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Alva O, Leroy A, Heiske M, Pereda-Loth V, Tisseyre L, Boland A, Deleuze JF, Rocha J, Schlebusch C, Fortes-Lima C, Stoneking M, Radimilahy C, Rakotoarisoa JA, Letellier T, Pierron D. The loss of biodiversity in Madagascar is contemporaneous with major demographic events. Curr Biol 2022; 32:4997-5007.e5. [PMID: 36334586 DOI: 10.1016/j.cub.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large-bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.
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Affiliation(s)
- Omar Alva
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anaïs Leroy
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Margit Heiske
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Lenka Tisseyre
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000 Evry, France
| | - Jorge Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Cesar Fortes-Lima
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 75236 Uppsala, Sweden
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Villeurbanne, France
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | | | - Thierry Letellier
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France
| | - Denis Pierron
- Équipe de Médecine Evolutive, EVOLSAN faculté de chirurgie dentaire, Université Toulouse III, Toulouse, France.
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Heiske M, Alva O, Pereda-Loth V, Van Schalkwyk M, Radimilahy C, Letellier T, Rakotarisoa JA, Pierron D. Genetic evidence and historical theories of the Asian and African origins of the present Malagasy population. Hum Mol Genet 2021; 30:R72-R78. [PMID: 33481023 DOI: 10.1093/hmg/ddab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/23/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
The origin of the Malagasy population has been a subject of speculation since the 16th century. Contributions of African, Asian, Indian, Melanesian, Arabic and Persian populations have been suggested based on physical and cultural anthropology, oral tradition, linguistics and later also by archaeology. In the mid-20th century, increased knowledge of heredity rules and technical progress enabled the identification of African and Asian populations as main contributors. Recent access to the genomic landscape of Madagascar demonstrated pronounced regional variability in the relative contributions of these two ancestries, yet with significant presence of both African and Asian components throughout Madagascar. This article reviews the extent to which genetic results have settled historical questions concerning the origin of the Malagasy population. After an overview of the early literature, the genetic results of the 20th and 21th centuries are discussed and then complemented by the latest results in genome-wide analyses. While there is still much uncertainty regarding when, how and the circumstances under which the ancestors of the modern Malagasy population arrived on the island, we propose a scenario based on historical texts and genomic results.
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Affiliation(s)
- Margit Heiske
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Omar Alva
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | - Matthew Van Schalkwyk
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Chantal Radimilahy
- Musée d'Art et d'Archéologie, University of Antananarivo, Antananarivo, Madagascar
| | - Thierry Letellier
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
| | | | - Denis Pierron
- Équipe de Médecine Evolutive, Faculté de Chirurgie Dentaire URU EVOLSAN Université Toulouse III, France
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Pierron D, Pereda-Loth V, Mantel M, Moranges M, Bignon E, Alva O, Kabous J, Heiske M, Pacalon J, David R, Dinnella C, Spinelli S, Monteleone E, Farruggia MC, Cooper KW, Sell EA, Thomas-Danguin T, Bakke AJ, Parma V, Hayes JE, Letellier T, Ferdenzi C, Golebiowski J, Bensafi M. Smell and taste changes are early indicators of the COVID-19 pandemic and political decision effectiveness. Nat Commun 2020; 11:5152. [PMID: 33056983 PMCID: PMC7560893 DOI: 10.1038/s41467-020-18963-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
In response to the COVID-19 pandemic, many governments have taken drastic measures to avoid an overflow of intensive care units. Accurate metrics of disease spread are critical for the reopening strategies. Here, we show that self-reports of smell/taste changes are more closely associated with hospital overload and are earlier markers of the spread of infection of SARS-CoV-2 than current governmental indicators. We also report a decrease in self-reports of new onset smell/taste changes as early as 5 days after lockdown enforcement. Cross-country comparisons demonstrate that countries that adopted the most stringent lockdown measures had faster declines in new reports of smell/taste changes following lockdown than a country that adopted less stringent lockdown measures. We propose that an increase in the incidence of sudden smell and taste change in the general population may be used as an indicator of COVID-19 spread in the population.
