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Launay R, Chobert SC, Abby SS, Pierrel F, André I, Esque J. Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework. J Chem Inf Model 2024; 64:5175-5193. [PMID: 38710096 DOI: 10.1021/acs.jcim.4c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Ubiquinone (UQ) is a redox polyisoprenoid lipid found in the membranes of bacteria and eukaryotes that has important roles, notably one in respiratory metabolism, which sustains cellular bioenergetics. In Escherichia coli, several steps of the UQ biosynthesis take place in the cytosol. To perform these reactions, a supramolecular assembly called Ubi metabolon is involved. This latter is composed of seven proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, and UbiK), and its structural organization is unknown as well as its protein stoichiometry. In this study, a computational framework has been designed to predict the structure of this macromolecular assembly. In several successive steps, we explored the possible protein interactions as well as the protein stoichiometry, to finally obtain a structural organization of the complex. The use of AlphaFold2-based methods combined with evolutionary information enabled us to predict several models whose quality and confidence were further analyzed using different metrics and scores. Our work led to the identification of a "core assembly" that will guide functional and structural characterization of the Ubi metabolon.
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Affiliation(s)
- Romain Launay
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Jérémy Esque
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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2
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Fabra MA, Paredes-Fuentes AJ, Torralba Carnerero M, Moreno Férnandez de Ayala DJ, Arroyo Luque A, Sánchez Cuesta A, Staiano C, Sanchez-Pintos P, Luz Couce M, Tomás M, Marco-Hernández AV, Orellana C, Martínez F, Roselló M, Caro A, Oltra Soler JS, Monfort S, Sánchez A, Rausell D, Vitoria I, Del Toro M, Garcia-Cazorla A, Julia-Palacios NA, Jou C, Yubero D, López LC, Hernández Camacho JD, López Lluch G, Ballesteros Simarro M, Rodríguez Aguilera JC, Calvo GB, Cascajo Almenara MV, Artuch R, Santos-Ocaña C. New variants expand the neurological phenotype of COQ7 deficiency. J Inherit Metab Dis 2024. [PMID: 38973597 DOI: 10.1002/jimd.12776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
The protein encoded by COQ7 is required for CoQ10 synthesis in humans, hydroxylating 3-demethoxyubiquinol (DMQ10) in the second to last steps of the pathway. COQ7 mutations lead to a primary CoQ10 deficiency syndrome associated with a pleiotropic neurological disorder. This study shows the clinical, physiological, and molecular characterization of four new cases of CoQ10 primary deficiency caused by five mutations in COQ7, three of which have not yet been described, inducing mitochondrial dysfunction in all patients. However, the specific combination of the identified variants in each patient generated precise pathophysiological and molecular alterations in fibroblasts, which would explain the differential in vitro response to supplementation therapy. Our results suggest that COQ7 dysfunction could be caused by specific structural changes that affect the interaction with COQ9 required for the DMQ10 presentation to COQ7, the substrate access to the active site, and the maintenance of the active site structure. Remarkably, patients' fibroblasts share transcriptional remodeling, supporting a modification of energy metabolism towards glycolysis, which could be an adaptive mechanism against CoQ10 deficiency. However, transcriptional analysis of mitochondria-associated pathways showed distinct and dramatic differences between patient fibroblasts, which correlated with the extent of pathophysiological and neurological alterations observed in the probands. Overall, this study suggests that the combination of precise genetic diagnostics and the availability of new structural models of human proteins could help explain the origin of phenotypic pleiotropy observed in some genetic diseases and the different responses to available therapies.
