1
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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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2
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566839. [PMID: 38014142 PMCID: PMC10680789 DOI: 10.1101/2023.11.13.566839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
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 oxidative decarboxylation of CoQ precursors. These findings fill a major gap in the knowledge of eukaryotic CoQ biosynthesis, and shed new 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
- Lead contact
| | - Fabien Pierrel
- Université Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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3
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Mantle D, Millichap L, Castro-Marrero J, Hargreaves IP. Primary Coenzyme Q10 Deficiency: An Update. Antioxidants (Basel) 2023; 12:1652. [PMID: 37627647 PMCID: PMC10451954 DOI: 10.3390/antiox12081652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
Coenzyme Q10 (CoQ10) has a number of vital functions in all cells, both mitochondrial and extra-mitochondrial. In addition to its key role in mitochondrial oxidative phosphorylation, CoQ10 serves as a lipid soluble antioxidant and plays an important role in fatty acid beta-oxidation and pyrimidine and lysosomal metabolism, as well as directly mediating the expression of a number of genes, including those involved in inflammation. Due to the multiplicity of roles in cell function, it is not surprising that a deficiency in CoQ10 has been implicated in the pathogenesis of a wide range of disorders. CoQ10 deficiency is broadly divided into primary and secondary types. Primary CoQ10 deficiency results from mutations in genes involved in the CoQ10 biosynthetic pathway. In man, at least 10 genes are required for the biosynthesis of functional CoQ10, a mutation in any one of which can result in a deficit in CoQ10 status. Patients may respond well to oral CoQ10 supplementation, although the condition must be recognised sufficiently early, before irreversible tissue damage has occurred. In this article, we have reviewed clinical studies (up to March 2023) relating to the identification of these deficiencies, and the therapeutic outcomes of CoQ10 supplementation; we have attempted to resolve the disparities between previous review articles regarding the usefulness or otherwise of CoQ10 supplementation in these disorders. In addition, we have highlighted several of the potential problems relating to CoQ10 supplementation in primary CoQ10 deficiency, as well as identifying unresolved issues relating to these disorders that require further research.
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Affiliation(s)
| | - Lauren Millichap
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
| | - Jesus Castro-Marrero
- Rheumatology Research Group, ME/CFS Research Unit, Vall d’Hebron Research Institute, Universitat Autonoma de Barcelona, 08035 Barcelona, Spain;
| | - Iain P. Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
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4
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Wang S, Jain A, Novales NA, Nashner AN, Tran F, Clarke CF. Predicting and Understanding the Pathology of Single Nucleotide Variants in Human COQ Genes. Antioxidants (Basel) 2022; 11:antiox11122308. [PMID: 36552517 PMCID: PMC9774615 DOI: 10.3390/antiox11122308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Abstract
Coenzyme Q (CoQ) is a vital lipid that functions as an electron carrier in the mitochondrial electron transport chain and as a membrane-soluble antioxidant. Deficiencies in CoQ lead to metabolic diseases with a wide range of clinical manifestations. There are currently few treatments that can slow or stop disease progression. Primary CoQ10 deficiency can arise from mutations in any of the COQ genes responsible for CoQ biosynthesis. While many mutations in these genes have been identified, the clinical significance of most of them remains unclear. Here we analyzed the structural and functional impact of 429 human missense single nucleotide variants (SNVs) that give rise to amino acid substitutions in the conserved and functional regions of human genes encoding a high molecular weight complex known as the CoQ synthome (or Complex Q), consisting of the COQ3-COQ7 and COQ9 gene products. Using structures of COQ polypeptides, close homologs, and AlphaFold models, we identified 115 SNVs that are potentially pathogenic. Further biochemical characterizations in model organisms such as Saccharomyces cerevisiae are required to validate the pathogenicity of the identified SNVs. Collectively, our results will provide a resource for clinicians during patient diagnosis and guide therapeutic efforts toward combating primary CoQ10 deficiency.
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5
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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6
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Diessl J, Berndtsson J, Broeskamp F, Habernig L, Kohler V, Vazquez-Calvo C, Nandy A, Peselj C, Drobysheva S, Pelosi L, Vögtle FN, Pierrel F, Ott M, Büttner S. Manganese-driven CoQ deficiency. Nat Commun 2022; 13:6061. [PMID: 36229432 PMCID: PMC9563070 DOI: 10.1038/s41467-022-33641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Overexposure to manganese disrupts cellular energy metabolism across species, but the molecular mechanism underlying manganese toxicity remains enigmatic. Here, we report that excess cellular manganese selectively disrupts coenzyme Q (CoQ) biosynthesis, resulting in failure of mitochondrial bioenergetics. While respiratory chain complexes remain intact, the lack of CoQ as lipophilic electron carrier precludes oxidative phosphorylation and leads to premature cell and organismal death. At a molecular level, manganese overload causes mismetallation and proteolytic degradation of Coq7, a diiron hydroxylase that catalyzes the penultimate step in CoQ biosynthesis. Coq7 overexpression or supplementation with a CoQ headgroup analog that bypasses Coq7 function fully corrects electron transport, thus restoring respiration and viability. We uncover a unique sensitivity of a diiron enzyme to mismetallation and define the molecular mechanism for manganese-induced bioenergetic failure that is conserved across species.
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Affiliation(s)
- Jutta Diessl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Jens Berndtsson
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Filomena Broeskamp
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Carmela Vazquez-Calvo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Arpita Nandy
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Carlotta Peselj
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Sofia Drobysheva
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Network Aging Research, Heidelberg University, 69120, Heidelberg, Germany
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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7
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Fernández-del-Río L, Clarke CF. Coenzyme Q Biosynthesis: An Update on the Origins of the Benzenoid Ring and Discovery of New Ring Precursors. Metabolites 2021; 11:385. [PMID: 34198496 PMCID: PMC8231959 DOI: 10.3390/metabo11060385] [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] [Received: 05/15/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Coenzyme Q (ubiquinone or CoQ) is a conserved polyprenylated lipid essential for mitochondrial respiration. CoQ is composed of a redox-active benzoquinone ring and a long polyisoprenyl tail that serves as a membrane anchor. A classic pathway leading to CoQ biosynthesis employs 4-hydroxybenzoic acid (4HB). Recent studies with stable isotopes in E. coli, yeast, and plant and animal cells have identified CoQ intermediates and new metabolic pathways that produce 4HB. Stable isotope labeling has identified para-aminobenzoic acid as an alternate ring precursor of yeast CoQ biosynthesis, as well as other natural products, such as kaempferol, that provide ring precursors for CoQ biosynthesis in plants and mammals. In this review, we highlight how stable isotopes can be used to delineate the biosynthetic pathways leading to CoQ.