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Affiliation(s)
- Denis Pierron
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France.
| | - Veronica Pereda-Loth
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France
| | - Marylou Mantel
- Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, University Claude Bernard Lyon 1, Bron, France
| | - Maëlle Moranges
- Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, University Claude Bernard Lyon 1, Bron, France
| | - Emmanuelle Bignon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, France
| | - Omar Alva
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France
| | - Julie Kabous
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France
| | - Margit Heiske
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France
| | - Jody Pacalon
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, France
| | - Renaud David
- Université Côte d'Azur, CHU de Nice, Nice Memory Clinic, Nice, France
| | | | | | | | - Michael C Farruggia
- Interdepartmental Neuroscience Program, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Keiland W Cooper
- Department of Neurobiology and Behavior, University of California, Irvine, CA, 92697, USA
| | - Elizabeth A Sell
- Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Thierry Thomas-Danguin
- Centre des Sciences du Goût et de l'Alimentation, INRAE, CNRS, AgroSup-Dijon, University Bourgogne Franche-Comté, Dijon, France
| | - Alyssa J Bakke
- The Pennsylvania State University, Philadelphia, PA, 19104, USA
| | | | - John E Hayes
- The Pennsylvania State University, Philadelphia, PA, 19104, USA
| | - Thierry Letellier
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire; UMR5288; CNRS/Université Paul-Sabiater Toulouse III, Toulouse, 31400, France
| | - Camille Ferdenzi
- Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, University Claude Bernard Lyon 1, Bron, France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, France.
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, South Korea.
| | - Moustafa Bensafi
- Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, University Claude Bernard Lyon 1, Bron, France.
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Pierron D, Heiske M, Razafindrazaka H, Pereda-Loth V, Sanchez J, Alva O, Arachiche A, Boland A, Olaso R, Deleuze JF, Ricaut FX, Rakotoarisoa JA, Radimilahy C, Stoneking M, Letellier T. Strong selection during the last millennium for African ancestry in the admixed population of Madagascar. Nat Commun 2018; 9:932. [PMID: 29500350 PMCID: PMC5834599 DOI: 10.1038/s41467-018-03342-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/06/2018] [Indexed: 01/24/2023] Open
Abstract
While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.
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Affiliation(s)
- Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France.
| | - Margit Heiske
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
- Aix Marseille Univ., CNRS, EFS, ADES, Marseille, France
| | - Veronica Pereda-Loth
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Jazmin Sanchez
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Omar Alva
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Amal Arachiche
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Robert Olaso
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Jean-Francois Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Francois-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Jean-Aimé Rakotoarisoa
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, 101, Antananarivo, Madagascar
| | - Chantal Radimilahy
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, 101, Antananarivo, Madagascar
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
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Heiske M, Letellier T, Klipp E. Comprehensive mathematical model of oxidative phosphorylation valid for physiological and pathological conditions. FEBS J 2017. [PMID: 28646582 DOI: 10.1111/febs.14151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We developed a mathematical model of oxidative phosphorylation (OXPHOS) that allows for a precise description of mitochondrial function with respect to the respiratory flux and the ATP production. The model reproduced flux-force relationships under various experimental conditions (state 3 and 4, uncoupling, and shortage of respiratory substrate) as well as time courses, exhibiting correct P/O ratios. The model was able to reproduce experimental threshold curves for perturbations of the respiratory chain complexes, the F1 F0 -ATP synthase, the ADP/ATP carrier, the phosphate/OH carrier, and the proton leak. Thus, the model is well suited to study complex interactions within the OXPHOS system, especially with respect to physiological adaptations or pathological modifications, influencing substrate and product affinities or maximal catalytic rates. Moreover, it could be a useful tool to study the role of OXPHOS and its capacity to compensate or enhance physiopathologies of the mitochondrial and cellular energy metabolism.
