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1. Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages

Author

Rubén Barcia-Cruz, David Goudenège, Jorge A. Moura de Sousa, Damien Piel, Martial Marbouty, Eduardo P. C. Rocha, and Frédérique Le Roux

Subjects
Science
Abstract

Abstract Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here we identify a family of satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), that are broadly distributed in marine bacteria of the family Vibrionaceae. A typical PICMI is characterized by reduced gene content, does not encode genes for capsid remodelling, and packages its DNA as a concatemer. PICMIs integrate in the bacterial host genome next to the fis regulator, and encode three core proteins necessary for excision and replication. PICMIs are dependent on virulent phage particles to spread to other bacteria, and protect their hosts from other competitive phages without interfering with their helper phage. Thus, our work broadens our understanding of phage satellites and narrows down the minimal number of functions necessary to hijack a tailed phage.

Published
2024
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2. Mitochondrial DNA Haplogroups and Variants Predispose to Chagas Disease Cardiomyopathy

Author

Frédéric Gallardo, Pauline Brochet, David Goudenège, João Paulo Silva Nunes, Pauline Andrieux, Barbara Maria Ianni, Amanda Farage Frade, Charles Mady, Ronaldo Honorato Barros Santos, Andreia Kuramoto, Samuel Steffen, Antonio Noedir Stolf, Pablo Pomerantzeff, Alfredo Inacio Fiorelli, Edimar Alcides Bocchi, Cristina Wide Pissetti, Bruno Saba, Fabrício C. Dias, Marcelo Ferraz Sampaio, Fabio Antônio Gaiotto, José Antonio Marin-Neto, Abílio Fragata, Ricardo Costa Fernandes Zaniratto, Sergio Siqueira, Giselle De Lima Peixoto, Fernando Bacal, Paula Buck, Rafael Ribeiro Almeida, Hui Tzu Lin-Wang, André Schmidt, Mario Hiroyuki Hirata, Eduardo Antonio Donadi, Alexandre Costa Pereira, Virmondes Rodrigues Junior, Martino Martinelli, Michel Naslavsky, Jorge Kalil, Vincent Procaccio, Edecio Cunha-Neto, and Christophe Chevillard

Subjects
chagas, cardiomyopathy, mitochondria, haplogroups, variants, copy-number, Medicine
Abstract

Cardiomyopathies are major causes of heart failure. Chagas disease (CD) is caused by the parasite Trypanosoma cruzi, and it is endemic in Central and South America. Thirty percent of cases evolve into chronic chagas cardiomyopathy (CCC), which has worse prognosis as compared with other cardiomyopathies. In vivo bioenergetic analysis and ex vivo proteomic analysis of myocardial tissues highlighted worse mitochondrial dysfunction in CCC, and previous studies identified nuclear-encoded mitochondrial gene variants segregating with CCC. Here, we assessed the role of the mitochondrial genome through mtDNA copy number variations and mtDNA haplotyping and sequencing from heart or blood tissues of severe, moderate CCC and asymptomatic/indeterminate Chagas disease as well as healthy controls as an attempt to help decipher mitochondrial-intrinsic genetic involvement in Chagas disease development. We have found that the mtDNA copy number was significantly lower in CCC than in heart tissue from healthy individuals, while blood mtDNA content was similar among asymptomatic Chagas disease, moderate, and severe CCC patients. An MtDNA haplogrouping study has indicated that African haplogroups were over represented in the Chagas subject groups in comparison with healthy Brazilian individuals. The European lineage is associated with protection against cardiomyopathy and the macro haplogroup H is associated with increased risk towards CCC. Using mitochondria DNA sequencing, 84 mtDNA-encoded protein sequence pathogenic variants were associated with CCC. Among them, two variants were associated to left ventricular non-compaction and two to hypertrophic cardiomyopathy. The finding that mitochondrial protein-coding SNPs and mitochondrial haplogroups associate with risk of evolving to CCC is consistent with a key role of mitochondrial DNA in the development of chronic chagas disease cardiomyopathy.

Published
2023
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3. Co-Exposure of Cardiomyocytes to IFN-γ and TNF-α Induces Mitochondrial Dysfunction and Nitro-Oxidative Stress: Implications for the Pathogenesis of Chronic Chagas Disease Cardiomyopathy

Author

João Paulo Silva Nunes, Pauline Andrieux, Pauline Brochet, Rafael Ribeiro Almeida, Eduardo Kitano, André Kenji Honda, Leo Kei Iwai, Débora Andrade-Silva, David Goudenège, Karla Deysiree Alcântara Silva, Raquel de Souza Vieira, Débora Levy, Sergio Paulo Bydlowski, Frédéric Gallardo, Magali Torres, Edimar Alcides Bocchi, Miguel Mano, Ronaldo Honorato Barros Santos, Fernando Bacal, Pablo Pomerantzeff, Francisco Rafael Martins Laurindo, Priscila Camillo Teixeira, Helder I. Nakaya, Jorge Kalil, Vincent Procaccio, Christophe Chevillard, and Edecio Cunha-Neto

Subjects
mitochondrial dysfunction, chronic Chagas disease cardiomyopathy, interferon gamma, energy metabolism, mitochondria, Immunologic diseases. Allergy, RC581-607
Abstract

Infection by the protozoan Trypanosoma cruzi causes Chagas disease cardiomyopathy (CCC) and can lead to arrhythmia, heart failure and death. Chagas disease affects 8 million people worldwide, and chronic production of the cytokines IFN-γ and TNF-α by T cells together with mitochondrial dysfunction are important players for the poor prognosis of the disease. Mitochondria occupy 40% of the cardiomyocytes volume and produce 95% of cellular ATP that sustain the life-long cycles of heart contraction. As IFN-γ and TNF-α have been described to affect mitochondrial function, we hypothesized that IFN-γ and TNF-α are involved in the myocardial mitochondrial dysfunction observed in CCC patients. In this study, we quantified markers of mitochondrial dysfunction and nitro-oxidative stress in CCC heart tissue and in IFN-γ/TNF-α-stimulated AC-16 human cardiomyocytes. We found that CCC myocardium displayed increased levels of nitro-oxidative stress and reduced mitochondrial DNA as compared with myocardial tissue from patients with dilated cardiomyopathy (DCM). IFN-γ/TNF-α treatment of AC-16 cardiomyocytes induced increased nitro-oxidative stress and decreased the mitochondrial membrane potential (ΔΨm). We found that the STAT1/NF-κB/NOS2 axis is involved in the IFN-γ/TNF-α-induced decrease of ΔΨm in AC-16 cardiomyocytes. Furthermore, treatment with mitochondria-sparing agonists of AMPK, NRF2 and SIRT1 rescues ΔΨm in IFN-γ/TNF-α-stimulated cells. Proteomic and gene expression analyses revealed that IFN-γ/TNF-α-treated cells corroborate mitochondrial dysfunction, transmembrane potential of mitochondria, altered fatty acid metabolism and cardiac necrosis/cell death. Functional assays conducted on Seahorse respirometer showed that cytokine-stimulated cells display decreased glycolytic and mitochondrial ATP production, dependency of fatty acid oxidation as well as increased proton leak and non-mitochondrial oxygen consumption. Together, our results suggest that IFN-γ and TNF-α cause direct damage to cardiomyocytes’ mitochondria by promoting oxidative and nitrosative stress and impairing energy production pathways. We hypothesize that treatment with agonists of AMPK, NRF2 and SIRT1 might be an approach to ameliorate the progression of Chagas disease cardiomyopathy.

Published
2021
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4. Glutamate-Induced Deregulation of Krebs Cycle in Mitochondrial Encephalopathy Lactic Acidosis Syndrome Stroke-Like Episodes (MELAS) Syndrome Is Alleviated by Ketone Body Exposure

Author

Sophie Belal, David Goudenège, Cinzia Bocca, Florent Dumont, Juan Manuel Chao De La Barca, Valérie Desquiret-Dumas, Naïg Gueguen, Guillaume Geffroy, Rayane Benyahia, Selma Kane, Salim Khiati, Céline Bris, Tamas Aranyi, Daniel Stockholm, Aurore Inisan, Aurélie Renaud, Magalie Barth, Gilles Simard, Pascal Reynier, Franck Letournel, Guy Lenaers, Dominique Bonneau, Arnaud Chevrollier, and Vincent Procaccio

Subjects
mitochondrial diseases, mtDNA, MELAS syndrome, multi-omics, glutamate, tricarboxylic acid cycle, Biology (General), QH301-705.5
Abstract

(1) Background: The development of mitochondrial medicine has been severely impeded by a lack of effective therapies. (2) Methods: To better understand Mitochondrial Encephalopathy Lactic Acidosis Syndrome Stroke-like episodes (MELAS) syndrome, neuronal cybrid cells carrying different mutation loads of the m.3243A > G mitochondrial DNA variant were analysed using a multi-omic approach. (3) Results: Specific metabolomic signatures revealed that the glutamate pathway was significantly increased in MELAS cells with a direct correlation between glutamate concentration and the m.3243A > G heteroplasmy level. Transcriptomic analysis in mutant cells further revealed alterations in specific gene clusters, including those of the glutamate, gamma-aminobutyric acid pathways, and tricarboxylic acid (TCA) cycle. These results were supported by post-mortem brain tissue analysis from a MELAS patient, confirming the glutamate dysregulation. Exposure of MELAS cells to ketone bodies significantly reduced the glutamate level and improved mitochondrial functions, reducing the accumulation of several intermediate metabolites of the TCA cycle and alleviating the NADH-redox imbalance. (4) Conclusions: Thus, a multi-omic integrated approach to MELAS cells revealed glutamate as a promising disease biomarker, while also indicating that a ketogenic diet should be tested in MELAS patients.

