101
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Cogliati S, Cabrera-Alarcón JL, Enriquez JA. Regulation and functional role of the electron transport chain supercomplexes. Biochem Soc Trans 2021; 49:2655-2668. [PMID: 34747989 PMCID: PMC8786287 DOI: 10.1042/bst20210460] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are one of the most exhaustively investigated organelles in the cell and most attention has been paid to the components of the mitochondrial electron transport chain (ETC) in the last 100 years. The ETC collects electrons from NADH or FADH2 and transfers them through a series of electron carriers within multiprotein respiratory complexes (complex I to IV) to oxygen, therefore generating an electrochemical gradient that can be used by the F1-F0-ATP synthase (also named complex V) in the mitochondrial inner membrane to synthesize ATP. The organization and function of the ETC is a continuous source of surprises. One of the latest is the discovery that the respiratory complexes can assemble to form a variety of larger structures called super-complexes (SCs). This opened an unexpected level of complexity in this well-known and fundamental biological process. This review will focus on the current evidence for the formation of different SCs and will explore how they modulate the ETC organization according to the metabolic state. Since the field is rapidly growing, we also comment on the experimental techniques used to describe these SC and hope that this overview may inspire new technologies that will help to advance the field.
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Affiliation(s)
- Sara Cogliati
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | | | - Jose Antonio Enriquez
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
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102
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Kurane T, Matsunaga T, Ida T, Sawada K, Nishimura A, Fukui M, Umemura M, Nakayama M, Ohara N, Matsumoto S, Akaike T, Matsuzaki G, Takaesu G. GRIM-19 is a target of mycobacterial Zn 2+ metalloprotease 1 and indispensable for NLRP3 inflammasome activation. FASEB J 2021; 36:e22096. [PMID: 34907600 DOI: 10.1096/fj.202101074rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/16/2021] [Accepted: 11/29/2021] [Indexed: 11/11/2022]
Abstract
Tuberculosis is a communicable disease caused by Mycobacterium tuberculosis which primarily infects macrophages and establishes intracellular parasitism. A mycobacterial virulence factor Zn2+ metalloprotease 1 (Zmp1) is known to suppress interleukin (IL)-1β production by inhibiting caspase-1 resulting in phagosome maturation arrest. However, the molecular mechanism of caspase-1 inhibition by Zmp1 is still elusive. Here, we identified GRIM-19 (also known as NDUFA13), an essential subunit of mitochondrial respiratory chain complex I, as a novel Zmp1-binding protein. Using the CRISPR/Cas9 system, we generated GRIM-19 knockout murine macrophage cell line J774.1 and found that GRIM-19 is essential for IL-1β production during mycobacterial infection as well as in response to NLRP3 inflammasome-activating stimuli such as extracellular ATP or nigericin. We also found that GRIM-19 is required for the generation of mitochondrial reactive oxygen species and NLRP3-dependent activation of caspase-1. Loss of GRIM-19 or forced expression of Zmp1 resulted in a decrease in mitochondrial membrane potential. Our study revealed a previously unrecognized role of GRIM-19 as an essential regulator of NLRP3 inflammasome and a molecular mechanism underlying Zmp1-mediated suppression of IL-1β production during mycobacterial infection.
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Affiliation(s)
- Tomomi Kurane
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoaki Ida
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuko Sawada
- Molecular Microbiology Group, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Akira Nishimura
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Fukui
- Molecular Microbiology Group, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Masayuki Umemura
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.,Molecular Microbiology Group, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Masaaki Nakayama
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Naoya Ohara
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, Niigata, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Goro Matsuzaki
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.,Molecular Microbiology Group, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Giichi Takaesu
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.,Molecular Microbiology Group, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
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103
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Wang H, Zhang H, Wang Y, Brown ZJ, Xia Y, Huang Z, Shen C, Hu Z, Beane J, Ansa-Addo EA, Huang H, Tian D, Tsung A. Regulatory T-cell and neutrophil extracellular trap interaction contributes to carcinogenesis in non-alcoholic steatohepatitis. J Hepatol 2021; 75:1271-1283. [PMID: 34363921 DOI: 10.1016/j.jhep.2021.07.032] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Regulatory T-cells (Tregs) impair cancer immunosurveillance by creating an immunosuppressive environment that fosters tumor cell survival. Our previous findings demonstrated that neutrophil extracellular traps (NETs), which are involved both in innate and adaptive immunity, are abundant in livers affected by non-alcoholic steatohepatitis (NASH). However, how NETs interact with Tregs in the development of NASH-associated hepatocellular carcinoma (NASH-HCC) is not known. METHODS A choline-deficient, high-fat diet+diethylnitrosamine mouse model and the stelic animal model were utilized for NASH-HCC and a western diet mouse model was used for NASH development. Treg depletion was achieved using FoxP3-DTR mice. RNA sequencing was used to explore the mechanism by which NETs could regulate Treg differentiation. Bioenergetic analyses of naïve CD4+ T-cells were assessed by Seahorse. RESULTS Although the absolute number of CD4+ T-cells is lower in NASH livers, the Treg subpopulation is selectively increased. Depleting Tregs dramatically inhibits HCC initiation and progression in NASH. There is a positive correlation between increased NET and hepatic Treg levels. RNA sequencing data reveals that NETs impact gene expression profiles in naïve CD4+ T-cells, with the most differentially expressed genes being those involved in mitochondrial oxidative phosphorylation. By facilitating mitochondrial respiration, NETs can promote Treg differentiation. Metabolic reprogramming of naïve CD4+ T-cells by NETs requires toll-like receptor 4. Blockade of NETs in vivo using Pad4-/- mice or DNase I treatment reduces the activity of Tregs. CONCLUSIONS Tregs can suppress immunosurveillance in the premalignant stages of NASH. NETs facilitate the crosstalk between innate and adaptive immunity in NASH by promoting Treg activity through metabolic reprogramming. Therapies targeting NETs and Treg interactions could offer a potential strategy for preventing HCC in patients with NASH. LAY SUMMARY Regulatory T-cells (Tregs) can promote tumor development by suppressing cancer immunosurveillance, but their role in carcinogenesis during non-alcoholic steatohepatitis (NASH) progression is unknown. Herein, we discovered that selectively increased intrahepatic Tregs can promote an immunosuppressive environment in NASH livers. Neutrophil extracellular traps (NETs) link innate and adaptive immunity by promoting Treg differentiation via metabolic reprogramming of naïve CD4+ T-cells. This mechanism could be targeted to prevent liver cancer in patients with NASH.
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Affiliation(s)
- Han Wang
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA; Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongji Zhang
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Yu Wang
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA; Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zachary J Brown
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Yujia Xia
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA; Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zheng Huang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chengli Shen
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Zhiwei Hu
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Joal Beane
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Ephraim A Ansa-Addo
- Pelotonia Institute for Immuno-Oncology and Division of Medical Oncology, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Hai Huang
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Allan Tsung
- Division of Surgical Oncology, Department of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.
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104
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van de Wal M, Adjobo-Hermans M, Keijer J, Schirris T, Homberg J, Wieckowski MR, Grefte S, van Schothorst EM, van Karnebeek C, Quintana A, Koopman WJH. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain 2021; 145:45-63. [PMID: 34849584 PMCID: PMC8967107 DOI: 10.1093/brain/awab426] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases. With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (complex I) induce isolated complex I deficiency and Leigh syndrome. This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA-encoded NDUFS4 gene, encoding the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) of complex I, induce ‘mitochondrial complex I deficiency, nuclear type 1’ (MC1DN1) and Leigh syndrome in paediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the Leigh syndrome pathomechanism and intervention testing. Here, we review and discuss the role of complex I and NDUFS4 mutations in human mitochondrial disease, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/Leigh syndrome pathomechanism and its therapeutic targeting.
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Affiliation(s)
- Melissa van de Wal
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Merel Adjobo-Hermans
- Department of Biochemistry (286), RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom Schirris
- Department of Pharmacology and Toxicology, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Judith Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Clara van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Albert Quintana
- Mitochondrial Neuropathology Laboratory, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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105
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Warnsmann V, Meisterknecht J, Wittig I, Osiewacz HD. Aging of Podospora anserina Leads to Alterations of OXPHOS and the Induction of Non-Mitochondrial Salvage Pathways. Cells 2021; 10:cells10123319. [PMID: 34943827 PMCID: PMC8699231 DOI: 10.3390/cells10123319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023] Open
Abstract
The accumulation of functionally impaired mitochondria is a key event in aging. Previous works with the fungal aging model Podospora anserina demonstrated pronounced age-dependent changes of mitochondrial morphology and ultrastructure, as well as alterations of transcript and protein levels, including individual proteins of the oxidative phosphorylation (OXPHOS). The identified protein changes do not reflect the level of the whole protein complexes as they function in-vivo. In the present study, we investigated in detail the age-dependent changes of assembled mitochondrial protein complexes, using complexome profiling. We observed pronounced age-depen-dent alterations of the OXPHOS complexes, including the loss of mitochondrial respiratory supercomplexes (mtRSCs) and a reduction in the abundance of complex I and complex IV. Additionally, we identified a switch from the standard complex IV-dependent respiration to an alternative respiration during the aging of the P. anserina wild type. Interestingly, we identified proteasome components, as well as endoplasmic reticulum (ER) proteins, for which the recruitment to mitochondria appeared to be increased in the mitochondria of older cultures. Overall, our data demonstrate pronounced age-dependent alterations of the protein complexes involved in energy transduction and suggest the induction of different non-mitochondrial salvage pathways, to counteract the age-dependent mitochondrial impairments which occur during aging.