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Affiliation(s)
- Margit Heiske
- Laboratoire d'Anthropologie Moléculaire et Imaginérie de Synthèse, Médecine Evolutive, UMR 5288 CNRS, Faculté de Médecine, Université de Toulouse, France.,Theoretische Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin, Germany
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imaginérie de Synthèse, Médecine Evolutive, UMR 5288 CNRS, Faculté de Médecine, Université de Toulouse, France
| | - Edda Klipp
- Theoretische Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin, Germany
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Heiske M, Nazaret C, Mazat JP. Modeling the respiratory chain complexes with biothermokinetic equations - the case of complex I. Biochim Biophys Acta 2014; 1837:1707-16. [PMID: 25064016 DOI: 10.1016/j.bbabio.2014.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 07/09/2014] [Accepted: 07/16/2014] [Indexed: 12/16/2022]
Abstract
The mitochondrial respiratory chain plays a crucial role in energy metabolism and its dysfunction is implicated in a wide range of human diseases. In order to understand the global expression of local mutations in the rate of oxygen consumption or in the production of adenosine triphosphate (ATP) it is useful to have a mathematical model in which the changes in a given respiratory complex are properly modeled. Our aim in this paper is to provide thermodynamics respecting and structurally simple equations to represent the kinetics of each isolated complexes which can, assembled in a dynamical system, also simulate the behavior of the respiratory chain, as a whole, under a large set of different physiological and pathological conditions. On the example of the reduced nicotinamide adenine dinucleotide (NADH)-ubiquinol-oxidoreductase (complex I) we analyze the suitability of different types of rate equations. Based on our kinetic experiments we show that very simple rate laws, as those often used in many respiratory chain models, fail to describe the kinetic behavior when applied to a wide concentration range. This led us to adapt rate equations containing the essential parameters of enzyme kinetic, maximal velocities and Henri-Michaelis-Menten like-constants (KM and KI) to satisfactorily simulate these data.
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Affiliation(s)
- Margit Heiske
- Université de Bordeaux, Bordeaux, France; Institut für Biologie Theoretische Biophysik Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin, Germany; Laboratoire de métabolisme énergétique cellulaire, IBGC - CNRS UMR 5095, 1 Rue Camille Saint Saëns, 33077 Bordeaux, France
| | - Christine Nazaret
- Institut de Mathématiques de Bordeaux, ENSTBB-Institut Polytechnique de Bordeaux, France
| | - Jean-Pierre Mazat
- Université de Bordeaux, Bordeaux, France; Laboratoire de métabolisme énergétique cellulaire, IBGC - CNRS UMR 5095, 1 Rue Camille Saint Saëns, 33077 Bordeaux, France.
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Mazat JP, Ransac S, Heiske M, Devin A, Rigoulet M. Mitochondrial energetic metabolism-some general principles. IUBMB Life 2013; 65:171-9. [DOI: 10.1002/iub.1138] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/23/2012] [Indexed: 11/10/2022]
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Ransac S, Heiske M, Mazat JP. From in silico to in spectro kinetics of respiratory complex I. Biochim Biophys Acta 2012; 1817:1958-69. [PMID: 22510388 DOI: 10.1016/j.bbabio.2012.03.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/28/2012] [Accepted: 03/29/2012] [Indexed: 12/12/2022]
Abstract
An enzyme's activity is the consequence of its structure. The stochastic approach we developed to study the functioning of the respiratory complexes is based upon their 3D structure and their physical and chemical properties. Consequently it should predict their kinetic properties. In this paper we compare the predictions of our stochastic model derived for the complex I with a number of experiments performed with a large range of complex I substrates and products. A good fit was found between the experiments and the prediction of our stochastic approach. We show that, due to the spatial separation of the two half redox reactions (NADH/NAD and Q/QH(2)), the kinetics cannot necessarily obey a simple mechanism (ordered or ping-pong for instance). A plateau in the kinetics is observed at high substrates concentrations, well evidenced in the double reciprocal plots, which is explained by the limiting rate of quinone reduction as compared with the oxidation of NADH at the other end of complex I. Moreover, we show that the set of the seven redox reactions in between the two half redox reactions (NADH/NAD and Q/QH(2)) acts as an electron buffer. An inhibition of complex I activity by quinone is observed at high concentration of this molecule, which cannot be explained by a simple stochastic model based on the known structure. We hypothesize that the distance between the catalytic site close to N2 (iron/sulfur redox center that transfers electrons to quinone) and the membrane forces the quinone/quinol to take several positions in between these sites. We represent these possible positions by an extra site necessarily occupied by the quinone/quinol molecules on their way to the redox site. With this hypothesis, we are able to fit the kinetic experiments over a large range of substrates and products concentrations. The slow rate constants derived for the transition between the two sites could be an indication of a conformational change of the enzyme during the quinone/quinol movement. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Stéphane Ransac
- Institute of Biochemistry and Genetics of the Cell, Bordeaux cedex, France
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Pierron D, Opazo JC, Heiske M, Papper Z, Uddin M, Chand G, Wildman DE, Romero R, Goodman M, Grossman LI. Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PLoS One 2011; 6:e26269. [PMID: 22028846 PMCID: PMC3196546 DOI: 10.1371/journal.pone.0026269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/23/2011] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.
