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von Känel C, Oeljeklaus S, Wenger C, Stettler P, Harsman A, Warscheid B, Schneider A. Intermembrane space-localized TbTim15 is an essential subunit of the single mitochondrial inner membrane protein translocase of trypanosomes. Mol Microbiol 2024; 121:1112-1126. [PMID: 38622999 DOI: 10.1111/mmi.15262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
All mitochondria import >95% of their proteins from the cytosol. This process is mediated by protein translocases in the mitochondrial membranes, whose subunits are generally highly conserved. Most eukaryotes have two inner membrane protein translocases (TIMs) that are specialized to import either presequence-containing or mitochondrial carrier proteins. In contrast, the parasitic protozoan Trypanosoma brucei has a single TIM complex consisting of one conserved and five unique subunits. Here, we identify candidates for new subunits of the TIM or the presequence translocase-associated motor (PAM) using a protein-protein interaction network of previously characterized TIM and PAM subunits. This analysis reveals that the trypanosomal TIM complex contains an additional trypanosomatid-specific subunit, designated TbTim15. TbTim15 is associated with the TIM complex, lacks transmembrane domains, and localizes to the intermembrane space. TbTim15 is essential for procyclic and bloodstream forms of trypanosomes. It contains two twin CX9C motifs and mediates import of both presequence-containing and mitochondrial carrier proteins. While the precise function of TbTim15 in mitochondrial protein import is unknown, our results are consistent with the notion that it may function as an import receptor for the non-canonical trypanosomal TIM complex.
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Affiliation(s)
- Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Philip Stettler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anke Harsman
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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2
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Povea-Cabello S, Brischigliaro M, Fernández-Vizarra E. Emerging mechanisms in the redox regulation of mitochondrial cytochrome c oxidase assembly and function. Biochem Soc Trans 2024; 52:873-885. [PMID: 38526156 DOI: 10.1042/bst20231183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
In eukaryotic cells, mitochondria perform cellular respiration through a series of redox reactions ultimately reducing molecular oxygen to water. The system responsible for this process is the respiratory chain or electron transport system (ETS) composed of complexes I-IV. Due to its function, the ETS is the main source of reactive oxygen species (ROS), generating them on both sides of the mitochondrial inner membrane, i.e. the intermembrane space (IMS) and the matrix. A correct balance between ROS generation and scavenging is important for keeping the cellular redox homeostasis and other important aspects of cellular physiology. However, ROS generated in the mitochondria are important signaling molecules regulating mitochondrial biogenesis and function. The IMS contains a large number of redox sensing proteins, containing specific Cys-rich domains, that are involved in ETS complex biogenesis. The large majority of these proteins function as cytochrome c oxidase (COX) assembly factors, mainly for the handling of copper ions necessary for the formation of the redox reactive catalytic centers. A particular case of ROS-regulated COX assembly factor is COA8, whose intramitochondrial levels are increased by oxidative stress, promoting COX assembly and/or protecting the enzyme from oxidative damage. In this review, we will discuss the current knowledge concerning the role played by ROS in regulating mitochondrial activity and biogenesis, focusing on the COX enzyme and with a special emphasis on the functional role exerted by the redox sensitive Cys residues contained in the COX assembly factors.
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Affiliation(s)
- Suleva Povea-Cabello
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Michele Brischigliaro
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Erika Fernández-Vizarra
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
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3
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Drekolia MK, Karantanou C, Wittig I, Li Y, Fuhrmann DC, Brüne B, Katsouda A, Hu J, Papapetropoulos A, Bibli SI. Loss of cardiac mitochondrial complex I persulfidation impairs NAD + homeostasis in aging. Redox Biol 2024; 69:103014. [PMID: 38171255 PMCID: PMC10792955 DOI: 10.1016/j.redox.2023.103014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024] Open
Abstract
Protein persulfidation is a significant post-translational modification that involves addition of a sulfur atom to the cysteine thiol group and is facilitated by sulfide species. Persulfidation targets reactive cysteine residues within proteins, influencing their structure and/or function across various biological systems. This modification is evolutionarily conserved and plays a crucial role in preventing irreversible cysteine overoxidation, a process that becomes prominent with aging. While, persulfidation decreases with age, its levels in the aged heart and the functional implications of such a reduction in cardiac metabolism remain unknown. Here we interrogated the cardiac persulfydome in wild-type adult mice and age-matched mice lacking the two sulfide generating enzymes, namely cystathionine gamma lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (3MST). Our findings revealed that cardiac persulfidated proteins in wild type hearts are less abundant compared to those in other organs, with a primary involvement in mitochondrial metabolic processes. We further focused on one specific target, NDUFB7, which undergoes persulfidation by both CSE and 3MST derived sulfide species. In particular, persulfidation of cysteines C80 and C90 in NDUFB7 protects the protein from overoxidation and maintains the complex I activity in cardiomyocytes. As the heart ages, the levels of CSE and 3MST in cardiomyocytes decline, leading to reduced NDUFB7 persulfidation and increased cardiac NADH/NAD+ ratio. Collectively, our data provide compelling evidence for a direct link between cardiac persulfidation and mitochondrial complex I activity, which is compromised in aging.
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Affiliation(s)
- Maria-Kyriaki Drekolia
- Department of Vascular Dysfunction, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt Am Main, Germany
| | - Christina Karantanou
- Department of Vascular Dysfunction, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt Am Main, Germany
| | - Ilka Wittig
- Institute for Cardiovascular Physiology, Goethe-University Frankfurt, Germany
| | - Yuanyuan Li
- Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dominik C Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Antonia Katsouda
- Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Laboratory of Pharmacology, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Jiong Hu
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt Am Main, Germany; Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Andreas Papapetropoulos
- Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Laboratory of Pharmacology, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece.
| | - Sofia-Iris Bibli
- Department of Vascular Dysfunction, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt Am Main, Germany; German Center of Cardiovascular Research (DZHK), Germany.
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4
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Xiang H, Tang H, He Q, Sun J, Yang Y, Kong L, Wang Y. NDUFA8 is transcriptionally regulated by EP300/H3K27ac and promotes mitochondrial respiration to support proliferation and inhibit apoptosis in cervical cancer. Biochem Biophys Res Commun 2024; 693:149374. [PMID: 38096616 DOI: 10.1016/j.bbrc.2023.149374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Cervical cancer, a common malignancy in women, poses a significant health burden worldwide. In this study, we aimed to investigate the expression, function, and potential mechanisms of NADH: ubiquinone oxidoreductase subunit A8 (NDUFA8) in cervical cancer. The Gene Expression Profiling Interactive Analysis (GEPIA) database and immunohistochemical scoring were used to analyze NDUFA8 expression in cervical cancer tissues and normal tissues. Quantitative real-time PCR and Western blot analyses were performed to assess the expression level of NDUFA8 in cervical cancer cell lines. NDUFA8 knockdown or overexpression experiments were conducted to evaluate its impact on cell proliferation and apoptosis. The mitochondrial respiratory status was analyzed by measuring cellular oxygen consumption, adenosine triphosphate (ATP) levels, and the expression levels of Mitochondrial Complex I activity, and Mitochondrial Complex IV-associated proteins Cytochrome C Oxidase Subunit 5B (COX5B) and COX6C. NDUFA8 exhibited high expression levels in cervical cancer tissues, and these levels were correlated with reduced survival rates. A significant upregulation of NDUFA8 expression was observed in cervical cancer cell lines compared to normal cells. Silencing NDUFA8 hindered cell proliferation, promoted apoptosis, and concurrently suppressed cellular mitochondrial respiration, resulting in decreased levels of available ATP. Conversely, NDUFA8 overexpression induced the opposite effects. Herein, we also found that E1A Binding Protein P300 (EP300) overexpression facilitated Histone H3 Lysine 27 (H3K27) acetylation enrichment, enhancing the activity of the NDUFA8 promoter region. NDUFA8, which is highly expressed in cervical cancer, is regulated by transcriptional control via EP300/H3K27 acetylation. By promoting mitochondrial respiration, NDUFA8 contributes to cervical cancer cell proliferation and apoptosis. These findings provide novel insights into NDUFA8 as a therapeutic target in cervical cancer.
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Affiliation(s)
- Huaguo Xiang
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China.
| | - Hongping Tang
- Department of Pathology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, 518028, China
| | - Qingqing He
- Department of Clinical Laboratory, The Second People's Hospital of Shenzhen, Shenzhen, 518025, China
| | - Junfang Sun
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
| | - Yihui Yang
- Department of Pathology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, 518028, China
| | - Lingyue Kong
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
| | - Yingzhen Wang
- Department of Clinical Laboratory, Fuyong People's Hospital of Baoan District, Shenzhen, 518103, China
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5
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Harada H, Moriya K, Kobuchi H, Ishihara N, Utsumi T. Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7. Sci Rep 2023; 13:22991. [PMID: 38151566 PMCID: PMC10752898 DOI: 10.1038/s41598-023-50390-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023] Open
Abstract
The present study examined human N-myristoylated proteins that specifically localize to mitochondria among the 1,705 human genes listed in MitoProteome, a mitochondrial protein database. We herein employed a strategy utilizing cellular metabolic labeling with a bioorthogonal myristic acid analog in transfected COS-1 cells established in our previous studies. Four proteins, DMAC1, HCCS, NDUFB7, and PLGRKT, were identified as N-myristoylated proteins that specifically localize to mitochondria. Among these proteins, DMAC1 and NDUFB7 play critical roles in the assembly of complex I of the mitochondrial respiratory chain. DMAC1 functions as an assembly factor, and NDUFB7 is an accessory subunit of complex I. An analysis of the intracellular localization of non-myristoylatable G2A mutants revealed that protein N-myristoylation occurring on NDUFB7 was important for the mitochondrial localization of this protein. Furthermore, an analysis of the role of the CHCH domain in NDUFB7 using Cys to Ser mutants revealed that it was essential for the mitochondrial localization of NDUFB7. Therefore, the present results showed that NDUFB7, a vital component of human mitochondrial complex I, was N-myristoylated, and protein N-myrisotylation and the CHCH domain were both indispensable for the specific targeting and localization of NDUFB7 to mitochondria.