Published
2022
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5. Long-Term Persistence of Mitochondrial DNA Instability in HIV-Exposed Uninfected Children during and after Exposure to Antiretroviral Drugs and HIV

Author

Valérie Desquiret-Dumas, Morgana D’Ottavi, Audrey Monnin, David Goudenège, Nicolas Méda, Amélie Vizeneux, Chipepo Kankasa, Thorkild Tylleskar, Céline Bris, Vincent Procaccio, Nicolas Nagot, Philippe Van de Perre, Pascal Reynier, and Jean-Pierre Molès

Subjects
HIV, neonates, mitochondria, clinical outcomes, neurodevelopment, genetic alterations, Biology (General), QH301-705.5
Abstract

HIV-exposed uninfected (HEU) children show impaired health outcomes during childhood. A high rate of mitochondrial DNA (mtDNA) instability was reported in the blood of HEU at birth. We aimed to explore the relationship between these health outcomes and mtDNA deletions over time in a case series of 24 HEU children. MtDNA instability was assessed by deep sequencing and analyzed by eKLIPse-v2 algorithm at three time points, namely birth, 1 year, and 6 years of age. Association between mtDNA deletion and health outcomes, including growth, clinical, and neurodevelopmental parameters, were explored using univariate statistical analyses and after stratification with relevant variables. HEU children were selected with an equal male:female ratio. An elevated number of mtDNA deletions and duplications events was observed at 7 days’ post-partum. Median heteroplasmy increased at one year of life and then returned to baseline by six years of age. The mtDNA instability was acquired and was not transmitted by the mother. No risk factors were significantly associated with mtDNA instability. In this small case series, we did not detect any association between any health outcome at 6 years and mtDNA instability measures. A significant effect modification of the association between the duration of maternal prophylaxis and child growth was observed after stratification with heteroplasmy rate. Genomic instability persists over time among HEU children but, despite its extension, stays subclinical at six years.

Published
2022
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6. Use of Next-Generation Sequencing for the Molecular Diagnosis of 1,102 Patients With a Autosomal Optic Neuropathy

Author

Majida Charif, Céline Bris, David Goudenège, Valérie Desquiret-Dumas, Estelle Colin, Alban Ziegler, Vincent Procaccio, Pascal Reynier, Dominique Bonneau, Guy Lenaers, and Patrizia Amati-Bonneau

Subjects
inherited optic neuropathies, mitochondrial disorders, molecular diagnosis, next generation sequencing, retinal ganglia cells, Neurology. Diseases of the nervous system, RC346-429
Abstract

Advances in next-generation sequencing (NGS) facilitate the diagnosis of genetic disorders. To evaluate its use for the molecular diagnosis of inherited optic neuropathy (ION), a blinding disease caused by the degeneration of retinal ganglion cells, we performed genetic analysis using targeted NGS of 22 already known and candidate genes in a cohort of 1,102 affected individuals. The panel design, library preparation, and sequencing reactions were performed using the Ion AmpliSeq technology. Pathogenic variants were detected in 16 genes in 245 patients (22%), including 186 (17%) and 59 (5%) dominant and recessive cases, respectively. Results confirmed that OPA1 variants are responsible for the majority of dominant IONs, whereas ACO2 and WFS1 variants are also frequently involved in both dominant and recessive forms of ION. All pathogenic variants were found in genes encoding proteins involved in the mitochondrial function, highlighting the importance of mitochondria in the survival of retinal ganglion cells.

Published
2021
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7. Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders

Author

Aurélien Trimouille, Naïg Gueguen, C. Rouzier, Pascal Reynier, Christophe Verny, Patrizia Amati-Bonneau, Dominique Bonneau, Marie Laure Martin-Negrier, Claude Jardel, Samira Ait-El-Mkadem Saadi, Magalie Barth, Julien Cassereau, Franck Letournel, David Goudenège, Céline Bris, Benoit Rucheton, Estelle Colin, Magot Armelle, Stéphane Allouche, Sylvie Bannwarth, Véronique Paquis-Flucklinger, Abdel Slama, Yann Péréon, Valérie Desquiret-Dumas, Vincent Procaccio, Guy Lenaers, Pauline Gaignard, and Marco Spinazzi

Subjects
Adult, Genetics, Mitochondrial DNA, Mitochondrial Diseases, Nuclear gene, Mitochondrial disease, Breakpoint, Mitochondrial genome maintenance, High-Throughput Nucleotide Sequencing, Biology, medicine.disease, DNA, Mitochondrial, Heteroplasmy, Human genetics, Mitochondria, Genome, Mitochondrial, medicine, Humans, Gene, Genetics (clinical), Sequence Deletion
Abstract

Diseases caused by defects in mitochondrial DNA (mtDNA) maintenance machinery, leading to mtDNA deletions, form a specific group of disorders. However, mtDNA deletions also appear during aging, interfering with those resulting from mitochondrial disorders. Here, using next-generation sequencing (NGS) data processed by eKLIPse and data mining, we established criteria distinguishing age-related mtDNA rearrangements from those due to mtDNA maintenance defects. MtDNA deletion profiles from muscle and urine patient samples carrying pathogenic variants in nuclear genes involved in mtDNA maintenance (n = 40) were compared with age-matched controls (n = 90). Seventeen additional patient samples were used to validate the data mining model. Overall, deletion number, heteroplasmy level, deletion locations, and the presence of repeats at deletion breakpoints were significantly different between patients and controls, especially in muscle samples. The deletion number was significantly relevant in adults, while breakpoint repeat lengths surrounding deletions were discriminant in young subjects. Altogether, eKLIPse analysis is a powerful tool for measuring the accumulation of mtDNA deletions between patients of different ages, as well as in prioritizing novel variants in genes involved in mtDNA stability.

Published
2021
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8. Divergence in bacterial ecology is reflected by difference in population genetic structure, phage-predator load and host range

Author

Karine Cahier, Damien Piel, Rubén Barcia-Cruz, David Goudenège, K. Mathias Wegner, Marc Monot, Jesús L Romalde, and Frédérique Le Roux

Abstract

Phages depend on their bacterial host to replicate, but how habitat, density and diversity of the host population drive phage ecology is not well understood. Here, we addressed this question by comparing two populations of marine bacteria and their phages collected during a time series sampling in an oyster farm. Vibrio crassostreae reproduces more specifically in oysters. This population is genetically structured into clades of near clonal strains favoring infection by closely related phages and leading to a modular structure of the phage-bacterial infection network. Vibrio chagasii, on the other hand, blooms in the water column from where it can colonize oysters via filter-feeding. We found higher phage predation pressure on V. chagasii that did not result from a broader host range of the phages but rather from a greater burst size generating more infectious particles in the environment. We showed that contrasting patterns of genetic diversity for host and phage lead to different infection network architectures. We also provided evidence that a bloom of phages generates epigenetic and genetic variability that can be selected to counteract host defense systems.

Published
2022
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9. Next-generation sequencing of Tunisian Leigh syndrome patients reveals novel variations: impact for diagnosis and treatment

Author

Meriem Hechmi, Majida Charif, Ichraf Kraoua, Meriem Fassatoui, Hamza Dallali, Valerie Desquiret-Dumas, Céline Bris, David Goudenège, Cyrine Drissi, Saïd Galaï, Slah Ouerhani, Vincent Procaccio, Patrizia Amati-Bonneau, Sonia Abdelhak, Ilhem Ben Youssef-Turki, Guy Lenaers, and Rym Kefi

Subjects
Nucleocytoplasmic Transport Proteins, Biophysics, Biotin, High-Throughput Nucleotide Sequencing, Membrane Transport Proteins, Cell Biology, DNA, Mitochondrial, Mitochondrial Membrane Transport Proteins, Biochemistry, Mitochondrial Proteins, Mutation, Humans, Thiamine, Leigh Disease, Child, Molecular Biology
Abstract

Mitochondrial cytopathies, among which the Leigh syndrome (LS), are caused by variants either in the mitochondrial or the nuclear genome, affecting the oxidative phosphorylation process. The aim of the present study consisted in defining the molecular diagnosis of a group of Tunisian patients with LS. Six children, belonging to five Tunisian families, with clinical and imaging presentations suggestive of LS were recruited. Whole mitochondrial DNA and targeted next-generation sequencing of a panel of 281 nuclear genes involved in mitochondrial physiology were performed. Bioinformatic analyses were achieved in order to identify deleterious variations. A single m.10197G>A (p.Ala47Thr) variant was found in the mitochondrial MT-ND3 gene in one patient, while the others were related to autosomal homozygous variants: two c.1412delA (p.Gln471ArgfsTer42) and c.1264A>G (p.Thr422Ala) in SLC19A3, one c.454C>G (p.Pro152Ala) in SLC25A19 and one c.122G>A (p.Gly41Asp) in ETHE1. Our findings demonstrate the usefulness of genomic investigations to improve LS diagnosis in consanguineous populations and further allow for treating the patients harboring variants in SLC19A3 and SLC25A19 that contribute to thiamine transport, by thiamine and biotin supplementation. Considering the Tunisian genetic background, the newly identified variants could be screened in patients with similar clinical presentation in related populations.