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Affiliation(s)
- Denis Pierron
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Juan C. Opazo
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Instituto de Ecologia y Evolucion, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Margit Heiske
- Laboratoire de Physiopathologie Mitochondriale, INSERM, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | - Zack Papper
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Monica Uddin
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- School of Public Health, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gopi Chand
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Derek E. Wildman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
- Department Of Obstetrics and Gynecology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Perinatology Research Branch, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland and Detroit, Michigan, United States of America
| | - Morris Goodman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
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Chang I, Heiske M, Letellier T, Wallace D, Baldi P. Modeling of mitochondria bioenergetics using a composable chemiosmotic energy transduction rate law: theory and experimental validation. PLoS One 2011; 6:e14820. [PMID: 21931590 PMCID: PMC3169640 DOI: 10.1371/journal.pone.0014820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 05/12/2011] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial bioenergetic processes are central to the production of cellular energy, and a decrease in the expression or activity of enzyme complexes responsible for these processes can result in energetic deficit that correlates with many metabolic diseases and aging. Unfortunately, existing computational models of mitochondrial bioenergetics either lack relevant kinetic descriptions of the enzyme complexes, or incorporate mechanisms too specific to a particular mitochondrial system and are thus incapable of capturing the heterogeneity associated with these complexes across different systems and system states. Here we introduce a new composable rate equation, the chemiosmotic rate law, that expresses the flux of a prototypical energy transduction complex as a function of: the saturation kinetics of the electron donor and acceptor substrates; the redox transfer potential between the complex and the substrates; and the steady-state thermodynamic force-to-flux relationship of the overall electro-chemical reaction. Modeling of bioenergetics with this rate law has several advantages: (1) it minimizes the use of arbitrary free parameters while featuring biochemically relevant parameters that can be obtained through progress curves of common enzyme kinetics protocols; (2) it is modular and can adapt to various enzyme complex arrangements for both in vivo and in vitro systems via transformation of its rate and equilibrium constants; (3) it provides a clear association between the sensitivity of the parameters of the individual complexes and the sensitivity of the system's steady-state. To validate our approach, we conduct in vitro measurements of ETC complex I, III, and IV activities using rat heart homogenates, and construct an estimation procedure for the parameter values directly from these measurements. In addition, we show the theoretical connections of our approach to the existing models, and compare the predictive accuracy of the rate law with our experimentally fitted parameters to those of existing models. Finally, we present a complete perturbation study of these parameters to reveal how they can significantly and differentially influence global flux and operational thresholds, suggesting that this modeling approach could help enable the comparative analysis of mitochondria from different systems and pathological states. The procedures and results are available in Mathematica notebooks at http://www.igb.uci.edu/tools/sb/mitochondria-modeling.html.
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Affiliation(s)
- Ivan Chang
- Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
- Institute of Genomic Biology, University of California Irvine, Irvine, California, United States of America
| | - Margit Heiske
- INSERM U688, University of Bordeaux-2, Bordeaux, France
| | | | - Douglas Wallace
- Department of Biochemistry, University of California Irvine, Irvine, California, United States of America
- Center for Mitochondrial and Molecular Medicine and Genetics (MAMMAG), University of California Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California Irvine, Irvine, California, United States of America
| | - Pierre Baldi
- Institute of Genomic Biology, University of California Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California Irvine, Irvine, California, United States of America
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Pierron D, Chang I, Arachiche A, Heiske M, Thomas O, Borlin M, Pennarun E, Murail P, Thoraval D, Rocher C, Letellier T. Mutation rate switch inside Eurasian mitochondrial haplogroups: impact of selection and consequences for dating settlement in Europe. PLoS One 2011; 6:e21543. [PMID: 21738700 PMCID: PMC3125290 DOI: 10.1371/journal.pone.0021543] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 06/03/2011] [Indexed: 01/27/2023] Open
Abstract
R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration “out of Africa” and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario.
