coelho
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal
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264
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Saura P, Kaila VRI. Molecular dynamics and structural models of the cyanobacterial NDH-1 complex. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2019; 1860:201-208. [PMID: 30448269 PMCID: PMC6358722 DOI: 10.1016/j.bbabio.2018.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
Abstract
NDH-1 is a gigantic redox-driven proton pump linked with respiration and cyclic electron flow in cyanobacterial cells. Based on experimentally resolved X-ray and cryo-EM structures of the respiratory complex I, we derive here molecular models of two isoforms of the cyanobacterial NDH-1 complex involved in redox-driven proton pumping (NDH-1L) and CO2-fixation (NDH-1MS). Our models show distinct structural and dynamic similarities to the core architecture of the bacterial and mammalian respiratory complex I. We identify putative plastoquinone-binding sites that are coupled by an electrostatic wire to the proton pumping elements in the membrane domain of the enzyme. Molecular simulations suggest that the NDH-1L isoform undergoes large-scale hydration changes that support proton-pumping within antiporter-like subunits, whereas the terminal subunit of the NDH-1MS isoform lacks such structural motifs. Our work provides a putative molecular blueprint for the complex I-analogue in the photosynthetic energy transduction machinery and demonstrates that general mechanistic features of the long-range proton-pumping machinery are evolutionary conserved in the complex I-superfamily.
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Affiliation(s)
- Patricia Saura
- Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstraße 4, Garching D-85747, Germany
| | - Ville R I Kaila
- Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstraße 4, Garching D-85747, Germany.
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265
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Jussupow A, Di Luca A, Kaila VRI. How cardiolipin modulates the dynamics of respiratory complex I. SCIENCE ADVANCES 2019; 5:eaav1850. [PMID: 30906865 PMCID: PMC6426460 DOI: 10.1126/sciadv.aav1850] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/30/2019] [Indexed: 05/19/2023]
Abstract
Cardiolipin modulates the activity of membrane-bound respiratory enzymes that catalyze biological energy transduction. The respiratory complex I functions as the primary redox-driven proton pump in mitochondrial and bacterial respiratory chains, and its activity is strongly enhanced by cardiolipin. However, despite recent advances in the structural biology of complex I, cardiolipin-specific interaction mechanisms currently remain unknown. On the basis of millisecond molecular simulations, we suggest that cardiolipin binds to proton-pumping subunits of complex I and induces global conformational changes that modulate the accessibility of the quinone substrate to the enzyme. Our findings provide key information on the coupling between complex I dynamics and activity and suggest how biological membranes modulate the structure and activity of proteins.
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266
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Banba A, Tsuji A, Kimura H, Murai M, Miyoshi H. Defining the mechanism of action of S1QELs, specific suppressors of superoxide production in the quinone-reaction site in mitochondrial complex I. J Biol Chem 2019; 294:6550-6561. [PMID: 30824536 DOI: 10.1074/jbc.ra119.007687] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
Site-specific suppressors of superoxide production (named S1QELs) in the quinone-reaction site in mitochondrial respiratory complex I during reverse electron transfer have been previously reported; however, their mechanism of action remains elusive. Using bovine heart submitochondrial particles, we herein investigated the effects of S1QELs on complex I functions. We found that the inhibitory effects of S1QELs on complex I are distinctly different from those of other known quinone-site inhibitors. For example, the inhibitory potencies of S1QELs significantly varied depending on the direction of electron transfer (forward or reverse). S1QELs marginally suppressed the specific chemical modification of Asp160 in the 49-kDa subunit, located deep in the quinone-binding pocket, by the tosyl chemistry reagent AL1. S1QELs also failed to suppress the binding of a photoreactive quinazoline-type inhibitor ([125I]AzQ) to the 49-kDa subunit. Moreover, a photoaffinity labeling experiment with photoreactive S1QEL derivatives indicated that they bind to a segment in the ND1 subunit that is not considered to make up the binding pocket for quinone or inhibitors. These results indicate that unlike known quinone-site inhibitors, S1QELs do not occupy the quinone- or inhibitor-binding pocket; rather, they may indirectly modulate the quinone-redox reactions by inducing structural changes of the pocket through binding to ND1. We conclude that this indirect effect may be a prerequisite for S1QELs' direction-dependent modulation of electron transfer. This, in turn, may be responsible for the suppression of superoxide production during reverse electron transfer without significantly interfering with forward electron transfer.
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Affiliation(s)
- Atsushi Banba
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Atsuhito Tsuji
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hironori Kimura
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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267
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Abstract
Single-particle electron cryomicroscopy (cryo-EM) has led to a revolution in structural work on mammalian respiratory complex I. Complex I (mitochondrial NADH:ubiquinone oxidoreductase), a membrane-bound redox-driven proton pump, is one of the largest and most complicated enzymes in the mammalian cell. Rapid progress, following the first 5-Å resolution data on bovine complex I in 2014, has led to a model for mouse complex I at 3.3-Å resolution that contains 96% of the 8,518 residues and to the identification of different particle classes, some of which are assigned to biochemically defined states. Factors that helped improve resolution, including improvements to biochemistry, cryo-EM grid preparation, data collection strategy, and image processing, are discussed. Together with recent structural data from an ancient relative, membrane-bound hydrogenase, cryo-EM on mammalian complex I has provided new insights into the proton-pumping machinery and a foundation for understanding the enzyme's catalytic mechanism.