Published
2022
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10. Usefulness of combined sequencing of the mitochondrial genome and a targeted panel of nuclear genes involved in mitochondrial diseases

Author

Adrien Bloch, Fanny Mochel, Benoit Rucheton, Foudil Lamari, David Goudenège, Sylvie Bannwarth, Réseau MitoDiag, Dominique Bonnefont-Rousselot, Sandrine Filaut, Flavie Ader, Vincent Procaccio, Laura Legrand, Véronique Fressart, and Pascale Richard

Subjects
Mitochondrial DNA, Mitochondrial Diseases, Nuclear gene, Mitochondrial disease, First line, Mutant, Reproducibility of Results, General Medicine, Computational biology, Biology, medicine.disease, DNA, Mitochondrial, Mitochondria, Nuclear DNA, Genome, Mitochondrial, medicine, Humans, Numt, Gene
Abstract

The molecular study of mitochondrial diseases, essential for diagnosis, is special due to the dual genetic origin of these pathologies: mitochondrial DNA and nuclear DNA. Complete mtDNA sequencing still remains the first line diagnostic test followed if negative, by resequencing panels of several hundred mitochondrially-encoded nuclear genes. This strategy, with an initial entire mtDNA sequencing, is currently justified by the presence of nuclear mitochondrial DNA sequences (NUMTs) in the nuclear genome. We designed a resequencing panel combining the mtDNA and 135 nuclear genes which was evaluated compared to the performances of the standard mtDNA sequencing. Method validation was performed on the reading depth and reproducibility of the results. Thirty patients were analyzed by both methods. We were able to demonstrate that NUMTs did not impact the mtDNA sequencing quality, as the identified variants and mutant loads were identical with the reference mtDNA sequencing method. Reading depths were higher than the recommendations of the MitoDiag French diagnostic network, for the entire mtDNA for muscle and for 70% of the mtDNA for blood. These results highlight the usefulness of combining both mtDNA and mitochondrially nuclear-encoded genes and thus obtain more complete results and faster turnaround time for mitochondrial disease patients.

Published
2021
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11. Next-Generation Sequencing Identifies Novel

Author

Majida, Charif, Arnaud, Chevrollier, Naïg, Gueguen, Selma, Kane, Céline, Bris, David, Goudenège, Valerie, Desquiret-Dumas, Isabelle, Meunier, Fanny, Mochel, Luc, Jeanjean, Fanny, Varenne, Vincent, Procaccio, Pascal, Reynier, Dominique, Bonneau, Patrizia, Amati-Bonneau, and Guy, Lenaers

Subjects
Mitochondrial Proteins, Mitochondrial Diseases, Optic Atrophy, Autosomal Dominant, High-Throughput Nucleotide Sequencing, Humans, Peptide Hydrolases
Abstract

Dominant Optic Atrophy (DOA) is one of the most common inherited mitochondrial diseases, leading to blindness. It is caused by the chronic degeneration of the retinal ganglion cells (RGCs) and their axons forming the optic nerve. Until now, DOA has been mainly associated with genes encoding proteins involved in mitochondrial network dynamics. Using next-generation and exome sequencing, we identified for the first time heterozygous

Published
2022

12. Phage-host coevolution in natural populations

Author

Damien Piel, Maxime Bruto, Yannick Labreuche, François Blanquart, David Goudenège, Rubén Barcia-Cruz, Sabine Chenivesse, Sophie Le Panse, Adèle James, Javier Dubert, Bruno Petton, Erica Lieberman, K. Mathias Wegner, Fatima A. Hussain, Kathryn M. Kauffman, Martin F. Polz, David Bikard, Sylvain Gandon, Eduardo P. C. Rocha, Frédérique Le Roux, Unité de Physiologie Fonctionnelle des Organismes Marins, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Universidade de Santiago de Compostela [Spain] (USC ), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Civil and Environmental Engineering [Cambridge] (CEE), Massachusetts Institute of Technology (MIT), Eligo Bioscience, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Universität Wien, Biologie de Synthèse - Synthetic biology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), We thank M. A. Petit, M. Blokesch, M. Sullivan and A. Bernheim for valuable suggestions, M. Touchon and A. Bernheim for assistance with vibrio genome annotation, Z. Chaplain for the illustrations and help during the time series sampling, the staff of the station Ifremer Argenton and Bouin, the ABIMS (Roscoff) and LABGeM (Evry) platforms for technical assistance, Z. Allouche, Biomics Platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA, and G. Riddihough from Life Science Editors for help with the manuscript. This work was supported by funding from the Agence Nationale de la Recherche (ANR-16-CE32-0008-01, REVENGE, ANR-20-CE35-0014, RESISTE), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 884988, Advanced ERC Dynamic) to F.L.R. and Ifremer to D.P. The work was further supported by a grant from the Simons Foundation (LIFE ID 572792) to M.F.P. Part of the Vibrio crassostreae genome sequencing was conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript., ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-16-CE32-0008,REVENGE,L'huître comme niche de l'évolution et l'émergence de vibrios pathogènes(2016), ANR-20-CE35-0014,RESISTE,Comprendre l'évolution de la résistance aux antimicrobiens chez les vibrios environnementaux(2020), European Project: 884988,ERC-2019-ADG,DYNAMIC(2021), Le Roux, Frédérique, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, L'huître comme niche de l'évolution et l'émergence de vibrios pathogènes - - REVENGE2016 - ANR-16-CE32-0008 - AAPG2016 - VALID, Comprendre l'évolution de la résistance aux antimicrobiens chez les vibrios environnementaux - - RESISTE2020 - ANR-20-CE35-0014 - AAPG2020 - VALID, A mechanistic approach to understand microbiome-viriome dynamics in nature - DYNAMIC - - ERC-2019-ADG2021-01-01 - 2025-12-31 - 884988 - VALID, Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Physiologie Fonctionnelle des Organismes Marins (PFOM), Laboratoire de Biologie Intégrative (LBI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Alfred Wegener Institute for Polar and Marine Research (AWI), University of Vienna [Vienna], Institut Pasteur [Paris] (IP), and Génétique des génomes - Genetics of Genomes (UMR 3525)

Subjects
Water microbiology, Microbiology (medical), MESH: Host Specificity, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Immunology, Cell Biology, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Applied Microbiology and Biotechnology, Microbiology, Host Specificity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Bacteriophages, MESH: Bacteriophages, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Viral genetics, Coevolution, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting cooccurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site. bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

Published
2022
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13. Dominant

Author

Majida, Charif, Naïg, Gueguen, Marc, Ferré, Zouhair, Elkarhat, Salim, Khiati, Morgane, LeMao, Arnaud, Chevrollier, Valerie, Desquiret-Dumas, David, Goudenège, Céline, Bris, Selma, Kane, Jennifer, Alban, Stéphanie, Chupin, Céline, Wetterwald, Leonardo, Caporali, Francesca, Tagliavini, Chiara, LaMorgia, Michele, Carbonelli, Neringa, Jurkute, Abdelhamid, Barakat, Philippe, Gohier, Christophe, Verny, Magalie, Barth, Vincent, Procaccio, Dominique, Bonneau, Xavier, Zanlonghi, Isabelle, Meunier, Nicole, Weisschuh, Simone, Schimpf-Linzenbold, Felix, Tonagel, Ulrich, Kellner, Patrick, Yu-Wai-Man, Valerio, Carelli, Bernd, Wissinger, Patrizia, Amati-Bonneau, Pascal, Reynier, and Guy, Lenaers

Subjects
mitochondria, AcademicSubjects/SCI01870, Original Article, AcademicSubjects/MED00310, Krebs cycle, eye diseases, ACO2, aconitase 2, optic neuropathy
Abstract

Biallelic mutations in ACO2, encoding the mitochondrial aconitase 2, have been identified in individuals with neurodegenerative syndromes, including infantile cerebellar retinal degeneration and recessive optic neuropathies (locus OPA9). By screening European cohorts of individuals with genetically unsolved inherited optic neuropathies, we identified 61 cases harbouring variants in ACO2, among whom 50 carried dominant mutations, emphasizing for the first time the important contribution of ACO2 monoallelic pathogenic variants to dominant optic atrophy. Analysis of the ophthalmological and clinical data revealed that recessive cases are affected more severely than dominant cases, while not significantly earlier. In addition, 27% of the recessive cases and 11% of the dominant cases manifested with extraocular features in addition to optic atrophy. In silico analyses of ACO2 variants predicted their deleterious impacts on ACO2 biophysical properties. Skin derived fibroblasts from patients harbouring dominant and recessive ACO2 mutations revealed a reduction of ACO2 abundance and enzymatic activity, and the impairment of the mitochondrial respiration using citrate and pyruvate as substrates, while the addition of other Krebs cycle intermediates restored a normal respiration, suggesting a possible short-cut adaptation of the tricarboxylic citric acid cycle. Analysis of the mitochondrial genome abundance disclosed a significant reduction of the mitochondrial DNA amount in all ACO2 fibroblasts. Overall, our data position ACO2 as the third most frequently mutated gene in autosomal inherited optic neuropathies, after OPA1 and WFS1, and emphasize the crucial involvement of the first steps of the Krebs cycle in the maintenance and survival of retinal ganglion cells., Graphical Abstract Graphical Abstract, By screening European cohorts of individuals with genetically unsolved inherited optic neuropathies, Charif et al. report 61 new cases harbouring variants in ACO2, among whom 50 with dominant mutations, emphasizing for the first time the important contribution of ACO2 monoallelic pathogenic variants to dominant optic atrophy.