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Affiliation(s)
- María Alcázar Fabra
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Abraham J Paredes-Fuentes
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Manuel Torralba Carnerero
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
| | - Daniel J Moreno Férnandez de Ayala
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Antonio Arroyo Luque
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Ana Sánchez Cuesta
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Carmine Staiano
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Paula Sanchez-Pintos
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Hospital de Santiago de Compostela, IDIS, CIBERER, MetabERN, Santiago de Compostela, Spain
- GCV14/ER/5 CIBERER, Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - María Luz Couce
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Hospital de Santiago de Compostela, IDIS, CIBERER, MetabERN, Santiago de Compostela, Spain
- GCV14/ER/5 CIBERER, Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - Miguel Tomás
- Hospital Universitari i Politècnic La Fe, Servicio de Neuropediatría, Valencia, Spain
| | | | - Carmen Orellana
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | - Francisco Martínez
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | - Mónica Roselló
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | - Alfonso Caro
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | | | - Sandra Monfort
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | - Alejandro Sánchez
- Hospital Universitari i Politècnic La Fe, Unidad de Genética, Valencia, Spain
| | - Dolores Rausell
- Hospital Universitari i Politècnic La Fe, Servicio de Análisis Clínicos, Valencia, Spain
| | - Isidro Vitoria
- Hospital Universitari i Politècnic La Fe, Unidad de Metabolopatías, Valencia, Spain
| | - Mireia Del Toro
- Pediatric Neurology Unit, Hospital Universitari Vall d'Hebron, CIBERER, MetabERN, Barcelona, Spain
- Instituto de Salud Carlos III, Barcelona, Spain
| | - Angels Garcia-Cazorla
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Natalia A Julia-Palacios
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Cristina Jou
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Delia Yubero
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Luis Carlos López
- Departamento de Fisiología, Facultad de Medicina, Centro de Investigación Biomédica, Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | - Juan Diego Hernández Camacho
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Guillermo López Lluch
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Manuel Ballesteros Simarro
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Juan Carlos Rodríguez Aguilera
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Gloria Brea Calvo
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - María Victoria Cascajo Almenara
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Rafael Artuch
- Hospital San Joan de Deu, Barcelona, Spain
- Unidad U703 CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Carlos Santos-Ocaña
- Departamento de Fisiología, Anatomía y Biología Celular, CABD, Universidad Pablo de Olavide, Sevilla, Spain
- Unidad U729 CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
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3
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Zuccaro KE, Abriata LA, Pinto Meireles FT, Moss FR, Frost A, Dal Peraro M, Aydin H. Cardiolipin clustering promotes mitochondrial membrane dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595226. [PMID: 38826344 PMCID: PMC11142133 DOI: 10.1101/2024.05.21.595226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cardiolipin (CL) is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the precise mechanisms through which CL influences mitochondrial morphology are not well understood. In this study, employing molecular dynamics (MD) simulations, we observed CL localize near the membrane-binding sites of the mitochondrial fusion protein Optic Atrophy 1 (OPA1). To validate these findings experimentally, we developed a bromine-labeled CL probe to enhance cryoEM contrast and characterize the structure of OPA1 assemblies bound to the CL-brominated lipid bilayers. Our images provide direct evidence of interactions between CL and two conserved motifs within the paddle domain (PD) of OPA1, which control membrane-shaping mechanisms. We further observed a decrease in membrane remodeling activity for OPA1 in lipid compositions with increasing concentrations of monolyso-cardiolipin (MLCL). Suggesting that the partial replacement of CL by MLCL accumulation, as observed in Barth syndrome-associated mutations of the tafazzin phospholipid transacylase, compromises the stability of protein-membrane interactions. Our analyses provide insights into how biological membranes regulate the mechanisms governing mitochondrial homeostasis.
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Affiliation(s)
- Kelly E. Zuccaro
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Fernando Teixeira Pinto Meireles
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Frank R. Moss
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Halil Aydin
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
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4
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Pettenuzzo I, Carli S, Sánchez-Cuesta A, Isidori F, Montanari F, Grippa M, Lanzoni G, Ambrosetti I, Di Pisa V, Cordelli DM, Mondardini MC, Pippucci T, Ragni L, Cenacchi G, Costa R, Lima M, Capristo MA, Tropeano CV, Caporali L, Carelli V, Brunelli E, Maffei M, Ahmed Sheikhmaye H, Fetta A, Brea-Calvo G, Garone C. COQ7 defect causes prenatal onset of mitochondrial CoQ 10 deficiency with cardiomyopathy and gastrointestinal obstruction. Eur J Hum Genet 2024:10.1038/s41431-024-01615-w. [PMID: 38702428 DOI: 10.1038/s41431-024-01615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
COQ7 pathogenetic variants cause primary CoQ10 deficiency and a clinical phenotype of encephalopathy, peripheral neuropathy, or multisystemic disorder. Early diagnosis is essential for promptly starting CoQ10 supplementation. Here, we report novel compound heterozygous variants in the COQ7 gene responsible for a prenatal onset (20 weeks of gestation) of hypertrophic cardiomyopathy and intestinal dysmotility in a Bangladesh consanguineous family with two affected siblings. The main clinical findings were dysmorphisms, recurrent intestinal occlusions that required ileostomy, left ventricular non-compaction cardiomyopathy, ascending aorta dilation, arterial hypertension, renal dysfunction, diffuse skin desquamation, axial hypotonia, neurodevelopmental delay, and growth retardation. Exome sequencing revealed compound heterozygous rare variants in the COQ7 gene, c.613_617delGCCGGinsCAT (p.Ala205HisfsTer48) and c.403A>G (p.Met135Val). In silico analysis and functional in vitro studies confirmed the pathogenicity of the variants responsible for abolished activities of complexes I + III and II + III in muscle homogenate, severe decrease of CoQ10 levels, and reduced basal and maximal respiration in patients' fibroblasts. The first proband deceased at 14 months of age, whereas supplementation with a high dose of CoQ10 (30 mg/kg/day) since the first days of life modified the clinical course in the second child, showing a recovery of milestones acquirement at the last follow-up (18 months of age). Our study expands the clinical spectrum of primary CoQ10 deficiency due to COQ7 gene defects and highlights the essential role of multidisciplinary and combined approaches for a timely diagnosis.