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Affiliation(s)
- Verena Warnsmann
- Institute of Molecular Biosciences, Faculty of Biosciences, Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jana Meisterknecht
- Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Goethe-University, Theodor-Stein-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Goethe-University, Theodor-Stein-Kai 7, 60590 Frankfurt am Main, Germany
| | - Heinz D Osiewacz
- Institute of Molecular Biosciences, Faculty of Biosciences, Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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106
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Jain S, Hu C, Kluza J, Ke W, Tian G, Giurgiu M, Bleilevens A, Campos AR, Charbono A, Stickeler E, Maurer J, Holinski-Feder E, Vaisburg A, Bureik M, Luo G, Marchetti P, Cheng Y, Wolf DA. Metabolic targeting of cancer by a ubiquinone uncompetitive inhibitor of mitochondrial complex I. Cell Chem Biol 2021; 29:436-450.e15. [PMID: 34852219 DOI: 10.1016/j.chembiol.2021.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/12/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022]
Abstract
SMIP004-7 is a small molecule inhibitor of mitochondrial respiration with selective in vivo anti-cancer activity through an as-yet unknown molecular target. We demonstrate here that SMIP004-7 targets drug-resistant cancer cells with stem-like features by inhibiting mitochondrial respiration complex I (NADH:ubiquinone oxidoreductase, complex I [CI]). Instead of affecting the quinone-binding site targeted by most CI inhibitors, SMIP004-7 and its cytochrome P450-dependent activated metabolite(s) have an uncompetitive mechanism of inhibition involving a distinct N-terminal region of catalytic subunit NDUFS2 that leads to rapid disassembly of CI. SMIP004-7 and an improved chemical analog selectively engage NDUFS2 in vivo to inhibit the growth of triple-negative breast cancer transplants, a response mediated at least in part by boosting CD4+ and CD8+ T cell-mediated immune surveillance. Thus, SMIP004-7 defines an emerging class of ubiquinone uncompetitive CI inhibitors for cell autonomous and microenvironmental metabolic targeting of mitochondrial respiration in cancer.
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Affiliation(s)
- Shashi Jain
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92024, USA
| | - Cheng Hu
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'An South Road, Xiamen, China
| | - Jerome Kluza
- Université de Lille, CNRS, Inserm, CHU Lille, Institut pour la Recherche sur le Cancer de Lille, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, 59000 Lille, France
| | - Wei Ke
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'An South Road, Xiamen, China
| | - Guiyou Tian
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'An South Road, Xiamen, China
| | | | - Andreas Bleilevens
- Department of Obstetrics and Gynecology, University of Aachen, Aachen, Germany
| | | | - Adriana Charbono
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92024, USA
| | - Elmar Stickeler
- Department of Obstetrics and Gynecology, University of Aachen, Aachen, Germany
| | - Jochen Maurer
- Department of Obstetrics and Gynecology, University of Aachen, Aachen, Germany
| | - Elke Holinski-Feder
- MGZ Medical Genetics Center Munich, 80335 Munich, Germany; Department of Medicine IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Arkadii Vaisburg
- Crocus Laboratories Inc., Montreal, QC, Canada; NuChem Sciences Inc., Montreal, QC, Canada
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Guangcheng Luo
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Philippe Marchetti
- Université de Lille, CNRS, Inserm, CHU Lille, Institut pour la Recherche sur le Cancer de Lille, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, 59000 Lille, France; Centre de Bio-Pathologie, Banque de Tissus, CHU of Lille, Lille, France
| | - Yabin Cheng
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'An South Road, Xiamen, China.
| | - Dieter A Wolf
- State Key Laboratory of Stress Biology and Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiang'An South Road, Xiamen, China; MGZ Medical Genetics Center Munich, 80335 Munich, Germany; Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich, 81675 Munich, Germany.
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107
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Legro NR, Kumar A, Aliu E. Case report of atypical Leigh syndrome in an adolescent male with novel biallelic variants in NDUFAF5 and review of the natural history of NDUFAF5-related disorders. Am J Med Genet A 2021; 188:896-899. [PMID: 34797029 DOI: 10.1002/ajmg.a.62568] [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: 09/21/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
NDUFAF5 encodes a Complex I assembly factor which is critical to the modification of a core subunit, NDUFS7, in early Complex I factor assembly. Mutations in NDUFAF5 have been previously shown to cause Complex I deficiency leading to mitochondrial respiratory chain impairment. More than 15 individuals affected by variants in NDUFAF5 have been described; however, there is phenotypic heterogeneity within this cohort. Some individuals display features of classical Leigh syndrome with early onset neurodegeneration whereas others live into early adulthood with progressive neurological deficits. Here, we present a clinical report of a 17-year-old African American individual with compound heterozygous mutations in NDUFAF5. The individual presented with childhood onset bilateral optic atrophy and developed progressive neuromuscular decline with relatively preserved cognition over time.
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Affiliation(s)
- Nicole R Legro
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.,Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Ashutosh Kumar
- Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.,Division of Neurology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ermal Aliu
- Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA.,Division of Medical Genetics, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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108
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An in vitro system to silence mitochondrial gene expression. Cell 2021; 184:5824-5837.e15. [PMID: 34672953 DOI: 10.1016/j.cell.2021.09.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/10/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022]
Abstract
The human mitochondrial genome encodes thirteen core subunits of the oxidative phosphorylation system, and defects in mitochondrial gene expression lead to severe neuromuscular disorders. However, the mechanisms of mitochondrial gene expression remain poorly understood due to a lack of experimental approaches to analyze these processes. Here, we present an in vitro system to silence translation in purified mitochondria. In vitro import of chemically synthesized precursor-morpholino hybrids allows us to target translation of individual mitochondrial mRNAs. By applying this approach, we conclude that the bicistronic, overlapping ATP8/ATP6 transcript is translated through a single ribosome/mRNA engagement. We show that recruitment of COX1 assembly factors to translating ribosomes depends on nascent chain formation. By defining mRNA-specific interactomes for COX1 and COX2, we reveal an unexpected function of the cytosolic oncofetal IGF2BP1, an RNA-binding protein, in mitochondrial translation. Our data provide insight into mitochondrial translation and innovative strategies to investigate mitochondrial gene expression.
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109
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Guerrero‐Castillo S, van Strien J, Brandt U, Arnold S. Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome. EMBO J 2021; 40:e108648. [PMID: 34542926 PMCID: PMC8561636 DOI: 10.15252/embj.2021108648] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
So-called ρ0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How cells adapt to survive ablation of oxidative phosphorylation remains poorly understood. Complexome profiling analysis of ρ0 cells covered 1,002 mitochondrial proteins and revealed changes in abundance and organization of numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies of complexes that would normally contain components encoded by mitochondrial DNA, we observed widespread reorganization of the complexome. This included distinct changes in the expression pattern of adenine nucleotide carrier isoforms, other mitochondrial transporters, and components of the protein import machinery. Remarkably, ablation of mitochondrial DNA hardly affected the complexes organizing cristae junctions indicating that the altered cristae morphology in ρ0 mitochondria predominantly resulted from the loss of complex V dimers required to impose narrow curvatures to the inner membrane. Our data provide a comprehensive resource for in-depth analysis of remodeling of the mitochondrial complexome in response to respiratory deficiency.
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Affiliation(s)
- Sergio Guerrero‐Castillo
- Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- University Children's Research@Kinder‐UKEUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Joeri van Strien
- Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Center for Molecular and Biomolecular InformaticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Ulrich Brandt
- Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Susanne Arnold
- Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
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110
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Xia C, Lou B, Fu Z, Mohsen AW, Shen AL, Vockley J, Kim JJP. Molecular mechanism of interactions between ACAD9 and binding partners in mitochondrial respiratory complex I assembly. iScience 2021; 24:103153. [PMID: 34646991 PMCID: PMC8497999 DOI: 10.1016/j.isci.2021.103153] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 09/16/2021] [Indexed: 01/05/2023] Open
Abstract
The dual function protein ACAD9 catalyzes α,β-dehydrogenation of fatty acyl-CoA thioesters in fatty acid β-oxidation and is an essential chaperone for mitochondrial respiratory complex I (CI) assembly. ACAD9, ECSIT, and NDUFAF1 interact to form the core mitochondrial CI assembly complex. Current studies examine the molecular mechanism of ACAD9/ECSIT/NDUFAF1interactions. ACAD9 binds to the carboxy-terminal half and NDUFAF1 to the amino-terminal half of ECSIT. Binary complexes are unstable and aggregate easily, while the ACAD9/ECSIT/NDUFAF1 ternary complex is soluble and highly stable. Molecular modeling and small-angle X-ray scattering studies identified intra-complex interaction sites and binding sites for other assembly factors. Binding of ECSIT at the ETF binding site in the amino-terminal domain of ACAD9 is consistent with observed loss of FAD and enzymatic activity and demonstrates that the two functions of ACAD9 are mutually exclusive. Mapping of 42 known pathogenic mutations onto the homology-modeled ACAD9 structure provides structural insights into pathomechanisms of CI deficiency.
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Affiliation(s)
- Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Baoying Lou
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Zhuji Fu
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anna L. Shen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jerry Vockley
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jung-Ja P. Kim
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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111
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Hevler JF, Zenezeni Chiozzi R, Cabrera-Orefice A, Brandt U, Arnold S, Heck AJR. Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain. Proc Natl Acad Sci U S A 2021; 118:e2106950118. [PMID: 34548399 PMCID: PMC8488679 DOI: 10.1073/pnas.2106950118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
Combining mass spectrometry-based chemical cross-linking and complexome profiling, we analyzed the interactome of heart mitochondria. We focused on complexes of oxidative phosphorylation and found that dimeric apoptosis-inducing factor 1 (AIFM1) forms a defined complex with ∼10% of monomeric cytochrome c oxidase (COX) but hardly interacts with respiratory chain supercomplexes. Multiple AIFM1 intercross-links engaging six different COX subunits provided structural restraints to build a detailed atomic model of the COX-AIFM12 complex (PDBDEV_00000092). An application of two complementary proteomic approaches thus provided unexpected insight into the macromolecular organization of the mitochondrial complexome. Our structural model excludes direct electron transfer between AIFM1 and COX. Notably, however, the binding site of cytochrome c remains accessible, allowing formation of a ternary complex. The discovery of the previously overlooked COX-AIFM12 complex and clues provided by the structural model hint at potential roles of AIFM1 in oxidative phosphorylation biogenesis and in programmed cell death.