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Affiliation(s)
| | - Catherine F. Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA;
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8
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Alcázar-Fabra M, Rodríguez-Sánchez F, Trevisson E, Brea-Calvo G. Primary Coenzyme Q deficiencies: A literature review and online platform of clinical features to uncover genotype-phenotype correlations. Free Radic Biol Med 2021; 167:141-180. [PMID: 33677064 DOI: 10.1016/j.freeradbiomed.2021.02.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/13/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022]
Abstract
Primary Coenzyme Q (CoQ) deficiencies are clinically heterogeneous conditions and lack clear genotype-phenotype correlations, complicating diagnosis and prognostic assessment. Here we present a compilation of all the symptoms and patients with primary CoQ deficiency described in the literature so far and analyse the most common clinical manifestations associated with pathogenic variants identified in the different COQ genes. In addition, we identified new associations between the age of onset of symptoms and different pathogenic variants, which could help to a better diagnosis and guided treatment. To make these results useable for clinicians, we created an online platform (https://coenzymeQbiology.github.io/clinic-CoQ-deficiency) about clinical manifestations of primary CoQ deficiency that will be periodically updated to incorporate new information published in the literature. Since CoQ primary deficiency is a rare disease, the available data are still limited, but as new patients are added over time, this tool could become a key resource for a more efficient diagnosis of this pathology.
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Affiliation(s)
- María Alcázar-Fabra
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA and CIBERER, Instituto de Salud Carlos III, Seville, 41013, Spain
| | | | - Eva Trevisson
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, 35128, Italy; Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padova, 35128, 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.
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9
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Nishida I, Yanai R, Matsuo Y, Kaino T, Kawamukai M. Benzoic acid inhibits Coenzyme Q biosynthesis in Schizosaccharomyces pombe. PLoS One 2020; 15:e0242616. [PMID: 33232355 PMCID: PMC7685456 DOI: 10.1371/journal.pone.0242616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023] Open
Abstract
Coenzyme Q (CoQ, ubiquinone) is an essential component of the electron transport system in aerobic organisms. Human type CoQ10, which has 10 units of isoprene in its quinone structure, is especially valuable as a food supplement. Therefore, studying the biosynthesis of CoQ10 is important not only for increasing metabolic knowledge, but also for improving biotechnological production. Herein, we show that Schizosaccharomyces pombe utilizes p-aminobenzoate (PABA) in addition to p-hydroxybenzoate (PHB) as a precursor for CoQ10 synthesis. We explored compounds that affect the synthesis of CoQ10 and found benzoic acid (Bz) at >5 μg/mL inhibited CoQ biosynthesis without accumulation of apparent CoQ intermediates. This inhibition was counteracted by incubation with a 10-fold lower amount of PABA or PHB. Overexpression of PHB-polyprenyl transferase encoded by ppt1 (coq2) also overcame the inhibition of CoQ biosynthesis by Bz. Inhibition by Bz was efficient in S. pombe and Schizosaccharomyces japonicus, but less so in Saccharomyces cerevisiae, Aureobasidium pullulans, and Escherichia coli. Bz also inhibited a S. pombe ppt1 (coq2) deletion strain expressing human COQ2, and this strain also utilized PABA as a precursor of CoQ10. Thus, Bz is likely to inhibit prenylation reactions involving PHB or PABA catalyzed by Coq2.
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Affiliation(s)
- Ikuhisa Nishida
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Ryota Yanai
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Yasuhiro Matsuo
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Tomohiro Kaino
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Makoto Kawamukai
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
- * E-mail:
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10
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Rhodoquinone in bacteria and animals: Two distinct pathways for biosynthesis of this key electron transporter used in anaerobic bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148278. [DOI: 10.1016/j.bbabio.2020.148278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
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11
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Disorders of Human Coenzyme Q10 Metabolism: An Overview. Int J Mol Sci 2020; 21:ijms21186695. [PMID: 32933108 PMCID: PMC7555759 DOI: 10.3390/ijms21186695] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022] Open
Abstract
Coenzyme Q10 (CoQ10) has a number of vital functions in all cells, both mitochondrial and extramitochondrial. In addition to its key role in mitochondrial oxidative phosphorylation, CoQ10 serves as a lipid soluble antioxidant, plays an important role in fatty acid, pyrimidine and lysosomal metabolism, as well as directly mediating the expression of a number of genes, including those involved in inflammation. In view of the central role of CoQ10 in cellular metabolism, it is unsurprising that a CoQ10 deficiency is linked to the pathogenesis of a range of disorders. CoQ10 deficiency is broadly classified into primary or secondary deficiencies. Primary deficiencies result from genetic defects in the multi-step biochemical pathway of CoQ10 synthesis, whereas secondary deficiencies can occur as result of other diseases or certain pharmacotherapies. In this article we have reviewed the clinical consequences of primary and secondary CoQ10 deficiencies, as well as providing some examples of the successful use of CoQ10 supplementation in the treatment of disease.