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Affiliation(s)
- Denis Pierron
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Ivan Chang
- Institute of Genomic Biology, University of California Irvine, Irvine, California, United States of America
| | - Amal Arachiche
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Margit Heiske
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Olivier Thomas
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Marine Borlin
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Erwan Pennarun
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
| | - Pacal Murail
- Laboratoire d'Anthropologie des Populations du Passé PACEA UMR 5199, CNRS - Université Bordeaux 1, Talence, France
| | - Didier Thoraval
- Institut de Biochimie et Génétique Cellulaires UMR 5095, CNRS - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Christophe Rocher
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
| | - Thierry Letellier
- Laboratoire de Physiopathologie Mitochondriale U688, INSERM - Université Victor Segalen-Bordeaux 2, Bordeaux, France
- * E-mail:
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Taanman JW, Heiske M, Letellier T. Measurement of kinetic parameters of human platelet DNA polymerase gamma. Methods 2010; 51:374-8. [PMID: 20227504 DOI: 10.1016/j.ymeth.2010.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/07/2010] [Accepted: 03/09/2010] [Indexed: 11/18/2022] Open
Abstract
Synthesis of mitochondrial DNA is performed by DNA polymerase gamma. Mutations in POLG, the gene encoding the catalytic subunit of DNA polymerase gamma, are a major cause of neurological disease. A large proportion of patients carry rare nucleotide substitutions leading to single amino acid changes. Confirming that these replacements are pathogenic can be problematic without biochemical evidence. Here, we provide a hands-on protocol for an in vitro kinetic assay of DNA polymerase gamma which allows assessment of the K(m) and V(max) for the incoming nucleotide of the polymerization reaction. To avoid measurement of contaminating nuclear DNA polymerases, platelet extracts are used since platelets do not contain a nucleus. Moreover, platelets have the advantage of being obtainable relatively non-invasively. Polymerization activity is determined by measurement of the incorporation of radioactive thymidine 5'-triphosphate (dTTP) on the homopolymeric RNA substrate poly(rA).oligo(dT)(12-18). To further minimize nuclear DNA polymerase activity, aphidicolin, an inhibitor of most nuclear DNA polymerases, is included in the reaction. In addition, reactions are carried out in the absence and presence of the competitive inhibitor of DNA polymerase gamma, 2',3'-dideoxythymidine 5'-triphosphate (ddTTP), to allow calculation of the ddTTP-sensitive incorporation. With this method, platelets from healthy control subjects extracted with 3% Triton X-100 showed a K(m) for dTTP of 1.42 microM and a V(max) of 0.83 pmol min(-1)mg(-1).
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Affiliation(s)
- Jan-Willem Taanman
- Department of Clinical Neurosciences, Institute of Neurology, University College London, Rowland Hill Street, London NW3 2PF, United Kingdom.
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Nazaret C, Heiske M, Thurley K, Mazat JP. Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production. J Theor Biol 2008; 258:455-64. [PMID: 19007794 DOI: 10.1016/j.jtbi.2008.09.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 07/18/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
Mitochondria play a central role in cellular energetic metabolism. The essential parts of this metabolism are the tricarboxylic acid (TCA) cycle, the respiratory chain and the adenosine triphosphate (ATP) synthesis machinery. Here a simplified model of these three metabolic components with a limited set of differential equations is presented. The existence of a steady state is demonstrated and results of numerical simulations are presented. The relevance of a simple model to represent actual in vivo behavior is discussed.
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Affiliation(s)
- Christine Nazaret
- IMB UMR CNRS 5251-ESTBB, Université de Bordeaux 2, 146 rue Léo-Saignat, F 33076 Bordeaux-Cedex, France.
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