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Affiliation(s)
- Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Riccardo Zenezeni Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands;
- Netherlands Proteomics Center, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
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112
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Marrocco A, Frawley K, Pearce LL, Peterson J, O'Brien JP, Mullett SJ, Wendell SG, St Croix CM, Mischler SE, Ortiz LA. Metabolic Adaptation of Macrophages as Mechanism of Defense against Crystalline Silica. THE JOURNAL OF IMMUNOLOGY 2021; 207:1627-1640. [PMID: 34433619 DOI: 10.4049/jimmunol.2000628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/08/2021] [Indexed: 11/19/2022]
Abstract
Silicosis is a lethal pneumoconiosis for which no therapy is available. Silicosis is a global threat, and more than 2.2 million people per year are exposed to silica in the United States. The initial response to silica is mediated by innate immunity. Phagocytosis of silica particles by macrophages is followed by recruitment of mitochondria to phagosomes, generation of mitochondrial reactive oxygen species, and cytokine (IL-1β, TNF-α, IFN-β) release. In contrast with LPS, the metabolic remodeling of silica-exposed macrophages is unclear. This study contrasts mitochondrial and metabolic alterations induced by LPS and silica on macrophages and correlates them with macrophage viability and cytokine production, which are central to the pathogenesis of silicosis. Using high-resolution respirometer and liquid chromatography-high-resolution mass spectrometry, we determined the effects of silica and LPS on mitochondrial respiration and determined changes in central carbon metabolism of murine macrophage cell lines RAW 264.7 and IC-21. We show that silica induces metabolic reprogramming of macrophages. Silica, as well as LPS, enhances glucose uptake and increases aerobic glycolysis in macrophages. In contrast with LPS, silica affects mitochondria respiration, reducing complex I and enhancing complex II activity, to sustain cell viability. These mitochondrial alterations are associated in silica, but not in LPS-exposed macrophages, with reductions of tricarboxylic acid cycle intermediates, including succinate, itaconate, glutamate, and glutamine. Furthermore, in contrast with LPS, these silica-induced metabolic adaptations do not correlate with IL-1β or TNF-α production, but with the suppressed release of IFN-β. Our data highlight the importance of complex II activity and tricarboxylic acid cycle remodeling to macrophage survival and cytokine-mediated inflammation in silicosis.
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Affiliation(s)
- Antonella Marrocco
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA
| | - Krystin Frawley
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA
| | - Linda L Pearce
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA
| | - James Peterson
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA
| | - James P O'Brien
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Steven J Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA.,Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, PA
| | - Stacy G Wendell
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA.,Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, PA.,Clinical Translational Science Institute, University of Pittsburgh, Pittsburgh, PA; and
| | | | - Steven E Mischler
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA
| | - Luis A Ortiz
- Department of Environmental and Occupational Health, Graduate School of Public Health at the University of Pittsburgh, Pittsburgh, PA;
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113
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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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114
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Ha JH, Jayaraman M, Yan M, Dhanasekaran P, Isidoro C, Song YS, Dhanasekaran DN. Identification of GNA12-driven gene signatures and key signaling networks in ovarian cancer. Oncol Lett 2021; 22:719. [PMID: 34429759 PMCID: PMC8371953 DOI: 10.3892/ol.2021.12980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
With the focus on defining the oncogenic network stimulated by lysophosphatidic acid (LPA) in ovarian cancer, the present study sought to interrogate the oncotranscriptome regulated by the LPA-mediated signaling pathway. LPA, LPA-receptor (LPAR) and LPAR-activated G protein 12 α-subunit, encoded by G protein subunit α 12 (GNA12), all serve an important role in ovarian cancer progression. While the general signaling mechanism regulated by LPA/LPAR/GNA12 has previously been characterized, the global transcriptomic network regulated by GNA12 in ovarian cancer pathophysiology remains largely unknown. To define the LPA/LPAR/GNA12-orchestrated oncogenic networks in ovarian cancer, transcriptomic and bioinformatical analyses were conducted using SKOV3 cells, in which the expression of GNA12 was silenced. Array analysis was performed in Agilent SurePrint G3 Human Comparative Genomic Hybridization 8×60 microarray platform. The array results were validated using Kuramochi cells. Gene and functional enrichment analyses were performed using Database for Annotation, Visualization and Integrated Discovery, Search Tool for Retrieval of Interacting Genes and Cytoscape algorithms. The results indicated a paradigm in which GNA12 drove ovarian cancer progression by upregulating a pro-tumorigenic network with AKT1, VEGFA, TGFB1, BCL2L1, STAT3, insulin-like growth factor 1 and growth hormone releasing hormone as critical hub and/or bottleneck nodes. Moreover, GNA12 downregulated a growth-suppressive network involving proteasome 20S subunit (PSM) β6, PSM α6, PSM ATPase 5, ubiquitin conjugating enzyme E2 E1, PSM non-ATPase 10, NDUFA4 mitochondrial complex-associated, NADH:ubiquinone oxidoreductase subunit B8 and anaphase promoting complex subunit 1 as hub or bottleneck nodes. In addition to providing novel insights into the LPA/LPAR/GNA12-regulated oncogenic networks in ovarian cancer, the present study identified several potential nodes in this network that could be assessed for targeted therapy.
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Affiliation(s)
- Ji-Hee Ha
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Muralidharan Jayaraman
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Mingda Yan
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Padmaja Dhanasekaran
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Ciro Isidoro
- Laboratory of Molecular Pathology and NanoBioImaging, Department of Health Sciences, University of Eastern Piedmont, I-17-28100 Novara, Italy
| | - Yong-Sang Song
- Department of Obstetrics and Gynecology, Cancer Research Institute, College of Medicine, Seoul National University, Seoul 151-921, Republic of Korea
| | - Danny N Dhanasekaran
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
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115
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Mabanglo MF, Bhandari V, Houry WA. Substrates and interactors of the ClpP protease in the mitochondria. Curr Opin Chem Biol 2021; 66:102078. [PMID: 34446368 DOI: 10.1016/j.cbpa.2021.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022]
Abstract
The ClpP protease is found across eukaryotic and prokaryotic organisms. It is well-characterized in bacteria where its function is important in maintaining protein homeostasis. Along with its ATPase partners, it has been shown to play critical roles in the regulation of enzymes involved in important cellular pathways. In eukaryotes, ClpP is found within cellular organelles. Proteomic studies have begun to characterize the role of this protease in the mitochondria through its interactions. Here, we discuss the proteomic techniques used to identify its interactors and present an atlas of mitochondrial ClpP substrates. The ClpP substrate pool is extensive and consists of proteins involved in essential mitochondrial processes such as the Krebs cycle, oxidative phosphorylation, translation, fatty acid metabolism, and amino acid metabolism. Discoveries of these associations have begun to illustrate the functional significance of ClpP in human health and disease.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada.
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116
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Adaptive optimization of the OXPHOS assembly line partially compensates lrpprc-dependent mitochondrial translation defects in mice. Commun Biol 2021; 4:989. [PMID: 34413467 PMCID: PMC8376967 DOI: 10.1038/s42003-021-02492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Mouse models of genetic mitochondrial disorders are generally used to understand specific molecular defects and their biochemical consequences, but rarely to map compensatory changes allowing survival. Here we took advantage of the extraordinary mitochondrial resilience of hepatic Lrpprc knockout mice to explore this question using native proteomics profiling and lipidomics. In these mice, low levels of the mtRNA binding protein LRPPRC induce a global mitochondrial translation defect and a severe reduction (>80%) in the assembly and activity of the electron transport chain (ETC) complex IV (CIV). Yet, animals show no signs of overt liver failure and capacity of the ETC is preserved. Beyond stimulation of mitochondrial biogenesis, results show that the abundance of mitoribosomes per unit of mitochondria is increased and proteostatic mechanisms are induced in presence of low LRPPRC levels to preserve a balance in the availability of mitochondrial- vs nuclear-encoded ETC subunits. At the level of individual organelles, a stabilization of residual CIV in supercomplexes (SCs) is observed, pointing to a role of these supramolecular arrangements in preserving ETC function. While the SC assembly factor COX7A2L could not contribute to the stabilization of CIV, important changes in membrane glycerophospholipid (GPL), most notably an increase in SC-stabilizing cardiolipins species (CLs), were observed along with an increased abundance of other supramolecular assemblies known to be stabilized by, and/or participate in CL metabolism. Together these data reveal a complex in vivo network of molecular adjustments involved in preserving mitochondrial integrity in energy consuming organs facing OXPHOS defects, which could be therapeutically exploited. Cuillerier et al. investigate compensatory mechanisms underlying survival of mice with a liver-specific knockout of the mitochondrial mRNA-binding protein Lrpprc. They propose various mechanisms operating along the OXPHOS assembly line, including mitochondrial biogenesis, mitochondrial ribosome upregulation and preferential supercomplex assembly, that could compensate lack of LRPPRC and allow survival of these mice.
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117
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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118
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Hilander T, Jackson CB, Robciuc M, Bashir T, Zhao H. The roles of assembly factors in mammalian mitoribosome biogenesis. Mitochondrion 2021; 60:70-84. [PMID: 34339868 DOI: 10.1016/j.mito.2021.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
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Affiliation(s)
- Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Finland.
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Tanzeela Bashir
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Key Laboratory of Stem Cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guangxi, China.