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12
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Wang Y, Hekimi S. Micellization of coenzyme Q by the fungicide caspofungin allows for safe intravenous administration to reach extreme supraphysiological concentrations. Redox Biol 2020; 36:101680. [PMID: 32810741 PMCID: PMC7451649 DOI: 10.1016/j.redox.2020.101680] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022] Open
Abstract
Coenzyme Q10 (CoQ10; also known as ubiquinone) is a vital, redox-active membrane component that functions as obligate electron transporter in the mitochondrial respiratory chain, as cofactor in other enzymatic processes and as antioxidant. CoQ10 supplementation has been widely investigated for treating a variety of acute and chronic conditions in which mitochondrial function or oxidative stress play a role. In addition, it is used as replacement therapy in patients with CoQ deficiency including inborn primary CoQ10 deficiency due to mutations in CoQ10-biosynthetic genes as well as secondary CoQ10 deficiency, which is frequently observed in patients with mitochondrial disease syndrome and in other conditions. However, despite many tests and some promising results, whether CoQ10 treatment is beneficial in any indication has remained inconclusive. Because CoQ10 is highly insoluble, it is only available in oral formulations, despite its very poor oral bioavailability. Using a novel model of CoQ-deficient cells, we screened a library of FDA-approved drugs for an activity that could increase the uptake of exogenous CoQ10 by the cell. We identified the fungicide caspofungin as capable of increasing the aqueous solubility of CoQ10 by several orders of magnitude. Caspofungin is a mild surfactant that solubilizes CoQ10 by forming nano-micelles with unique properties favoring stability and cellular uptake. Intravenous administration of the formulation in mice achieves unprecedented increases in CoQ10 plasma levels and in tissue uptake, with no observable toxicity. As it contains only two safe components (caspofungin and CoQ10), this injectable formulation presents a high potential for clinical safety and efficacy. Coenzyme Q10 (CoQ10) can be solubilized by the antifungal drug caspofungin (CF). CF is a mild surfactant and solubilizes CoQ10 in water by forming micellar structures with a high CoQ10 content. CF/CoQ10 micelles have unique properties favoring rapid and efficient uptake into cells and mitochondria. CF/CoQ10 micelles can be intravenously administrated without signs of toxicity. Intravenous administration of CF/CoQ10 in mice achieves unprecedented elevation of CoQ10 plasma levels and tissue uptake.
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Affiliation(s)
- Ying Wang
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montreal, Quebec, Canada.
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13
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Alves R, Kastora SL, Gomes-Gonçalves A, Azevedo N, Rodrigues CF, Silva S, Demuyser L, Van Dijck P, Casal M, Brown AJP, Henriques M, Paiva S. Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source. NPJ Biofilms Microbiomes 2020; 6:4. [PMID: 31993211 PMCID: PMC6978337 DOI: 10.1038/s41522-020-0114-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
Candida glabrata is an important human fungal pathogen known to trigger serious infections in immune-compromised individuals. Its ability to form biofilms, which exhibit high tolerance to antifungal treatments, has been considered as an important virulence factor. However, the mechanisms involving antifungal resistance in biofilms and the impact of host niche environments on these processes are still poorly defined. In this study, we performed a whole-transcriptome analysis of C. glabrata biofilm cells exposed to different environmental conditions and constraints in order to identify the molecular pathways involved in fluconazole resistance and understand how acidic pH niches, associated with the presence of acetic acid, are able to modulate these responses. We show that fluconazole treatment induces gene expression reprogramming in a carbon source and pH-dependent manner. This is particularly relevant for a set of genes involved in DNA replication, ergosterol, and ubiquinone biosynthesis. We also provide additional evidence that the loss of mitochondrial function is associated with fluconazole resistance, independently of the growth condition. Lastly, we propose that C. glabrata Mge1, a cochaperone involved in iron metabolism and protein import into the mitochondria, is a key regulator of fluconazole susceptibility during carbon and pH adaptation by reducing the metabolic flux towards toxic sterol formation. These new findings suggest that different host microenvironments influence directly the physiology of C. glabrata, with implications on how this pathogen responds to antifungal treatment. Our analyses identify several pathways that can be targeted and will potentially prove to be useful for developing new antifungals to treat biofilm-based infections.
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Grants
- MR/M026663/1 Medical Research Council
- MR/N006364/1 Medical Research Council
- MR/N006364/2 Medical Research Council
- This study was supported by the Portuguese National Funding Agency for Science, Research and Technology FCT (grant PTDC/BIAMIC/5184/2014). RA received FCT PhD fellowship (PD/BD/113813/2015). The authors gratefully acknowledge Edinburgh Genomics for RNA-Seq library preparation and sequencing. The work on CBMA was supported by the strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569). The work on CEB was supported by PEst-OE/EQB/LA0023/2013, from FCT, “BioHealth - Biotechnology and Bioengineering approaches to improve health quality", Ref. NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER and the project “Consolidating Research Expertize and Resources on Cellular and Molecular Biotechnology at CEB/IBB”, Ref. FCOMP-01-0124-FEDER-027462. The work in Aberdeen was also supported by the European Research Council through the advanced grant “STRIFE” (C-2009-AdG-249793), by the UK Medical Research Council (MR/M026663/1) and by the Medical Research Council Center for Medical Mycology and the University of Aberdeen (MR/N006364/1). The work at KU Leuven was supported by the Federation of European Biochemical Societies (FEBS) through a short-term fellowship awarded to RA and by the Fund for Scientific Research Flanders (FWO; WO.009.16N).
- Federation of European Biochemical Societies (FEBS)
- Strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569)
- European Research Council through the advanced grant “STRIFE” (C-2009-AdG-249793), UK Medical Research Council (MR/M026663/1) and Medical Research Council Center for Medical Mycology and the University of Aberdeen (MR/N006364/1
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Affiliation(s)
- Rosana Alves
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Stavroula L. Kastora
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
| | - Alexandra Gomes-Gonçalves
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Nuno Azevedo
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Célia F. Rodrigues
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
- LEPABE, Department of Chemical Engineering, University of Porto, Porto, Portugal
| | - Sónia Silva
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Flanders, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Margarida Casal
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Alistair J. P. Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
- MRC Center for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, UK
| | - Mariana Henriques
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Center for Biological Engineering, University of Minho, Braga, Portugal
| | - Sandra Paiva
- Center of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
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14
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Wang Y, Hekimi S. The Complexity of Making Ubiquinone. Trends Endocrinol Metab 2019; 30:929-943. [PMID: 31601461 DOI: 10.1016/j.tem.2019.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022]
Abstract
Ubiquinone (UQ, coenzyme Q) is an essential electron transfer lipid in the mitochondrial respiratory chain. It is a main source of mitochondrial reactive oxygen species (ROS) but also has antioxidant properties. This mix of characteristics is why ubiquinone supplementation is considered a potential therapy for many diseases involving mitochondrial dysfunction. Mutations in the ubiquinone biosynthetic pathway are increasingly being identified in patients. Furthermore, secondary ubiquinone deficiency is a common finding associated with mitochondrial disorders and might exacerbate these conditions. Recent developments have suggested that ubiquinone biosynthesis occurs in discrete domains of the mitochondrial inner membrane close to ER-mitochondria contact sites. This spatial requirement for ubiquinone biosynthesis could be the link between secondary ubiquinone deficiency and mitochondrial dysfunction, which commonly results in loss of mitochondrial structural integrity.