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Affiliation(s)
- Haruna Harada
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Koko Moriya
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Hirotsugu Kobuchi
- Department of Cell Chemistry, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Naotada Ishihara
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Toshihiko Utsumi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan.
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan.
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6
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Zigo M, Kerns K, Sutovsky P. The Ubiquitin-Proteasome System Participates in Sperm Surface Subproteome Remodeling during Boar Sperm Capacitation. Biomolecules 2023; 13:996. [PMID: 37371576 DOI: 10.3390/biom13060996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Sperm capacitation is a complex process endowing biological and biochemical changes to a spermatozoon for a successful encounter with an oocyte. The present study focused on the role of the ubiquitin-proteasome system (UPS) in the remodeling of the sperm surface subproteome. The sperm surface subproteome from non-capacitated and in vitro capacitated (IVC) porcine spermatozoa, with and without proteasomal inhibition, was selectively isolated. The purified sperm surface subproteome was analyzed using high-resolution, quantitative liquid chromatography-mass spectrometry (LC-MS) in four replicates. We identified 1680 HUGO annotated proteins, out of which we found 91 to be at least 1.5× less abundant (p < 0.05) and 141 to be at least 1.5× more abundant (p < 0.05) on the surface of IVC spermatozoa. These proteins were associated with sperm capacitation, hyperactivation, metabolism, acrosomal exocytosis, and fertilization. Abundances of 14 proteins were found to be significantly different (p < 0.05), exceeding a 1.5-fold abundance between the proteasomally inhibited (100 µM MG132) and vehicle control (0.2% ethanol) groups. The proteins NIF3L1, CSE1L, NDUFB7, PGLS, PPP4C, STK39, and TPRG1L were found to be more abundant; while BPHL, GSN, GSPT1, PFDN4, STYXL1, TIMM10, and UBXN4 were found to be less abundant in proteasomally inhibited IVC spermatozoa. Despite the UPS having a narrow range of targets, it modulated sperm metabolism and binding by regulating susceptible surface proteins. Changes in CSE1L, PFDN4, and STK39 during in vitro capacitation were confirmed using immunocytochemistry, image-based flow cytometry, and Western blotting. The results confirmed the active participation of the UPS in the extensive sperm surface proteome remodeling that occurs during boar sperm capacitation. This work will help us to identify new pharmacological mechanisms to positively or negatively modulate sperm fertilizing ability in food animals and humans.
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Affiliation(s)
- Michal Zigo
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
| | - Karl Kerns
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Peter Sutovsky
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO 65211, USA
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7
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Kisty EA, Saart EC, Weerapana E. Identifying Redox-Sensitive Cysteine Residues in Mitochondria. Antioxidants (Basel) 2023; 12:992. [PMID: 37237858 PMCID: PMC10215197 DOI: 10.3390/antiox12050992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The mitochondrion is the primary energy generator of a cell and is a central player in cellular redox regulation. Mitochondrial reactive oxygen species (mtROS) are the natural byproducts of cellular respiration that are critical for the redox signaling events that regulate a cell's metabolism. These redox signaling pathways primarily rely on the reversible oxidation of the cysteine residues on mitochondrial proteins. Several key sites of this cysteine oxidation on mitochondrial proteins have been identified and shown to modulate downstream signaling pathways. To further our understanding of mitochondrial cysteine oxidation and to identify uncharacterized redox-sensitive cysteines, we coupled mitochondrial enrichment with redox proteomics. Briefly, differential centrifugation methods were used to enrich for mitochondria. These purified mitochondria were subjected to both exogenous and endogenous ROS treatments and analyzed by two redox proteomics methods. A competitive cysteine-reactive profiling strategy, termed isoTOP-ABPP, enabled the ranking of the cysteines by their redox sensitivity, due to a loss of reactivity induced by cysteine oxidation. A modified OxICAT method enabled a quantification of the percentage of reversible cysteine oxidation. Initially, we assessed the cysteine oxidation upon treatment with a range of exogenous hydrogen peroxide concentrations, which allowed us to differentiate the mitochondrial cysteines by their susceptibility to oxidation. We then analyzed the cysteine oxidation upon inducing reactive oxygen species generation via the inhibition of the electron transport chain. Together, these methods identified the mitochondrial cysteines that were sensitive to endogenous and exogenous ROS, including several previously known redox-regulated cysteines and uncharacterized cysteines on diverse mitochondrial proteins.
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8
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Lee JJ, Kang HJ, Kim SS, Charton C, Kim J, Lee JK. Unraveling the Transcriptomic Signatures of Homologous Recombination Deficiency in Ovarian Cancers. Adv Biol (Weinh) 2022; 6:e2200060. [PMID: 36116121 DOI: 10.1002/adbi.202200060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/03/2022] [Indexed: 01/28/2023]
Abstract
Homologous recombination deficiency (HRD) is a crucial driver of tumorigenesis by inducing impaired repair of double-stranded DNA breaks. Although HRD possibly triggers the production of numerous tumor neoantigens that sufficiently stimulate and activate various tumor-immune responses, a comprehensive understanding of the HRD-associated tumor microenvironment is elusive. To investigate the effect of HRD on the selective enrichment of transcriptomic signatures, 294 cases from The Cancer Genome Atlas-Ovarian Cancer project with both RNA-sequencing and SNP array data are analyzed. Differentially expressed gene analysis and network analysis are performed to identify HRD-specific signatures. Gene-sets associated with mitochondrial activation, including enhanced oxidative phosphorylation (OxPhos), are significantly enriched in the HRD-high group. Furthermore, a wide range of immune cell activation signatures is enriched in HRD-high cases of high-grade serous ovarian cancer (HGSOC). On further cell-type-specific analysis, M1-like macrophage genes are significantly enriched in HRD-high HGSOC cases, whereas M2-macrophage-related genes are not. The immune-response-associated genomic features, including tumor mutation rate, neoantigens, and tumor mutation burdens, correlated with HRD scores. In conclusion, the results of this study highlight the biological properties of HRD, including enhanced energy metabolism, increased tumor neoantigens and tumor mutation burdens, and consequent exacerbation of immune responses, particularly the enrichment of M1-like macrophages in HGSOC cases.
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Affiliation(s)
- Jae Jun Lee
- Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Hyun Ju Kang
- Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Stephanie S Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Clémentine Charton
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Jinho Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Jin-Ku Lee
- Medical Research Center, Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
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9
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Salscheider SL, Gerlich S, Cabrera-Orefice A, Peker E, Rothemann RA, Murschall LM, Finger Y, Szczepanowska K, Ahmadi ZA, Guerrero-Castillo S, Erdogan A, Becker M, Ali M, Habich M, Petrungaro C, Burdina N, Schwarz G, Klußmann M, Neundorf I, Stroud DA, Ryan MT, Trifunovic A, Brandt U, Riemer J. AIFM1 is a component of the mitochondrial disulfide relay that drives complex I assembly through efficient import of NDUFS5. EMBO J 2022; 41:e110784. [PMID: 35859387 PMCID: PMC9434101 DOI: 10.15252/embj.2022110784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022] Open
Abstract
The mitochondrial intermembrane space protein AIFM1 has been reported to mediate the import of MIA40/CHCHD4, which forms the import receptor in the mitochondrial disulfide relay. Here, we demonstrate that AIFM1 and MIA40/CHCHD4 cooperate beyond this MIA40/CHCHD4 import. We show that AIFM1 and MIA40/CHCHD4 form a stable long‐lived complex in vitro, in different cell lines, and in tissues. In HEK293 cells lacking AIFM1, levels of MIA40 are unchanged, but the protein is present in the monomeric form. Monomeric MIA40 neither efficiently interacts with nor mediates the import of specific substrates. The import defect is especially severe for NDUFS5, a subunit of complex I of the respiratory chain. As a consequence, NDUFS5 accumulates in the cytosol and undergoes rapid proteasomal degradation. Lack of mitochondrial NDUFS5 in turn results in stalling of complex I assembly. Collectively, we demonstrate that AIFM1 serves two overlapping functions: importing MIA40/CHCHD4 and constituting an integral part of the disulfide relay that ensures efficient interaction of MIA40/CHCHD4 with specific substrates.