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119
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Diverse mitochondrial abnormalities in a new cellular model of TAFFAZZIN deficiency are remediated by cardiolipin-interacting small molecules. J Biol Chem 2021; 297:101005. [PMID: 34314685 PMCID: PMC8384898 DOI: 10.1016/j.jbc.2021.101005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/11/2021] [Accepted: 07/22/2021] [Indexed: 11/26/2022] Open
Abstract
Barth syndrome (BTHS) is an X-linked disorder of mitochondrial phospholipid metabolism caused by pathogenic variants in TAFFAZIN, which results in abnormal cardiolipin (CL) content in the inner mitochondrial membrane. To identify unappreciated pathways of mitochondrial dysfunction in BTHS, we utilized an unbiased proteomics strategy and identified that complex I (CI) of the mitochondrial respiratory chain and the mitochondrial quality control protease presenilin-associated rhomboid-like protein (PARL) are altered in a new HEK293–based tafazzin-deficiency model. Follow-up studies confirmed decreased steady state levels of specific CI subunits and an assembly factor in the absence of tafazzin; this decrease is in part based on decreased transcription and results in reduced CI assembly and function. PARL, a rhomboid protease associated with the inner mitochondrial membrane with a role in the mitochondrial response to stress, such as mitochondrial membrane depolarization, is increased in tafazzin-deficient cells. The increased abundance of PARL correlates with augmented processing of a downstream target, phosphoglycerate mutase 5, at baseline and in response to mitochondrial depolarization. To clarify the relationship between abnormal CL content, CI levels, and increased PARL expression that occurs when tafazzin is missing, we used blue-native PAGE and gene expression analysis to determine that these defects are remediated by SS-31 and bromoenol lactone, pharmacologic agents that bind CL or inhibit CL deacylation, respectively. These findings have the potential to enhance our understanding of the cardiac pathology of BTHS, where defective mitochondrial quality control and CI dysfunction have well-recognized roles in the pathology of diverse forms of cardiac dysfunction.
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120
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Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021; 22:ijms22157809. [PMID: 34360575 PMCID: PMC8346016 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.
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121
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Murari A, Rhooms SK, Garcia C, Liu T, Li H, Mishra B, Deshong C, Owusu-Ansah E. Dissecting the concordant and disparate roles of NDUFAF3 and NDUFAF4 in mitochondrial complex I biogenesis. iScience 2021; 24:102869. [PMID: 34386730 PMCID: PMC8346666 DOI: 10.1016/j.isci.2021.102869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/12/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022] Open
Abstract
Distinct sub-assemblies (modules) of mitochondrial complex I (CI) are assembled with the assistance of CI Assembly Factors (CIAFs) through mechanisms that are incompletely defined. Here, using genetic analyses in Drosophila, we report that when either of the CIAFs – NDUFAF3 or NDUFAF4 – is disrupted, biogenesis of the Q-, N-, and PP-b-modules of CI is impaired. This is due, at least in part, to the compromised integration of NDUFS3 and NDUFS5 into the Q-, and PP-b-modules, respectively, coupled with a destabilization of another CIAF, TIMMDC1, in assembly intermediates. Notably, forced expression of NDUFAF4 rescues the biogenesis defects in the Q-module and some aspects of the defects in the PP-b-module of CI when NDUFAF3 is disrupted. Altogether, our studies furnish new fundamental insights into the mechanism by which NDUFAF3 and NDUFAF4 regulate CI assembly and raises the possibility that certain point mutations in NDUFAF3 may be rescued by overexpression of NDUFAF4. Disruption of NDUFAF3 and NDUFAF4 in Drosophila muscles destabilizes TIMMDC1 NDUFAF3 and NDUFAF4 regulate biogenesis of the N, Q, and Pp modules NDUFAF4 ameliorates some of the CI biogenesis defects in NDUFAF3 mutants
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Affiliation(s)
- Anjaneyulu Murari
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shauna-Kay Rhooms
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Christian Garcia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University - New Jersey Medical School, Newark, NJ 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University - New Jersey Medical School, Newark, NJ 07103, USA
| | - Bibhuti Mishra
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cassie Deshong
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
- The Robert N. Butler Columbia Aging Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Corresponding author
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122
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Knapp-Wilson A, Pereira GC, Buzzard E, Ford HC, Richardson A, Corey RA, Neal C, Verkade P, Halestrap AP, Gold VAM, Kuwabara PE, Collinson I. Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health. J Cell Sci 2021; 134:jcs258399. [PMID: 34106255 PMCID: PMC8277142 DOI: 10.1242/jcs.258399] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial supercomplexes form around a conserved core of monomeric complex I and dimeric complex III; wherein a subunit of the former, NDUFA11, is conspicuously situated at the interface. We identified nduf-11 (B0491.5) as encoding the Caenorhabditis elegans homologue of NDUFA11. Animals homozygous for a CRISPR-Cas9-generated knockout allele of nduf-11 arrested at the second larval (L2) development stage. Reducing (but not eliminating) expression using RNAi allowed development to adulthood, enabling characterisation of the consequences: destabilisation of complex I and its supercomplexes and perturbation of respiratory function. The loss of NADH dehydrogenase activity was compensated by enhanced complex II activity, with the potential for detrimental reactive oxygen species (ROS) production. Cryo-electron tomography highlighted aberrant morphology of cristae and widening of both cristae junctions and the intermembrane space. The requirement of NDUF-11 for balanced respiration, mitochondrial morphology and development presumably arises due to its involvement in complex I and supercomplex maintenance. This highlights the importance of respiratory complex integrity for health and the potential for its perturbation to cause mitochondrial disease. This article has an associated First Person interview with Amber Knapp-Wilson, joint first author of the paper.
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Affiliation(s)
| | | | - Emma Buzzard
- Living Systems Institute, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
- College of Life and Environmental Sciences,Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Holly C. Ford
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Chris Neal
- Wolfson Bioimaging Facility, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Vicki A. M. Gold
- Living Systems Institute, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
- College of Life and Environmental Sciences,Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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123
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van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS, Evers F, Fernandez-Vizarra E, Guerrero-Castillo S, Kooij TWA, Páleníková P, Pardo M, Ugalde C, Wittig I, Wöhlbrand L, Brandt U, Arnold S, Huynen MA. CEDAR, an online resource for the reporting and exploration of complexome profiling data. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148411. [PMID: 33722514 DOI: 10.1016/j.bbabio.2021.148411] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Complexome profiling is an emerging 'omics' approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
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Affiliation(s)
- Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander Haupt
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Center for Biological Signalling Studies (BIOSS) and Center for Integrative Signalling Studies (CIBSS), 79104 Freiburg, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Alfredo Cabrera-Orefice
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jyoti S Choudhary
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Felix Evers
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Sergio Guerrero-Castillo
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Taco W A Kooij
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Cristina Ugalde
- Hospital 12 de Octubre Research Institute, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Ilka Wittig
- Functional Proteomics, Medical School, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Arnold
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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124
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Peruzzotti-Jametti L, Willis CM, Hamel R, Krzak G, Pluchino S. Metabolic Control of Smoldering Neuroinflammation. Front Immunol 2021; 12:705920. [PMID: 34249016 PMCID: PMC8262770 DOI: 10.3389/fimmu.2021.705920] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Compelling evidence exists that patients with chronic neurological conditions, which includes progressive multiple sclerosis, display pathological changes in neural metabolism and mitochondrial function. However, it is unknown if a similar degree of metabolic dysfunction occurs also in non-neural cells in the central nervous system. Specifically, it remains to be clarified (i) the full extent of metabolic changes in tissue-resident microglia and infiltrating macrophages after prolonged neuroinflammation (e.g., at the level of chronic active lesions), and (ii) whether these alterations underlie a unique pathogenic phenotype that is amenable for therapeutic targeting. Herein, we discuss how cell metabolism and mitochondrial function govern the function of chronic active microglia and macrophages brain infiltrates and identify new metabolic targets for therapeutic approaches aimed at reducing smoldering neuroinflammation.
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Affiliation(s)
- Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Cory M Willis
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Regan Hamel
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Grzegorz Krzak
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Stefano Pluchino
- Department of Clinical Neurosciences and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
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125
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Bi H, Guo H, Wang Q, Zhang X, Zhao Y, Li J, Zhao W, Tuo H, Zhang Y. A Novel Variation in the Mitochondrial Complex I Assembly Factor NDUFAF5 Causes Isolated Bilateral Striatal Necrosis in Childhood. Front Neurol 2021; 12:675616. [PMID: 34177781 PMCID: PMC8223072 DOI: 10.3389/fneur.2021.675616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 01/30/2023] Open
Abstract
Background: Bilateral striatal necrosis (BSN) is characterized by symmetrical degeneration, predominantly of the caudate and putamen nucleus, in the basal ganglia. It is associated with numerous acquired and hereditary neuro-developmental and motor dysfunction-related pathological conditions. BSN results in high morbidity and mortality among infants and children, and its diagnosis is clinically challenging due to several overlapping disease phenotypes. Therefore, a precise genetic diagnosis is urgently needed for accurate genetic counseling and improved prognostic outcomes as well. Objective: To identify novel missense mutations in the NDUFAF5 gene as a cause of childhood BSN in members of a Chinese family and summarize the clinical characteristics of patients with the NDUFAF5 gene mutations. Methods: This study included a large family living in a remote northwestern area of China. Three siblings developed a neurological disorder characterized by generalized dystonia within the first decade of their lives. Cerebral computed tomography (CT) and magnetic resonance imaging (MRI) showed bilateral lesions of the putamen. Biochemical and genetic approaches were used to identify the cause of BSN. Results: Sequence analysis showed no pathogenic variation in PANK2, SLC25A19, SLC19A3, and NUP62 genes and in the entire mitochondrial genome as well. Whole-exome sequencing revealed compound heterozygous mutations consisting of NDUFAF5:c.425A > C(p.E142A) and c.836T > G (p.M279R). The father, a healthy sister, and a healthy brother of the affected siblings carried the c.836T > G mutation, and the mother carried the c.425A > C mutation. These variants were absent in 100 ethnically matched non-BSN controls. In silico analysis demonstrated that the E142A and M279R mutations in NDUFAF5 protein significantly perturbed the normal conformation of the protein due to alterations in the hydrogen bonding patterns around the evolutionarily conserved catalytic domains, leading to its loss of function in the early stage of mitochondrial complex I assembly. Conclusions: We identified a novel compound heterozygous mutation (c.425A > C and c.836T > G) in the NDUFAF5 gene as the potential cause of autosomal recessive childhood BSN, which extended the pathogenic variation spectrum of the NDUFAF5 gene. This study provides substantial evidence for further improvement of genetic counseling and better clinical management of BSN affected individuals.