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Affiliation(s)
- Ahmed-Noor A Agip
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; , , ,
| | - James N Blaza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; , , , .,Current affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Justin G Fedor
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; , , ,
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; , , ,
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268
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Affiliation(s)
- Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, Route 772, 6525 GA Nijmegen, Netherlands.
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269
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Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature 2019; 566:411-414. [PMID: 30742075 DOI: 10.1038/s41586-019-0921-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022]
Abstract
Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis1,2. NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms3,4 and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP+ molecule reduced4,5. NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants3,6. However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH3,5,6, and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin3-5,7. Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical.
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270
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Ligas J, Pineau E, Bock R, Huynen MA, Meyer EH. The assembly pathway of complex I in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:447-459. [PMID: 30347487 DOI: 10.1111/tpj.14133] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 05/23/2023]
Abstract
All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin for many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme in the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved.
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Affiliation(s)
- Joanna Ligas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Emmanuelle Pineau
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Centre for Mitochondrial Medicine, Radboud University, Nijmegen, The Netherlands
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, 67084, Strasbourg, France
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271
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Tran KN, Niu S, Ichiye T. Reduction potential calculations of the Fe–S clusters in
Thermus thermophilus
respiratory complex I. J Comput Chem 2019; 40:1248-1256. [DOI: 10.1002/jcc.25785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Kelly N. Tran
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Shuqiang Niu
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Toshiko Ichiye
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
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272
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Stepanova A, Konrad C, Manfredi G, Springett R, Ten V, Galkin A. The dependence of brain mitochondria reactive oxygen species production on oxygen level is linear, except when inhibited by antimycin A. J Neurochem 2019; 148:731-745. [PMID: 30582748 DOI: 10.1111/jnc.14654] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 01/22/2023]
Abstract
Reactive oxygen species (ROS) are by-products of physiological mitochondrial metabolism that are involved in several cellular signaling pathways as well as tissue injury and pathophysiological processes, including brain ischemia/reperfusion injury. The mitochondrial respiratory chain is considered a major source of ROS; however, there is little agreement on how ROS release depends on oxygen concentration. The rate of H2 O2 release by intact brain mitochondria was measured with an Amplex UltraRed assay using a high-resolution respirometer (Oroboros) equipped with a fluorescent optical module and a system of controlled gas flow for varying the oxygen concentration. Three types of substrates were used: malate and pyruvate, succinate and glutamate, succinate alone or glycerol 3-phosphate. For the first time we determined that, with any substrate used in the absence of inhibitors, H2 O2 release by respiring brain mitochondria is linearly dependent on the oxygen concentration. We found that the highest rate of H2 O2 release occurs in conditions of reverse electron transfer when mitochondria oxidize succinate or glycerol 3-phosphate. H2 O2 production by complex III is significant only in the presence of antimycin A and, in this case, the oxygen dependence manifested mixed (linear and hyperbolic) kinetics. We also demonstrated that complex II in brain mitochondria could contribute to ROS generation even in the absence of its substrate succinate when the quinone pool is reduced by glycerol 3-phosphate. Our results underscore the critical importance of reverse electron transfer in the brain, where a significant amount of succinate can be accumulated during ischemia providing a backflow of electrons to complex I at the early stages of reperfusion. Our study also demonstrates that ROS generation in brain mitochondria is lower under hypoxic conditions than in normoxia. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Anna Stepanova
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, UK.,Department of Pediatrics, Columbia University, New York, NY, USA
| | - Csaba Konrad
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Roger Springett
- Cardiovascular Division, King's College London, British Heart Foundation Centre of Excellence London, London, UK
| | - Vadim Ten
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Alexander Galkin
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, UK.,Department of Pediatrics, Columbia University, New York, NY, USA
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273