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Affiliation(s)
| | - Sarah Gerlich
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Esra Peker
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | | | | | - Yannik Finger
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Karolina Szczepanowska
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Zeinab Alsadat Ahmadi
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alican Erdogan
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Mark Becker
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Muna Ali
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Markus Habich
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | | | - Nele Burdina
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Institute for Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Merlin Klußmann
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Ines Neundorf
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Aleksandra Trifunovic
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jan Riemer
- Institute for Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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10
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Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
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Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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11
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Short AK, Thai CW, Chen Y, Kamei N, Pham AL, Birnie MT, Bolton JL, Mortazavi A, Baram TZ. Single-Cell Transcriptional Changes in Hypothalamic Corticotropin-Releasing Factor-Expressing Neurons After Early-Life Adversity Inform Enduring Alterations in Vulnerabilities to Stress. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 3:99-109. [PMID: 36712559 PMCID: PMC9874075 DOI: 10.1016/j.bpsgos.2021.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Mental health and vulnerabilities to neuropsychiatric disorders involve the interplay of genes and environment, particularly during sensitive developmental periods. Early-life adversity (ELA) and stress promote vulnerabilities to stress-related affective disorders, yet it is unknown how transient ELA dictates lifelong neuroendocrine and behavioral reactions to stress. The population of hypothalamic corticotropin-releasing factor (CRF)-expressing neurons that regulate stress responses is a promising candidate to mediate the long-lasting influences of ELA on stress-related behavioral and hormonal responses via enduring transcriptional and epigenetic mechanisms. Methods Capitalizing on a well-characterized model of ELA, we examined ELA-induced changes in gene expression profiles of CRF-expressing neurons in the hypothalamic paraventricular nucleus of developing male mice. We used single-cell RNA sequencing on isolated CRF-expressing neurons. We determined the enduring functional consequences of transcriptional changes on stress reactivity in adult ELA mice, including hormonal responses to acute stress, adrenal weights as a measure of chronic stress, and behaviors in the looming shadow threat task. Results Single-cell transcriptomics identified distinct and novel CRF-expressing neuronal populations, characterized by both their gene expression repertoire and their neurotransmitter profiles. ELA-provoked expression changes were selective to specific subpopulations and affected genes involved in neuronal differentiation, synapse formation, energy metabolism, and cellular responses to stress and injury. Importantly, these expression changes were impactful, apparent from adrenal hypertrophy and augmented behavioral responses to stress in adulthood. Conclusions We uncover a novel repertoire of stress-regulating CRF cell types differentially affected by ELA and resulting in augmented stress vulnerability, with relevance to the origins of stress-related affective disorders.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Christina W. Thai
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California
| | - Yuncai Chen
- Department of Pediatrics, University of California Irvine, Irvine, California
| | - Noriko Kamei
- Department of Pediatrics, University of California Irvine, Irvine, California
| | - Aidan L. Pham
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Matthew T. Birnie
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Jessica L. Bolton
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California,Department of Neurology, University of California Irvine, Irvine, California,Address correspondence to Tallie Z. Baram, M.D., Ph.D.
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12
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Geldon S, Fernández-Vizarra E, Tokatlidis K. Redox-Mediated Regulation of Mitochondrial Biogenesis, Dynamics, and Respiratory Chain Assembly in Yeast and Human Cells. Front Cell Dev Biol 2021; 9:720656. [PMID: 34557489 PMCID: PMC8452992 DOI: 10.3389/fcell.2021.720656] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022] Open
Abstract
Mitochondria are double-membrane organelles that contain their own genome, the mitochondrial DNA (mtDNA), and reminiscent of its endosymbiotic origin. Mitochondria are responsible for cellular respiration via the function of the electron oxidative phosphorylation system (OXPHOS), located in the mitochondrial inner membrane and composed of the four electron transport chain (ETC) enzymes (complexes I-IV), and the ATP synthase (complex V). Even though the mtDNA encodes essential OXPHOS components, the large majority of the structural subunits and additional biogenetical factors (more than seventy proteins) are encoded in the nucleus and translated in the cytoplasm. To incorporate these proteins and the rest of the mitochondrial proteome, mitochondria have evolved varied, and sophisticated import machineries that specifically target proteins to the different compartments defined by the two membranes. The intermembrane space (IMS) contains a high number of cysteine-rich proteins, which are mostly imported via the MIA40 oxidative folding system, dependent on the reduction, and oxidation of key Cys residues. Several of these proteins are structural components or assembly factors necessary for the correct maturation and function of the ETC complexes. Interestingly, many of these proteins are involved in the metalation of the active redox centers of complex IV, the terminal oxidase of the mitochondrial ETC. Due to their function in oxygen reduction, mitochondria are the main generators of reactive oxygen species (ROS), on both sides of the inner membrane, i.e., in the matrix and the IMS. ROS generation is important due to their role as signaling molecules, but an excessive production is detrimental due to unwanted oxidation reactions that impact on the function of different types of biomolecules contained in mitochondria. Therefore, the maintenance of the redox balance in the IMS is essential for mitochondrial function. In this review, we will discuss the role that redox regulation plays in the maintenance of IMS homeostasis as well as how mitochondrial ROS generation may be a key regulatory factor for ETC biogenesis, especially for complex IV.
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Affiliation(s)
| | - Erika Fernández-Vizarra
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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13
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Li M, Tian X, Li X, Huang M, Huang S, Wu Y, Jiang M, Shi Y, Shi L, Wang Z. Diverse energy metabolism patterns in females in Neodon fuscus, Lasiopodomys brandtii, and Mus musculus revealed by comparative transcriptomics under hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147130. [PMID: 34088150 DOI: 10.1016/j.scitotenv.2021.147130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
The effects of global warming and anthropogenic disturbance force animals to migrate from lower to higher elevations to find suitable new habitats. As such migrations increase hypoxic stress on the animals, it is important to understand how plateau- and plain-dwelling animals respond to low-oxygen environments. We used comparative transcriptomics to explore the response of Neodon fuscus, Lasiopodomys brandtii, and Mus musculus skeletal muscle tissues to hypoxic conditions. Results indicate that these species have adopted different oxygen transport and energy metabolism strategies for dealing with a hypoxic environment. N. fuscus promotes oxygen transport by increasing hemoglobin synthesis and reduces the risk of thrombosis through cooperative regulation of genes, including Fga, Fgb, Alb, and Ttr; genes such as Acs16, Gpat4, and Ndufb7 are involved in regulating lipid synthesis, fatty acid β-oxidation, hemoglobin synthesis, and electron-linked transmission, thereby maintaining a normal energy supply in hypoxic conditions. In contrast, the oxygen-carrying capacity and angiogenesis of red blood cells in L. brandtii are promoted by genes in the CYP and COL families; this species maintains its bodily energy supply by enhancing the pentose phosphate pathway and mitochondrial fatty acid synthesis pathway. However, under hypoxia, M. musculus cannot effectively transport additional oxygen; thus, its cell cycle, proliferation, and migration are somewhat affected. Given its lack of hypoxic tolerance experience, M. musculus also shows significantly reduced oxidative phosphorylation levels under hypoxic conditions. Our results suggest that the glucose capacity of M. musculus skeletal muscle does not provide sufficient energy during hypoxia; thus, we hypothesize that it supplements its bodily energy by synthesizing ketone bodies. For the first time, we describe the energy metabolism pathways of N. fuscus and L. brandtii skeletal muscle tissues under hypoxic conditions. Our findings, therefore, improve our understanding of how vertebrates thrive in high altitude and plain habitats when faced with hypoxic conditions.
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Affiliation(s)
- Mengyang Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shuang Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Mengwan Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; School of Physical Education (Main campus), Zhengzhou University, Zhengzhou 450001, Henan, China.
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14
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Needs HI, Protasoni M, Henley JM, Prudent J, Collinson I, Pereira GC. Interplay between Mitochondrial Protein Import and Respiratory Complexes Assembly in Neuronal Health and Degeneration. Life (Basel) 2021; 11:432. [PMID: 34064758 PMCID: PMC8151517 DOI: 10.3390/life11050432] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
The fact that >99% of mitochondrial proteins are encoded by the nuclear genome and synthesised in the cytosol renders the process of mitochondrial protein import fundamental for normal organelle physiology. In addition to this, the nuclear genome comprises most of the proteins required for respiratory complex assembly and function. This means that without fully functional protein import, mitochondrial respiration will be defective, and the major cellular ATP source depleted. When mitochondrial protein import is impaired, a number of stress response pathways are activated in order to overcome the dysfunction and restore mitochondrial and cellular proteostasis. However, prolonged impaired mitochondrial protein import and subsequent defective respiratory chain function contributes to a number of diseases including primary mitochondrial diseases and neurodegeneration. This review focuses on how the processes of mitochondrial protein translocation and respiratory complex assembly and function are interlinked, how they are regulated, and their importance in health and disease.
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Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Margherita Protasoni
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Julien Prudent
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Gonçalo C. Pereira
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
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15
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Correia SP, Moedas MF, Naess K, Bruhn H, Maffezzini C, Calvo-Garrido J, Lesko N, Wibom R, Schober FA, Jemt A, Stranneheim H, Freyer C, Wedell A, Wredenberg A. Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7. Hum Mutat 2021; 42:378-384. [PMID: 33502047 DOI: 10.1002/humu.24173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/18/2020] [Accepted: 01/24/2021] [Indexed: 01/18/2023]
Abstract
Mutations in structural subunits and assembly factors of complex I of the oxidative phosphorylation system constitute the most common cause of mitochondrial respiratory chain defects. Such mutations can present a wide range of clinical manifestations, varying from mild deficiencies to severe, lethal disorders. We describe a patient presenting intrauterine growth restriction and anemia, which displayed postpartum hypertrophic cardiomyopathy, lactic acidosis, encephalopathy, and a severe complex I defect with fatal outcome. Whole genome sequencing revealed an intronic biallelic mutation in the NDUFB7 gene (c.113-10C>G) and splicing pattern alterations in NDUFB7 messenger RNA were confirmed by RNA Sequencing. The detected variant resulted in a significant reduction of the NDUFB7 protein and reduced complex I activity. Complementation studies with expression of wild-type NDUFB7 in patient fibroblasts normalized complex I function. Here we report a case with a primary complex I defect due to a homozygous mutation in an intron region of the NDUFB7 gene.