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Affiliation(s)
- Hongyan Bi
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Qianfei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yaming Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jimei Li
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Weiqin Zhao
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Houzhen Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongbo Zhang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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126
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Páleníková P, Harbour ME, Prodi F, Minczuk M, Zeviani M, Ghelli A, Fernández-Vizarra E. Duplexing complexome profiling with SILAC to study human respiratory chain assembly defects. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148395. [PMID: 33600785 DOI: 10.1016/j.bbabio.2021.148395] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022]
Abstract
Complexome Profiling (CP) combines size separation, by electrophoresis or other means, of native multimeric complexes with protein identification by mass spectrometry (MS). Peptide MS analysis of the multiple fractions in which the sample is separated, results in the creation of protein abundance profiles in function of molecular size, providing a visual output of the assembly status of a group of proteins of interest. Stable isotope labeling by amino acids in cell culture (SILAC) is an established quantitative proteomics technique that allows duplexing in the MS analysis as well as the comparison of relative protein abundances between the samples, which are processed and analyzed together. Combining SILAC and CP permitted the direct comparison of migration and abundance of the proteins present in the mitochondrial respiratory chain complexes in two different samples. This analysis, however, introduced a level of complexity in data processing for which bioinformatic tools had to be developed in order to generate the normalized protein abundance profiles. The advantages and challenges of using of this type of analysis for the characterization of two cell lines carrying pathological variants in MT-CO3 and MT-CYB is reviewed. An additional unpublished example of SILAC-CP of a cell line with an in-frame 18-bp deletion in MT-CYB is presented. In these cells, in contrast to other MT-CYB deficient models, a small proportion of complex III2 is formed and it is found associated with fully assembled complex I. This analysis also revealed a profuse accumulation of assembly intermediates containing complex III subunits UQCR10 and CYC1, as well as a profound early-stage complex IV assembly defect.
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Affiliation(s)
- Petra Páleníková
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Federica Prodi
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Michal Minczuk
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Massimo Zeviani
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna Ghelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Erika Fernández-Vizarra
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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127
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Le Vasseur M, Friedman J, Jost M, Xu J, Yamada J, Kampmann M, Horlbeck MA, Salemi MR, Phinney BS, Weissman JS, Nunnari J. Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells. eLife 2021; 10:67624. [PMID: 34034859 PMCID: PMC8154037 DOI: 10.7554/elife.67624] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/10/2021] [Indexed: 01/01/2023] Open
Abstract
Dysfunction of the mitochondrial electron transport chain (mETC) is a major cause of human mitochondrial diseases. To identify determinants of mETC function, we screened a genome-wide human CRISPRi library under oxidative metabolic conditions with selective inhibition of mitochondrial Complex III and identified ovarian carcinoma immunoreactive antigen (OCIA) domain-containing protein 1 (OCIAD1) as a Complex III assembly factor. We find that OCIAD1 is an inner mitochondrial membrane protein that forms a complex with supramolecular prohibitin assemblies. Our data indicate that OCIAD1 is required for maintenance of normal steady-state levels of Complex III and the proteolytic processing of the catalytic subunit cytochrome c1 (CYC1). In OCIAD1 depleted mitochondria, unprocessed CYC1 is hemylated and incorporated into Complex III. We propose that OCIAD1 acts as an adaptor within prohibitin assemblies to stabilize and/or chaperone CYC1 and to facilitate its proteolytic processing by the IMMP2L protease.
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Affiliation(s)
- Maxence Le Vasseur
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Jonathan Friedman
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, United States
| | - Jiawei Xu
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Justin Yamada
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, United States.,Chan-Zuckerberg Biohub, San Francisco, United States
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States
| | - Michelle R Salemi
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, Davis, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.,Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
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128
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Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Life (Basel) 2021; 11:life11050455. [PMID: 34069703 PMCID: PMC8161149 DOI: 10.3390/life11050455] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex of the respiratory chain. Complex I couples electron transfer to vectorial proton translocation across the inner mitochondrial membrane. The L shaped structure of complex I is divided into a membrane arm and a matrix arm. Fourteen central subunits are conserved throughout species, while some 30 accessory subunits are typically found in eukaryotes. Complex I dysfunction is associated with mutations in the nuclear and mitochondrial genome, resulting in a broad spectrum of neuromuscular and neurodegenerative diseases. Accessory subunit NDUFS4 in the matrix arm is a hot spot for mutations causing Leigh or Leigh-like syndrome. In this review, we focus on accessory subunits of the matrix arm and discuss recent reports on the function of accessory subunit NDUFS4 and its interplay with NDUFS6, NDUFA12, and assembly factor NDUFAF2 in complex I assembly.
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129
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Haumann S, Boix J, Knuever J, Bieling A, Vila Sanjurjo A, Elson JL, Blakely EL, Taylor RW, Riet N, Abken H, Kashkar H, Hornig-Do HT, Wiesner RJ. Mitochondrial DNA mutations induce mitochondrial biogenesis and increase the tumorigenic potential of Hodgkin and Reed-Sternberg cells. Carcinogenesis 2021; 41:1735-1745. [PMID: 32255484 DOI: 10.1093/carcin/bgaa032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 11/14/2022] Open
Abstract
Functioning mitochondria are crucial for cancer metabolism, but aerobic glycolysis is still considered to be an important pathway for energy production in many tumor cells. Here we show that two well established, classic Hodgkin lymphoma (cHL) cell lines harbor deleterious variants within mitochondrial DNA (mtDNA) and thus exhibit reduced steady-state levels of respiratory chain complexes. However, instead of resulting in the expected bioenergetic defect, these mtDNA variants evoke a retrograde signaling response that induces mitochondrial biogenesis and ultimately results in increased mitochondrial mass as well as function and enhances proliferation in vitro as well as tumor growth in mice in vivo. When complex I assembly was impaired by knockdown of one of its subunits, this led to further increased mitochondrial mass and function and, consequently, further accelerated tumor growth in vivo. In contrast, inhibition of mitochondrial respiration in vivo by the mitochondrial complex I inhibitor metformin efficiently slowed down growth. We conclude that, as a new mechanism, mildly deleterious mtDNA variants in cHL cancer cells cause an increase of mitochondrial mass and enhanced function as a compensatory effect using a retrograde signaling pathway, which provides an obvious advantage for tumor growth.
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Affiliation(s)
- Sophie Haumann
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Pediatrics, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Julia Boix
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jana Knuever
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Dermatology, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Angela Bieling
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Anton Vila Sanjurjo
- Grupo GIBE, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade de A Coruña (UDC), A Coruña, Spain
| | - Joanna L Elson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne UK
| | - Nicole Riet
- Department I for Internal Medicine, Medical Faculty and University of Cologne, 50931 Cologne, Germany
| | - Hinrich Abken
- Department I for Internal Medicine, Medical Faculty and University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,RCI, Regensburg Center for Interventional Immunology, Chair Gene-Immunotherapy, University Hospital Regensburg, Regensburg, Germany
| | - Hamid Kashkar
- Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Institute of Medical Microbiology, Immunology and Hygiene, Medical Faculty and University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Hue-Tran Hornig-Do
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Rudolf J Wiesner
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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130
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Multiplexed complexome profiling using tandem mass tags. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148448. [PMID: 34015258 DOI: 10.1016/j.bbabio.2021.148448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022]
Abstract
Complexome profiling is a rapidly spreading, powerful technique to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly, and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time of mass spectrometry analyses. Here, we report an improved process workflow that implements tandem mass tags for multiplexing complexome profiling. This workflow substantially reduces the number of samples and measuring time without compromising protein identification or quantification reliability. In profiles from mitochondrial fractions of cells recovering from chloramphenicol treatment, tandem mass tags-multiplexed complexome profiling exhibited migration patterns of mature ATP synthase (complex V) and assembly intermediates that were consistent in composition and abundance with profiles obtained by the label-free approach. Reporter ion quantifications of proteins and complexes unaffected by the chloramphenicol treatment presented less variation in comparison to the label-free method. Incorporation of tandem mass tags enabled an efficient and robust complexome profiling analysis and may foster broader application for protein complex profiling in biomedical research and diagnostics.
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131
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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: 12] [Impact Index Per Article: 4.0] [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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Xiong W, Yuan Z, Wang T, Wu S, Xiong Y, Yao Y, Yang Y, Wu H. Quercitrin Attenuates Acetaminophen-Induced Acute Liver Injury by Maintaining Mitochondrial Complex I Activity. Front Pharmacol 2021; 12:586010. [PMID: 34025394 PMCID: PMC8131832 DOI: 10.3389/fphar.2021.586010] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
The flavonoid quercitrin has a strong antioxidant property. It is also reported to have a protective effect on the liver. However, the mechanism by which it exerts a protective effect on the liver is not fully understood. The objective of this article is to confirm the protective effect of quercitrin extracted from Albiziae flos on acetaminophen (APAP)-induced liver injury and to explain its mechanism. In the in vivo study, quercitrin was administered orally to BALB/c mice at a dose of 50, 100, and 200 mg/kg for seven consecutive days. APAP (300 mg/kg) was injected intraperitoneally after a last dose of quercitrin was administered. Determination of alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), interleukin 6 (IL-6), tumor necrosis factor α (TNF-α), reactive oxygen species (ROS), superoxide dismutase (SOD), glutathione (GSH), glutathione peroxidase (GSH-Px), catalase (CAT), and malondialdehyde (MDA) levels showed that quercitrin effectively attenuated APAP-induced acute liver injury in mice. Results of the in vitro study showed that quercitrin reduced the levels of ROS, protected mitochondria from damage, and restored the activity of mitochondrial complex I in APAP-treated L-02 cells. The addition of rotenone which is an inhibitor of complex I blocked the protective effect of quercitrin. The expression of mitochondrial complex I was also maintained by quercitrin. Our results suggest that quercitrin can maintain the level of mitochondrial complex I in injured cells and restore its activity, which reduces the production of ROS, protects the mitochondria from oxidative stress, and has a protective effect on the liver.