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Affiliation(s)
- Ilaria Pettenuzzo
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'età Pediatrica, Bologna, Italy
| | - Sara Carli
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- Center for Applied Biomedical Research, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
| | - Ana Sánchez-Cuesta
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA and CIBERER, Instituto de Salud Carlos III, Seville, 41013, Spain
| | - Federica Isidori
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Mina Grippa
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Giulia Lanzoni
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Irene Ambrosetti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Veronica Di Pisa
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'età Pediatrica, Bologna, Italy
| | - Duccio Maria Cordelli
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'età Pediatrica, Bologna, Italy
| | - Maria Cristina Mondardini
- Pediatric Anesthesia and Intensive Care Unit, Department of Woman's and Child's Health, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
| | - Luca Ragni
- Pediatric Cardiology and Adult Congenital Heart Disease Program, Department of Cardio-Thoracic and Vascular Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Roberta Costa
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Mario Lima
- Pediatric Surgery Department, IRCCS Sant'Orsola-Malpighi Polyclinic, Alma Mater Studiorum-University of Bologna, 40126, Bologna, Italy
| | | | | | - Leonardo Caporali
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Elena Brunelli
- Obstetric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna University of Bologna, Bologna, Italia
| | - Monica Maffei
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di neuroradiologia con tecniche ad elevata complessità, Bologna, Italia
| | - Hodman Ahmed Sheikhmaye
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di neuroradiologia con tecniche ad elevata complessità, Bologna, Italia
| | - Anna Fetta
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'età Pediatrica, Bologna, Italy
| | - Gloria Brea-Calvo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA and CIBERER, Instituto de Salud Carlos III, Seville, 41013, Spain
| | - Caterina Garone
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy.
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'età Pediatrica, Bologna, Italy.
- Center for Applied Biomedical Research, Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy.
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5
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Qiu Y, Xiong Y, Wang L, Zhu M, Tan D, Hong D. Homozygous variant in COQ7 causes autosomal recessive hereditary spastic paraplegia. Ann Clin Transl Neurol 2024; 11:1067-1074. [PMID: 38439593 PMCID: PMC11021622 DOI: 10.1002/acn3.52037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/14/2024] [Accepted: 02/24/2024] [Indexed: 03/06/2024] Open
Abstract
Biallelic mutations in the coenzyme Q7 (COQ7) encoding gene were recently identified as a genetic cause of distal hereditary motor neuropathy. Here, we explored the clinical, electrophysiological, pathological, and genetic characteristics of a Chinese patient with spastic paraplegia associated with recessive variants in COQ7. This patient carried a novel c.322C>A (p.Pro108Thr) homozygous variant. Sural biopsy revealed mild mixed axonal and demyelinating degeneration. Immunoblotting showed a significant decrease in the COQ7 protein level in the patient's fibroblasts. This study confirmed that COQ7 variant as a genetic cause of HSP, and further extended spastic paraplegia to the phenotypic spectrum of COQ7-related disorders.