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Affiliation(s)
- Sandrina P Correia
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Marco F Moedas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helene Bruhn
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Javier Calvo-Garrido
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Lesko
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florian A Schober
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anders Jemt
- Department of Microbiology, Tumour and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Christoph Freyer
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wredenberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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16
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Tort F, Barredo E, Parthasarathy R, Ugarteburu O, Ferrer-Cortès X, García-Villoria J, Gort L, González-Quintana A, Martín MA, Fernández-Vizarra E, Zeviani M, Ribes A. Biallelic mutations in NDUFA8 cause complex I deficiency in two siblings with favorable clinical evolution. Mol Genet Metab 2020; 131:349-357. [PMID: 33153867 DOI: 10.1016/j.ymgme.2020.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023]
Abstract
Isolated complex I (CI) deficiency is the most common cause of oxidative phosphorylation (OXPHOS) dysfunction. Whole-exome sequencing identified biallelic mutations in NDUFA8 (c.[293G > T]; [293G > T], encoding for an accessory subunit of CI, in two siblings with a favorable clinical evolution. The individuals reported here are practically asymptomatic, with the exception of slight failure to thrive and some language difficulties at the age of 6 and 9 years, respectively. These observations are remarkable since the vast majority of patients with CI deficiency, including the only NDUFA8 patient reported so far, showed an extremely poor clinical outcome. Western blot studies demonstrated that NDUFA8 protein was strongly reduced in the patients' fibroblasts and muscle extracts. In addition, there was a marked and specific decrease in the steady-state levels of CI subunits. BN-PAGE demonstrated an isolated defect in the assembly and the activity of CI with impaired supercomplexes formation and abnormal accumulation of CI subassemblies. Confocal microscopy analysis in fibroblasts showed rounder mitochondria and diminished branching degree of the mitochondrial network. Functional complementation studies demonstrated disease-causality for the identified mutation as lentiviral transduction with wild-type NDUFA8 cDNA restored the steady-state levels of CI subunits and completely recovered the deficient enzymatic activity in immortalized mutant fibroblasts. In summary, we provide additional evidence of the involvement of NDUFA8 as a mitochondrial disease-causing gene associated with altered mitochondrial morphology, CI deficiency, impaired supercomplexes formation, and very mild progression of the disease.
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Affiliation(s)
- Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | | | | | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Xenia Ferrer-Cortès
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Laura Gort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Adrián González-Quintana
- Laboratorio de Enfermedades Mitocondriales, Servicio de Bioquímica, Instituto de Investigación Hospital, 12 de Octubre (imas12), CIBERER, Madrid, Spain
| | - Miguel A Martín
- Laboratorio de Enfermedades Mitocondriales, Servicio de Bioquímica, Instituto de Investigación Hospital, 12 de Octubre (imas12), CIBERER, Madrid, Spain
| | | | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain.
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17
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Cupo RR, Shorter J. Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. eLife 2020; 9:e55279. [PMID: 32573439 PMCID: PMC7343390 DOI: 10.7554/elife.55279] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Cells have evolved specialized protein disaggregases to reverse toxic protein aggregation and restore protein functionality. In nonmetazoan eukaryotes, the AAA+ disaggregase Hsp78 resolubilizes and reactivates proteins in mitochondria. Curiously, metazoa lack Hsp78. Hence, whether metazoan mitochondria reactivate aggregated proteins is unknown. Here, we establish that a mitochondrial AAA+ protein, Skd3 (human ClpB), couples ATP hydrolysis to protein disaggregation and reactivation. The Skd3 ankyrin-repeat domain combines with conserved AAA+ elements to enable stand-alone disaggregase activity. A mitochondrial inner-membrane protease, PARL, removes an autoinhibitory peptide from Skd3 to greatly enhance disaggregase activity. Indeed, PARL-activated Skd3 solubilizes α-synuclein fibrils connected to Parkinson's disease. Human cells lacking Skd3 exhibit reduced solubility of various mitochondrial proteins, including anti-apoptotic Hax1. Importantly, Skd3 variants linked to 3-methylglutaconic aciduria, a severe mitochondrial disorder, display diminished disaggregase activity (but not always reduced ATPase activity), which predicts disease severity. Thus, Skd3 is a potent protein disaggregase critical for human health.
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Affiliation(s)
- Ryan R Cupo
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
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18
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Yatsuka Y, Kishita Y, Formosa LE, Shimura M, Nozaki F, Fujii T, Nitta KR, Ohtake A, Murayama K, Ryan MT, Okazaki Y. A homozygous variant in NDUFA8 is associated with developmental delay, microcephaly, and epilepsy due to mitochondrial complex I deficiency. Clin Genet 2020; 98:155-165. [PMID: 32385911 DOI: 10.1111/cge.13773] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial complex I deficiency is caused by pathogenic variants in mitochondrial and nuclear genes associated with complex I structure and assembly. We report the case of a patient with NDUFA8-related mitochondrial disease. The patient presented with developmental delay, microcephaly, and epilepsy. His fibroblasts showed apparent biochemical defects in mitochondrial complex I. Whole-exome sequencing revealed that the patient carried a homozygous variant in NDUFA8. His fibroblasts showed a reduction in the protein expression level of not only NDUFA8, but also the other complex I subunits, consistent with assembly defects. The enzyme activity of complex I and oxygen consumption rate were restored by reintroducing wild-typeNDUFA8 cDNA into patient fibroblasts. The functional properties of the variant in NDUFA8 were also investigated using NDUFA8 knockout cells expressing wild-type or mutated NDUFA8 cDNA. These experiments further supported the pathogenicity of the variant in complex I assembly. This is the first report describing that the loss of NDUFA8, which has not previously been associated with mitochondrial disease, causes severe defect in the assembly of mitochondrial complex I, leading to progressive neurological and developmental abnormalities.
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Affiliation(s)
- Yukiko Yatsuka
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yoshihito Kishita
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Fumihito Nozaki
- Department of Pediatrics, Shiga Medical Center for Children, Moriyama, Japan
| | - Tatsuya Fujii
- Department of Pediatrics, Shiga Medical Center for Children, Moriyama, Japan
| | - Kazuhiro R Nitta
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Akira Ohtake
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan.,Department of Pediatrics and Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yasushi Okazaki
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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19
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AIF meets the CHCHD4/Mia40-dependent mitochondrial import pathway. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165746. [PMID: 32105825 DOI: 10.1016/j.bbadis.2020.165746] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023]
Abstract
In the mitochondria of healthy cells, Apoptosis-Inducing factor (AIF) is required for the optimal functioning of the respiratory chain machinery, mitochondrial integrity, cell survival, and proliferation. In all analysed species, it was revealed that the downregulation or depletion of AIF provokes mainly the post-transcriptional loss of respiratory chain Complex I protein subunits. Recent progress in the field has revealed that AIF fulfils its mitochondrial pro-survival function by interacting physically and functionally with CHCHD4, the evolutionarily-conserved human homolog of yeast Mia40. The redox-regulated CHCHD4/Mia40-dependent import machinery operates in the intermembrane space of the mitochondrion and controls the import of a set of nuclear-encoded cysteine-motif carrying protein substrates. In addition to their participation in the biogenesis of specific respiratory chain protein subunits, CHCHD4/Mia40 substrates are also implicated in the control of redox regulation, antioxidant response, translation, lipid homeostasis and mitochondrial ultrastructure and dynamics. Here, we discuss recent insights on the AIF/CHCHD4-dependent protein import pathway and review current data concerning the CHCHD4/Mia40 protein substrates in metazoan. Recent findings and the identification of disease-associated mutations in AIF or in specific CHCHD4/Mia40 substrates have highlighted these proteins as potential therapeutic targets in a variety of human disorders.
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20
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Subrahmanian N, Castonguay AD, Fatnes TA, Hamel PP. Chlamydomonas reinhardtii as a plant model system to study mitochondrial complex I dysfunction. PLANT DIRECT 2020; 4:e00200. [PMID: 32025618 PMCID: PMC6996877 DOI: 10.1002/pld3.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Mitochondrial complex I, a proton-pumping NADH: ubiquinone oxidoreductase, is required for oxidative phosphorylation. However, the contribution of several human mutations to complex I deficiency is poorly understood. The unicellular alga Chlamydomonas reinhardtii was utilized to study complex I as, unlike in mammals, mutants with complete loss of the holoenzyme are viable. From a forward genetic screen for complex I-deficient insertional mutants, six mutants exhibiting complex I deficiency with assembly defects were isolated. Chlamydomonas mutants isolated from our screens, lacking the subunits NDUFV2 and NDUFB10, were used to reconstruct and analyze the effect of two human mutations in these subunit-encoding genes. The K209R substitution in NDUFV2, reported in Parkinson's disease patients, did not significantly affect the enzyme activity or assembly. The C107S substitution in the NDUFB10 subunit, reported in a case of fatal infantile cardiomyopathy, is part of a conserved C-(X)11-C motif. The cysteine substitutions, at either one or both positions, still allowed low levels of holoenzyme formation, indicating that this motif is crucial for complex I function but not strictly essential for assembly. We show that the algal mutants provide a simple and useful platform to delineate the consequences of patient mutations on complex I function.