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Affiliation(s)
- Weichen Xiong
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Zixin Yuan
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Tianshun Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Songtao Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yiyi Xiong
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yunfeng Yao
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yanfang Yang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.,Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, China.,Collaborative Innovation Center of Traditional Chinese Medicine of New Products for Geriatrics Hubei Province, Wuhan, China.,Key Laboratory of Traditional Chinese Medicine Resource and Compound Preparation Ministry of Education, Hubei University of Chinese Medicine, Wuhan, China
| | - Hezhen Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.,Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, China.,Collaborative Innovation Center of Traditional Chinese Medicine of New Products for Geriatrics Hubei Province, Wuhan, China.,Key Laboratory of Traditional Chinese Medicine Resource and Compound Preparation Ministry of Education, Hubei University of Chinese Medicine, Wuhan, China
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133
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Gonzalez-Franquesa A, Stocks B, Chubanava S, Hattel HB, Moreno-Justicia R, Peijs L, Treebak JT, Zierath JR, Deshmukh AS. Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity. Cell Rep 2021; 35:109180. [PMID: 34038727 DOI: 10.1016/j.celrep.2021.109180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of supercomplexes have typically relied upon antibody-based quantification, often limited to a single subunit per respiratory complex. To provide a deeper insight into mitochondrial and supercomplex plasticity, we combine native electrophoresis and mass spectrometry to determine the supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We quantify 422 mitochondrial proteins within 10 supercomplex bands in which we show the debated presence of complexes II and V. Exercise-induced mitochondrial biogenesis results in non-stoichiometric changes in subunits and incorporation into supercomplexes. We uncover the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits after exercise. Furthermore, exercise affects the complexing of Lactb, an obesity-associated mitochondrial protein, and ubiquinone biosynthesis proteins. Knockdown of ubiquinone biosynthesis proteins leads to alterations in mitochondrial respiration. Our approach can be applied to broad biological systems. In this instance, comprehensively analyzing respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.
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Affiliation(s)
- Alba Gonzalez-Franquesa
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Ben Stocks
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sabina Chubanava
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Helle B Hattel
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Roger Moreno-Justicia
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lone Peijs
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen 2200, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark.
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134
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Hernansanz-Agustín P, Enríquez JA. Functional segmentation of CoQ and cyt c pools by respiratory complex superassembly. Free Radic Biol Med 2021; 167:232-242. [PMID: 33722627 DOI: 10.1016/j.freeradbiomed.2021.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/23/2021] [Accepted: 03/07/2021] [Indexed: 12/25/2022]
Abstract
Electron transfer between respiratory complexes is an essential step for the efficiency of the mitochondrial oxidative phosphorylation. Until recently, it was stablished that ubiquinone and cytochrome c formed homogenous single pools in the inner mitochondrial membrane which were not influenced by the presence of respiratory supercomplexes. However, this idea was challenged by the fact that bottlenecks in electron transfer appeared after disruption of supercomplexes into their individual complexes. The postulation of the plasticity model embraced all these observations and concluded that complexes and supercomplexes co-exist and are dedicated to a spectrum of metabolic requirements. Here, we review the involvement of superassembly in complex I stability, the role of supercomplexes in ROS production and the segmentation of the CoQ and cyt c pools, together with their involvement in signaling and disease. Taking apparently conflicting literature we have built up a comprehensive model for the segmentation of CoQ and cyt c mediated by supercomplexes, discuss the current limitations and provide a prospect of the current knowledge in the field.
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Affiliation(s)
- Pablo Hernansanz-Agustín
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III CNIC, Melchor Fernández Almagro 3, Madrid, 28029, Spain.
| | - José Antonio Enríquez
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III CNIC, Melchor Fernández Almagro 3, Madrid, 28029, Spain; Centro de Investigaciones Biomédicas en Red de Fragilidad y Envejecimiento Saludable-CIBERFES. Av. Monforte de Lemos, 3-5. Pabellón 11, Planta 0 28029, Madrid, Spain.
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135
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Nolte H, Langer T. ComplexFinder: A software package for the analysis of native protein complex fractionation experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148444. [PMID: 33940038 DOI: 10.1016/j.bbabio.2021.148444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/28/2022]
Abstract
Identification of protein complexes and quantitative distribution of a single protein across different complexes are fundamental to unravel cellular mechanisms and of biological and clinical relevance. A recently introduced method, complexome profiling, combines fractionation techniques to separate native protein complexes with high-resolution mass spectrometry and allows to identify protein complexes in an unbiased manner. Due to recent advances in mass spectrometry instrumentation, the analysis time can be reduced dramatically while the coverage of thousands of proteins remains constant, which leads to an increased data acquisition rate and reduces the burden to initiate such complex experiments. Therefore, the development of novel computational pipelines for the analysis of such comprehensive complexome profiles is required. Usually, potential complex formations are assembled by correlation analysis. However, a major challenge in such an analysis is, that a protein can occur in multiple complexes of varying composition. Hence, signal profiles of proteins of the same complex might show high local similarities but do correlate poorly over all acquired fractions. Here, we describe ComplexFinder; a python-based computational pipeline that enables machine-learning based prediction of novel protein-protein interactions incorporating numerous measures of distance between signal profiles. Importantly, each signal profile is represented by an ensemble of peak-like models. These models allow the calculation of local similarities, enabling peak-centric comparison between biological conditions and the estimation of the composition of specific complexes. From the predicted protein-protein interactions, a protein connectivity network is constructed, which is used to assemble proteins into macromolecular complexes incorporating peak-centric information. ComplexFinder enables the peak-centric analysis of complexome profiling data utilizing various LC-MS/MS quantification strategies including label-free, SILAC, TMT as well as pulseSILAC. The source code is freely available at https://github.com/hnolcol/ComplexFinder.
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Affiliation(s)
- Hendrik Nolte
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann Str. 9b, 50931 Cologne, Germany.
| | - Thomas Langer
- Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann Str. 9b, 50931 Cologne, Germany; Institute of Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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136
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Martinez-Lopez JE, Coleman O, Meleady P, Clynes M. Transfection of miR-31* boosts oxidative phosphorylation metabolism in the mitochondria and enhances recombinant protein production in Chinese hamster ovary cells. J Biotechnol 2021; 333:86-96. [PMID: 33940052 DOI: 10.1016/j.jbiotec.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
MicroRNAs are increasingly being used to enhance relevant pathways of interest during CHO cell line development and to optimise biopharmaceutical production processes. Previous studies have demonstrated that genetic manipulation of microRNAs has led to the development of highly productive phenotypes by increasing cell density through modifying the cell cycle, extending the culture lifespan by delaying apoptotic mechanisms, or improving the energetic flux by targeting mitochondrial metabolism. Re-programming mitochondrial metabolism has arisen as a potential area of interest due to the potential to decrease the Warburg effect and increase cell specific productivity with significant impact on the manufacture of recombinant therapeutic proteins. In this study, we have demonstrated a role for miR-31* to enhance specific productivity in CHO cells by boosting oxidative phosphorylation in the mitochondria. A detailed analysis of the mitochondrial metabolism revealed that miR-31* transfection increases basal oxygen consumption and spare respiratory capacity that leads to an increase in ATP production. Additionally, a proteomic analysis unveiled a number of potential targets involved in fatty acid metabolism and the TCA cycle, both implicated in mitochondrial metabolism. This data demonstrates a potential role for miR-31* to reprogramme the mitochondrial energetic metabolism and increase recombinant protein production in CHO cells.
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Affiliation(s)
- Jesus E Martinez-Lopez
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
| | - Orla Coleman
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland.
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, D09 NR58, Ireland
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137
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Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:32. [PMID: 34549195 PMCID: PMC8451152 DOI: 10.1038/s43586-021-00029-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.
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Affiliation(s)
- Josie A. Christopher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Charlotte Stadler
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Claire E. Martin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David G. Rattray
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana Mahdessian
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS and CIBSS Signaling Research Centers, University of Freiburg, Freiburg, Germany
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Kathryn S. Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
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138
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Optic atrophy-associated TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I. Proc Natl Acad Sci U S A 2021; 118:2019665118. [PMID: 33879611 DOI: 10.1073/pnas.2019665118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mitochondrial disease is a debilitating condition with a diverse genetic etiology. Here, we report that TMEM126A, a protein that is mutated in patients with autosomal-recessive optic atrophy, participates directly in the assembly of mitochondrial complex I. Using a combination of genome editing, interaction studies, and quantitative proteomics, we find that loss of TMEM126A results in an isolated complex I deficiency and that TMEM126A interacts with a number of complex I subunits and assembly factors. Pulse-labeling interaction studies reveal that TMEM126A associates with the newly synthesized mitochondrial DNA (mtDNA)-encoded ND4 subunit of complex I. Our findings indicate that TMEM126A is involved in the assembly of the ND4 distal membrane module of complex I. In addition, we find that the function of TMEM126A is distinct from its paralogue TMEM126B, which acts in assembly of the ND2-module of complex I.
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139
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D'Angelo L, Astro E, De Luise M, Kurelac I, Umesh-Ganesh N, Ding S, Fearnley IM, Gasparre G, Zeviani M, Porcelli AM, Fernandez-Vizarra E, Iommarini L. NDUFS3 depletion permits complex I maturation and reveals TMEM126A/OPA7 as an assembly factor binding the ND4-module intermediate. Cell Rep 2021; 35:109002. [PMID: 33882309 PMCID: PMC8076766 DOI: 10.1016/j.celrep.2021.109002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/25/2021] [Accepted: 03/25/2021] [Indexed: 11/25/2022] Open
Abstract
Complex I (CI) is the largest enzyme of the mitochondrial respiratory chain, and its defects are the main cause of mitochondrial disease. To understand the mechanisms regulating the extremely intricate biogenesis of this fundamental bioenergetic machine, we analyze the structural and functional consequences of the ablation of NDUFS3, a non-catalytic core subunit. We show that, in diverse mammalian cell types, a small amount of functional CI can still be detected in the complete absence of NDUFS3. In addition, we determine the dynamics of CI disassembly when the amount of NDUFS3 is gradually decreased. The process of degradation of the complex occurs in a hierarchical and modular fashion in which the ND4 module remains stable and bound to TMEM126A. We, thus, uncover the function of TMEM126A, the product of a disease gene causing recessive optic atrophy as a factor necessary for the correct assembly and function of CI.