Published
2021

14. Warburg-like effect is a hallmark of complex I assembly defects

Author

Naïg Gueguen, Anaïs Lebert, Guy Lenaers, Patrizia Amati-Bonneau, Magalie Barth, Mariame Selma Kane, Cédric Gadras, Pascal Reynier, David Goudenège, Dominique Bonneau, Valérie Desquiret-Dumas, Stéphanie Leruez, Stéphanie Chupin, Daniel Henrion, Morgane Le Mao, Céline Wetterwald, Vincent Procaccio, Salim Khiati, Géraldine Leman, Guillaume Geffroy, Lydie Tessier, Arnaud Chevrollier, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Angers (UA), ARN : régulations naturelle et artificielle, Université Bordeaux Segalen - Bordeaux 2-Institut Européen de Chimie et de Biologie-Institut National de la Santé et de la Recherche Médicale (INSERM), Mitochondrie : Régulations et Pathologie, Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de Biochimie et Génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Réseau Maladies Métaboliques, Hôpitaux Universitaires du Grand Ouest, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Physiopathologie et thérapie des déficits sensoriels et moteurs, and Université Montpellier 2 - Sciences et Techniques (UM2)-IFR76-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, Mitochondrial Diseases, [SDV]Life Sciences [q-bio], Citric Acid Cycle, Regulator, 03 medical and health sciences, 0302 clinical medicine, Humans, Glycolysis, RNA, Small Interfering, Overproduction, Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Principal Component Analysis, Reactive oxygen species, Electron Transport Complex I, ATP synthase, biology, Catabolism, NADH Dehydrogenase, Fibroblasts, Pyruvate dehydrogenase complex, Warburg effect, Mitochondria, Cell biology, 030104 developmental biology, Metabolic Engineering, chemistry, 030220 oncology & carcinogenesis, biology.protein, Molecular Medicine, RNA Interference, Reactive Oxygen Species
Abstract

Due to its pivotal role in NADH oxidation and ATP synthesis, mitochondrial complex I (CI) emerged as a crucial regulator of cellular metabolism. A functional CI relies on the sequential assembly of nuclear- and mtDNA-encoded subunits; however, whether CI assembly status is involved in the metabolic adaptations in CI deficiency still remains largely unknown. Here, we investigated the relationship between CI functions, its structure and the cellular metabolism in 29 patient fibroblasts representative of most CI mitochondrial diseases. Our results show that, contrary to the generally accepted view, a complex I deficiency does not necessarily lead to a glycolytic switch, i.e. the so-called Warburg effect, but that this particular metabolic adaptation is a feature of CI assembly defect. By contrast, a CI functional defect without disassembly induces a higher catabolism to sustain the oxidative metabolism. Mechanistically, we demonstrate that reactive oxygen species overproduction by CI assembly intermediates and subsequent AMPK-dependent Pyruvate Dehydrogenase inactivation are key players of this metabolic reprogramming. Thus, this study provides a two-way-model of metabolic responses to CI deficiencies that are central not only in defining therapeutic strategies for mitochondrial diseases, but also in all pathophysiological conditions involving a CI deficiency.

Published
2019
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15. Next generation sequencing in family with MNGIE syndrome associated to optic atrophy: Novel homozygous POLG mutation in the C-terminal sub-domain leading to mtDNA depletion

Author

David Goudenège, Pascal Reynier, Majida Charif, Rahma Felhi, Dominique Bonneau, Mongia Hachicha, Lamia Sfaihi, Céline Bris, Leila Ammar-Keskes, Guy Lenaers, Patrizia Amati-Bonneau, Valérie Desquiret-Dumas, Vincent Procaccio, Faiza Fakhfakh, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Hedi Chaker Hospital [Sfax], Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Pediatrics, Mitochondrie : Régulations et Pathologie, Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiopathologie et thérapie des déficits sensoriels et moteurs, Université Montpellier 2 - Sciences et Techniques (UM2)-IFR76-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, This work was supported by the Ministry of Higher Education and Scientific Research in Tunisia, University of Sfax. We acknowledge the support from the Institut National de la Santé et de la Recherche Médicale (INSERM), France, Centre National de la Recherche Scientifique (CNRS), France, the Université d'Angers, the University Hospital of Angers, the Région Pays de Loire and Angers Loire Métropole, France., and We would like to thank all the member of the family for their cooperation in the present study.

Subjects
Male, 0301 basic medicine, Mitochondrial DNA, Nuclear gene, Adolescent, [SDV]Life Sciences [q-bio], Clinical Biochemistry, MtDNA depletion, Oxidative phosphorylation, Biology, OPA1, DNA, Mitochondrial, Biochemistry, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Muscular Dystrophy, Oculopharyngeal, Mitochondrial Encephalomyopathies, medicine, Humans, Thymidine phosphorylase, Child, ComputingMilieux_MISCELLANEOUS, Genetics, Ophthalmoplegia, mtDNA depletion, Intestinal Pseudo-Obstruction, Biochemistry (medical), Pathogenic variants, General Medicine, medicine.disease, DNA Polymerase gamma, 3. Good health, Optic Atrophy, Cytosol, 030104 developmental biology, POLG, 030220 oncology & carcinogenesis, MNGIE, Mutation
Abstract

Introduction Mitochondrial diseases are a group of disorders caused mainly by the impairment of the mitochondrial oxidative phosphorylation process, due to mutations either in the mitochondrial or nuclear genome. Among them, the mitochondrial neuro-gastrointestinal encephalo-myopathy (MNGIE) syndrome affects adolescents or young adults, and is mostly caused by TYMP mutations encoding a cytosolic thymidine phosphorylase (TP). Patients and methods The present study reports the molecular investigation by next-generation re-sequencing of 281 nuclear genes, encoding mitochondrial proteins, of consanguineous family including two individuals with MNGIE syndrome associated to optic atrophy. Bioinformatic analysis was also performed in addition to mtDNA deletion screening and mtDNA copy number quantification in blood of the two patients which were carried out by solf clipping program and qPCR respectively. Results Next-generation re-sequencing revealed a novel homozygous c.2391G > T POLG mutation (p.M797I) co-occurring with the hypomorphic c.1311A > G OPA1 variant (p.I437M). Analysis of the mitochondrial genome in the two patients disclosed mtDNA depletion in blood, but no deletion. Bio-informatics investigations supported the pathogenicity of the novel POLG mutation that is located in the C-terminal subdomain and might change POLG 3D structure, stability and function. Conclusion The novel homozygous p.M797I POLG mutation is responsible for MNGIE combined to optic atrophy and mtDNA depletion in the two patients.

Published
2019
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16. Dominant ACO2 mutations are a frequent cause of isolated optic atrophy

Author

Chiara LaMorgia, Pascal Reynier, Céline Wetterwald, Vincent Procaccio, Simone Schimpf-Linzenbold, Bernd Wissinger, Valérie Desquiret-Dumas, Stéphanie Chupin, Felix Tonagel, Leonardo Caporali, Selma Kane, Valerio Carelli, Magalie Barth, Naïg Gueguen, Xavier Zanlonghi, Majida Charif, Patrick Yu-Wai-Man, Neringa Jurkute, Morgane LeMao, Francesca Tagliavini, David Goudenège, Zouhair Elkarhat, Céline Bris, Marc Ferré, Jennifer Alban, Isabelle Meunier, Guy Lenaers, Arnaud Chevrollier, Abdelhamid Barakat, Ulrich Kellner, Patrizia Amati-Bonneau, Christophe Verny, Salim Khiati, Nicole Weisschuh, Philippe Gohier, Michele Carbonelli, Dominique Bonneau, Charif, Majida, Gueguen, Naïg, Ferré, Marc, Elkarhat, Zouhair, Khiati, Salim, LeMao, Morgane, Chevrollier, Arnaud, Desquiret-Dumas, Valerie, Goudenège, David, Bris, Céline, Kane, Selma, Alban, Jennifer, Chupin, Stéphanie, Wetterwald, Céline, Caporali, Leonardo, Tagliavini, Francesca, LaMorgia, Chiara, Carbonelli, Michele, Jurkute, Neringa, Barakat, Abdelhamid, Gohier, Philippe, Verny, Christophe, Barth, Magalie, Procaccio, Vincent, Bonneau, Dominique, Zanlonghi, Xavier, Meunier, Isabelle, Weisschuh, Nicole, Schimpf-Linzenbold, Simone, Tonagel, Felix, Kellner, Ulrich, Yu-Wai-Man, Patrick, Carelli, Valerio, Wissinger, Bernd, Amati-Bonneau, Patrizia, Reynier, Pascal, Lenaers, Guy, Université Mohamed 1 Oujda MAROC, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Université d'Angers (UA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), University of Bologna/Università di Bologna, Maggiore-Bellaria Hospital [Bologna], University College of London [London] (UCL), Moorfields Eye Hospital [London], Cambridge University Hospitals - NHS (CUH), University of Cambridge [UK] (CAM), Clinique Jules-Vernes [Nantes], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), University of Tübingen, Molecular Genetics Laboratory [Tuebingen, Germany] (Centre for Ophthalmology), Institute for Ophthalmic Research [Tuebingen, Germany]-University Clinics Tuebingen [Germany], Rare Retinal Disease Center [Siegburg, Germany], AugenZentrum Siegburg-MVZ ADTC Siegburg GmbH [Germany], and LENAERS, Guy