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Affiliation(s)
- Yusen Qiu
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
- Rare Disease CenterThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Ying Xiong
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Lulu Wang
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Min Zhu
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
- Rare Disease CenterThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Dandan Tan
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
- Rare Disease CenterThe First Affiliated Hospital of Nanchang UniversityNanchangChina
| | - Daojun Hong
- Department of NeurologyThe First Affiliated Hospital of Nanchang UniversityNanchangChina
- Rare Disease CenterThe First Affiliated Hospital of Nanchang UniversityNanchangChina
- Institute of Neurology, Jiangxi Academy of Clinical Medical Science, The First Affiliated Hospital, Jiangxi Medical CollegeNanchang UniversityNanchangChina
- Key Laboratory of Rare Neurological Diseases of Jiangxi Provincial Health Commission, Jiangxi Medical CollegeNanchang UniversityNanchangChina
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6
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Pelosi L, Morbiato L, Burgardt A, Tonello F, Bartlett AK, Guerra RM, Ferizhendi KK, Desbats MA, Rascalou B, Marchi M, Vázquez-Fonseca L, Agosto C, Zanotti G, Roger-Margueritat M, Alcázar-Fabra M, García-Corzo L, Sánchez-Cuesta A, Navas P, Brea-Calvo G, Trevisson E, Wendisch VF, Pagliarini DJ, Salviati L, Pierrel F. COQ4 is required for the oxidative decarboxylation of the C1 carbon of coenzyme Q in eukaryotic cells. Mol Cell 2024; 84:981-989.e7. [PMID: 38295803 DOI: 10.1016/j.molcel.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 03/10/2024]
Abstract
Coenzyme Q (CoQ) is a redox lipid that fulfills critical functions in cellular bioenergetics and homeostasis. CoQ is synthesized by a multi-step pathway that involves several COQ proteins. Two steps of the eukaryotic pathway, the decarboxylation and hydroxylation of position C1, have remained uncharacterized. Here, we provide evidence that these two reactions occur in a single oxidative decarboxylation step catalyzed by COQ4. We demonstrate that COQ4 complements an Escherichia coli strain deficient for C1 decarboxylation and hydroxylation and that COQ4 displays oxidative decarboxylation activity in the non-CoQ producer Corynebacterium glutamicum. Overall, our results substantiate that COQ4 contributes to CoQ biosynthesis, not only via its previously proposed structural role but also via the oxidative decarboxylation of CoQ precursors. These findings fill a major gap in the knowledge of eukaryotic CoQ biosynthesis and shed light on the pathophysiology of human primary CoQ deficiency due to COQ4 mutations.
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Affiliation(s)
- Ludovic Pelosi
- Université Grenoble Alpes, CNRS UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Laura Morbiato
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology, and Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | | | - Abigail K Bartlett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Bérengère Rascalou
- Université Grenoble Alpes, CNRS UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Marco Marchi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Luis Vázquez-Fonseca
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Caterina Agosto
- Pediatric Pain and Palliative Care Unit, Department of Women and Children's Health, University Hospital of Padova, 35128 Padova, Italy
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padua, Italy
| | | | - María Alcázar-Fabra
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and CIBERER, Sevilla, Spain
| | - Laura García-Corzo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and CIBERER, Sevilla, Spain
| | - Ana Sánchez-Cuesta
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and CIBERER, Sevilla, Spain
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and CIBERER, Sevilla, Spain
| | - Gloria Brea-Calvo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and CIBERER, Sevilla, Spain
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology, and Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, 35128 Padova, Italy; Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padua, Padua 35131, Italy.
| | - Fabien Pierrel
- Université Grenoble Alpes, CNRS UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France.
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7
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Herrero Martín JC, Salegi Ansa B, Álvarez-Rivera G, Domínguez-Zorita S, Rodríguez-Pombo P, Pérez B, Calvo E, Paradela A, Miguez DG, Cifuentes A, Cuezva JM, Formentini L. An ETFDH-driven metabolon supports OXPHOS efficiency in skeletal muscle by regulating coenzyme Q homeostasis. Nat Metab 2024; 6:209-225. [PMID: 38243131 PMCID: PMC10896730 DOI: 10.1038/s42255-023-00956-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/30/2023] [Indexed: 01/21/2024]
Abstract
Coenzyme Q (Q) is a key lipid electron transporter, but several aspects of its biosynthesis and redox homeostasis remain undefined. Various flavoproteins reduce ubiquinone (oxidized form of Q) to ubiquinol (QH2); however, in eukaryotes, only oxidative phosphorylation (OXPHOS) complex III (CIII) oxidizes QH2 to Q. The mechanism of action of CIII is still debated. Herein, we show that the Q reductase electron-transfer flavoprotein dehydrogenase (ETFDH) is essential for CIII activity in skeletal muscle. We identify a complex (comprising ETFDH, CIII and the Q-biosynthesis regulator COQ2) that directs electrons from lipid substrates to the respiratory chain, thereby reducing electron leaks and reactive oxygen species production. This metabolon maintains total Q levels, minimizes QH2-reductive stress and improves OXPHOS efficiency. Muscle-specific Etfdh-/- mice develop myopathy due to CIII dysfunction, indicating that ETFDH is a required OXPHOS component and a potential therapeutic target for mitochondrial redox medicine.