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Manoj KM, Parashar A, David Jacob V, Ramasamy S. Aerobic respiration: proof of concept for the oxygen-centric murburn perspective. J Biomol Struct Dyn 2019; 37:4542-4556. [PMID: 30488771 DOI: 10.1080/07391102.2018.1552896] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The inner mitochondrial membrane protein complexes (I-V) and prokaryotic respiratory machinery are examined for a deeper understanding of their structure-function correlations and dynamics. In silico analysis of the structure of complexes I-IV, docking studies and erstwhile literature confirm that they carry sites which are in close proximity to DROS (diffusible reactive oxygen species) generating redox centers. These findings provide supportive evidence for the newly proposed oxygen-centric chemical-coupling mechanism (murburn concept), wherein DROS catalyzes the esterification of inorganic phosphate to ADP. Further, in a reductionist system, we demonstrate that a DROS (like superoxide) can effectively esterify inorganic phosphate to ADP. The impact of these findings and the interactive dynamics of classical inhibitors (rotenone and cyanide), uncouplers (dinitrophenol and uncoupling protein) and other toxins (atractyloside and oligomycin) are briefly discussed. Highlights • Earlier perception: Complexes (I-IV) pump protons and Complex V make ATP (aided by protons) • Herein: Respiratory molecular machinery is probed for new structure-function correlations • Analyses: Quantitative arguments discount proton-centric ATP synthesis in mitochondria and bacteria • In silico data: ADP-binding sites and O2/ diffusible reactive oxygen species (DROS)-accessible channels are unveiled in respiratory proteins • In vitro data: Using luminometry, ATP synthesis is demonstrated from ADP, Pi and superoxide • Inference: Findings agree with decentralized ADP-Pi activation via oxygen-centric murburn scheme Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research , Vadlamudi , Guntur, Andhra Pradesh, India
| | | | - Surjith Ramasamy
- Department of Biotechnology, Indian Institute of Technology Guwahati , Guwahati , Assam, India
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274
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Majmudar JD, Feng X, Fox NG, Nabhan JF, Towle T, Ma T, Gooch R, Bulawa C, Yue WW, Martelli A. 4'-Phosphopantetheine and long acyl chain-dependent interactions are integral to human mitochondrial acyl carrier protein function. MEDCHEMCOMM 2019; 10:209-220. [PMID: 30881609 DOI: 10.1039/c8md00489g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/23/2018] [Indexed: 11/21/2022]
Abstract
The mitochondrial acyl carrier protein (human ACPM, yeast Acp1) is an essential mitochondrial protein. Through binding of nascent acyl chains on the serine (S112)-bound 4'-phosphopantetheine (4'-PP) cofactor, ACPM is involved in mitochondrial fatty acid synthesis and lipoic acid biogenesis. Recently, yeast Acp1 was found to interact with several mitochondrial complexes, including the iron-sulfur (Fe-S) cluster biosynthesis and respiratory complexes, via the binding to LYRM proteins, a family of proteins involved in assembly/stability of complexes. Importantly, the interaction of LYRM proteins with Acp1 was shown to be essential in maintaining integrity of mitochondrial complexes. In human, recent structures show that ACPM binding to LYRM proteins involves acyl chains attached to the 4'-PP cofactor. Here, we performed an detailed characterization of the mitochondrial interactome of human ACPM by mass spectrometry (MS) and demonstrate the crucial role of the 4'-PP cofactor in most of ACPM interactions. Specifically, we show that ACPM interacts with endogenous Fe-S cluster complex components through binding of the LYRM protein ISD11/LYRM4. Using knockdown experiments, we further determine that ACPM is essential for the stability of mitochondrial respiratory complexes I, II and III, as well as the Fe-S cluster biosynthesis complex. Finally, using native MS and a top-down MS approach, we show that C14, C16 and C18 3-keto-acyl chains on ACPM are implicated in binding to ISD11 through analysis of the recombinant ACPM-ISD11 complex. Taken together, our data provide novel understanding of the role of 4'-PP- and long acyl chains-dependent interactions in human ACPM function.
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Affiliation(s)
- Jaimeen D Majmudar
- Chemical Biology, Medicine Design , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Xidong Feng
- Discovery Sciences , Worldwide Research and Development , Pfizer Inc. , Eastern Point Road , Groton , CT 06340 , USA
| | - Nicholas G Fox
- Structural Genomics Consortium , Nuffield Department of Clinical Medicine , University of Oxford , OX3 7DQ , UK
| | - Joseph F Nabhan
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Theresa Towle
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Tiffany Ma
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Renea Gooch
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Christine Bulawa
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Wyatt W Yue
- Structural Genomics Consortium , Nuffield Department of Clinical Medicine , University of Oxford , OX3 7DQ , UK
| | - Alain Martelli
- Rare Disease Research Unit , Worldwide Research and Development , Pfizer Inc. , 610 Main Street , Cambridge , MA 02139 , USA .
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275
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Wolters JC, Permentier HP, Bakker BM, Bischoff R. Targeted Proteomics to Study Mitochondrial Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:101-117. [PMID: 31452138 DOI: 10.1007/978-981-13-8367-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Targeted mass spectrometry in the selected or parallel reaction monitoring (SRM or PRM) mode is a widely used methodology to quantify proteins based on so-called signature or proteotypic peptides. SRM has the advantage of being able to quantify a range of proteins in a single analysis, for example, to measure the level of enzymes comprising a biochemical pathway. In this chapter, we will detail how to set up an SRM assay on the example of the mitochondrial protein succinate dehydrogenase [ubiquinone] flavoprotein subunit (mouse UniProt-code Q8K2B3). First, we will outline the in silico assay design including the choice of peptides based on a range of properties. We will further delineate different quantification strategies and introduce the reader to LC-MS assay development including the selection of the optimal peptide charge state and fragment ions as well as a discussion of the dynamic range of detection. The chapter will close with an application from the area of mitochondrial biology related to the quantification of a set of proteins isolated from mouse liver mitochondria in a study on mitochondrial respiratory flux decline in aging mouse muscle.