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Affiliation(s)
- Ying Wang
- Department of Biology, McGill University, Montreal, Canada
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15
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Lindahl PA. A comprehensive mechanistic model of iron metabolism in Saccharomyces cerevisiae. Metallomics 2019; 11:1779-1799. [PMID: 31531508 DOI: 10.1039/c9mt00199a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ironome of budding yeast (circa 2019) consists of approximately 139 proteins and 5 nonproteinaceous species. These proteins were grouped according to location in the cell, type of iron center(s), and cellular function. The resulting 27 groups were used, along with an additional 13 nonprotein components, to develop a mesoscale mechanistic model that describes the import, trafficking, metallation, and regulation of iron within growing yeast cells. The model was designed to be simultaneously mutually autocatalytic and mutually autoinhibitory - a property called autocatinhibitory that should be most realistic for simulating cellular biochemical processes. The model was assessed at the systems' level. General conclusions are presented, including a new perspective on understanding regulatory mechanisms in cellular systems. Some unsettled issues are described. This model, once fully developed, has the potential to mimic the phenotype (at a coarse-grain level) of all iron-related genetic mutations in this simple and well-studied eukaryote.
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Affiliation(s)
- Paul A Lindahl
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-3255, USA.
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16
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Vanillic Acid Restores Coenzyme Q Biosynthesis and ATP Production in Human Cells Lacking COQ6. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:3904905. [PMID: 31379988 PMCID: PMC6652073 DOI: 10.1155/2019/3904905] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 11/18/2022]
Abstract
Coenzyme Q (CoQ), a redox-active lipid, is comprised of a quinone group and a polyisoprenoid tail. It is an electron carrier in the mitochondrial respiratory chain, a cofactor of other mitochondrial dehydrogenases, and an essential antioxidant. CoQ requires a large set of enzymes for its biosynthesis; mutations in genes encoding these proteins cause primary CoQ deficiency, a clinically and genetically heterogeneous group of diseases. Patients with CoQ deficiency often respond to oral CoQ10 supplementation. Treatment is however problematic because of the low bioavailability of CoQ10 and the poor tissue delivery. In recent years, bypass therapy using analogues of the precursor of the aromatic ring of CoQ has been proposed as a promising alternative. We have previously shown using a yeast model that vanillic acid (VA) can bypass mutations of COQ6, a monooxygenase required for the hydroxylation of the C5 carbon of the ring. In this work, we have generated a human cell line lacking functional COQ6 using CRISPR/Cas9 technology. We show that these cells cannot synthesize CoQ and display severe ATP deficiency. Treatment with VA can recover CoQ biosynthesis and ATP production. Moreover, these cells display increased ROS production, which is only partially corrected by exogenous CoQ, while VA restores ROS to normal levels. Furthermore, we show that these cells accumulate 3-decaprenyl-1,4-benzoquinone, suggesting that in mammals, the decarboxylation and C1 hydroxylation reactions occur before or independently of the C5 hydroxylation. Finally, we show that COQ6 isoform c (transcript NM_182480) does not encode an active enzyme. VA can be produced in the liver by the oxidation of vanillin, a nontoxic compound commonly used as a food additive, and crosses the blood-brain barrier. These characteristics make it a promising compound for the treatment of patients with CoQ deficiency due to COQ6 mutations.
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17
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Del Borrello S, Lautens M, Dolan K, Tan JH, Davie T, Schertzberg MR, Spensley MA, Caudy AA, Fraser AG. Rhodoquinone biosynthesis in C. elegans requires precursors generated by the kynurenine pathway. eLife 2019; 8:e48165. [PMID: 31232688 PMCID: PMC6656428 DOI: 10.7554/elife.48165] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/22/2019] [Indexed: 02/05/2023] Open
Abstract
Parasitic helminths infect over a billion humans. To survive in the low oxygen environment of their hosts, these parasites use unusual anaerobic metabolism - this requires rhodoquinone (RQ), an electron carrier that is made by very few animal species. Crucially RQ is not made or used by any parasitic hosts and RQ synthesis is thus an ideal target for anthelmintics. However, little is known about how RQ is made and no drugs are known to block RQ synthesis. C. elegans makes RQ and can use RQ-dependent metabolic pathways - here, we use C. elegans genetics to show that tryptophan degradation via the kynurenine pathway is required to generate the key amine-containing precursors for RQ synthesis. We show that C. elegans requires RQ for survival in hypoxic conditions and, finally, we establish a high throughput assay for drugs that block RQ-dependent metabolism. This may drive the development of a new class of anthelmintic drugs. This study is a key first step in understanding how RQ is made in parasitic helminths.
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Affiliation(s)
| | | | | | - June H Tan
- The Donnelly CentreUniversity of TorontoTorontoCanada
| | - Taylor Davie
- The Donnelly CentreUniversity of TorontoTorontoCanada
| | | | - Mark A Spensley
- The Donnelly CentreUniversity of TorontoTorontoCanada
- Whole Animal PhenotypingPhenalysys IncTorontoCanada
| | - Amy A Caudy
- The Donnelly CentreUniversity of TorontoTorontoCanada
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18
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Eisenberg-Bord M, Tsui HS, Antunes D, Fernández-Del-Río L, Bradley MC, Dunn CD, Nguyen TPT, Rapaport D, Clarke CF, Schuldiner M. The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis. ACTA ACUST UNITED AC 2019; 2:2515256418825409. [PMID: 30937424 PMCID: PMC6441334 DOI: 10.1177/2515256418825409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loss of the endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) complex that resides in contact sites between the yeast ER and mitochondria leads to impaired respiration; however, the reason for that is not clear. We find that in ERMES null mutants, there is an increase in the level of mRNAs encoding for biosynthetic enzymes of coenzyme Q6 (CoQ6), an essential electron carrier of the mitochondrial respiratory chain. We show that the mega complexes involved in CoQ6 biosynthesis (CoQ synthomes) are destabilized in ERMES mutants. This, in turn, affects the level and distribution of CoQ6 within the cell, resulting in reduced mitochondrial CoQ6. We suggest that these outcomes contribute to the reduced respiration observed in ERMES mutants. Fluorescence microscopy experiments demonstrate close proximity between the CoQ synthome and ERMES, suggesting a spatial coordination. The involvement of the ER-mitochondria contact site in regulation of CoQ6 biogenesis highlights an additional level of communication between these two organelles.