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Affiliation(s)
- Juan Cruz Herrero Martín
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Beñat Salegi Ansa
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Gerardo Álvarez-Rivera
- Laboratorio Foodomics, Instituto de Investigación en Ciencias de la Alimentación (CIAL), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Sonia Domínguez-Zorita
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigación Universitaria La Paz (IDIPAZ), Madrid, Spain
| | - Belén Pérez
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigación Universitaria La Paz (IDIPAZ), Madrid, Spain
| | - Enrique Calvo
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Madrid, Spain
| | - Alberto Paradela
- Proteomics Unit, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - David G Miguez
- Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Departamento de Física de la Materia Condensada, IFIMAC, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Alejandro Cifuentes
- Laboratorio Foodomics, Instituto de Investigación en Ciencias de la Alimentación (CIAL), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - José M Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
- Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Laura Formentini
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
- Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid (UAM), Madrid, Spain.
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8
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Zhang XY, Dong HL, Wu ZY. Axonal Charcot-Marie-Tooth disease due to COQ7 mutation: expanding the genetic and clinical spectrum. Brain 2023; 146:e117-e119. [PMID: 37343138 DOI: 10.1093/brain/awad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Xin-Yun Zhang
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hai-Lin Dong
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310009, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310012, China
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9
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González-Arzola K, Díaz-Quintana A. Mitochondrial Factors in the Cell Nucleus. Int J Mol Sci 2023; 24:13656. [PMID: 37686461 PMCID: PMC10563088 DOI: 10.3390/ijms241713656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The origin of eukaryotic organisms involved the integration of mitochondria into the ancestor cell, with a massive gene transfer from the original proteobacterium to the host nucleus. Thus, mitochondrial performance relies on a mosaic of nuclear gene products from a variety of genomes. The concerted regulation of their synthesis is necessary for metabolic housekeeping and stress response. This governance involves crosstalk between mitochondrial, cytoplasmic, and nuclear factors. While anterograde and retrograde regulation preserve mitochondrial homeostasis, the mitochondria can modulate a wide set of nuclear genes in response to an extensive variety of conditions, whose response mechanisms often merge. In this review, we summarise how mitochondrial metabolites and proteins-encoded either in the nucleus or in the organelle-target the cell nucleus and exert different actions modulating gene expression and the chromatin state, or even causing DNA fragmentation in response to common stress conditions, such as hypoxia, oxidative stress, unfolded protein stress, and DNA damage.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Consejo Superior de Investigaciones Científicas—Universidad de Sevilla—Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio Díaz-Quintana
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
- Instituto de Investigaciones Químicas—cicCartuja, Universidad de Sevilla—C.S.I.C, 41092 Seville, Spain
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10
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Wongkittichote P, Duque Lasio ML, Magistrati M, Pathak S, Sample B, Carvalho DR, Ortega AB, Castro MAA, de Gusmao CM, Toler TL, Bellacchio E, Dallabona C, Shinawi M. Phenotypic, molecular, and functional characterization of COQ7-related primary CoQ 10 deficiency: Hypomorphic variants and two distinct disease entities. Mol Genet Metab 2023; 139:107630. [PMID: 37392700 PMCID: PMC10995746 DOI: 10.1016/j.ymgme.2023.107630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
Primary coenzyme Q10 (CoQ10) deficiency is a group of inborn errors of metabolism caused by defects in CoQ10 biosynthesis. Biallelic pathogenic variants in COQ7, encoding mitochondrial 5-demethoxyubiquinone hydroxylase, have been reported in nine patients from seven families. We identified five new patients with COQ7-related primary CoQ10 deficiency, performed clinical assessment of the patients, and studied the functional effects of current and previously reported COQ7 variants and potential treatment options. The main clinical features included a neonatal-onset presentation with severe neuromuscular, cardiorespiratory and renal involvement and a late-onset disease presenting with progressive neuropathy, lower extremity weakness, abnormal gait, and variable developmental delay. Baker's yeast orthologue of COQ7, CAT5, is required for growth on oxidative carbon sources and cat5Δ strain demonstrates oxidative growth defect. Expression of wild-type CAT5 could completely rescue the defect; however, yeast CAT5 harboring equivalent human pathogenic variants could not. Interestingly, cat5Δ yeast harboring p.Arg57Gln (equivalent to human p.Arg54Gln), p.Arg112Trp (equivalent to p.Arg107Trp), p.Ile69Asn (equivalent to p.Ile66Asn) and combination of p.Lys108Met and p.Leu116Pro (equivalent to the complex allele p.[Thr103Met;Leu111Pro]) partially rescued the growth defects, indicating these variants are hypomorphic alleles. Supplementation with 2,4 dihydroxybenzoic acid (2,4-diHB) rescued the growth defect of both the leaky and severe mutants. Overexpression of COQ8 and 2,4-diHB supplementation synergistically restored oxidative growth and respiratory defect. Overall, we define two distinct disease presentations of COQ7-related disorder with emerging genotype-phenotype correlation and validate the use of the yeast model for functional studies of COQ7 variants.