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Affiliation(s)
- Justina C Wolters
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
- Laboratory of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
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276
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Shen X, Pu Z, Chen X, Murphy RW, Shen Y. Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes. Front Genet 2019; 10:925. [PMID: 31632444 PMCID: PMC6785628 DOI: 10.3389/fgene.2019.00925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/04/2019] [Indexed: 02/05/2023] Open
Abstract
Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic respiration. Analyses of the available 2,161 complete mitochondrial genomes of 1,042 fishes, including 115 deep-sea species, detect signals of positive selection in mitochondrial genes in nine branches of deep-sea fishes. Aerobic metabolism yields much more energy per unit of source material than anaerobic metabolism. The adaptive evolution of the mtDNA may reflect that aerobic metabolism plays a more important role than anaerobic metabolism in deep-sea fishes, whose energy sources (food) are extremely limited. This strategy maximizes the usage of energy sources. Eleven mitochondrial genes have convergent/parallel amino acid changes between branches of deep-sea fishes. Thus, these amino acid sites may be functionally important in the acquisition of energy, and reflect convergent evolution during their independent invasion of the harsh deep-sea ecological niche.
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Affiliation(s)
- Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
- *Correspondence: Yongyi Shen,
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277
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278
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Uno S, Kimura H, Murai M, Miyoshi H. Exploring the quinone/inhibitor-binding pocket in mitochondrial respiratory complex I by chemical biology approaches. J Biol Chem 2018; 294:679-696. [PMID: 30425100 DOI: 10.1074/jbc.ra118.006056] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/10/2018] [Indexed: 11/06/2022] Open
Abstract
NADH-quinone oxidoreductase (respiratory complex I) couples NADH-to-quinone electron transfer to the translocation of protons across the membrane. Even though the architecture of the quinone-access channel in the enzyme has been modeled by X-ray crystallography and cryo-EM, conflicting findings raise the question whether the models fully reflect physiologically relevant states present throughout the catalytic cycle. To gain further insights into the structural features of the binding pocket for quinone/inhibitor, we performed chemical biology experiments using bovine heart sub-mitochondrial particles. We synthesized ubiquinones that are oversized (SF-UQs) or lipid-like (PC-UQs) and are highly unlikely to enter and transit the predicted narrow channel. We found that SF-UQs and PC-UQs can be catalytically reduced by complex I, albeit only at moderate or low rates. Moreover, quinone-site inhibitors completely blocked the catalytic reduction and the membrane potential formation coupled to this reduction. Photoaffinity-labeling experiments revealed that amiloride-type inhibitors bind to the interfacial domain of multiple core subunits (49 kDa, ND1, and PSST) and the 39-kDa supernumerary subunit, although the latter does not make up the channel cavity in the current models. The binding of amilorides to the multiple target subunits was remarkably suppressed by other quinone-site inhibitors and SF-UQs. Taken together, the present results are difficult to reconcile with the current channel models. On the basis of comprehensive interpretations of the present results and of previous findings, we discuss the physiological relevance of these models.
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Affiliation(s)
- Shinpei Uno
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hironori Kimura
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- From the Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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279
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Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO. Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 2018; 14:e1007735. [PMID: 30399141 PMCID: PMC6219761 DOI: 10.1371/journal.pgen.1007735] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023] Open
Abstract
Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.
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Affiliation(s)
- Wen C. Aw
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard G. Melvin
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Neil A. Youngson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Michael R. Garvin
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Yifang Hu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña (UDC), Campus Zapateira s/n, A Coruña, Spain
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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280
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Larosa V, Remacle C. Insights into the respiratory chain and oxidative stress. Biosci Rep 2018; 38:BSR20171492. [PMID: 30201689 PMCID: PMC6167499 DOI: 10.1042/bsr20171492] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 01/13/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive reduced oxygen molecules that result from aerobic metabolism. The common forms are the superoxide anion (O2∙-) and hydrogen peroxide (H2O2) and their derived forms, hydroxyl radical (HO∙) and hydroperoxyl radical (HOO∙). Their production sites in mitochondria are reviewed. Even though being highly toxic products, ROS seem important in transducing information from dysfunctional mitochondria. Evidences of signal transduction mediated by ROS in mitochondrial deficiency contexts are then presented in different organisms such as yeast, mammals or photosynthetic organisms.
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Affiliation(s)
- Véronique Larosa
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
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281
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Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps. Nat Commun 2018; 9:4500. [PMID: 30374105 PMCID: PMC6206036 DOI: 10.1038/s41467-018-06955-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron transfer onto ubiquinone triggers the concerted rearrangement of three protein loops of subunits ND1, ND3, and 49-kDa thereby generating the power-stoke driving proton pumping. Here we show that fixing loop TMH1-2ND3 to the nearby subunit PSST via a disulfide bridge introduced by site-directed mutagenesis reversibly disengages proton pumping without impairing ubiquinone reduction, inhibitor binding or the Active/Deactive transition. The X-ray structure of mutant complex I indicates that the disulfide bridge immobilizes but does not displace the tip of loop TMH1-2ND3. We conclude that movement of loop TMH1-2ND3 located at the ubiquinone-binding pocket is required to drive proton pumping corroborating one of the central predictions of our model for the mechanism of energy conversion by complex I proposed earlier. Proton pumping of mitochondrial complex I depends on the reduction of ubiquinone but the molecular mechanism of energy conversion is unclear. Here, the authors provide structural and biochemical evidence showing that movement of loop TMH1-2 in complex I subunit ND3 is required to drive proton pumping.