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Affiliation(s)
- Nitya Subrahmanian
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Plant Cellular and Molecular Biology Graduate ProgramThe Ohio State UniversityColumbusOHUSA
| | - Andrew David Castonguay
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Molecular Genetics Graduate ProgramThe Ohio State UniversityColumbusOHUSA
| | - Thea Aspelund Fatnes
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Present address:
Fürst Medical LaboratoryOsloNorway
| | - Patrice Paul Hamel
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Department of Biological Chemistry and PharmacologyThe Ohio State UniversityColumbusOHUSA
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Cerebral mitochondrial electron transport chain dysfunction in multiple system atrophy and Parkinson's disease. Sci Rep 2019; 9:6559. [PMID: 31024027 PMCID: PMC6484105 DOI: 10.1038/s41598-019-42902-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/25/2019] [Indexed: 11/08/2022] Open
Abstract
Multiple system atrophy (MSA) is a neurodegenerative disease characterised by glial cytoplasmic inclusions (GCIs), containing α-synuclein. Mutated COQ2, encoding an enzyme essential for co-enzyme Q10 (CoQ10) biosynthesis, has been associated with MSA. CoQ10 is an electron carrier in the mitochondrial electron transport chain (ETC) and antioxidant. It has been shown to be deficient in MSA brain tissue, thus implicating mitochondrial dysfunction in MSA. To investigate mitochondrial dysfunction in MSA further we examined ETC activity in MSA and control brain tissue, compared with Parkinson's disease (PD) where mitochondrial dysfunction is known to be important. Using cerebellar and occipital white matter ETC complex I, II/III and IV activities were measured spectrophotometrically, selected individual components of the ETC were assessed by immunoblotting and cellular complex IV activity was analysed by enzyme histochemistry. We show decreased complex II/III activity with increased complex I and IV activity in MSA cerebellar white matter. This corresponds with the deficit in CoQ10 previously described in MSA and reflects the high regional pathological burden of GCIs. This study highlights mitochondrial dysfunction in MSA pathogenesis, suggests an influence on selective regional vulnerability to disease and points to shared disease mechanisms in α-synucleinopathies.
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22
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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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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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Abstract
Mitochondria are the power stations of the eukaryotic cell, using the energy released by the oxidation of glucose and other sugars to produce ATP. Electrons are transferred from NADH, produced in the citric acid cycle in the mitochondrial matrix, to oxygen by a series of large protein complexes in the inner mitochondrial membrane, which create a transmembrane electrochemical gradient by pumping protons across the membrane. The flow of protons back into the matrix via a proton channel in the ATP synthase leads to conformational changes in the nucleotide binding pockets and the formation of ATP. The three proton pumping complexes of the electron transfer chain are NADH-ubiquinone oxidoreductase or complex I, ubiquinone-cytochrome c oxidoreductase or complex III, and cytochrome c oxidase or complex IV. Succinate dehydrogenase or complex II does not pump protons, but contributes reduced ubiquinone. The structures of complex II, III and IV were determined by x-ray crystallography several decades ago, but complex I and ATP synthase have only recently started to reveal their secrets by advances in x-ray crystallography and cryo-electron microscopy. The complexes I, III and IV occur to a certain extent as supercomplexes in the membrane, the so-called respirasomes. Several hypotheses exist about their function. Recent cryo-electron microscopy structures show the architecture of the respirasome with near-atomic detail. ATP synthase occurs as dimers in the inner mitochondrial membrane, which by their curvature are responsible for the folding of the membrane into cristae and thus for the huge increase in available surface that makes mitochondria the efficient energy plants of the eukaryotic cell.
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Affiliation(s)
- Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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25
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Severe riboflavin deficiency induces alterations in the hepatic proteome of starter Pekin ducks. Br J Nutr 2017; 118:641-650. [PMID: 29185933 DOI: 10.1017/s0007114517002641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Suboptimal vitamin B2 status is encountered globally. Riboflavin deficiency depresses growth and results in a fatty liver. The underlying mechanisms remain to be established and an overview of molecular alterations is lacking. We investigated hepatic proteome changes induced by riboflavin deficiency to explain its effects on growth and hepatic lipid metabolism. In all, 360 1-d-old Pekin ducks were divided into three groups of 120 birds each, with twelve replicates and ten birds per replicate. For 21 d, the ducks were fed ad libitum a control diet (CAL), a riboflavin-deficient diet (RD) or were pair-fed with the control diet to the mean daily intake of the RD group (CPF). When comparing RD with CAL and CPF, growth depression, liver enlargement, liver lipid accumulation and enhanced liver SFA (C6 : 0, C12 : 0, C16 : 0, C18 : 0) were observed. In RD, thirty-two proteins were enhanced and thirty-one diminished (>1·5-fold) compared with CAL and CPF. Selected proteins were confirmed by Western blotting. The diminished proteins are mainly involved in fatty acid β-oxidation and the mitochondrial electron transport chain (ETC), whereas the enhanced proteins are mainly involved in TAG and cholesterol biosynthesis. RD causes liver lipid accumulation and growth depression probably by impairing fatty acid β-oxidation and ETC. These findings contribute to our understanding of the mechanisms of liver lipid metabolic disorders due to RD.
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26
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Massoz S, Hanikenne M, Bailleul B, Coosemans N, Radoux M, Miranda-Astudillo H, Cardol P, Larosa V, Remacle C. In vivo chlorophyll fluorescence screening allows the isolation of a Chlamydomonas mutant defective for NDUFAF3, an assembly factor involved in mitochondrial complex I assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:584-595. [PMID: 28857403 DOI: 10.1111/tpj.13677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 05/16/2023]
Abstract
The qualitative screening method used to select complex I mutants in the microalga Chlamydomonas, based on reduced growth under heterotrophic conditions, is not suitable for high-throughput screening. In order to develop a fast screening method based on measurements of chlorophyll fluorescence, we first demonstrated that complex I mutants displayed decreased photosystem II efficiency in the genetic background of a photosynthetic mutation leading to reduced formation of the electrochemical proton gradient in the chloroplast (pgrl1 mutation). In contrast, single mutants (complex I and pgrl1 mutants) could not be distinguished from the wild type by their photosystem II efficiency under the conditions tested. We next performed insertional mutagenesis on the pgrl1 mutant. Out of about 3000 hygromycin-resistant insertional transformants, 46 had decreased photosystem II efficiency and three were complex I mutants. One of the mutants was tagged and whole genome sequencing identified the resistance cassette in NDUFAF3, a homolog of the human NDUFAF3 gene, encoding for an assembly factor involved in complex I assembly. Complemented strains showed restored complex I activity and assembly. Overall, we describe here a screening method which is fast and particularly suited for the identification of Chlamydomonas complex I mutants.
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Affiliation(s)
- Simon Massoz
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Marc Hanikenne
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- InBioS - Functional Genomics and Plant Molecular Imaging, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Benjamin Bailleul
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Nadine Coosemans
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Michèle Radoux
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Hector Miranda-Astudillo
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Pierre Cardol
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Véronique Larosa
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
| | - Claire Remacle
- InBioS - Genetics and Physiology of Microalgae, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
- PhytoSYSTEMS, Chemin de la vallée, 4, 4000 Liège, University of Liège, Belgium
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27
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Complementary transcriptomic and proteomic analyses reveal regulatory mechanisms of milk protein production in dairy cows consuming different forages. Sci Rep 2017; 7:44234. [PMID: 28290485 PMCID: PMC5349593 DOI: 10.1038/srep44234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 11/19/2022] Open
Abstract
Forage plays a critical role in the milk production of dairy cows; however, the mechanisms regulating bovine milk synthesis in dairy cows fed high forage rations with different basal forage types are not well-understood. In the study, rice straw (RS, low-quality) and alfalfa hay (AH, high-quality) diets were fed to lactating cows to explore how forage quality affected the molecular mechanisms regulating milk production using RNA-seq transcriptomic method with iTRAQ proteomic technique. A total of 554 transcripts (423 increased and 131 decreased) and 517 proteins (231 up-regulated and 286 down-regulated) were differentially expressed in the mammary glands of the two groups. The correlation analysis demonstrated seven proteins (six up-regulated and one down-regulated) had consistent mRNA expression. Functional analysis of the differentially expressed transcripts/proteins suggested that enhanced capacity for energy and fatty acid metabolism, increased protein degradation, reduced protein synthesis, decreased amino acid metabolism and depressed cell growth were related to RS consumption. The results indicated cows consuming RS diets may have had depressed milk protein synthesis because these animals had decreased capacity for protein synthesis, enhanced proteolysis, inefficient energy generation and reduced cell growth. Additional work evaluating RS- and AH-based rations may help better isolate molecular adaptations to low nutrient availability during lactation.