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Affiliation(s)
- Parith Wongkittichote
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maria Laura Duque Lasio
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sheel Pathak
- Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Daniel Rocha Carvalho
- SARAH Network Rehabilitation Hospitals, Genetic Unit, Brasilia, Federal District, Brazil
| | | | - Matheus Augusto Araújo Castro
- Mendelics Genomic Analyses, Sao Paulo, Brazil; Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo HCFMUSP, São Paulo, SP, Brazil
| | - Claudio M de Gusmao
- Mendelics Genomic Analyses, Sao Paulo, Brazil; Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo HCFMUSP, São Paulo, SP, Brazil
| | - Tomi L Toler
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Emanuele Bellacchio
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA.
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11
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von der Malsburg A, Sapp GM, Zuccaro KE, von Appen A, Moss FR, Kalia R, Bennett JA, Abriata LA, Dal Peraro M, van der Laan M, Frost A, Aydin H. Structural mechanism of mitochondrial membrane remodelling by human OPA1. Nature 2023; 620:1101-1108. [PMID: 37612504 PMCID: PMC10875962 DOI: 10.1038/s41586-023-06441-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate1-3. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fusion of the mitochondrial inner membrane4,5. Despite its fundamental importance, the molecular mechanisms by which OPA1 modulates mitochondrial morphology are unclear. Here, using a combination of cellular and structural analyses, we illuminate the molecular mechanisms that are key to OPA1-dependent membrane remodelling and fusion. Human OPA1 embeds itself into cardiolipin-containing membranes through a lipid-binding paddle domain. A conserved loop within the paddle domain inserts deeply into the bilayer, further stabilizing the interactions with cardiolipin-enriched membranes. OPA1 dimerization through the paddle domain promotes the helical assembly of a flexible OPA1 lattice on the membrane, which drives mitochondrial fusion in cells. Moreover, the membrane-bending OPA1 oligomer undergoes conformational changes that pull the membrane-inserting loop out of the outer leaflet and contribute to the mechanics of membrane remodelling. Our findings provide a structural framework for understanding how human OPA1 shapes mitochondrial morphology and show us how human disease mutations compromise OPA1 functions.
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Affiliation(s)
- Alexander von der Malsburg
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Gracie M Sapp
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Kelly E Zuccaro
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Alexander von Appen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank R Moss
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA
| | - Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy A Bennett
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin van der Laan
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Altos Labs, Bay Area Institute of Science, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Halil Aydin
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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12
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Jacquier A, Theuriet J, Fontaine F, Mosbach V, Lacoste N, Ribault S, Risson V, Carras J, Coudert L, Simonet T, Latour P, Stojkovic T, Piard J, Cosson A, Lesca G, Bouhour F, Allouche S, Puccio H, Pegat A, Schaeffer L. Homozygous COQ7 mutation: a new cause of potentially treatable distal hereditary motor neuropathy. Brain 2023; 146:3470-3483. [PMID: 36454683 PMCID: PMC10393394 DOI: 10.1093/brain/awac453] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/30/2022] [Accepted: 11/20/2022] [Indexed: 08/03/2023] Open
Abstract
Distal hereditary motor neuropathy represents a group of motor inherited neuropathies leading to distal weakness. We report a family of two brothers and a sister affected by distal hereditary motor neuropathy in whom a homozygous variant c.3G>T (p.1Met?) was identified in the COQ7 gene. This gene encodes a protein required for coenzyme Q10 biosynthesis, a component of the respiratory chain in mitochondria. Mutations of COQ7 were previously associated with severe multi-organ disorders characterized by early childhood onset and developmental delay. Using patient blood samples and fibroblasts derived from a skin biopsy, we investigated the pathogenicity of the variant of unknown significance c.3G>T (p.1Met?) in the COQ7 gene and the effect of coenzyme Q10 supplementation in vitro. We showed that this variation leads to a severe decrease in COQ7 protein levels in the patient's fibroblasts, resulting in a decrease in coenzyme Q10 production and in the accumulation of 6-demethoxycoenzyme Q10, the COQ7 substrate. Interestingly, such accumulation was also found in the patient's plasma. Normal coenzyme Q10 and 6-demethoxycoenzyme Q10 levels were restored in vitro by using the coenzyme Q10 