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282
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Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z. An electron transfer path connects subunits of a mycobacterial respiratory supercomplex. Science 2018; 362:science.aat8923. [PMID: 30361386 DOI: 10.1126/science.aat8923] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/10/2018] [Indexed: 11/02/2022]
Abstract
We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from Mycobacterium smegmatis. It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis.
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Affiliation(s)
- Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Ao Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Wenxin Ji
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ruogu Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhui Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Lu Yu
- High Magnetic Field Laboratory, CAS, Hefei 230031, China
| | - Changlin Tian
- High Magnetic Field Laboratory, CAS, Hefei 230031, China.,Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jingwen Li
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK
| | - Hsin-Yung Yen
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK.,OMass Technologies, Begbroke Science Park, Woodstock Rd, Yarnton, Kidlington OX5 1PF, UK
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China
| | - Yuna Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Minze Jia
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhiyong Lou
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK
| | - Luet-Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China. .,University of Chinese Academy of Sciences, Beijing, China
| | - Quan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Science, Nankai University, Tianjin 300353, China. .,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200031, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing 100101, China.,Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
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283
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Daghistani HM, Rajab BS, Kitmitto A. Three-dimensional electron microscopy techniques for unravelling mitochondrial dysfunction in heart failure and identification of new pharmacological targets. Br J Pharmacol 2018; 176:4340-4359. [PMID: 30225980 PMCID: PMC6887664 DOI: 10.1111/bph.14499] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/30/2018] [Accepted: 08/18/2018] [Indexed: 12/23/2022] Open
Abstract
A hallmark of heart failure is mitochondrial dysfunction leading to a bioenergetics imbalance in the myocardium. Consequently, there is much interest in targeting mitochondrial abnormalities to attenuate the pathogenesis of heart failure. This review discusses (i) how electron microscopy (EM) techniques have been fundamental for the current understanding of mitochondrial structure–function, (ii) the paradigm shift in resolutions now achievable by 3‐D EM techniques due to the introduction of direct detection devices and phase plate technology, and (iii) the application of EM for unravelling mitochondrial pathological remodelling in heart failure. We further consider the tremendous potential of multi‐scale EM techniques for the development of therapeutics, structure‐based ligand design and for delineating how a drug elicits nanostructural effects at the molecular, organelle and cellular levels. In conclusion, 3‐D EM techniques have entered a new era of structural biology and are poised to play a pivotal role in discovering new therapies targeting mitochondria for treating heart failure. Linked Articles This article is part of a themed section on Mitochondrial Pharmacology: Featured Mechanisms and Approaches for Therapy Translation. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.22/issuetoc
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Affiliation(s)
- Hussam M Daghistani
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Bodour S Rajab
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ashraf Kitmitto
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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284
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Burschel S, Kreuzer Decovic D, Nuber F, Stiller M, Hofmann M, Zupok A, Siemiatkowska B, Gorka M, Leimkühler S, Friedrich T. Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli
NADH:ubiquinone oxidoreductase (complex I). Mol Microbiol 2018; 111:31-45. [DOI: 10.1111/mmi.14137] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Sabrina Burschel
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Doris Kreuzer Decovic
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
| | - Franziska Nuber
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Marie Stiller
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Maud Hofmann
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Arkadiusz Zupok
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Beata Siemiatkowska
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Michal Gorka
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Silke Leimkühler
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
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285
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Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kühlbrandt W, Zickermann V. Cryo-EM structure of respiratory complex I at work. eLife 2018; 7:39213. [PMID: 30277212 PMCID: PMC6168287 DOI: 10.7554/elife.39213] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
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Affiliation(s)
- Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Karin Siegmund
- Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Volker Zickermann
- Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany.,Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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286
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Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. Cytonuclear integration and co-evolution. Nat Rev Genet 2018; 19:635-648. [PMID: 30018367 PMCID: PMC6469396 DOI: 10.1038/s41576-018-0035-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes. Advances in structural biology and comparative genomics are yielding important insights into the evolution of such complexes, including correlated sequence changes and recruitment of novel subunits. Thus, chimeric cytonuclear complexes provide a powerful window into the mechanisms of molecular co-evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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287
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Habich M, Salscheider SL, Riemer J. Cysteine residues in mitochondrial intermembrane space proteins: more than just import. Br J Pharmacol 2018; 176:514-531. [PMID: 30129023 DOI: 10.1111/bph.14480] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/20/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