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28
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Chursa U, Nuñez-Durán E, Cansby E, Amrutkar M, Sütt S, Ståhlman M, Olsson BM, Borén J, Johansson ME, Bäckhed F, Johansson BR, Sihlbom C, Mahlapuu M. Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle. Diabetologia 2017; 60:553-567. [PMID: 27981357 PMCID: PMC6518105 DOI: 10.1007/s00125-016-4171-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
AIMS/HYPOTHESIS Understanding the molecular networks controlling ectopic lipid deposition and insulin responsiveness in skeletal muscle is essential for developing new strategies to treat type 2 diabetes. We recently identified serine/threonine protein kinase 25 (STK25) as a critical regulator of liver steatosis, hepatic lipid metabolism and whole body glucose and insulin homeostasis. Here, we assessed the role of STK25 in control of ectopic fat storage and insulin responsiveness in skeletal muscle. METHODS Skeletal muscle morphology was studied by histological examination, exercise performance and insulin sensitivity were assessed by treadmill running and euglycaemic-hyperinsulinaemic clamp, respectively, and muscle lipid metabolism was analysed by ex vivo assays in Stk25 transgenic and wild-type mice fed a high-fat diet. Lipid accumulation and mitochondrial function were also studied in rodent myoblasts overexpressing STK25. Global quantitative phosphoproteomics was performed in skeletal muscle of Stk25 transgenic and wild-type mice fed a high-fat diet to identify potential downstream mediators of STK25 action. RESULTS We found that overexpression of STK25 in transgenic mice fed a high-fat diet increases intramyocellular lipid accumulation, impairs skeletal muscle mitochondrial function and sarcomeric ultrastructure, and induces perimysial and endomysial fibrosis, thereby reducing endurance exercise capacity and muscle insulin sensitivity. Furthermore, we observed enhanced lipid accumulation and impaired mitochondrial function in rodent myoblasts overexpressing STK25, demonstrating an autonomous action for STK25 within cells. Global phosphoproteomic analysis revealed alterations in the total abundance and phosphorylation status of different target proteins located predominantly to mitochondria and sarcomeric contractile elements in Stk25 transgenic vs wild-type muscle, respectively, providing a possible molecular mechanism for the observed phenotype. CONCLUSIONS/INTERPRETATION STK25 emerges as a new regulator of the complex interplay between lipid storage, mitochondrial energetics and insulin action in skeletal muscle, highlighting the potential of STK25 antagonists for type 2 diabetes treatment.
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Affiliation(s)
- Urszula Chursa
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Esther Nuñez-Durán
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Emmelie Cansby
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Manoj Amrutkar
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Silva Sütt
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden
| | - Marcus Ståhlman
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jan Borén
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria E Johansson
- Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Bengt R Johansson
- Institute of Biomedicine, Electron Microscopy Unit, University of Gothenburg, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Margit Mahlapuu
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Sahlgrenska University Hospital, Blå stråket 5, SE-41345, Gothenburg, Sweden.
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Gómez-Serrano M, Camafeita E, López JA, Rubio MA, Bretón I, García-Consuegra I, García-Santos E, Lago J, Sánchez-Pernaute A, Torres A, Vázquez J, Peral B. Differential proteomic and oxidative profiles unveil dysfunctional protein import to adipocyte mitochondria in obesity-associated aging and diabetes. Redox Biol 2016; 11:415-428. [PMID: 28064117 PMCID: PMC5220168 DOI: 10.1016/j.redox.2016.12.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/19/2022] Open
Abstract
Human age-related diseases, including obesity and type 2 diabetes (T2DM), have long been associated to mitochondrial dysfunction; however, the role for adipose tissue mitochondria in these conditions remains unknown. We have tackled the impact of aging and T2DM on adipocyte mitochondria from obese patients by quantitating not only the corresponding abundance changes of proteins, but also the redox alterations undergone by Cys residues thereof. For that, we have resorted to a high-throughput proteomic approach based on isobaric labeling, liquid chromatography and mass spectrometry. The alterations undergone by the mitochondrial proteome revealed aging- and T2DM-specific hallmarks. Thus, while a global decrease of oxidative phosphorylation (OXPHOS) subunits was found in aging, the diabetic patients exhibited a reduction of specific OXPHOS complexes as well as an up-regulation of the anti-oxidant response. Under both conditions, evidence is shown for the first time of a link between increased thiol protein oxidation and decreased protein abundance in adipose tissue mitochondria. This association was stronger in T2DM, where OXPHOS mitochondrial- vs. nuclear-encoded protein modules were found altered, suggesting impaired mitochondrial protein translocation and complex assembly. The marked down-regulation of OXPHOS oxidized proteins and the alteration of oxidized Cys residues related to protein import through the redox-active MIA (Mitochondrial Intermembrane space Assembly) pathway support that defects in protein translocation to the mitochondria may be an important underlying mechanism for mitochondrial dysfunction in T2DM and physiological aging. The present draft of redox targets together with the quantification of protein and oxidative changes may help to better understand the role of oxidative stress in both a physiological process like aging and a pathological condition like T2DM.
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Affiliation(s)
- María Gómez-Serrano
- Instituto de Investigaciones Biomédicas, Alberto Sols, (IIBM); Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid (CSIC-UAM), Madrid 28029, Spain
| | - Emilio Camafeita
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Juan A López
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Miguel A Rubio
- Department of Endocrinology, Hospital Clínico San Carlos (IDISSC), Facultad de Medicina, Universidad Complutense, Madrid 28040, Spain
| | - Irene Bretón
- Department of Endocrinology and Nutrition, Hospital General Universitario Gregorio Marañón (IISGM), Madrid 28007, Spain
| | - Inés García-Consuegra
- Instituto de Investigación, Hospital Universitario 12 de Octubre (i+12), Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid 28029, Spain
| | - Eva García-Santos
- Instituto de Investigaciones Biomédicas, Alberto Sols, (IIBM); Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid (CSIC-UAM), Madrid 28029, Spain
| | - Jesús Lago
- Department of Surgery, Hospital General Universitario Gregorio Marañón (IISGM), Madrid 28007, Spain
| | - Andrés Sánchez-Pernaute
- Department of Surgery, Hospital Clínico San Carlos (IDISSC), Facultad de Medicina, Universidad Complutense, Madrid 28040, Spain
| | - Antonio Torres
- Department of Surgery, Hospital Clínico San Carlos (IDISSC), Facultad de Medicina, Universidad Complutense, Madrid 28040, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Belén Peral
- Instituto de Investigaciones Biomédicas, Alberto Sols, (IIBM); Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid (CSIC-UAM), Madrid 28029, Spain.
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30
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Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes. Nature 2016; 537:644-648. [PMID: 27654913 DOI: 10.1038/nature19774] [Citation(s) in RCA: 359] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 08/18/2016] [Indexed: 02/06/2023]
Abstract
Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII2CIV (the respirasome)-a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.
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Affiliation(s)
- James A Letts
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Karol Fiedorczuk
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
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31
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Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. Atomic structure of the entire mammalian mitochondrial complex I. Nature 2016; 538:406-410. [PMID: 27595392 DOI: 10.1038/nature19794] [Citation(s) in RCA: 359] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022]
Abstract
Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,MRC Mitochondrial Biology Unit, Cambridge CB2 0XY, UK
| | - James A Letts
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | | | - Karol Kaszuba
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, UK
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
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Mitochondrial disulfide relay and its substrates: mechanisms in health and disease. Cell Tissue Res 2016; 367:59-72. [DOI: 10.1007/s00441-016-2481-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/18/2016] [Indexed: 01/06/2023]
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Zhu J, Vinothkumar KR, Hirst J. Structure of mammalian respiratory complex I. Nature 2016; 536:354-358. [PMID: 27509854 PMCID: PMC5027920 DOI: 10.1038/nature19095] [Citation(s) in RCA: 395] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/08/2016] [Indexed: 12/17/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner membrane. Mammalian complex I1 contains 45 subunits, comprising 14 core subunits that house the catalytic machinery and are conserved from bacteria to humans, and a mammalian-specific cohort of 31 supernumerary subunits1,2. Knowledge about the structures and functions of the supernumerary subunits is fragmentary. Here, we describe a 4.2 Å resolution single-particle cryoEM structure of complex I from Bos taurus. We locate and model all 45 subunits to provide the entire structure of the mammalian complex. Furthermore, computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally-dynamic regions and match biochemical descriptions of the ‘active-to-deactive’ enzyme transition that occurs during hypoxia3,4. Thus, our structures provide a foundation for understanding complex I assembly5 and the effects of mutations that cause clinically-relevant complex I dysfunctions6, insights into the structural and functional roles of the supernumerary subunits, and new information on the mechanism and regulation of catalysis.