precursor 2,4-dihydroxybenzoic acid, thus bypassing the COQ7 requirement. Coenzyme Q10 biosynthesis deficiency is known to impair the mitochondrial respiratory chain. Seahorse experiments showed that the patient's cells mainly rely on glycolysis to maintain sufficient ATP production. Consistently, the replacement of glucose by galactose in the culture medium of these cells reduced their proliferation rate. Interestingly, normal proliferation was restored by coenzyme Q10 supplementation of the culture medium, suggesting a therapeutic avenue for these patients. Altogether, we have identified the first example of recessive distal hereditary motor neuropathy caused by a homozygous variation in the COQ7 gene, which should thus be included in the gene panels used to diagnose peripheral inherited neuropathies. Furthermore, 6-demethoxycoenzyme Q10 accumulation in the blood can be used to confirm the pathogenic nature of the mutation. Finally, supplementation with coenzyme Q10 or derivatives should be considered to prevent the progression of COQ7-related peripheral inherited neuropathy in diagnosed patients.
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Affiliation(s)
- Arnaud Jacquier
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Centre de Biotechnologie Cellulaire, CBC Biotec, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Julian Theuriet
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Hôpital Neurologique Pierre Wertheimer, Service d’électroneuromyographie et de pathologies neuromusculaires, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Fanny Fontaine
- Service de Biochimie, CHU de Caen, UMRS 1237 PhIND, Université de Caen, Caen, France
| | - Valentine Mosbach
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Nicolas Lacoste
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Shams Ribault
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Hôpital Henry Gabrielle, Service de Médecine Physique et de Réadaptation, CHU de Lyon—Hospices Civils de Lyon (HCL), Saint-Genis-Laval, France
| | - Valérie Risson
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Julien Carras
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Laurent Coudert
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Thomas Simonet
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Philippe Latour
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Unité fonctionnelle de neurogénétique moléculaire, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Tanya Stojkovic
- Institut de Myologie, Hôpital Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
| | - Juliette Piard
- Centre de Génétique Humaine, CHU, Besançon, France
- UMR-Inserm 1231 GAD, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, Dijon, France
| | - Anne Cosson
- Neurologie Électrophysiologie Clinique, CHU Jean-Minjoz, Besançon, France
| | - Gaëtan Lesca
- Service de génétique, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Françoise Bouhour
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Hôpital Neurologique Pierre Wertheimer, Service d’électroneuromyographie et de pathologies neuromusculaires, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Stéphane Allouche
- Service de Biochimie, CHU de Caen, UMRS 1237 PhIND, Université de Caen, Caen, France
| | - Hélène Puccio
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
| | - Antoine Pegat
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Hôpital Neurologique Pierre Wertheimer, Service d’électroneuromyographie et de pathologies neuromusculaires, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
| | - Laurent Schaeffer
- Pathophysiology and Genetics of Neuron and Muscle, CNRS UMR 5261, INSERM U1315, Université Lyon1, Faculté de Médecine Lyon Est, Lyon, France
- Centre de Biotechnologie Cellulaire, CBC Biotec, CHU de Lyon—Hospices Civils de Lyon (HCL) groupement Est, Bron, France
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13
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Staiano C, García-Corzo L, Mantle D, Turton N, Millichap LE, Brea-Calvo G, Hargreaves I. Biosynthesis, Deficiency, and Supplementation of Coenzyme Q. Antioxidants (Basel) 2023; 12:1469. [PMID: 37508007 PMCID: PMC10375973 DOI: 10.3390/antiox12071469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Originally identified as a key component of the mitochondrial respiratory chain, Coenzyme Q (CoQ or CoQ10 for human tissues) has recently been revealed to be essential for many different redox processes, not only in the mitochondria, but elsewhere within other cellular membrane types. Cells rely on endogenous CoQ biosynthesis, and defects in this still-not-completely understood pathway result in primary CoQ deficiencies, a group of conditions biochemically characterised by decreased tissue CoQ levels, which in turn are linked to functional defects. Secondary CoQ deficiencies may result from a wide variety of cellular dysfunctions not directly linked to primary synthesis. In this article, we review the current knowledge on CoQ biosynthesis, the defects leading to diminished CoQ10 levels in human tissues and their associated clinical manifestations.