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Affiliation(s)
| | - Hui S Tsui
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Diana Antunes
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Lucía Fernández-Del-Río
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Michelle C Bradley
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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19
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Hajj Chehade M, Pelosi L, Fyfe CD, Loiseau L, Rascalou B, Brugière S, Kazemzadeh K, Vo CDT, Ciccone L, Aussel L, Couté Y, Fontecave M, Barras F, Lombard M, Pierrel F. A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone. Cell Chem Biol 2019; 26:482-492.e7. [PMID: 30686758 DOI: 10.1016/j.chembiol.2018.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023]
Abstract
Ubiquinone (UQ) is a polyprenylated lipid that is conserved from bacteria to humans and is crucial to cellular respiration. How the cell orchestrates the efficient synthesis of UQ, which involves the modification of extremely hydrophobic substrates by multiple sequential enzymes, remains an unresolved issue. Here, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway in Escherichia coli. The SCP2 domain of UbiJ forms an extended hydrophobic cavity that binds UQ intermediates inside the 1-MDa Ubi complex. We purify the Ubi complex from cytoplasmic extracts and demonstrate that UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. Collectively, our results document a rare case of stable metabolon and highlight how the supramolecular organization of soluble enzymes allows the modification of hydrophobic substrates in a hydrophilic environment.
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Affiliation(s)
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Cameron David Fyfe
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Laurent Loiseau
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France
| | - Bérengère Rascalou
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Sabine Brugière
- Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | | | - Chau-Duy-Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Lidia Ciccone
- SOLEIL Synchrotron, L'Orme des Merisiers, 91198 Gif-sur-Yvette, France
| | - Laurent Aussel
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Frédéric Barras
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France; SAMe Unit, Department de Microbiologie, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France.
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20
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Subramanian K, Jochem A, Le Vasseur M, Lewis S, Paulson BR, Reddy TR, Russell JD, Coon JJ, Pagliarini DJ, Nunnari J. Coenzyme Q biosynthetic proteins assemble in a substrate-dependent manner into domains at ER-mitochondria contacts. J Cell Biol 2019; 218:1353-1369. [PMID: 30674579 PMCID: PMC6446851 DOI: 10.1083/jcb.201808044] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/05/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022] Open
Abstract
CoQ lipids are built at the mitochondrial inner membrane by a multicomponent pathway. Subramanian et al. reveal that CoQ pathway components assemble via CoQ intermediates into domains at ER–mitochondria contacts, suggesting that CoQ domains function as metabolons that facilitate processive CoQ production and distribution. Coenzyme Q (CoQ) lipids are ancient electron carriers that, in eukaryotes, function in the mitochondrial respiratory chain. In mitochondria, CoQ lipids are built by an inner membrane–associated, multicomponent, biosynthetic pathway via successive steps of isoprenyl tail polymerization, 4-hydroxybenzoate head-to-tail attachment, and head modification, resulting in the production of CoQ. In yeast, we discovered that head-modifying CoQ pathway components selectively colocalize to multiple resolvable domains in vivo, representing supramolecular assemblies. In cells engineered with conditional ON or OFF CoQ pathways, domains were strictly correlated with CoQ production and substrate flux, respectively, indicating that CoQ lipid intermediates are required for domain formation. Mitochondrial CoQ domains were also observed in human cells, underscoring their conserved functional importance. CoQ domains within cells were highly enriched adjacent to ER–mitochondria contact sites. Together, our data suggest that CoQ domains function to facilitate substrate accessibility for processive and efficient CoQ production and distribution in cells.
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Affiliation(s)
- Kelly Subramanian
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI
| | - Maxence Le Vasseur
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
| | - Samantha Lewis
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
| | | | | | - Jason D Russell
- Morgridge Institute for Research, Madison, WI.,Genome Center of Wisconsin, Madison, WI
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI.,Genome Center of Wisconsin, Madison, WI.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA
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21
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An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. Mol Cell 2019; 73:763-774.e10. [PMID: 30661980 DOI: 10.1016/j.molcel.2018.11.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/16/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.
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22
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Degli Esposti M. A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria. Genome Biol Evol 2018; 9:3039-3053. [PMID: 29106540 PMCID: PMC5714133 DOI: 10.1093/gbe/evx225] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 12/15/2022] Open
Abstract
Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochondria and bacteria. Nonorthologous proteins can also contribute to some biochemical steps as originally uncovered in Escherichia coli, which is the best studied organism for Q biosynthesis in prokaryotes. However, the origin of the biosynthetic pathway of Q has remained obscure. Here, I show by genome analysis that Q biosynthesis originated in cyanobacteria and then diversified in anaerobic alpha proteobacteria which have extant relatives in members of the Rhodospirillaceae family. Two distinct biochemical pathways diverged when ambient oxygen reached current levels on earth, one leading to the well-known series of Ubi genes found in E. coli, and the other containing CoQ proteins originally found in eukaryotes. Extant alpha proteobacteria show Q biosynthesis pathways that are more similar to that present in mitochondria than to that of E. coli. Hence, this work clarifies not only the origin but also the evolution of Q biosynthesis from bacteria to mitochondria.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genoa, Italy.,Center for Genomic Sciences, Universidad National Autonoma de Mexico Campus of Cuernavaca, Cuernavaca, Morelos, Mexico
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Reduction in the levels of CoQ biosynthetic proteins is related to an increase in lifespan without evidence of hepatic mitohormesis. Sci Rep 2018; 8:14013. [PMID: 30228311 PMCID: PMC6143522 DOI: 10.1038/s41598-018-32190-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/26/2018] [Indexed: 01/05/2023] Open
Abstract
Mitohormesis is an adaptive response induced by a mild mitochondrial stress that promotes longevity and metabolic health in different organisms. This mechanism has been proposed as the cause of the increase in the survival in Coq7+/- (Mclk1+/-) mice, which show hepatic reduction of COQ7, early mitochondrial dysfunction and increased oxidative stress. Our study shows that the lack of COQ9 in Coq9Q95X mice triggers the reduction of COQ7, COQ6 and COQ5, which results in an increase in life expectancy. However, our results reveal that the hepatic CoQ levels are not decreased and, therefore, neither mitochondrial dysfunction or increased oxidative stress are observed in liver of Coq9Q95X mice. These data point out the tissue specific differences in CoQ biosynthesis. Moreover, our results suggest that the effect of reduced levels of COQ7 on the increased survival in Coq9Q95X mice may be due to mitochondrial mechanisms in non-liver tissues or to other unknown mechanisms.