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Affiliation(s)
- Luigi D'Angelo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Elisa Astro
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Nikkitha Umesh-Ganesh
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Shujing Ding
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK
| | - Ian M Fearnley
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Massimo Zeviani
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK; Venetian Institute of Molecular Medicine, 35128 Padua, Italy; Department of Neurosciences, University of Padua, 35128 Padua, Italy
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy; Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell'Emilia, Italy
| | - Erika Fernandez-Vizarra
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY Cambridge, UK; Institute of Molecular, Cell and Systems Biology, University of Glasgow, G12 8QQ Glasgow, UK.
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy.
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140
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Organization of the Respiratory Supercomplexes in Cells with Defective Complex III: Structural Features and Metabolic Consequences. Life (Basel) 2021; 11:life11040351. [PMID: 33920624 PMCID: PMC8074069 DOI: 10.3390/life11040351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial respiratory chain encompasses four oligomeric enzymatic complexes (complex I, II, III and IV) which, together with the redox carrier ubiquinone and cytochrome c, catalyze electron transport coupled to proton extrusion from the inner membrane. The protonmotive force is utilized by complex V for ATP synthesis in the process of oxidative phosphorylation. Respiratory complexes are known to coexist in the membrane as single functional entities and as supramolecular aggregates or supercomplexes (SCs). Understanding the assembly features of SCs has relevant biomedical implications because defects in a single protein can derange the overall SC organization and compromise the energetic function, causing severe mitochondrial disorders. Here we describe in detail the main types of SCs, all characterized by the presence of complex III. We show that the genetic alterations that hinder the assembly of Complex III, not just the activity, cause a rearrangement of the architecture of the SC that can help to preserve a minimal energetic function. Finally, the major metabolic disturbances associated with severe SCs perturbation due to defective complex III are discussed along with interventions that may circumvent these deficiencies.
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141
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Fang H, Ye X, Xie J, Li Y, Li H, Bao X, Yang Y, Lin Z, Jia M, Han Q, Zhu J, Li X, Zhao Q, Yang Y, Lyu J. A membrane arm of mitochondrial complex I sufficient to promote respirasome formation. Cell Rep 2021; 35:108963. [PMID: 33852835 DOI: 10.1016/j.celrep.2021.108963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/25/2021] [Accepted: 03/16/2021] [Indexed: 01/02/2023] Open
Abstract
The assembly pathways of mitochondrial respirasome (supercomplex I+III2+IV) are not fully understood. Here, we show that an early sub-complex I assembly, rather than holo-complex I, is sufficient to initiate mitochondrial respirasome assembly. We find that a distal part of the membrane arm of complex I (PD-a module) is a scaffold for the incorporation of complexes III and IV to form a respirasome subcomplex. Depletion of PD-a, rather than other complex I modules, decreases the steady-state levels of complexes III and IV. Both HEK293T cells lacking TIMMDC1 and patient-derived cells with disease-causing mutations in TIMMDC1 showed accumulation of this respirasome subcomplex. This suggests that TIMMDC1, previously known as a complex-I assembly factor, may function as a respirasome assembly factor. Collectively, we provide a detailed, cooperative assembly model in which most complex-I subunits are added to the respirasome subcomplex in the lateral stages of respirasome assembly.
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Affiliation(s)
- Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China.
| | - Xianglai Ye
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Jie Xie
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Yuanyuan Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Haiyan Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Xinzhu Bao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Yue Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Zifan Lin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Manli Jia
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Qing Han
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Jingjing Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Xueyun Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiongya Zhao
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, Hangzhou 310000, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing 100000, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325000, China; Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, Hangzhou 310000, China.
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142
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Murari A, Rhooms SK, Goparaju NS, Villanueva M, Owusu-Ansah E. An antibody toolbox to track complex I assembly defines AIF's mitochondrial function. J Cell Biol 2021; 219:152090. [PMID: 32936885 PMCID: PMC7659709 DOI: 10.1083/jcb.202001071] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/01/2020] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
An ability to comprehensively track the assembly intermediates (AIs) of complex I (CI) biogenesis in Drosophila will enable the characterization of the precise mechanism(s) by which various CI regulators modulate CI assembly. Accordingly, we generated 21 novel antibodies to various mitochondrial proteins and used this resource to characterize the mechanism by which apoptosis-inducing factor (AIF) regulates CI biogenesis by tracking the AI profile observed when AIF expression is impaired. We find that when the AIF–Mia40 translocation complex is disrupted, the part of CI that transfers electrons to ubiquinone is synthesized but fails to progress in the CI biosynthetic pathway. This is associated with a reduction in intramitochondrial accumulation of the Mia40 substrate, MIC19. Importantly, knockdown of either MIC19 or MIC60, components of the mitochondrial contact site and cristae organizing system (MICOS), fully recapitulates the AI profile observed when AIF is inhibited. Thus, AIF’s effect on CI assembly is principally due to compromised intramitochondrial transport of the MICOS complex.
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Affiliation(s)
- Anjaneyulu Murari
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY
| | - Shauna-Kay Rhooms
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY
| | - Naga Sri Goparaju
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY
| | - Maximino Villanueva
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY
| | - Edward Owusu-Ansah
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY.,The Robert N. Butler Columbia Aging Center, Columbia University Medical Center, New York, NY
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143
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TMEM70 and TMEM242 help to assemble the rotor ring of human ATP synthase and interact with assembly factors for complex I. Proc Natl Acad Sci U S A 2021; 118:2100558118. [PMID: 33753518 PMCID: PMC8020751 DOI: 10.1073/pnas.2100558118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human mitochondrial ATP synthase is a molecular machine with a rotary action bound in the inner organellar membranes. Turning of the rotor, driven by a proton motive force, provides energy to make ATP from ADP and phosphate. Among the 29 component proteins of 18 kinds, ATP6 and ATP8 are mitochondrial gene products, and the rest are nuclear gene products that are imported into the organelle. The ATP synthase is assembled from them via intermediate modules representing the main structural elements of the enzyme. One such module is the c8-ring, which provides the membrane sector of the enzyme's rotor, and its assembly is influenced by another transmembrane (TMEM) protein, TMEM70. We have shown that subunit c interacts with TMEM70 and another hitherto unidentified mitochondrial transmembrane protein, TMEM242. Deletion of TMEM242, similar to deletion of TMEM70, affects but does not completely eliminate the assembly of ATP synthase, and to a lesser degree the assembly of respiratory enzyme complexes I, III, and IV. Deletion of TMEM70 and TMEM242 together prevents assembly of ATP synthase and the impact on complex I is enhanced. Removal of TMEM242, but not of TMEM70, also affects the introduction of subunits ATP6, ATP8, j, and k into the enzyme. TMEM70 and TMEM242 interact with the mitochondrial complex I assembly (the MCIA) complex that supports assembly of the membrane arm of complex I. The interactions of TMEM70 and TMEM242 with MCIA could be part of either the assembly of ATP synthase and complex I or the regulation of their levels.
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144
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Subrahmanian N, LaVoie MJ. Is there a special relationship between complex I activity and nigral neuronal loss in Parkinson's disease? A critical reappraisal. Brain Res 2021; 1767:147434. [PMID: 33745923 PMCID: PMC9520341 DOI: 10.1016/j.brainres.2021.147434] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/25/2021] [Accepted: 03/12/2021] [Indexed: 12/21/2022]
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disease manifesting both motor and non-motor symptoms. The motor features are generally ascribed to the selective loss of dopamine neurons within the substantia nigra pars compacta. While the precise etiology of PD remains elusive, multiple genetic and environmental elements have emerged as contributing factors. The discovery of MPTP-induced parkinsonism directed intense inquiry towards mitochondrial pathways, with a specific focus on mitochondrial complex I. Consisting of more than 40 subunits, complex I is the first enzyme of the electron transport chain that is required for mitochondrial ATP production. In this review, we present a critical analysis of studies assessing the prevalence and specificity of mitochondrial complex I deficiency in PD. In addition, we take the novel view of incorporating the features of genetically-defined bona fide complex I disorders and the prevalence of nigral involvement in such cases. Through this innovative bi-directional view, we consider both complex I changes in a disease of the substantia nigra and nigral changes in diseases of complex I. We assess the strength of association between nigral cell loss and complex I deficits, as well as the oft under-appreciated heterogeneity of complex I deficiency disorders and the variability of the PD data.
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Affiliation(s)
- Nitya Subrahmanian
- Department of Neurology, University of Florida, Gainesville, FL 32610, USA
| | - Matthew J LaVoie
- Department of Neurology, University of Florida, Gainesville, FL 32610, USA.