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Affiliation(s)
- Jiapeng Zhu
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Kutti R Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
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The origin of the supernumerary subunits and assembly factors of complex I: A treasure trove of pathway evolution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:971-9. [PMID: 27048931 DOI: 10.1016/j.bbabio.2016.03.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 11/20/2022]
Abstract
We review and document the evolutionary origin of all complex I assembly factors and nine supernumerary subunits from protein families. Based on experimental data and the conservation of critical residues we identify a spectrum of protein function conservation between the complex I representatives and their non-complex I homologs. This spectrum ranges from proteins that have retained their molecular function but in which the substrate specificity may have changed or have become more specific, like NDUFAF5, to proteins that have lost their original molecular function and critical catalytic residues like NDUFAF6. In between are proteins that have retained their molecular function, which however appears unrelated to complex I, like ACAD9, or proteins in which amino acids of the active site are conserved but for which no enzymatic activity has been reported, like NDUFA10. We interpret complex I evolution against the background of molecular evolution theory. Complex I supernumerary subunits and assembly factors appear to have been recruited from proteins that are mitochondrial and/or that are expressed when complex I is active. Within the evolution of complex I and its assembly there are many cases of neofunctionalization after gene duplication, like ACAD9 and TMEM126B, one case of subfunctionalization: ACPM1 and ACPM2 in Yarrowia lipolytica, and one case in which a complex I protein itself appears to have been the source of a new protein from another complex: NDUFS6 gave rise to cytochrome c oxidase subunit COX4/COX5b. Complex I and its assembly can therewith be regarded as a treasure trove for pathway evolution. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Sánchez-Caballero L, Guerrero-Castillo S, Nijtmans L. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:980-90. [PMID: 27040506 DOI: 10.1016/j.bbabio.2016.03.031] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Mammalian complex I is composed of 44 different subunits and its assembly requires at least 13 specific assembly factors. Proper function of the mitochondrial respiratory chain enzyme is of crucial importance for cell survival due to its major participation in energy production and cell signaling. Complex I assembly depends on the coordination of several crucial processes that need to be tightly interconnected and orchestrated by a number of assembly factors. The understanding of complex I assembly evolved from simple sequential concept to the more sophisticated modular assembly model describing a convoluted process. According to this model, the different modules assemble independently and associate afterwards with each other to form the final enzyme. In this review, we aim to unravel the complexity of complex I assembly and provide the latest insights in this fundamental and fascinating process. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Laura Sánchez-Caballero
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo Nijtmans
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
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Guarás A, Perales-Clemente E, Calvo E, Acín-Pérez R, Loureiro-Lopez M, Pujol C, Martínez-Carrascoso I, Nuñez E, García-Marqués F, Rodríguez-Hernández MA, Cortés A, Diaz F, Pérez-Martos A, Moraes CT, Fernández-Silva P, Trifunovic A, Navas P, Vazquez J, Enríquez JA. The CoQH2/CoQ Ratio Serves as a Sensor of Respiratory Chain Efficiency. Cell Rep 2016; 15:197-209. [PMID: 27052170 DOI: 10.1016/j.celrep.2016.03.009] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/03/2016] [Accepted: 02/27/2016] [Indexed: 02/01/2023] Open
Abstract
Electrons feed into the mitochondrial electron transport chain (mETC) from NAD- or FAD-dependent enzymes. A shift from glucose to fatty acids increases electron flux through FAD, which can saturate the oxidation capacity of the dedicated coenzyme Q (CoQ) pool and result in the generation of reactive oxygen species. To prevent this, the mETC superstructure can be reconfigured through the degradation of respiratory complex I, liberating associated complex III to increase electron flux via FAD at the expense of NAD. Here, we demonstrate that this adaptation is driven by the ratio of reduced to oxidized CoQ. Saturation of CoQ oxidation capacity induces reverse electron transport from reduced CoQ to complex I, and the resulting local generation of superoxide oxidizes specific complex I proteins, triggering their degradation and the disintegration of the complex. Thus, CoQ redox status acts as a metabolic sensor that fine-tunes mETC configuration in order to match the prevailing substrate profile.
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Affiliation(s)
- Adela Guarás
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Ester Perales-Clemente
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Enrique Calvo
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Rebeca Acín-Pérez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Marta Loureiro-Lopez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Claire Pujol
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Isabel Martínez-Carrascoso
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Estefanía Nuñez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Fernando García-Marqués
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - María Angeles Rodríguez-Hernández
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Ana Cortés
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Francisca Diaz
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Acisclo Pérez-Martos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Carlos T Moraes
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Patricio Fernández-Silva
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Sevilla 41013, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Sevilla 41013, Spain
| | - Jesús Vazquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Jose A Enríquez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain.
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Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:902-14. [PMID: 26921811 DOI: 10.1016/j.bbabio.2016.02.013] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ulrich Brandt
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany.
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Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
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39
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Modjtahedi N, Tokatlidis K, Dessen P, Kroemer G. Mitochondrial Proteins Containing Coiled-Coil-Helix-Coiled-Coil-Helix (CHCH) Domains in Health and Disease. Trends Biochem Sci 2016; 41:245-260. [PMID: 26782138 DOI: 10.1016/j.tibs.2015.12.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 11/19/2022]
Abstract
Members of the coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing protein family that carry (CX9C) type motifs are imported into the mitochondrion with the help of the disulfide relay-dependent MIA import pathway. These evolutionarily conserved proteins are emerging as new cellular factors that control mitochondrial respiration, redox regulation, lipid homeostasis, and membrane ultrastructure and dynamics. We discuss recent insights on the activity of known (CX9C) motif-carrying proteins in mammals and review current data implicating the Mia40/CHCHD4 import machinery in the regulation of their mitochondrial import. Recent findings and the identification of disease-associated mutations in specific (CX9C) motif-carrying proteins have highlighted members of this family of proteins as potential therapeutic targets in a variety of human disorders.
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Affiliation(s)
- Nazanine Modjtahedi
- Institut National de la Santé et de la Recherche Médicale, U1030, Villejuif, France; Gustave Roussy Cancer Campus, Villejuif, France; Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France.
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Philippe Dessen
- Gustave Roussy Cancer Campus, Villejuif, France; Faculty of Medicine, Université Paris-Saclay, Kremlin-Bicêtre, France; Groupe bioinformatique Gustave Roussy Cancer Campus, Villejuif, France
| | - Guido Kroemer
- Equipe 11 Labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Université Pierre et Marie Curie, Paris, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, AP-HP, France; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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40
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Letts JA, Sazanov LA. Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Curr Opin Struct Biol 2015; 33:135-45. [PMID: 26387075 DOI: 10.1016/j.sbi.2015.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/13/2015] [Accepted: 08/25/2015] [Indexed: 02/04/2023]
Abstract
The 1MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.
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Affiliation(s)
- James A Letts
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.
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41
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Structure of subcomplex Iβ of mammalian respiratory complex I leads to new supernumerary subunit assignments. Proc Natl Acad Sci U S A 2015; 112:12087-92. [PMID: 26371297 DOI: 10.1073/pnas.1510577112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial complex I (proton-pumping NADH:ubiquinone oxidoreductase) is an essential respiratory enzyme. Mammalian complex I contains 45 subunits: 14 conserved "core" subunits and 31 "supernumerary" subunits. The structure of Bos taurus complex I, determined to 5-Å resolution by electron cryomicroscopy, described the structure of the mammalian core enzyme and allowed the assignment of 14 supernumerary subunits. Here, we describe the 6.8-Å resolution X-ray crystallography structure of subcomplex Iβ, a large portion of the membrane domain of B. taurus complex I that contains two core subunits and a cohort of supernumerary subunits. By comparing the structures and composition of subcomplex Iβ and complex I, supported by comparisons with Yarrowia lipolytica complex I, we propose assignments for eight further supernumerary subunits in the structure. Our new assignments include two CHCH-domain containing subunits that contain disulfide bridges between CX9C motifs; they are processed by the Mia40 oxidative-folding pathway in the intermembrane space and probably stabilize the membrane domain. We also assign subunit B22, an LYR protein, to the matrix face of the membrane domain. We reveal that subunit B22 anchors an acyl carrier protein (ACP) to the complex, replicating the LYR protein-ACP structural module that was identified previously in the hydrophilic domain. Thus, we significantly extend knowledge of how the mammalian supernumerary subunits are arranged around the core enzyme, and provide insights into their roles in biogenesis and regulation.
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42
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Hangen E, Féraud O, Lachkar S, Mou H, Doti N, Fimia GM, Lam NV, Zhu C, Godin I, Muller K, Chatzi A, Nuebel E, Ciccosanti F, Flamant S, Bénit P, Perfettini JL, Sauvat A, Bennaceur-Griscelli A, Ser-Le Roux K, Gonin P, Tokatlidis K, Rustin P, Piacentini M, Ruvo M, Blomgren K, Kroemer G, Modjtahedi N. Interaction between AIF and CHCHD4 Regulates Respiratory Chain Biogenesis. Mol Cell 2015; 58:1001-14. [PMID: 26004228 DOI: 10.1016/j.molcel.2015.04.020] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/27/2015] [Accepted: 04/14/2015] [Indexed: 12/19/2022]
Abstract
Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein that, beyond its apoptotic function, is required for the normal expression of major respiratory chain complexes. Here we identified an AIF-interacting protein, CHCHD4, which is the central component of a redox-sensitive mitochondrial intermembrane space import machinery. Depletion or hypomorphic mutation of AIF caused a downregulation of CHCHD4 protein by diminishing its mitochondrial import. CHCHD4 depletion sufficed to induce a respiratory defect that mimicked that observed in AIF-deficient cells. CHCHD4 levels could be restored in AIF-deficient cells by enforcing its AIF-independent mitochondrial localization. This modified CHCHD4 protein reestablished respiratory function in AIF-deficient cells and enabled AIF-deficient embryoid bodies to undergo cavitation, a process of programmed cell death required for embryonic morphogenesis. These findings explain how AIF contributes to the biogenesis of respiratory chain complexes, and they establish an unexpected link between the vital function of AIF and the propensity of cells to undergo apoptosis.