Subjects
0301 basic medicine, Retinal degeneration, Mitochondrial DNA, [SDV]Life Sciences [q-bio], Biology, Mitochondrion, medicine.disease_cause, Retinal ganglion, Optic neuropathy, 03 medical and health sciences, 0302 clinical medicine, Atrophy, medicine, ACO2, Genetics, Mutation, General Engineering, medicine.disease, eye diseases, aconitase 2, optic neuropathy, [SDV] Life Sciences [q-bio], mitochondria, 030104 developmental biology, sense organs, Krebs cycle, 030217 neurology & neurosurgery, Optic nerve disorder
Abstract

Biallelic mutations in ACO2, encoding the mitochondrial aconitase 2, have been identified in individuals with neurodegenerative syndromes, including infantile cerebellar retinal degeneration and recessive optic neuropathies (locus OPA9). By screening European cohorts of individuals with genetically unsolved inherited optic neuropathies, we identified 61 cases harbouring variants in ACO2, among whom 50 carried dominant mutations, emphasizing for the first time the important contribution of ACO2 monoallelic pathogenic variants to dominant optic atrophy. Analysis of the ophthalmological and clinical data revealed that recessive cases are affected more severely than dominant cases, while not significantly earlier. In addition, 27% of the recessive cases and 11% of the dominant cases manifested with extraocular features in addition to optic atrophy. In silico analyses of ACO2 variants predicted their deleterious impacts on ACO2 biophysical properties. Skin derived fibroblasts from patients harbouring dominant and recessive ACO2 mutations revealed a reduction of ACO2 abundance and enzymatic activity, and the impairment of the mitochondrial respiration using citrate and pyruvate as substrates, while the addition of other Krebs cycle intermediates restored a normal respiration, suggesting a possible short-cut adaptation of the tricarboxylic citric acid cycle. Analysis of the mitochondrial genome abundance disclosed a significant reduction of the mitochondrial DNA amount in all ACO2 fibroblasts. Overall, our data position ACO2 as the third most frequently mutated gene in autosomal inherited optic neuropathies, after OPA1 and WFS1, and emphasize the crucial involvement of the first steps of the Krebs cycle in the maintenance and survival of retinal ganglion cells.

Published
2021
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17. Cancer/Testis Antigens into mitochondria: a hub between spermatogenesis, tumorigenesis and mitochondrial physiology adaptation

Author

Salim Khiati, Magalie Boguenet, Guy Lenaers, David Goudenège, Olivier R. Baris, Jade Aurriere, Pascale May-Panloup, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), and CCSD, Accord Elsevier

Subjects
0301 basic medicine, Male, [SDV]Life Sciences [q-bio], Physiology, Biology, Mitochondrion, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Antigen, Antigens, Neoplasm, Neoplasms, Testis, medicine, Humans, Spermatogenesis, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, Cancer, Cell Biology, medicine.disease, Mitochondria, Gene Expression Regulation, Neoplastic, [SDV] Life Sciences [q-bio], 030104 developmental biology, Localization, Tumorigenesis, Molecular Medicine, Cancer/testis antigens, Cancer/Testis Antigen, Adaptation, Carcinogenesis, 030217 neurology & neurosurgery
Abstract

International audience; Cancer/Testis Antigens (CTAs) genes are expressed only during spermatogenesis and tumorigenesis. Both processes share common specific metabolic adaptation related to energy supply, with a glucose to lactate gradient, leading to changes in mitochondrial physiology paralleling CTAs expression. In this review, we address the role of CTAs in mitochondria (mitoCTAs), by reviewing all published data, and assessing the putative localization of CTAs by screening for the presence of a mitochondrial targeting sequence (MTS). We evidenced that among the 276 CTAs, five were already shown to interfere with mitochondrial activities and 67 display a potential MTS.

Published
2020
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18. Mutations in aARS genes revealed by targeted next-generation sequencing in patients with mitochondrial diseases

Author

Rim Kallel, Vincent Procaccio, Patrizia Amati-Bonneau, Faiza Fakhfakh, Majida Charif, Rahma Felhi, Agnès Guichet, Valérie Desquiret-Dumas, Dominique Bonneau, Emna Mkaouar-Rebai, Mongia Hachicha, Pascal Reynier, Guy Lenaers, David Goudenège, Céline Bris, Lamia Sfaihi, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)

Subjects
0301 basic medicine, Male, Nuclear gene, Mitochondrial Diseases, Mitochondrial disease, [SDV]Life Sciences [q-bio], Aspartate-tRNA Ligase, Aminoacylation, Biology, DNA sequencing, Amino Acyl-tRNA Synthetases, Mitochondrial Proteins, 03 medical and health sciences, 0302 clinical medicine, Genetics, medicine, Humans, Child, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, Genetic Association Studies, chemistry.chemical_classification, Alanine-tRNA Ligase, Homozygote, High-Throughput Nucleotide Sequencing, Translation (biology), General Medicine, medicine.disease, 3. Good health, Mitochondria, Pedigree, 030104 developmental biology, Enzyme, chemistry, 030220 oncology & carcinogenesis, Child, Preschool, RNA splicing, Mutation, Female
Abstract

Mitochondrial diseases are a clinically heterogeneous group of multisystemic disorders that arise as a result of various mitochondrial dysfunctions. Autosomal recessive aARS deficiencies represent a rapidly growing group of severe rare inherited mitochondrial diseases, involving multiple organs, and currently without curative option. They might be related to defects of mitochondrial aminoacyl t-RNA synthetases (mtARS) that are ubiquitous enzymes involved in mitochondrial aminoacylation and the translation process. Here, using NGS analysis of 281 nuclear genes encoding mitochondrial proteins, we identified 4 variants in different mtARS in three patients from unrelated Tunisian families, with clinical features of mitochondrial disorders. Two homozygous variants were found in KARS (c.683C>T) and AARS2 (c.1150-4C>G), respectively in two patients, while two heterozygous variants in EARS2 (c.486-7C>G) and DARS2 (c.1456C>T) were concomitantly found in the third patient. Bio-informatics investigations predicted their pathogenicity and deleterious effects on pre-mRNA splicing and on protein stability. Thus, our results suggest that mtARS mutations are common in Tunisian patients with mitochondrial diseases.

Published
2020
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19. First characterization of LHON pedigrees in North Africa

Author

Nisrine Aboussair, Céline Bris, Mostafa Kandil, Halima Nahili, David Goudenège, Patrizia Amati-Bonneau, Abdelhamid Barakat, Majida Charif, Aymane Bouzidi, Najat Sifeddine, Guy Lenaers, Kenza Dafir, Vincent Procaccio, Valérie Desquiret-Dumas, Ghita Amalou, Meriem Elqabli, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Pedigree chart, North africa, Optic Atrophy, Hereditary, Leber, DNA, Mitochondrial, Genealogy, Pedigree, 03 medical and health sciences, Ophthalmology, 0302 clinical medicine, Geography, Africa, Northern, Mutation, Correspondence, 030221 ophthalmology & optometry, Humans, 030217 neurology & neurosurgery, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020
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20. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

Author

Pascal Reynier, Dominique Bonneau, Vincent Procaccio, Céline Bris, Estelle Colin, Virginie Hoffmann, Véronique Paquis-Flucklinger, Patrizia Amati-Bonneau, Claude Jardel, Benoit Rucheton, Guy Lenaers, Valérie Desquiret-Dumas, David Goudenège, Sylvie Bannwarth, Anne-Sophie Lebre, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB), Service de génétique médicale, Centre Hospitalier Universitaire de Nice (CHU Nice)-Hôpital l'Archet, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Service de génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Mitochondrie : Régulations et Pathologie, Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiopathologie et thérapie des déficits sensoriels et moteurs, Université Montpellier 2 - Sciences et Techniques (UM2)-IFR76-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)

Subjects
0301 basic medicine, Mitochondrial DNA, Mitochondrial Diseases, Nuclear gene, Mitochondrial disease, [SDV]Life Sciences [q-bio], Computational biology, 030105 genetics & heredity, Biology, DNA, Mitochondrial, DNA sequencing, 03 medical and health sciences, Genotype, medicine, Humans, Gene, Genetic Association Studies, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Sequence Deletion, Base Sequence, Breakpoint, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, medicine.disease, Phenotype, Mitochondria, 030104 developmental biology, Software
Abstract

Accurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data. The methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance. eKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ). Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.