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Coenzyme Q 10 deficiencies: pathways in yeast and humans. Essays Biochem 2018; 62:361-376. [PMID: 29980630 PMCID: PMC6056717 DOI: 10.1042/ebc20170106] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/08/2018] [Accepted: 05/14/2018] [Indexed: 12/23/2022]
Abstract
Coenzyme Q (ubiquinone or CoQ) is an essential lipid that plays a role in mitochondrial respiratory electron transport and serves as an important antioxidant. In human and yeast cells, CoQ synthesis derives from aromatic ring precursors and the isoprene biosynthetic pathway. Saccharomyces cerevisiae coq mutants provide a powerful model for our understanding of CoQ biosynthesis. This review focusses on the biosynthesis of CoQ in yeast and the relevance of this model to CoQ biosynthesis in human cells. The COQ1–COQ11 yeast genes are required for efficient biosynthesis of yeast CoQ. Expression of human homologs of yeast COQ1–COQ10 genes restore CoQ biosynthesis in the corresponding yeast coq mutants, indicating profound functional conservation. Thus, yeast provides a simple yet effective model to investigate and define the function and possible pathology of human COQ (yeast or human gene involved in CoQ biosynthesis) gene polymorphisms and mutations. Biosynthesis of CoQ in yeast and human cells depends on high molecular mass multisubunit complexes consisting of several of the COQ gene products, as well as CoQ itself and CoQ intermediates. The CoQ synthome in yeast or Complex Q in human cells, is essential for de novo biosynthesis of CoQ. Although some human CoQ deficiencies respond to dietary supplementation with CoQ, in general the uptake and assimilation of this very hydrophobic lipid is inefficient. Simple natural products may serve as alternate ring precursors in CoQ biosynthesis in both yeast and human cells, and these compounds may act to enhance biosynthesis of CoQ or may bypass certain deficient steps in the CoQ biosynthetic pathway.
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Abstract
Prenylquinones are isoprenoid compounds with a characteristic quinone structure and isoprenyl tail that are ubiquitous in almost all living organisms. There are four major prenylquinone classes: ubiquinone (UQ), menaquinone (MK), plastoquinone (PQ), and rhodoquinone (RQ). The quinone structure and isoprenyl tail length differ among organisms. UQ, PQ, and RQ contain benzoquinone, while MK contains naphthoquinone. UQ, MK, and RQ are involved in oxidative phosphorylation, while PQ functions in photosynthetic electron transfer. Some organisms possess two types of prenylquinones; Escherichia coli has UQ8 and MK8, and Caenorhabditis elegans has UQ9 and RQ9. Crystal structures of most of the enzymes involved in MK synthesis have been solved. Studies on the biosynthesis and functions of quinones have advanced recently, including for phylloquinone (PhQ), which has a phytyl moiety instead of an isoprenyl tail. Herein, the synthesis and applications of prenylquinones are reviewed.
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Affiliation(s)
- Makoto Kawamukai
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
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26
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Stefely JA, Pagliarini DJ. Biochemistry of Mitochondrial Coenzyme Q Biosynthesis. Trends Biochem Sci 2017; 42:824-843. [PMID: 28927698 DOI: 10.1016/j.tibs.2017.06.008] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 11/16/2022]
Abstract
Coenzyme Q (CoQ, ubiquinone) is a redox-active lipid produced across all domains of life that functions in electron transport and oxidative phosphorylation and whose deficiency causes human diseases. Yet, CoQ biosynthesis has not been fully defined in any organism. Several proteins with unclear molecular functions facilitate CoQ biosynthesis through unknown means, and multiple steps in the pathway are catalyzed by currently unidentified enzymes. Here we highlight recent progress toward filling these knowledge gaps through both traditional biochemistry and cutting-edge 'omics' approaches. To help fill the remaining gaps, we present questions framed by the recently discovered CoQ biosynthetic complex and by putative biophysical barriers. Mapping CoQ biosynthesis, metabolism, and transport pathways has great potential to enhance treatment of numerous human diseases.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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Xia H, Tang Q, Song J, Ye J, Wu H, Zhang H. A yigP mutant strain is a small colony variant of E. coli and shows pleiotropic antibiotic resistance. Can J Microbiol 2017; 63:961-969. [PMID: 28915357 DOI: 10.1139/cjm-2017-0347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Small colony variants (SCVs) are a commonly observed subpopulation of bacteria that have a small colony size and distinctive biochemical characteristics. SCVs are more resistant than the wild type to some antibiotics and usually cause persistent infections in the clinic. SCV studies have been very active during the past 2 decades, especially Staphylococcus aureus SCVs. However, fewer studies on Escherichia coli SCVs exist, so we studied an E. coli SCV during an experiment involving the deletion of the yigP locus. PCR and DNA sequencing revealed that the SCV was attributable to a defect in the yigP function. Furthermore, we investigated the antibiotic resistance profile of the E. coli SCV and it showed increased erythromycin, kanamycin, and d-cycloserine resistance, but collateral sensitivity to ampicillin, polymyxin, chloramphenicol, tetracycline, rifampin, and nalidixic acid. We tried to determine the association between yigP and the pleiotropic antibiotic resistance of the SCV by analyzing biofilm formation, cellular morphology, and coenzyme Q (Q8) production. Our results indicated that impaired Q8 biosynthesis was the primary factor that contributed to the increased resistance and collateral sensitivity of the SCV. This study offers a novel genetic basis for E. coli SCVs and an insight into the development of alternative antimicrobial strategies for clinical therapy.