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Affiliation(s)
- Emilie Hangen
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France
| | - Olivier Féraud
- Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; INSERM U935, 94805 Villejuif, France; ESTeam Paris Sud, Stem Cell Core Facility, Institut André Lwoff, 94800 Villejuif, France
| | - Sylvie Lachkar
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France
| | - Haiwei Mou
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France
| | - Nunzianna Doti
- Istituto di Biostrutture e Bioimmagini, CNR, 80134 Napoli, Italy
| | - Gian Maria Fimia
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS "L. Spallanzani," 00149 Rome, Italy; Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce 73100, Italy
| | - Ngoc-Vy Lam
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Isabelle Godin
- Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; INSERM U1009, 94805 Villejuif, France
| | - Kevin Muller
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France
| | - Afroditi Chatzi
- Institute of Molecular Cell and Systems Biology, University of Glasgow, G12 8QQ Glasgow, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion Crete 70013, Greece
| | - Esther Nuebel
- Institute of Molecular Cell and Systems Biology, University of Glasgow, G12 8QQ Glasgow, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion Crete 70013, Greece
| | - Fabiola Ciccosanti
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS "L. Spallanzani," 00149 Rome, Italy
| | - Stéphane Flamant
- Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; INSERM U935, 94805 Villejuif, France
| | - Paule Bénit
- INSERM UMR1141, Hôpital Robert Debré, 75019 Paris, France; Faculté de Médecine Denis Diderot, Université Paris 7, 75013 Paris, France
| | - Jean-Luc Perfettini
- Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; Cell Death and Aging Team, Gustave Roussy, 94805 Villejuif, France; INSERM U1030, Gustave Roussy, 94805 Villejuif, France
| | - Allan Sauvat
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Cell Biology and Metabolomics Platforms, Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France
| | - Annelise Bennaceur-Griscelli
- Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; INSERM U935, 94805 Villejuif, France; ESTeam Paris Sud, Stem Cell Core Facility, Institut André Lwoff, 94800 Villejuif, France; Laboratoire d'Hématologie, Hôpital Paul Brousse AP-HP, 94800 Villejuif, France
| | - Karine Ser-Le Roux
- Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; Animal and Veterinary Resources, 94805 Villejuif, France
| | - Patrick Gonin
- Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Sud/Paris XI, 94270 Kremlin Bicêtre, France; Animal and Veterinary Resources, 94805 Villejuif, France
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, University of Glasgow, G12 8QQ Glasgow, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion Crete 70013, Greece
| | - Pierre Rustin
- INSERM UMR1141, Hôpital Robert Debré, 75019 Paris, France; Faculté de Médecine Denis Diderot, Université Paris 7, 75013 Paris, France
| | - Mauro Piacentini
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS "L. Spallanzani," 00149 Rome, Italy; Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, 80134 Napoli, Italy
| | - Klas Blomgren
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Pediatrics, University of Gothenburg, The Queen Silvia Children's Hospital, 40530 Gothenburg, Sweden; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Guido Kroemer
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France; Cell Biology and Metabolomics Platforms, Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France.
| | - Nazanine Modjtahedi
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, UMRS 1138, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Center, 94805 Villejuif, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75006 Paris, France.
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Jeong JC, Chen X. A New Semantic Functional Similarity over Gene Ontology. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:322-334. [PMID: 26357220 DOI: 10.1109/tcbb.2014.2343963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Identifying functionally similar or closely related genes and gene products has significant impacts on biological and clinical studies as well as drug discovery. In this paper, we propose an effective and practically useful method measuring both gene and gene product similarity by integrating the topology of gene ontology, known functional domains and their functional annotations. The proposed method is comprehensively evaluated through statistical analysis of the similarities derived from sequence, structure and phylogenetic profiles, and clustering analysis of disease genes clusters. Our results show that the proposed method clearly outperforms other conventional methods. Furthermore, literature analysis also reveals that the proposed method is both statistically and biologically promising for identifying functionally similar genes or gene products. In particular, we demonstrate that the proposed functional similarity metric is capable of discoverying new disease related genes or gene products.
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Jiang J, Briedé JJ, Jennen DGJ, Van Summeren A, Saritas-Brauers K, Schaart G, Kleinjans JCS, de Kok TMCM. Increased mitochondrial ROS formation by acetaminophen in human hepatic cells is associated with gene expression changes suggesting disruption of the mitochondrial electron transport chain. Toxicol Lett 2015; 234:139-50. [PMID: 25704631 DOI: 10.1016/j.toxlet.2015.02.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/15/2015] [Accepted: 02/17/2015] [Indexed: 12/16/2022]
Abstract
Acetaminophen (APAP) overdosage results in hepatotoxicity, but the underlying molecular mechanisms are still not completely understood. In the current study, we focused on mitochondrial-specific oxidative liver injury induced by APAP exposure. Owning to genetic polymorphisms in the CYP2E1 gene or varying inducibility by xenobiotics, the CYP2E1 mRNA level and protein activity vary extensively among individuals. As CYP2E1 is a known ROS generating enzyme, we chose HepG2 to minimize CYP2E1-induced ROS formation, which will help us better understand the APAP induced mitochondrial-specific hepatotoxicity in a subpopulation with low CYP2E1 activity. HepG2 cells were exposed to a low and toxic dose (0.5 and 10mM) of APAP and analyzed at four time points for genome-wide gene expression. Mitochondria were isolated and electron spin resonance spectroscopy was performed to measure the formation of mitochondrial ROS. The yield of ATP was measured to confirm the impact of the toxic dose of APAP on cellular energy production. Our results indicate that 10mM APAP significantly influences the expression of mitochondrial protein-encoding genes in association with an increase in mitochondrial ROS formation. Additionally, 10mM APAP affects the expression of genes encoding the subunits of electron transport chain (ETC) complexes, which may alter normal mitochondrial functions by disrupting the assembly, stability, and structural integrity of ETC complexes, leading to a measurable depletion of ATP, and cell death. The expression of mitochondrium-specific antioxidant enzyme, SOD2, is reduced which may limit the ROS scavenging ability and cause imbalance of the mitochondrial ROS homeostasis. Overall, transcriptome analysis reveals the molecular processes involved in the observed APAP-induced increase of mitochondrial ROS formation and the associated APAP-induced oxidative stress.
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Affiliation(s)
- Jian Jiang
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands.
| | - Jacob J Briedé
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Anke Van Summeren
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Karen Saritas-Brauers
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Gert Schaart
- Department of Human Movement Sciences, School of nutrition, Toxicology and metabolism (NUTRIM) Maastricht University Medical Centre, 6200 MD Maastricht, the Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
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Vinothkumar KR, Zhu J, Hirst J. Architecture of mammalian respiratory complex I. Nature 2014; 515:80-84. [PMID: 25209663 PMCID: PMC4224586 DOI: 10.1038/nature13686] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/17/2014] [Indexed: 12/18/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases.
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Affiliation(s)
- Kutti R Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jiapeng Zhu
- MRC Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY, UK
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Abstract
Mitochondrial complex I has a molecular mass of almost 1 MDa and comprises more than 40 polypeptides. Fourteen central subunits harbour the bioenergetic core functions. We are only beginning to understand the significance of the numerous accessory subunits. The present review addresses the role of accessory subunits for assembly, stability and regulation of complex I and for cellular functions not directly associated with redox-linked proton translocation.
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A scaffold of accessory subunits links the peripheral arm and the distal proton-pumping module of mitochondrial complex I. Biochem J 2011; 437:279-88. [PMID: 21545356 DOI: 10.1042/bj20110359] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a very large membrane protein complex with a central function in energy metabolism. Complex I from the aerobic yeast Yarrowia lipolytica comprises 14 central subunits that harbour the bioenergetic core functions and at least 28 accessory subunits. Despite progress in structure determination, the position of individual accessory subunits in the enzyme complex remains largely unknown. Proteomic analysis of subcomplex Iδ revealed that it lacked eleven subunits, including the central subunits ND1 and ND3 forming the interface between the peripheral and the membrane arm in bacterial complex I. This unexpected observation provided insight into the structural organization of the connection between the two major parts of mitochondrial complex I. Combining recent structural information, biochemical evidence on the assignment of individual subunits to the subdomains of complex I and sequence-based predictions for the targeting of subunits to different mitochondrial compartments, we derived a model for the arrangement of the subunits in the membrane arm of mitochondrial complex I.
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Abstract
The prokaryotic and eukaryotic homologues of complex I (proton-pumping NADH:quinone oxidoreductase) perform the same function in energy transduction, but the eukaryotic enzymes are twice as big as their prokaryotic cousins, and comprise three times as many subunits. Fourteen core subunits are conserved in all complexes I, and are sufficient for catalysis - so why are the eukaryotic enzymes embellished by so many supernumerary or accessory subunits? In this issue of the Biochemical Journal, Angerer et al. have provided new evidence to suggest that the supernumerary subunits are important for enzyme stability. This commentary aims to put this suggestion into context.
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Understanding mitochondrial complex I assembly in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:851-62. [PMID: 21924235 DOI: 10.1016/j.bbabio.2011.08.010] [Citation(s) in RCA: 298] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/17/2011] [Accepted: 08/27/2011] [Indexed: 12/12/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the largest multimeric enzyme complex of the mitochondrial respiratory chain, which is responsible for electron transport and the generation of a proton gradient across the mitochondrial inner membrane to drive ATP production. Eukaryotic complex I consists of 14 conserved subunits, which are homologous to the bacterial subunits, and more than 26 accessory subunits. In mammals, complex I consists of 45 subunits, which must be assembled correctly to form the properly functioning mature complex. Complex I dysfunction is the most common oxidative phosphorylation (OXPHOS) disorder in humans and defects in the complex I assembly process are often observed. This assembly process has been difficult to characterize because of its large size, the lack of a high resolution structure for complex I, and its dual control by nuclear and mitochondrial DNA. However, in recent years, some of the atomic structure of the complex has been resolved and new insights into complex I assembly have been generated. Furthermore, a number of proteins have been identified as assembly factors for complex I biogenesis and many patients carrying mutations in genes associated with complex I deficiency and mitochondrial diseases have been discovered. Here, we review the current knowledge of the eukaryotic complex I assembly process and new insights from the identification of novel assembly factors. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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