Published
2019
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21. Dominant mutations in mtDNA maintenance gene SSBP1 cause optic atrophy and foveopathy

Author

Cécile Delettre, Gaël Manes, Mélanie Quiles, Guy Lenaers, Marie O. Pequignot, Ulrich Kellner, Béatrice Bocquet, Helmut Wilhelm, Chantal Cazevieille, Audrey Sénéchal, Maria Solà, Fenna Hensen, Bernd Wissinger, Emmanuelle Sarzi, Camille Piro-Mégy, Xavier Zanlonghi, Aleix Tarrés-Solé, David Goudenège, Agathe Roubertie, Nicole Weisschuh, Christian P. Hamel, Majida Charif, Johannes N. Spelbrink, Arka Chakraborty, Agnès Muller, Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Physiopathologie et thérapie des déficits sensoriels et moteurs, Université Montpellier 2 - Sciences et Techniques (UM2)-IFR76-Institut National de la Santé et de la Recherche Médicale (INSERM), Neuroimmunologie des annélides (NA), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Institute of Human Genetics [Erlangen, Allemagne], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Institute for Ophthalmic Research [Tübingen, Germany] (Centre for Ophthalmology), University of Tübingen, Service Exploration Fonctionnelle de la Vision, Clinique Sourdille, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, European Commission, Ministerio de Educación y Formación Profesional (España), LENAERS, Guy, and Institut des Neurosciences de Montpellier (INM)

Subjects
0301 basic medicine, Male, genetic structures, [SDV]Life Sciences [q-bio], Mitochondrion, GTP Phosphohydrolases, 0302 clinical medicine, Missense mutation, Child, ComputingMilieux_MISCELLANEOUS, Genetics, Aged, 80 and over, Neurodegeneration, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], General Medicine, Middle Aged, 3. Good health, Mitochondria, [SDV] Life Sciences [q-bio], DNA-Binding Proteins, 030220 oncology & carcinogenesis, Female, Research Article, Adult, DNA Replication, Mitochondrial DNA, Adolescent, Mutation, Missense, Biology, DNA-binding protein, DNA, Mitochondrial, Mitochondrial Proteins, 03 medical and health sciences, Atrophy, All institutes and research themes of the Radboud University Medical Center, Optic Atrophy, Autosomal Dominant, Exome Sequencing, medicine, Humans, Gene, Aged, Binding protein, medicine.disease, eye diseases, Ophthalmology, 030104 developmental biology, Commentary, sense organs
Abstract

© 2020, Piro-Mégy et al., Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDSs), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutations in single-strand binding protein 1 (SSBP1) in 5 unrelated families, leading to the R38Q and R107Q amino acid changes in the mitochondrial single-stranded DNA-binding protein, a crucial protein involved in mtDNA replication. All affected individuals presented optic atrophy, associated with foveopathy in half of the cases. To uncover the structural features underlying SSBP1 mutations, we determined a revised SSBP1 crystal structure. Structural analysis suggested that both mutations affect dimer interactions and presumably distort the DNA-binding region. Using patient fibroblasts, we validated that the R38Q variant destabilizes SSBP1 dimer/tetramer formation, affects mtDNA replication, and induces mtDNA depletion. Our study showing that mutations in SSBP1 cause a form of dominant optic atrophy frequently accompanied with foveopathy brings insights into mtDNA maintenance disorders., This study was supported by the Spanish Ministry of Science, Innovation and Universities, MINECO (BFU2015-70645-R, RTI2018-101015-B-100 to MS), the Generalitat de Catalunya (2014-SGR-997 and 2017-SGR-1192 to MS), and the European Union (FP7-HEALTH-2012-306029-2 to MS). ATS was awarded with an FPU fellowship from the Ministry of Education, Professional Formation (MEFP). The Structural Biology Unit at IBMB-CSIC is a “Maria de Maeztu” Unit of Excellence awarded by MINECO (MDM-2014-0435). This work was supported by the “Prinses Beatrix Spierfonds” and the “Stichting Spieren voor Spieren” (W.OR15-05 to JNS).

Published
2019
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22. Mitochondrial DNA Instability Is Common in HIV-Exposed Uninfected Newborns

Author

Chipepo Kankasa, Vincent Procaccio, Philippe Van de Perre, Valérie Desquiret-Dumas, Mandisa Singata-Madliki, Nicolas Nagot, Céline Bris, Audrey Monnin, Thorkild Tylleskär, Nicolas Meda, David Goudenège, Pascal Reynier, Jean Pierre Moles, Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Etablissement Français du Sang Provence-Alpes Côte-d'Azur et Corse (EFS), Université des Antilles (UA), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Fort Hare, University of Bergen (UiB), and BONIZEC, Sandrine

Subjects
MtDNA deletions, Mitochondrial DNA, Human immunodeficiency virus (HIV), Physiology, Mitochondrion, Nucleotide level, medicine.disease_cause, Genome, Article, 03 medical and health sciences, [SDV.MHEP.PED] Life Sciences [q-bio]/Human health and pathology/Pediatrics, birth, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicine, 030212 general & internal medicine, 030304 developmental biology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, 0303 health sciences, business.industry, HIV, genomic alterations, General Medicine, Heteroplasmy, mitochondria, pediatric, Child population, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ARV, business
Abstract

Worldwide, one million HIV-exposed uninfected (HEU) children are born yearly, and chronic health impairments have been reported in these children. Mitochondrial DNA (mtDNA) instability and altered mtDNA content have been evidenced in these children, but an exhaustive characterization of altered mitochondrial genomes has never been reported. We applied deep mtDNA sequencing coupled to the deletion identification algorithm eKLIPse to the blood of HEU neonates (n = 32), which was compared with healthy controls (n = 15). Dried blood spots (DBS) from African HEU children were collected seven days after birth between November 2009 and May 2012. DBS from French healthy controls were collected at birth (or &lt, 3 days of life) in 2012 and in 2019. In contrast to the absence of mtDNA instability observed at the nucleotide level, we identified significant amounts of heteroplasmic mtDNA deletions in 75% of HEU children and in none of controls. The heteroplasmy rate of the 62 mtDNA deletions identified varied from 0.01% to up to 50%, the highest rates being broadly compatible with bioenergetic defect and clinical expression. mtDNA integrity is commonly affected in HEU neonates. The nature of the deletions suggests a mechanism related to aging or tumor-associated mtDNA instability. This child population may be at risk of additional mtDNA genetic alterations considering that they will be exposed to other mitotoxic drugs including antiretroviral or anti-tuberculosis treatment.

Published
2021
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23. A single regulatory gene is sufficient to alterVibrio aestuarianuspathogenicity in oysters

Author

Didier Mazel, Bruno Petton, Annick Jacq, Jean-Louis Nicolas, Delphine Tourbiez, Alexandra Calteau, Frédérique Le Roux, Sophie Mangenot, David Goudenège, Philippe Haffner, Astrid Lemire, Marie-Agnès Travers, and Yannick Labreuche

Subjects
Genetics, Comparative genomics, Oyster, biology, Virulence, Oyster farming, biology.organism_classification, Microbiology, Vibrio, Ostreidae, Phylogenetics, biology.animal, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Regulator gene
Abstract

Oyster diseases caused by pathogenic vibrios pose a major challenge to the sustainability of oyster farming. In France, since 2012 a disease affecting specifically adult oysters has been associated with the presence of Vibrio aestuarianus. Here, by combining genome comparison, phylogenetic analyses and high-throughput infections of strains isolated before or during the recent outbreaks, we show that virulent strains cluster into two V. aestuarianus lineages independently of the sampling dates. The bacterial lethal dose was not different between strains isolated before or after 2012. Hence, the emergence of a new highly virulent clonal strain is unlikely. Each lineage comprises nearly identical strains, the majority of them being virulent, suggesting that within these phylogenetically coherent virulent lineages a few strains have lost their pathogenicity. Comparative genomics allowed the identification of a single frameshift in a non-virulent strain. This mutation affects the varS gene that codes for a signal transduction histidine-protein kinase. Genetic analyses confirmed that varS is necessary for infection of oysters and for a secreted metalloprotease expression. For the first time in a Vibrio species, we show here that VarS is a key factor of pathogenicity.

Published
2015
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24. Deep sequencing shows that oocytes are not prone to accumulate mtDNA heteroplasmic mutations during ovarian ageing

Author

David Goudenège, Valérie Desquiret-Dumas, Philippe Descamps, Valérie Seegers, Céline Bris, M. Domin-Bernhard, Lisa Boucret, Vincent Procaccio, Véronique Ferré-L’Hotellier, Pierre-Emmanuel Bouet, Pascal Reynier, Pascale May-Panloup, Laboratoire de Biologie de la Reproduction [CHU Angers], Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Biochimie et Génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), Innate Immunity and Immunotherapy (CRCINA-ÉQUIPE 7), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Service de Gynécologie et Obstétrique [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-hôpital Sud, Service de Gynécologie-Obstétrique [CHU Angers], University Hospital of Angers, the University of Angers, France, and the French national research centers, Institut National de la Santé et de la Recherche Médicale (INSERM) and the Centre National de la Recherche Scientifique (CNRS)., Service de Gynécologie et Obstétrique [Rennes] = Gynaecology [Rennes], CHU Pontchaillou [Rennes], Bernardo, Elizabeth, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)

Subjects
Adult, 0301 basic medicine, Aging, Mitochondrial DNA, medicine.medical_treatment, Ovary, [SDV.CAN]Life Sciences [q-bio]/Cancer, Fertilization in Vitro, Biology, Real-Time Polymerase Chain Reaction, DNA, Mitochondrial, Deep sequencing, Andrology, 03 medical and health sciences, ovarian ageing, [SDV.CAN] Life Sciences [q-bio]/Cancer, medicine, Humans, Ovarian Reserve, Ovarian reserve, oocyte, Genetics, Cumulus Cells, Assisted reproductive technology, business.industry, mtDNA, Rehabilitation, Obstetrics and Gynecology, General Medicine, Ion semiconductor sequencing, Oocyte, Heteroplasmy, 3. Good health, mitochondria, 030104 developmental biology, medicine.anatomical_structure, Reproductive Medicine, Case-Control Studies, Mutation, Linear Models, Oocytes, Female, business, diminished ovarian reserve
Abstract