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Affiliation(s)
- Hui Xia
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Qiongwei Tang
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jie Song
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jiang Ye
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Haizhen Wu
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,b Department of Applied Biology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Huizhan Zhang
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,b Department of Applied Biology, East China University of Science and Technology, Shanghai, People's Republic of China
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28
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Xia H, Yang X, Tang Q, Ye J, Wu H, Zhang H. EsrE-A yigP Locus-Encoded Transcript-Is a 3' UTR sRNA Involved in the Respiratory Chain of E. coli. Front Microbiol 2017; 8:1658. [PMID: 28900423 PMCID: PMC5581919 DOI: 10.3389/fmicb.2017.01658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/15/2017] [Indexed: 01/20/2023] Open
Abstract
The yigP locus is widely conserved among γ-proteobacteria. Mutation of the yigP locus impacts aerobic growth of Gram-negative bacteria. However, the underlying mechanism of how the yigP locus influences aerobic growth remains largely unknown. Here, we demonstrated that the yigP locus in Escherichia coli encodes two transcripts; the mRNA of ubiquinone biosynthesis protein, UbiJ, and the 3′ untranslated region small regulatory RNA (sRNA), EsrE. EsrE is an independent transcript that is transcribed using an internal promoter of the yigP locus. Surprisingly, we found that both the EsrE sRNA and UbiJ protein were required for Q8 biosynthesis, and were sufficient to rescue the growth defect ascribed to deletion of the yigP locus. Moreover, our data showed that EsrE targeted multiple mRNAs involved in several cellular processes including murein biosynthesis and the tricarboxylic acid cycle. Among these targets, sdhD mRNA that encodes one subunit of succinate dehydrogenase (SDH), was significantly activated. Our findings provided an insight into the important function of EsrE in bacterial adaptation to various environments, as well as coordinating different aspects of bacterial physiology.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Xichen Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Qiongwei Tang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China.,Department of Applied Biology, East China University of Science and TechnologyShanghai, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China.,Department of Applied Biology, East China University of Science and TechnologyShanghai, China
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29
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He CH, Black DS, Allan CM, Meunier B, Rahman S, Clarke CF. Human COQ9 Rescues a coq9 Yeast Mutant by Enhancing Coenzyme Q Biosynthesis from 4-Hydroxybenzoic Acid and Stabilizing the CoQ-Synthome. Front Physiol 2017; 8:463. [PMID: 28736527 PMCID: PMC5500610 DOI: 10.3389/fphys.2017.00463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/16/2017] [Indexed: 11/18/2022] Open
Abstract
Coq9 is required for the stability of a mitochondrial multi-subunit complex, termed the CoQ-synthome, and the deamination step of Q intermediates that derive from para-aminobenzoic acid (pABA) in yeast. In human, mutations in the COQ9 gene cause neonatal-onset primary Q10 deficiency. In this study, we determined whether expression of human COQ9 could complement yeast coq9 point or null mutants. We found that expression of human COQ9 rescues the growth of the temperature-sensitive yeast mutant, coq9-ts19, on a non-fermentable carbon source and increases the content of Q6, by enhancing Q biosynthesis from 4-hydroxybenzoic acid (4HB). To study the mechanism for the rescue by human COQ9, we determined the steady-state levels of yeast Coq polypeptides in the mitochondria of the temperature-sensitive yeast coq9 mutant expressing human COQ9. We show that the expression of human COQ9 significantly increased steady-state levels of yeast Coq4, Coq6, Coq7, and Coq9 at permissive temperature. Human COQ9 polypeptide levels persisted at non-permissive temperature. A small amount of the human COQ9 co-purified with tagged Coq6, Coq6-CNAP, indicating that human COQ9 interacts with the yeast Q-biosynthetic complex. These findings suggest that human COQ9 rescues the yeast coq9 temperature-sensitive mutant by stabilizing the CoQ-synthome and increasing Q biosynthesis from 4HB. This finding provides a powerful approach to studying the function of human COQ9 using yeast as a model.
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Affiliation(s)
- Cuiwen H He
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, United States
| | - Dylan S Black
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, United States
| | - Christopher M Allan
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, United States
| | - Brigitte Meunier
- Institut de Biologie Intégrative de la Cellule, CEA, Centre National de la Recherche Scientifique, UPSud, Paris-Saclay UniversityGif-sur-Yvette, France
| | - Shamima Rahman
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation TrustLondon, United Kingdom.,Mitochondrial Research Group, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child HealthLondon, United Kingdom
| | - Catherine F Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, United States
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30
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Pierrel F. Impact of Chemical Analogs of 4-Hydroxybenzoic Acid on Coenzyme Q Biosynthesis: From Inhibition to Bypass of Coenzyme Q Deficiency. Front Physiol 2017; 8:436. [PMID: 28690551 PMCID: PMC5479927 DOI: 10.3389/fphys.2017.00436] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022] Open
Abstract
Coenzyme Q is a lipid that participates to important physiological functions. Coenzyme Q is synthesized in multiple steps from the precursor 4-hydroxybenzoic acid. Mutations in enzymes that participate to coenzyme Q biosynthesis result in primary coenzyme Q deficiency, a type of mitochondrial disease. Coenzyme Q10 supplementation of patients is the classical treatment but it shows limited efficacy in some cases. The molecular understanding of the coenzyme Q biosynthetic pathway allowed the design of experiments to bypass deficient biosynthetic steps with analogs of 4-hydroxybenzoic acid. These molecules provide the defective chemical group and can reactivate endogenous coenzyme Q biosynthesis as demonstrated recently in yeast, mammalian cell cultures, and mouse models of primary coenzyme Q deficiency. This mini review presents how the chemical properties of various analogs of 4-hydroxybenzoic acid dictate the effect of the molecules on CoQ biosynthesis and how the reactivation of endogenous coenzyme Q biosynthesis may achieve better results than exogenous CoQ10 supplementation.