The intermembrane space (IMS) is a very small mitochondrial sub-compartment with critical relevance for many cellular processes. IMS proteins fulfil important functions in transport of proteins, lipids, metabolites and metal ions, in signalling, in metabolism and in defining the mitochondrial ultrastructure. Our understanding of the IMS proteome has become increasingly refined although we still lack information on the identity and function of many of its proteins. One characteristic of many IMS proteins are conserved cysteines. Different post-translational modifications of these cysteine residues can have critical roles in protein function, localization and/or stability. The close localization to different ROS-producing enzyme systems, a dedicated machinery for oxidative protein folding, and a unique equipment with antioxidative systems, render the careful balancing of the redox and modification states of the cysteine residues, a major challenge in the IMS. In this review, we discuss different functions of human IMS proteins, the involvement of cysteine residues in these functions, the consequences of cysteine modifications and the consequences of cysteine mutations or defects in the machinery for disulfide bond formation in terms of human health. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
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Affiliation(s)
- Markus Habich
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Silja Lucia Salscheider
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
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288
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Sheikhizadeh Anari S, de Ridder D, Schranz ME, Smit S. Efficient inference of homologs in large eukaryotic pan-proteomes. BMC Bioinformatics 2018; 19:340. [PMID: 30257640 PMCID: PMC6158922 DOI: 10.1186/s12859-018-2362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/09/2018] [Indexed: 12/31/2022] Open
Abstract
Background Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, there is a need for efficient standalone tools to detect homologs in novel data. Results To address this, we present a fast method for detecting homology groups across a large number of individuals and/or species. We adopted a k-mer based approach which considerably reduces the number of pairwise protein alignments without sacrificing sensitivity. We demonstrate accuracy, scalability, efficiency and applicability of the presented method for detecting homology in large proteomes of bacteria, fungi, plants and Metazoa. Conclusions We clearly observed the trade-off between recall and precision in our homology inference. Favoring recall or precision strongly depends on the application. The clustering behavior of our program can be optimized for particular applications by altering a few key parameters. The program is available for public use at https://github.com/sheikhizadeh/pantools as an extension to our pan-genomic analysis tool, PanTools. Electronic supplementary material The online version of this article (10.1186/s12859-018-2362-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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289
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Wang Y, Hu SB, Wang MR, Yao RW, Wu D, Yang L, Chen LL. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nat Cell Biol 2018; 20:1145-1158. [DOI: 10.1038/s41556-018-0204-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/22/2018] [Indexed: 01/26/2023]
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290
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NMR as a Tool to Investigate the Processes of Mitochondrial and Cytosolic Iron-Sulfur Cluster Biosynthesis. Molecules 2018; 23:molecules23092213. [PMID: 30200358 PMCID: PMC6205161 DOI: 10.3390/molecules23092213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/03/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters, the ubiquitous protein cofactors found in all kingdoms of life, perform a myriad of functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. The biogenesis of Fe-S clusters is a multi-step process that involves the participation of many protein partners. Recent biophysical studies, involving X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and small angle X-ray scattering (SAXS), have greatly improved our understanding of these steps. In this review, after describing the biological importance of iron sulfur proteins, we focus on the contributions of NMR spectroscopy has made to our understanding of the structures, dynamics, and interactions of proteins involved in the biosynthesis of Fe-S cluster proteins.
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291
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Valach M, Léveillé-Kunst A, Gray MW, Burger G. Respiratory chain Complex I of unparalleled divergence in diplonemids. J Biol Chem 2018; 293:16043-16056. [PMID: 30166340 DOI: 10.1074/jbc.ra118.005326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial genes of Euglenozoa (Kinetoplastida, Diplonemea, and Euglenida) are notorious for being barely recognizable, raising the question of whether such divergent genes actually code for functional proteins. Here we demonstrate the translation and identify the function of five previously unassigned y genes encoded by mitochondrial DNA (mtDNA) of diplonemids. As is the rule in diplonemid mitochondria, y genes are fragmented, with gene pieces transcribed separately and then trans-spliced to form contiguous mRNAs. Further, y transcripts undergo massive RNA editing, including uridine insertions that generate up to 16-residue-long phenylalanine tracts, a feature otherwise absent from conserved mitochondrial proteins. By protein sequence analyses, MS, and enzymatic assays in Diplonema papillatum, we show that these y genes encode the subunits Nad2, -3, -4L, -6, and -9 of the respiratory chain Complex I (CI; NADH:ubiquinone oxidoreductase). The few conserved residues of these proteins are essentially those involved in proton pumping across the inner mitochondrial membrane and in coupling ubiquinone reduction to proton pumping (Nad2, -3, -4L, and -6) and in interactions with subunits containing electron-transporting Fe-S clusters (Nad9). Thus, in diplonemids, 10 CI subunits are mtDNA-encoded. Further, MS of D. papillatum CI allowed identification of 26 conventional and 15 putative diplonemid-specific nucleus-encoded components. Most conventional accessory subunits are well-conserved but unusually long, possibly compensating for the streamlined mtDNA-encoded components and for missing, otherwise widely distributed, conventional subunits. Finally, D. papillatum CI predominantly exists as a supercomplex I:III:IV that is exceptionally stable, making this protist an organism of choice for structural studies.