STUDY QUESTION Does ovarian ageing increase the number of heteroplasmic mitochondrial DNA (mtDNA) point mutations in oocytes? SUMMARY ANSWER Our results suggest that oocytes are not subject to the accumulation of mtDNA point mutations during ovarian ageing. WHAT IS KNOWN ALREADY Ageing is associated with the alteration of mtDNA integrity in various tissues. Primary oocytes, present in the ovary since embryonic life, may accumulate mtDNA mutations during the process of ovarian ageing. STUDY DESIGN, SIZE, DURATION This was an observational study of 53 immature oocyte-cumulus complexes retrieved from 35 women undergoing IVF at the University Hospital of Angers, France, from March 2013 to March 2014. The women were classified in two groups, one including 19 women showing signs of ovarian ageing objectified by a diminished ovarian reserve (DOR), and the other, including 16 women with a normal ovarian reserve (NOR), which served as a control group. PARTICIPANTS/MATERIALS, SETTING, METHODS mtDNA was extracted from isolated oocytes, and from their corresponding cumulus cells (CCs) considered as a somatic cell compartment. The average mtDNA content of each sample was assessed by using a quantitative real-time PCR technique. Deep sequencing was performed using the Ion Torrent Proton for Next-Generation Sequencing. Signal processing and base calling were done by the embedded pre-processing pipeline and the variants were analyzed using an in-house workflow. The distribution of the different variants between DOR and NOR patients, on one hand, and oocyte and CCs, on the other, was analyzed with the generalized mixed linear model to take into account the cluster of cells belonging to a given mother. MAIN RESULTS AND THE ROLE OF CHANCE There were no significant differences between the numbers of mtDNA variants between the DOR and the NOR patients, either in the oocytes (P = 0.867) or in the surrounding CCs (P = 0.154). There were also no differences in terms of variants with potential functional consequences. De-novo mtDNA variants were found in 28% of the oocytes and in 66% of the CCs with the mean number of variants being significantly different (respectively 0.321, SD = 0.547 and 1.075, SD = 1.158) (P < 0.0001). Variants with a potential functional consequence were also overrepresented in CCs compared with oocytes (P = 0.0019). LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Limitations may be due to the use of immature oocytes discarded during the assisted reproductive technology procedure, the small size of the sample, and the high-throughput sequencing technology that might not have detected heteroplasmy levels lower than 2%. WIDER IMPLICATIONS OF THE FINDINGS The alteration of mtDNA integrity in oocytes during ovarian ageing is a recurring question to which our pilot study suggests a reassuring answer. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the University Hospital of Angers, the University of Angers, France, and the French national research centers, INSERM and the CNRS. There are nocompeting interests.

Published
2017
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25. CLUH couples mitochondrial distribution to the energetic and metabolic status

Author

Valérie Desquiret-Dumas, Stéphanie Chupin, Rodolphe Perrot, Naïg Gueguen, Dominique Bonneau, David C. Logan, Ilaria Dalla Rosa, Vincent Procaccio, David Goudenège, Jamal Wakim, Morgane Le Mao, Guy Lenaers, Juan Manuel Chao de la Barca, Pascal Reynier, Florence Manero, Salim Khiati, Arnaud Chevrollier, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Inst Biol Sante, Université d'Angers (UA), Mill Hill Laboratory, The Francis Crick Institute [London], Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Region Pays de Loire and Angers Loire Metropole, Fondation VISIO, Ouvrir les Yeux, Union Nationale des Aveugles et Deficients Visuels, Association contre les Maladies Mitochondriales, Retina France, Kjer France, Inst MitoVasc, Equipe MitoLab, The Francis Crick Institute, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)

Subjects
0301 basic medicine, Mitochondrial translation, [SDV]Life Sciences [q-bio], Citric Acid Cycle, Oxidative phosphorylation, Biology, Mitochondrion, DNA, Mitochondrial, Oxidative Phosphorylation, 03 medical and health sciences, chemistry.chemical_compound, Adenosine Triphosphate, Ethidium, Humans, Metabolomics, Beta oxidation, Palmitoylcarnitine, Optical Imaging, RNA-Binding Proteins, Cell Biology, Metabolism, Cell size, Cell biology, Mitochondria, Citric acid cycle, 030104 developmental biology, chemistry, CLUH, Phosphatidylcholines, Mitochondrial dynamics, CRISPR-Cas Systems, Oxidation-Reduction, Adenosine triphosphate, Gene Deletion, DNA Damage, HeLa Cells
Abstract

Mitochondrial dynamics and distribution are critical for supplying ATP in response to energy demand. CLUH is a protein involved in mitochondrial distribution whose dysfunction leads to mitochondrial clustering, the metabolic consequences of which remain unknown. To gain insight into the role of CLUH on mitochondrial energy production and cellular metabolism, we have generated CLUH-knockout cells using CRISPR/Cas9. Mitochondrial clustering was associated with a smaller cell size and with decreased abundance of respiratory complexes, resulting in oxidative phosphorylation (OXPHOS) defects. This energetic impairment was found to be due to the alteration of mitochondrial translation and to a metabolic shift towards glucose dependency. Metabolomic profiling by mass spectroscopy revealed an increase in the concentration of some amino acids, indicating a dysfunctional Krebs cycle, and increased palmitoylcarnitine concentration, indicating an alteration of fatty acid oxidation, and a dramatic decrease in the concentrations of phosphatidylcholine and sphingomyeline, consistent with the decreased cell size. Taken together, our study establishes a clear function for CLUH in coupling mitochondrial distribution to the control of cell energetic and metabolic status.

Published
2017
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26. High-throughput sequencing revealed a novel SETX mutation in a Hungarian patient with amyotrophic lateral sclerosis

Author

Adrienn Sulák, Péter Klivényi, Katalin Farkas, Nóra Török, David Goudenège, Márta Széll, Kornélia Tripolszki, József I. Engelhardt, Dóra Török, Nikoletta Nagy, Vincent Procaccio, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, amyotrophic lateral sclerosis, Heterozygote, ALS4, Mutation, Missense, Biology, SETX gene, medicine.disease_cause, Lower motor neuron, 03 medical and health sciences, Behavioral Neuroscience, symbols.namesake, 0302 clinical medicine, C9orf72, medicine, Missense mutation, Humans, Amyotrophic lateral sclerosis, targeted sequencing, p.N264S missense mutation, Gene, Original Research, Aged, Genetics, Mutation, C9orf72 Protein, DNA Helicases, High-Throughput Nucleotide Sequencing, medicine.disease, Phenotype, Multifunctional Enzymes, proteins, 030104 developmental biology, medicine.anatomical_structure, Mendelian inheritance, symbols, motor neuron disease, RNA-Binding Protein FUS, Female, Missense, 030217 neurology & neurosurgery, RNA Helicases, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the degeneration of the motor neurons. To date, 126 genes have been implicated in ALS. Therefore, the heterogenous genetic background of ALS requires comprehensive genetic investigative approaches.METHODS: In this study, DNA from 28 Hungarian ALS patients was subjected to targeted high-throughput sequencing of the coding regions of three Mendelian ALS genes: , and .RESULTS: A novel heterozygous missense mutation (c.791A>G, p.N264S) of the gene was identified in a female patient presenting an atypical ALS phenotype, including adult onset and lower motor neuron impairment. No further mutations were detected in the other Mendelian ALS genes investigated.CONCLUSION: Our study contributes to the understanding of the genetic and phenotypic diversity of motor neuron diseases (MNDs). Our results also suggest that the elucidation of the genetic background of MNDs requires a complex approach, including the screening of both Mendelian and non-Mendelian genes.

Published
2017
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27. Genome sequence of Vibrio diabolicus and identification of the exopolysaccharide HE800 biosynthesis locus

Author

David, Goudenège, Vincent, Boursicot, Typhaine, Versigny, Sandrine, Bonnetot, Jacqueline, Ratiskol, Corinne, Sinquin, Gisèle, LaPointe, Frédérique, Le Rous, Frédérique Le, Roux, and Christine, Delbarre-Ladrat

Subjects
DNA, Bacterial, Sequence analysis, Molecular Sequence Data, Sequence Homology, Locus (genetics), Biosynthesis, Applied Microbiology and Biotechnology, Genome, Bacterial genetics, 03 medical and health sciences, Exopolysaccharide, Polysaccharides, Phylogenetics, Cluster Analysis, Seawater, Phylogeny, Vibrio, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, Sequence Analysis, DNA, General Medicine, biology.organism_classification, Biosynthetic Pathways, Genetic Loci, Vibrio diabolicus, Genome, Bacterial, Biotechnology
Abstract

Vibrio diabolicus, a marine bacterium originating from deep-sea hydrothermal vents, produces the HE800 exopolysaccharide with high value for biotechnological purposes, especially for human health. Its genome was sequenced and analyzed; phylogenetic analysis using the core genome revealed V. diabolicus is close to another deep-sea Vibrio sp. (Ex25) within the Harveyi clade and Alginolyticus group. A genetic locus homologous to the syp cluster from Vibrio fischeri was demonstrated to be involved in the HE800 production. However, few genetic particularities suggest that the regulation of syp expression may be different in V. diabolicus. The presence of several types of glycosyltransferases within the locus indicates a capacity to generate diversity in the glycosidic structure, which may confer an adaptability to environmental conditions. These results contribute to better understanding exopolysaccharide biosynthesis and for developing new efficient processes to produce this molecule for biotechnological applications.