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Affiliation(s)
- Fabien Pierrel
- Centre National de la Recherche Scientifique, Grenoble INP, TIMC-IMAG, University Grenoble AlpesGrenoble, France
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31
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Biosynthesis of 4-acetylantroquinonol B in Antrodia cinnamomea via a pathway related to coenzyme Q synthesis. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Payet LA, Leroux M, Willison JC, Kihara A, Pelosi L, Pierrel F. Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol 2016; 23:1241-1250. [PMID: 27693056 DOI: 10.1016/j.chembiol.2016.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/20/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Coenzyme Q (Q) is a redox lipid that is central for the energetic metabolism of eukaryotes. The biosynthesis of Q from the aromatic precursor 4-hydroxybenzoic acid (4-HB) is understood fairly well. However, biosynthetic details of how 4-HB is produced from tyrosine remain elusive. Here, we provide key insights into this long-standing biosynthetic problem by uncovering molecular details of the first and last reactions of the pathway in the yeast Saccharomyces cerevisiae, namely the deamination of tyrosine to 4-hydroxyphenylpyruvate by Aro8 and Aro9, and the oxidation of 4-hydroxybenzaldehyde to 4-HB by Hfd1. Inactivation of the HFD1 gene in yeast resulted in Q deficiency, which was rescued by the human enzyme ALDH3A1. This suggests that a similar pathway operates in animals, including humans, and led us to propose that patients with genetically unassigned Q deficiency should be screened for mutations in aldehyde dehydrogenase genes, especially ALDH3A1.
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Affiliation(s)
- Laurie-Anne Payet
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Mélanie Leroux
- CEA-Grenoble, DRF-BIG-CBM, UMR5249, 38000 Grenoble, France
| | | | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ludovic Pelosi
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Fabien Pierrel
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France.
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Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions. mSystems 2016; 1:mSystems00091-16. [PMID: 27822549 PMCID: PMC5069965 DOI: 10.1128/msystems.00091-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/05/2016] [Indexed: 11/27/2022] Open
Abstract
UQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a phylogenomic analysis of hydroxylases involved in UQ biosynthesis. Our results support the existence of at least two UQ hydroxylases in the proteobacterial ancestor, and yet, we show that their number varies from one to four in extant proteobacterial species. Our biochemical experiments demonstrated that bacteria containing only one or two UQ hydroxylases have developed generalist enzymes that are able to catalyze several steps of UQ biosynthesis. Our study documents a rare case where evolution favored the broadening of an enzyme’s regioselectivity, which resulted in gene loss in several proteobacterial species with small genomes. The ubiquitous ATP synthase uses an electrochemical gradient to synthesize cellular energy in the form of ATP. The production of this electrochemical gradient relies on liposoluble proton carriers like ubiquinone (UQ), which is used in the respiratory chains of eukaryotes and proteobacteria. The biosynthesis of UQ requires three hydroxylation reactions on contiguous positions of an aromatic ring. In Escherichia coli, each of three UQ flavin monooxygenases (FMOs), called UbiF, UbiH, and UbiI, modifies a single position of the aromatic ring. This pattern of three hydroxylation reactions/three proteins has been accepted as a paradigm in UQ biology. Using a phylogenetic analysis, we found that UbiF, UbiH, and UbiI are detected only in a small fraction of proteobacteria, and we identified two new types of UQ FMOs: UbiM, which is distributed in members of the alpha, beta, and gamma classes of proteobacteria, and UbiL, which is restricted to members of the alphaproteobacteria. Remarkably, the ubiL and ubiM genes were found in genomes with fewer than three UQ hydroxylase-encoding genes. We demonstrated, using biochemical approaches, that UbiL from Rhodospirillum rubrum and UbiM from Neisseria meningitidis hydroxylate, respectively, two and three positions of the aromatic ring during UQ biosynthesis. We conclude that bacteria have evolved a large repertoire of hydroxylase combinations for UQ biosynthesis, including pathways with either three specialist enzymes or pathways with one or two generalist enzymes of broader regioselectivity. The emergence of the latter is potentially related to genome reduction events. IMPORTANCE UQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a phylogenomic analysis of hydroxylases involved in UQ biosynthesis. Our results support the existence of at least two UQ hydroxylases in the proteobacterial ancestor, and yet, we show that their number varies from one to four in extant proteobacterial species. Our biochemical experiments demonstrated that bacteria containing only one or two UQ hydroxylases have developed generalist enzymes that are able to catalyze several steps of UQ biosynthesis. Our study documents a rare case where evolution favored the broadening of an enzyme’s regioselectivity, which resulted in gene loss in several proteobacterial species with small genomes.
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Acosta MJ, Vazquez Fonseca L, Desbats MA, Cerqua C, Zordan R, Trevisson E, Salviati L. Coenzyme Q biosynthesis in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1079-1085. [PMID: 27060254 DOI: 10.1016/j.bbabio.2016.03.036] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 01/11/2023]
Abstract
Coenzyme Q (CoQ, or ubiquinone) is a remarkable lipid that plays an essential role in mitochondria as an electron shuttle between complexes I and II of the respiratory chain, and complex III. It is also a cofactor of other dehydrogenases, a modulator of the permeability transition pore and an essential antioxidant. CoQ is synthesized in mitochondria by a set of at least 12 proteins that form a multiprotein complex. The exact composition of this complex is still unclear. Most of the genes involved in CoQ biosynthesis (COQ genes) have been studied in yeast and have mammalian orthologues. Some of them encode enzymes involved in the modification of the quinone ring of CoQ, but for others the precise function is unknown. Two genes appear to have a regulatory role: COQ8 (and its human counterparts ADCK3 and ADCK4) encodes a putative kinase, while PTC7 encodes a phosphatase required for the activation of Coq7. Mutations in human COQ genes cause primary CoQ(10) deficiency, a clinically heterogeneous mitochondrial disorder with onset from birth to the seventh decade, and with clinical manifestation ranging from fatal multisystem disorders, to isolated encephalopathy or nephropathy. The pathogenesis of CoQ(10) deficiency involves deficient ATP production and excessive ROS formation, but possibly other aspects of CoQ(10) function are implicated. CoQ(10) deficiency is unique among mitochondrial disorders since an effective treatment is available. Many patients respond to oral CoQ(10) supplementation. Nevertheless, treatment is still problematic because of the low bioavailability of the compound, and novel pharmacological approaches are currently being investigated. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Manuel Jesús Acosta
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Luis Vazquez Fonseca
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Cristina Cerqua
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Roberta Zordan
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy.
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, and IRP Città della Speranza, Padova, Italy.
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