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Affiliation(s)
- Matus Valach
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
| | - Alexandra Léveillé-Kunst
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
| | - Michael W Gray
- the Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Gertraud Burger
- From the Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec H3T 1J4, Canada and
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292
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Henderson R. Von der Elektronenkristallographie zur Einzelpartikel-KryoEM (Nobel-Aufsatz). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH Großbritannien
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293
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Abstract
Complex I couples the free energy released from quinone (Q) reduction to pump protons across the biological membrane in the respiratory chains of mitochondria and many bacteria. The Q reduction site is separated by a large distance from the proton-pumping membrane domain. To address the molecular mechanism of this long-range proton-electron coupling, we perform here full atomistic molecular dynamics simulations, free energy calculations, and continuum electrostatics calculations on complex I from Thermus thermophilus We show that the dynamics of Q is redox-state-dependent, and that quinol, QH2, moves out of its reduction site and into a site in the Q tunnel that is occupied by a Q analog in a crystal structure of Yarrowia lipolytica We also identify a second Q-binding site near the opening of the Q tunnel in the membrane domain, where the Q headgroup forms strong interactions with a cluster of aromatic and charged residues, while the Q tail resides in the lipid membrane. We estimate the effective diffusion coefficient of Q in the tunnel, and in turn the characteristic time for Q to reach the active site and for QH2 to escape to the membrane. Our simulations show that Q moves along the Q tunnel in a redox-state-dependent manner, with distinct binding sites formed by conserved residue clusters. The motion of Q to these binding sites is proposed to be coupled to the proton-pumping machinery in complex I.
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294
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Na S, Jurkovic S, Friedrich T, Koslowski T. Charge transfer through a fragment of the respiratory complex I and its regulation: an atomistic simulation approach. Phys Chem Chem Phys 2018; 20:20023-20032. [PMID: 30022212 DOI: 10.1039/c8cp02420k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We simulate electron transfer within a fragment of the NADH:ubiquinone oxidoreductase (respiratory complex I) of the hyperthermophilic bacterium Aquifex aeolicus. We apply molecular dynamics simulations, thermodynamic integration, and a thermodynamic network least squares analysis to compute two key parameters of Marcus' theory of charge transfer, the thermodynamic driving force and the reorganization energy. Intramolecular contributions to the Gibbs free energy differences of electron and hydrogen transfer processes, ΔG, are accessed by calibrating against experimental redox titration data. This approach permits the computation of the interactions between the species NAD+, FMNH2, N1a-, and N3-, and the construction of a free energy surface for the flow of electrons within the fragment. We find NAD+ to be a strong candidate for the regulation of charge transfer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße23a, 79104 Freiburg im Breisgau, Germany.
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295
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Parodi-Rullán RM, Chapa-Dubocq XR, Javadov S. Acetylation of Mitochondrial Proteins in the Heart: The Role of SIRT3. Front Physiol 2018; 9:1094. [PMID: 30131726 PMCID: PMC6090200 DOI: 10.3389/fphys.2018.01094] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
A growing number of studies have demonstrated the role of post-translational modifications of proteins, particularly acetylation, in human diseases including neurodegenerative and cardiovascular diseases, diabetes, cancer, and in aging. Acetylation of mitochondrial proteins has been shown to be involved in the pathogenesis of cardiac diseases such as myocardial infarction (ischemia-reperfusion) and heart failure. Indeed, over 60% of mitochondrial proteins contain acetylation sites, and most of these proteins are involved in mitochondrial bioenergetics. Mitochondrial non-enzymatic acetylation is enabled by acetyl-coenzyme A abundance and serves as the primary pathway of acetylation in mitochondria. Hence, regulation of enzymatic deacetylation becomes the most important mechanism to control acetylation/deacetylation of mitochondrial proteins. Acetylation/deacetylation of mitochondrial proteins has been regarded as a key regulator of mitochondrial metabolism and function. Proteins are deacetylated by NAD+-dependent deacetylases known as sirtuins (SIRTs). Among seven sirtuin isoforms, only SIRT3, SIRT4, and SIRT5 are localized in the mitochondria. SIRT3 is the main mitochondrial sirtuin which plays a key role in maintaining metabolic and redox balance in the mitochondria under physiological and pathological conditions. SIRT3 regulates the enzymatic activity of proteins involved in fatty acid oxidation, tricarboxylic acid cycle, electron transport chain, and oxidative phosphorylation. Although many enzymes have been identified as targets for SIRT3, cardiac-specific SIRT3 effects and regulations could differ from those in non-cardiac tissues. Therefore, it is important to elucidate the contribution of SIRT3 and mitochondrial protein acetylation/deacetylation in mitochondrial metabolism and cardiac dysfunction. Here, we summarize previous studies and provide a comprehensive analysis of the role of SIRT3 in mitochondria metabolism and bioenergetics under physiological conditions and in cardiac diseases. In addition, the review discusses mitochondrial protein acetylation as a potential target for cardioprotection.