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145
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Stenton SL, Sheremet NL, Catarino CB, Andreeva NA, Assouline Z, Barboni P, Barel O, Berutti R, Bychkov I, Caporali L, Capristo M, Carbonelli M, Cascavilla ML, Charbel Issa P, Freisinger P, Gerber S, Ghezzi D, Graf E, Heidler J, Hempel M, Heon E, Itkis YS, Javasky E, Kaplan J, Kopajtich R, Kornblum C, Kovacs-Nagy R, Krylova TD, Kunz WS, La Morgia C, Lamperti C, Ludwig C, Malacarne PF, Maresca A, Mayr JA, Meisterknecht J, Nevinitsyna TA, Palombo F, Pode-Shakked B, Shmelkova MS, Strom TM, Tagliavini F, Tzadok M, van der Ven AT, Vignal-Clermont C, Wagner M, Zakharova EY, Zhorzholadze NV, Rozet JM, Carelli V, Tsygankova PG, Klopstock T, Wittig I, Prokisch H. Impaired complex I repair causes recessive Leber's hereditary optic neuropathy. J Clin Invest 2021; 131:138267. [PMID: 33465056 PMCID: PMC7954600 DOI: 10.1172/jci138267] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is the most frequent mitochondrial disease and was the first to be genetically defined by a point mutation in mitochondrial DNA (mtDNA). A molecular diagnosis is achieved in up to 95% of cases, the vast majority of which are accounted for by 3 mutations within mitochondrial complex I subunit–encoding genes in the mtDNA (mtLHON). Here, we resolve the enigma of LHON in the absence of pathogenic mtDNA mutations. We describe biallelic mutations in a nuclear encoded gene, DNAJC30, in 33 unsolved patients from 29 families and establish an autosomal recessive mode of inheritance for LHON (arLHON), which to date has been a prime example of a maternally inherited disorder. Remarkably, all hallmarks of mtLHON were recapitulated, including incomplete penetrance, male predominance, and significant idebenone responsivity. Moreover, by tracking protein turnover in patient-derived cell lines and a DNAJC30-knockout cellular model, we measured reduced turnover of specific complex I N-module subunits and a resultant impairment of complex I function. These results demonstrate that DNAJC30 is a chaperone protein needed for the efficient exchange of complex I subunits exposed to reactive oxygen species and integral to a mitochondrial complex I repair mechanism, thereby providing the first example to our knowledge of a disease resulting from impaired exchange of assembled respiratory chain subunits.
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Affiliation(s)
- Sarah L Stenton
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Natalia L Sheremet
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Claudia B Catarino
- Department of Neurology, Friedrich-Baur-Institute, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Natalia A Andreeva
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Zahra Assouline
- Fédération de Génétique et Institut Imagine, Université Paris Descartes, Hôpital Necker Enfants Malades, Paris, France
| | | | - Ortal Barel
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Igor Bychkov
- Research Centre for Medical Genetics, Moscow, Russia
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | | | | | - Peter Charbel Issa
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Peter Freisinger
- Department of Pediatrics, Klinikum am Steinenberg, Reutlingen, Germany
| | - Sylvie Gerber
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Elisabeth Graf
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Juliana Heidler
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elise Heon
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, The University of Toronto, Toronto, Canada
| | - Yulya S Itkis
- Research Centre for Medical Genetics, Moscow, Russia
| | - Elisheva Javasky
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Josseline Kaplan
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | | | - Reka Kovacs-Nagy
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Wolfram S Kunz
- Department of Experimental Epileptology and Cognition Research, University of Bonn, Bonn, Germany
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Munich, Germany
| | - Pedro F Malacarne
- Institute for Cardiovascular Physiology, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | | | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Jana Meisterknecht
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Tatiana A Nevinitsyna
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Institute for Rare Diseases.,Talpiot Medical Leadership Program, and
| | - Maria S Shmelkova
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Tim M Strom
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany
| | | | - Michal Tzadok
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Amelie T van der Ven
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | | | - Nino V Zhorzholadze
- Federal State Budgetary Institution of Science "Research Institute of Eye Diseases," Moscow, Russia
| | - Jean-Michel Rozet
- Laboratory Genetics in Ophthalmology (LGO), INSERM UMR1163 - Institute of Genetic Diseases, Imagine. Paris, France
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | | | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital of the Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Ilka Wittig
- Functional Proteomics, Medical School, Goethe University, Frankfurt am Main, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
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146
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Wang T, Liu H, Itoh K, Oh S, Zhao L, Murata D, Sesaki H, Hartung T, Na CH, Wang J. C9orf72 regulates energy homeostasis by stabilizing mitochondrial complex I assembly. Cell Metab 2021; 33:531-546.e9. [PMID: 33545050 PMCID: PMC8579819 DOI: 10.1016/j.cmet.2021.01.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 04/06/2020] [Accepted: 01/08/2021] [Indexed: 12/31/2022]
Abstract
The haploinsufficiency of C9orf72 is implicated in the most common forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but the full spectrum of C9orf72 functions remains to be established. Here, we report that C9orf72 is a mitochondrial inner-membrane-associated protein regulating cellular energy homeostasis via its critical role in the control of oxidative phosphorylation (OXPHOS). The translocation of C9orf72 from the cytosol to the inter-membrane space is mediated by the redox-sensitive AIFM1/CHCHD4 pathway. In mitochondria, C9orf72 specifically stabilizes translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1), a crucial factor for the assembly of OXPHOS complex I. C9orf72 directly recruits the prohibitin complex to inhibit the m-AAA protease-dependent degradation of TIMMDC1. The mitochondrial complex I function is impaired in C9orf72-linked ALS/FTD patient-derived neurons. These results reveal a previously unknown function of C9orf72 in mitochondria and suggest that defective energy metabolism may underlie the pathogenesis of relevant diseases.
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Affiliation(s)
- Tao Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kie Itoh
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sungtaek Oh
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Liang Zhao
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daisuke Murata
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hiromi Sesaki
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Thomas Hartung
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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147
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Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J 2021; 477:4085-4132. [PMID: 33151299 PMCID: PMC7657662 DOI: 10.1042/bcj20190767] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1–F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
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148
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Maclean AE, Bridges HR, Silva MF, Ding S, Ovciarikova J, Hirst J, Sheiner L. Complexome profile of Toxoplasma gondii mitochondria identifies divergent subunits of respiratory chain complexes including new subunits of cytochrome bc1 complex. PLoS Pathog 2021; 17:e1009301. [PMID: 33651838 PMCID: PMC7987180 DOI: 10.1371/journal.ppat.1009301] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/23/2021] [Accepted: 01/11/2021] [Indexed: 12/30/2022] Open
Abstract
The mitochondrial electron transport chain (mETC) and F1Fo-ATP synthase are of central importance for energy and metabolism in eukaryotic cells. The Apicomplexa, important pathogens of humans causing diseases such as toxoplasmosis and malaria, depend on their mETC in every known stage of their complicated life cycles. Here, using a complexome profiling proteomic approach, we have characterised the Toxoplasma mETC complexes and F1Fo-ATP synthase. We identified and assigned 60 proteins to complexes II, IV and F1Fo-ATP synthase of Toxoplasma, of which 16 have not been identified previously. Notably, our complexome profile elucidates the composition of the Toxoplasma complex III, the target of clinically used drugs such as atovaquone. We identified two new homologous subunits and two new parasite-specific subunits, one of which is broadly conserved in myzozoans. We demonstrate all four proteins are essential for complex III stability and parasite growth, and show their depletion leads to decreased mitochondrial potential, supporting their assignment as complex III subunits. Our study highlights the divergent subunit composition of the apicomplexan mETC and F1Fo-ATP synthase complexes and sets the stage for future structural and drug discovery studies.
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Affiliation(s)
- Andrew E. Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Hannah R. Bridges
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Mariana F. Silva
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Shujing Ding
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
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149
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Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia‐Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler‐Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gabriele Giachin
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Romain Bouverot
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Samira Acajjaoui
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Melissa Saïdi
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Anaïs Chretien
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Maria Bacia‐Verloop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Luca Signor
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Philippe J. Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS CEA, Université Grenoble Alpes 71 avenue des Martyrs 38042 Grenoble France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL) Grenoble Outstation 71 avenue des Martyrs 38042 Grenoble France
| | - Darren J. Hart
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eaazhisai Kandiah
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Gordon Leonard
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Montserrat Soler‐Lopez
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
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150
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Novais AK, Deschêne K, Martel-Kennes Y, Roy C, Laforest JP, Lessard M, Matte JJ, Lapointe J. Weaning differentially affects mitochondrial function, oxidative stress, inflammation and apoptosis in normal and low birth weight piglets. PLoS One 2021; 16:e0247188. [PMID: 33606751 PMCID: PMC7894895 DOI: 10.1371/journal.pone.0247188] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/02/2021] [Indexed: 01/22/2023] Open
Abstract
Weaning is associated with increased occurrence of infections and diseases in piglets. Recent findings indicate that weaning induces mitochondrial dysfunction and oxidative stress conditions that more severely impact smaller piglets. The objective of this study was to characterize the molecular mechanisms underlying these physiological consequences and the relation with systemic inflammatory status in both normal and low birth weight (NBW and LBW) piglets throughout the peri-weaning period. To conduct the study, 30 sows were inseminated, and specific piglets from their litters were assigned to one of two experimental groups: NBW (n = 60, 1.73 ± 0.01 kg,) and LBW piglets weighing less than 1.2 kg (n = 60, 1.01 ± 0.01 kg). Then, 10 piglets from each group were selected at 14, 21 (weaning), 23, 25, 29 and 35 days of age to collect organ and plasma samples. Specific porcine RT2 Profiler™ PCR Arrays related to mitochondrial function, oxidative stress, inflammation and apoptosis processes were first used to target genes that are modulated after weaning in NBW piglets (d 23 and d 35 vs. d 14). Expression of selected genes was evaluated by quantitative PCR. These analyses revealed that expression of inflammatory genes CXCL10 and CCL19 increased after weaning in intestinal mucosa, while expression of genes encoding subunits of the mitochondrial respiratory chain was downregulated in liver and kidney of both groups. Interestingly, major modulators of mitophagy (BNIP3), cell survival (BCL2A1) and antioxidant defense system (TXNRD2, GPx3, HMOX1) were found to be highly expressed in NBW piglets. The systemic levels of TNF-α and IL1-β significantly increased following weaning and were higher in NBW piglets. These results provide novel information about the molecular origin of mitochondrial dysfunction and oxidative stress observed in weaned piglets and suggest that clearance of dysfunctional mitochondria, antioxidant defenses and inflammatory response are compromised in LBW piglets.
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Affiliation(s)
- Aliny K. Novais
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
- Department of Animal Science, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Karine Deschêne
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Yan Martel-Kennes
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
- Département des Sciences Animales, Université Laval, Ville de Québec, Québec, Canada
| | - Caroline Roy
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Jean-Paul Laforest
- Département des Sciences Animales, Université Laval, Ville de Québec, Québec, Canada
| | - Martin Lessard
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - J. Jacques Matte
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Jerome Lapointe
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
- * E-mail:
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