Published
2014
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28. Outer membrane vesicles are vehicles for the delivery ofVibrio tasmaniensisvirulence factors to oyster immune cells

Author

Sun Nyunt Wai, Yohann Couté, Audrey S. Vanhove, Guillaume M. Charrière, Frédérique Le Roux, Delphine Destoumieux-Garzón, David Goudenège, Sylvie Kieffer-Jaquinod, Marylise Duperthuy, and Benjamin Gourbal

Subjects
Proteases, Protease, medicine.medical_treatment, Intracellular parasite, Antimicrobial peptides, Virulence, Biology, Microbiology, 3. Good health, medicine, Bacterial outer membrane, Pathogen, Ecology, Evolution, Behavior and Systematics, Polymyxin B, medicine.drug
Abstract

Vibrio tasmaniensis LGP32, a facultative intracellular pathogen of oyster haemocytes, was shown here to release outer membrane vesicles (OMVs) both in the extracellular milieu and inside haemocytes. Intracellular release of OMVs occurred inside phagosomes of intact haemocytes having phagocytosed few vibrios as well as in damaged haemocytes containing large vacuoles heavily loaded with LGP32. The OMV proteome of LGP32 was shown to be rich in hydrolases (25%) including potential virulence factors such as proteases, lipases, phospholipases, haemolysins and nucleases. One major caseinase/gelatinase named Vsp for vesicular serine protease was found to be specifically secreted through OMVs in which it is enclosed. Vsp was shown to participate in the virulence phenotype of LGP32 in oyster experimental infections. Finally, OMVs were highly protective against antimicrobial peptides, increasing the minimal inhibitory concentration of polymyxin B by 16-fold. Protection was conferred by OMV titration of polymyxin B but did not depend on the activity of Vsp or another OMV-associated protease. Altogether, our results show that OMVs contribute to the pathogenesis of LGP32, being able to deliver virulence factors to host immune cells and conferring protection against antimicrobial peptides.

Published
2014
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29. Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters

Author

Typhaine Versigny, Astrid Lemire, Frédérique Le Roux, David Goudenège, Bruno Petton, Alexandra Calteau, Yannick Labreuche, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité Physiologie Fonctionnelle des Organismes marins, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), ANR-11-BSV7-0023,VIBRIOGEN,Les vibrios pathogènes d'invertébrés marins : un nouveau regard sur la virulence et les réservoirs de gènes permettant l'adaptation à la niche écologique(2011), Physiologie Fonctionnelle des Organismes Marins (PFOM), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Oyster, Population, Virulence, Genomics, Disease, Aquaculture, Microbiology, 03 medical and health sciences, biology.animal, host-pathogen interactions, Animals, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Vibrio, Comparative genomics, 0303 health sciences, education.field_of_study, Genome, biology, Base Sequence, 030306 microbiology, ACL, Bacterial, food and beverages, Gene Expression Regulation, Bacterial, biology.organism_classification, Ostreidae, Gene Expression Regulation, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial, Bacterial Outer Membrane Proteins
Abstract

International audience; Disease in oysters has been steadily rising over the past decade, threatening the long-term survival of commercial and natural stocks. Our understanding and management of such diseases are of critical importance as aquaculture is an important aspect of dealing with the approaching worldwide food shortage. Although some bacteria of the Vibrio genus isolated from diseased oysters have been demonstrated to be pathogenic by experimental infection, direct causality has not been established. Little is known about the dynamics of how the bacterial population hosted by oysters changes during disease progression. Combining experimental ecology, a high-throughput infection assay and genome sequencing, we show that the onset of disease in oysters is associated with progressive replacement of diverse benign colonizers by members of a phylogenetically coherent virulent population. Although the virulent population is genetically diverse, all members of that population can cause disease. Comparative genomics across virulent and nonvirulent populations identified candidate virulence factors that were clustered in population-specific genomic regions. Genetic analyses revealed that one gene for a candidate virulent factor, a putative outer membrane protein, is necessary for infection of oysters. Finally, analyses of oyster mortality following experimental infection suggest that disease onset can be facilitated by the presence of nonvirulent strains. This is a new form of polymicrobial disease, in which nonpathogenic strains contribute to increase mortality.

Published
2015
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30. Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

Author

Dominique Ansquer, Evelyne Krin, Martin F. Polz, Claudine Médigue, David Goudenège, Sophie Mangenot, Didier Mazel, Alexandra Calteau, Yannick Labreuche, Frédérique Le Roux, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Lagons, Ecosystèmes et Aquaculture Durable de Nouvelle Calédonie (LEADNC), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), MIT Parsons Laboratory, Massachusetts Institute of Technology (MIT), The present study has been supported by the Genoscope (appel d’offre 2007 and 2011) Région Bretagne (SAD Vibrigen 6633), the Institut Pasteur, the CNRS (UMR3525), the ANR blanc (11-BSV7-023-01 ‘VIBRIOGEN’) and Ifremer (DG post doctoral funding)., We acknowledge Dr Eliane Chung and Iony Manitra Razanajatovo for providing the strains isolated in Madagascar, Sophie Le Panse for the transmission electron microscopy analysis, the staff of the station Ifremer Nouvelle Calédonie, the ABIMS and LABGeM plateform for technical support, Dr Simonetta Gribaldo, Otto Cordero and Dr Cyrille Goarant for fruitful discussions and Dr Brigid Davis for critical reading of the manuscript., ANR-11-BSV7-0023,VIBRIOGEN,Les vibrios pathogènes d'invertébrés marins : un nouveau regard sur la virulence et les réservoirs de gènes permettant l'adaptation à la niche écologique(2011), Plasticité du Génome Bactérien, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Lagons, Ecosystèmes et Aquaculture Durable [Nouméa] (LEAD), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
[SDV]Life Sciences [q-bio], MESH: Virulence, phylogeny, MESH: Genome, Bacterial, Genome, MESH: Madagascar, MESH: Penaeidae, nigritoxin, MESH: Animals, MESH: Genetic Variation, vibrio, MESH: Phylogeny, Phylogeny, Genetics, 0303 health sciences, education.field_of_study, Phylogenetic tree, Virulence, MESH: Genomics, Genomics, Horizontal gene transfer, Shrimp, MESH: Microscopy, Electron, Transmission, horizontal gene transfer, Original Article, shrimp, Plasmids, Gene Transfer, Horizontal, Population, Bacterial Toxins, Locus (genetics), Biology, Microbiology, 03 medical and health sciences, Microscopy, Electron, Transmission, New Caledonia, Penaeidae, MESH: Vibrio, Phylogenetics, MESH: Plasmids, Madagascar, Animals, Nigritoxin, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Vibrio, Comparative genomics, 030306 microbiology, Genetic Variation, MESH: New Caledonia, MESH: Gene Transfer, Horizontal, virulence, MESH: Bacterial Toxins, Genome, Bacterial
Abstract

International audience; Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.

Published
2013
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31. SORGOdb: Superoxide Reductase Gene Ontology curated DataBase

Author

Céline Lucchetti-Miganeh, Frédérique Barloy-Hubler, Gilles Salbert, David Goudenège, David Thybert, Interactions cellulaires et moléculaires (ICM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Agence Nationale de la Recherche, Ministere de la Recherche , CLM, and Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), OXYGEN DETOXIFICATION, Architecture domain, DESULFURICANS ATCC 27774, lcsh:QR1-502, TREPONEMA-PALLIDUM, 010402 general chemistry, 01 natural sciences, Microbiology, lcsh:Microbiology, Neelaredoxin, Database, 03 medical and health sciences, chemistry.chemical_compound, MULTIPLE SEQUENCE ALIGNMENT, NONHEME IRON PROTEIN, Databases, Genetic, PYROCOCCUS-FURIOSUS, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Genetics, 0303 health sciences, biology, Superoxide, Gene ontology, ACTIVE-SITE, Active site, ARCHAEOGLOBUS-FULGIDUS NEELAREDOXIN, DESULFOVIBRIO-GIGAS NEELAREDOXIN, biology.organism_classification, DESULFOARCULUS-BAARSII, 0104 chemical sciences, Protein Structure, Tertiary, Biochemistry, chemistry, Superoxide reductase, biology.protein, Pyrococcus furiosus, Oxidoreductases
Abstract

Background Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated. Description SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010). Conclusions SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.

Published
2011
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33. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing

Author

Céline Bris, David Goudenege, Valérie Desquiret-Dumas, Majida Charif, Estelle Colin, Dominique Bonneau, Patrizia Amati-Bonneau, Guy Lenaers, Pascal Reynier, and Vincent Procaccio

Subjects
mitochondria, mitochondrial diseases, mitochondrial DNA, next generation sequencing, bioinformatics, mtDNA variant interpretation, Genetics, QH426-470
Abstract

The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.

Published
2018
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