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Affiliation(s)
- Rebecca M Parodi-Rullán
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - Xavier R Chapa-Dubocq
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - Sabzali Javadov
- Department of Physiology, University of Puerto Rico School of Medicine, San Juan, PR, United States
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296
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Cai K, Frederick RO, Dashti H, Markley JL. Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering. Structure 2018; 26:1127-1136.e4. [PMID: 29983374 PMCID: PMC6082693 DOI: 10.1016/j.str.2018.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 05/24/2018] [Indexed: 11/19/2022]
Abstract
Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.
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Affiliation(s)
- Kai Cai
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Ronnie O Frederick
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Hesam Dashti
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - John L Markley
- Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
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297
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Fiedorczuk K, Sazanov LA. Mammalian Mitochondrial Complex I Structure and Disease-Causing Mutations. Trends Cell Biol 2018; 28:835-867. [PMID: 30055843 DOI: 10.1016/j.tcb.2018.06.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Abstract
Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria; Present address: The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria.
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298
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Mitochondrial complex I in the post-ischemic heart: reperfusion-mediated oxidative injury and protein cysteine sulfonation. J Mol Cell Cardiol 2018; 121:190-204. [PMID: 30031815 DOI: 10.1016/j.yjmcc.2018.07.244] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Abstract
A serious consequence of ischemia-reperfusion injury (I/R) is oxidative damage leading to mitochondrial dysfunction. Such I/R-induced mitochondrial dysfunction is observed as impaired state 3 respiration and overproduction of O2-. The cascading ROS can propagate cysteine oxidation on mitochondrial complex I and add insult to injury. Herein we employed LC-MS/MS to identify protein sulfonation of complex I in mitochondria from the infarct region of rat hearts subjected to 30-min of coronary ligation and 24-h of reperfusion in vivo as well as the mitochondria of sham controls. Mitochondrial preparations from the I/R regions had enhanced sulfonation levels on the cysteine ligands of iron‑sulfur clusters, including N3 (C425), N1b (C92), N4 (C226), N2 (C158/C188), and N1a (C134/C139). The 4Fe-4S centers of N3, N1b, N4, and N2 are key redox-active components of complex I, thus sulfonation of metal-binding sites impaired the main electron transfer pathway. The binuclear N1a has a very low redox potential and an antioxidative function. Increased C134/C139 sulfonation by I/R impaired the N1a cluster, potentially contributing to overall O2- generation by the FMN moiety of complex I. MS analysis also revealed I/R-mediated increased sulfonation at the core subunits of 51 kDa (C125, C187, C206, C238, C255, C286), 75 kDa (C367, C554, C564, C727), 49 kDa (C146, C326, C347), and PSST (C188). These results were consistent with the consensus indicating that 51 kDa and 75 kDa are two of major subunits hosting regulatory thiols, and their enhanced sulfonation by I/R predisposed the myocardium to further oxidant stress with impaired ubiquinone reduction. MS analysis further showed I/R-mediated enhanced sulfonation at the supernumerary subunits of 42 kDa (C67, C112, C183, C253), 15 kDa (C43), and 13 kDa (C79). The 42 kDa protein is metazoan-specific, which was reported to stabilize mammalian complex I. C43 of the 15 kDa subunit forms an intramolecular disulfide bond with C56, which was reported to stabilize complex I structure. C79 of the 13 kDa subunit is involved in Zn2+-binding, which was reported functionally important for complex I assembly. C79 sulfonation by I/R was found to impair Zn2+-binding. No significant enhancement of protein sulfonation was observed in mitochondrial complex I from the rat heart subjected to 30-min ischemia alone in vivo despite a decreased state 3 respiration, suggesting that the physiologic conditions of hyperoxygenation during reperfusion mediated an increase in complex I sulfonation and oxidative injury. In conclusion, sulfonation of specific cysteines of complex I mediates I/R-induced mitochondrial dysfunction via impaired ETC activity, increasing •O2- production, and mediating redox dysfunction of complex I.
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299
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Assembly of mammalian oxidative phosphorylation complexes I-V and supercomplexes. Essays Biochem 2018; 62:255-270. [PMID: 30030361 PMCID: PMC6056720 DOI: 10.1042/ebc20170098] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 01/30/2023]
Abstract
The assembly of the five oxidative phosphorylation system (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process. The human enzymes comprise core proteins, performing the catalytic activities, and a large number of ‘supernumerary’ subunits that play essential roles in assembly, regulation and stability. The correct addition of prosthetic groups as well as chaperoning and incorporation of the structural components require a large number of factors, many of which have been found mutated in cases of mitochondrial disease. Nowadays, the mechanisms of assembly for each of the individual complexes are almost completely understood and the knowledge about the assembly factors involved is constantly increasing. On the other hand, it is now well established that complexes I, III and IV interact with each other, forming the so-called respiratory supercomplexes or ‘respirasomes’, although the pathways that lead to their formation are still not completely clear. This review is a summary of our current knowledge concerning the assembly of complexes I–V and of the supercomplexes.
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300
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Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nat Ecol Evol 2018; 2:1258-1267. [DOI: 10.1038/s41559-018-0606-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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