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Affiliation(s)
- Carmine Staiano
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Laura García-Corzo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | | | - Nadia Turton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Merseyside L3 5UX, UK
| | - Lauren E Millichap
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Merseyside L3 5UX, UK
| | - Gloria Brea-Calvo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Merseyside L3 5UX, UK
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14
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Hu M, Jiang Y, Xu JJ. Characterization of Arabidopsis thaliana Coq9 in the CoQ Biosynthetic Pathway. Metabolites 2023; 13:813. [PMID: 37512520 PMCID: PMC10385794 DOI: 10.3390/metabo13070813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Coenzyme Q, also known as ubiquinone, is a fat-soluble isoprene quinone that serves as a cofactor for numerous enzymes across all domains of life. However, the biosynthetic pathway for this important molecule in plants has been examined in only a limited number of studies. In yeast and mammals, Coq9, an isoprenoid-lipid-binding protein, is essential for CoQ biosynthesis. Previous studies showed that Arabidopsis thaliana Coq9 failed to complement the fission yeast Schizosaccharomyces pombe coq9 null mutant, and its function in plants remains unknown. In this study, we demonstrated that expression of Arabidopsis Coq9 rescued the growth of a yeast temperature-sensitive coq9 mutant and increased CoQ content. Phylogenetic analysis revealed that Coq9 is widely present in green plants. Green fluorescent protein (GFP) fusion experiments showed that Arabidopsis Coq9 is targeted to mitochondria. Disruption of the Coq9 gene in Arabidopsis results in lower amounts of CoQ. Our work suggests that plant Coq9 is required for efficient CoQ biosynthesis. These findings provide new insights into the evolution of CoQ biosynthesis in plants. The identification of Coq9 as a key player in CoQ biosynthesis in plants opens up new avenues for understanding the regulation of this important metabolic pathway.
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Affiliation(s)
- Mei Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yan Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
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15
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Orris B, Sung MW, Bhat S, Xu Y, Huynh KW, Han S, Johnson DC, Bosbach B, Shields DJ, Stivers JT. Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.544806. [PMID: 37398126 PMCID: PMC10312740 DOI: 10.1101/2023.06.15.544806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA, and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ~20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
| | | | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
| | | | | | | | - Darren C. Johnson
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - David J. Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - James T. Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
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Guerra RM, Pagliarini DJ. Coenzyme Q biochemistry and biosynthesis. Trends Biochem Sci 2023; 48:463-476. [PMID: 36702698 PMCID: PMC10106368 DOI: 10.1016/j.tibs.2022.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/26/2023]
Abstract
Coenzyme Q (CoQ) is a remarkably hydrophobic, redox-active lipid that empowers diverse cellular processes. Although most known for shuttling electrons between mitochondrial electron transport chain (ETC) complexes, the roles for CoQ are far more wide-reaching and ever-expanding. CoQ serves as a conduit for electrons from myriad pathways to enter the ETC, acts as a cofactor for biosynthetic and catabolic reactions, detoxifies damaging lipid species, and engages in cellular signaling and oxygen sensing. Many open questions remain regarding the biosynthesis, transport, and metabolism of CoQ, which hinders our ability to treat human CoQ deficiency. Here, we recount progress in filling these knowledge gaps, highlight unanswered questions, and underscore the need for novel tools to enable discoveries and improve the treatment of CoQ-related diseases.
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Affiliation(s)
- Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Departament of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Departament of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Bennett JA, Steward LR, Rudolph J, Voss AP, Aydin H. The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding. PLoS Biol 2022; 20:e3001899. [PMID: 36534696 PMCID: PMC9815587 DOI: 10.1371/journal.pbio.3001899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/05/2023] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and bioenergetics in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space (IMS), where it assembles into filaments to regulate the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates lipid metabolism.
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Affiliation(s)
- Jeremy A. Bennett
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Lottie R. Steward
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Adam P. Voss
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Halil Aydin
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
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