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Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain

Identifieur interne : 001E21 ( Main/Exploration ); précédent : 001E20; suivant : 001E22

Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH‐2 strain

Auteurs : Boyang Ji [France] ; Sheng-Da Zhang [France] ; Pascal Arnoux [France] ; Zoe Rouy [France] ; François Alberto [France] ; Nadège Philippe [France] ; Dorothée Murat [France] ; Wei-Jia Zhang [France, République populaire de Chine] ; Jean-Baptiste Rioux [France] ; Nicolas Ginet [France] ; Monique Sabaty [France] ; Sophie Mangenot [France] ; Nathalie Pradel [France] ; Jiesheng Tian [République populaire de Chine] ; Jing Yang [France, République populaire de Chine] ; Lichen Zhang [France] ; Wenyan Zhang [République populaire de Chine] ; Hongmiao Pan [République populaire de Chine] ; Bernard Henrissat [France] ; Pedro M. Coutinho [France] ; Ying Li [République populaire de Chine, France] ; Tian Xiao [République populaire de Chine, France] ; Claudine Médigue [France] ; Valérie Barbe [France] ; David Pignol [France] ; Emmanuel Talla [France] ; Long-Fei Wu [France]

Source :

RBID : ISTEX:C0D72C039B1913DF00DDF28B0AD54DB8B082BE3F

Abstract

Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.

Url:
DOI: 10.1111/1462-2920.12180


Affiliations:


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Le document en format XML

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<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Xiao, Tian" sort="Xiao, Tian" uniqKey="Xiao T" first="Tian" last="Xiao">Tian Xiao</name>
<affiliation wicri:level="1">
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao</wicri:regionArea>
<wicri:noRegion>Qingdao</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, F‐91057, Evry</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Centre National de la Recherche Scientifique, Unité Mixte de Recherche 80302 rue Gaston Crémieux, F‐91057, Evry</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>UEVE, Université d'Evry, boulevard François Mitterrand, F‐91025, Evry</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Barbe, Valerie" sort="Barbe, Valerie" uniqKey="Barbe V" first="Valérie" last="Barbe">Valérie Barbe</name>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Finition, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique‐Génoscope, 2 rue Gaston Crémieux, CP 5706 – 91057, Evry cedex</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Évry (Essonne)</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Pignol, David" sort="Pignol, David" uniqKey="Pignol D" first="David" last="Pignol">David Pignol</name>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Bioénergétique Cellulaire, Université Aix‐Marseille, CEA/DSV/IBEB, UMR 7265 CNRS/CEA, F‐13180, Saint‐Paul‐lez‐Durance</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Saint‐Paul‐lez‐Durance</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Talla, Emmanuel" sort="Talla, Emmanuel" uniqKey="Talla E" first="Emmanuel" last="Talla">Emmanuel Talla</name>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="1">
<country wicri:rule="url">France</country>
</affiliation>
</author>
<author>
<name sortKey="Wu, Long Ei" sort="Wu, Long Ei" uniqKey="Wu L" first="Long-Fei" last="Wu">Long-Fei Wu</name>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Chimie Bactérienne, Aix‐Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F‐13402, Marseille Cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire International Associé de la Bio‐Minéralisation et Nano‐Structures (LIA‐BioMNSL), Centre National de la Recherche Scientifique, F‐13402, Marseille cedex 20</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Provence-Alpes-Côte d'Azur</region>
<settlement type="city">Marseille</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series>
<title level="j" type="main">Environmental Microbiology</title>
<title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title>
<idno type="ISSN">1462-2912</idno>
<idno type="eISSN">1462-2920</idno>
<imprint>
<biblScope unit="vol">16</biblScope>
<biblScope unit="issue">2</biblScope>
<biblScope unit="page" from="525">525</biblScope>
<biblScope unit="page" to="544">544</biblScope>
<biblScope unit="page-count">20</biblScope>
<date type="published" when="2014-02">2014-02</date>
</imprint>
<idno type="ISSN">1462-2912</idno>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt>
<idno type="ISSN">1462-2912</idno>
</seriesStmt>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract">Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane‐bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH‐2. The high number of repeats and transposable elements account for the differences in QH‐2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH‐2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium‐quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH‐2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH‐2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH‐2 neither has TonB and TonB‐dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH‐2 to marine sediments in comparison with its closely related freshwater counterparts.</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>France</li>
<li>République populaire de Chine</li>
</country>
<region>
<li>Provence-Alpes-Côte d'Azur</li>
<li>Île-de-France</li>
</region>
<settlement>
<li>Marseille</li>
<li>Pékin</li>
<li>Saint‐Paul‐lez‐Durance</li>
<li>Évry (Essonne)</li>
</settlement>
</list>
<tree>
<country name="France">
<region name="Provence-Alpes-Côte d'Azur">
<name sortKey="Ji, Boyang" sort="Ji, Boyang" uniqKey="Ji B" first="Boyang" last="Ji">Boyang Ji</name>
</region>
<name sortKey="Alberto, Francois" sort="Alberto, Francois" uniqKey="Alberto F" first="François" last="Alberto">François Alberto</name>
<name sortKey="Arnoux, Pascal" sort="Arnoux, Pascal" uniqKey="Arnoux P" first="Pascal" last="Arnoux">Pascal Arnoux</name>
<name sortKey="Barbe, Valerie" sort="Barbe, Valerie" uniqKey="Barbe V" first="Valérie" last="Barbe">Valérie Barbe</name>
<name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name>
<name sortKey="Ginet, Nicolas" sort="Ginet, Nicolas" uniqKey="Ginet N" first="Nicolas" last="Ginet">Nicolas Ginet</name>
<name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name>
<name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name>
<name sortKey="Mangenot, Sophie" sort="Mangenot, Sophie" uniqKey="Mangenot S" first="Sophie" last="Mangenot">Sophie Mangenot</name>
<name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name>
<name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name>
<name sortKey="Medigue, Claudine" sort="Medigue, Claudine" uniqKey="Medigue C" first="Claudine" last="Médigue">Claudine Médigue</name>
<name sortKey="Murat, Dorothee" sort="Murat, Dorothee" uniqKey="Murat D" first="Dorothée" last="Murat">Dorothée Murat</name>
<name sortKey="Philippe, Nadege" sort="Philippe, Nadege" uniqKey="Philippe N" first="Nadège" last="Philippe">Nadège Philippe</name>
<name sortKey="Philippe, Nadege" sort="Philippe, Nadege" uniqKey="Philippe N" first="Nadège" last="Philippe">Nadège Philippe</name>
<name sortKey="Pignol, David" sort="Pignol, David" uniqKey="Pignol D" first="David" last="Pignol">David Pignol</name>
<name sortKey="Pignol, David" sort="Pignol, David" uniqKey="Pignol D" first="David" last="Pignol">David Pignol</name>
<name sortKey="Pradel, Nathalie" sort="Pradel, Nathalie" uniqKey="Pradel N" first="Nathalie" last="Pradel">Nathalie Pradel</name>
<name sortKey="Rioux, Jean Aptiste" sort="Rioux, Jean Aptiste" uniqKey="Rioux J" first="Jean-Baptiste" last="Rioux">Jean-Baptiste Rioux</name>
<name sortKey="Rouy, Zoe" sort="Rouy, Zoe" uniqKey="Rouy Z" first="Zoe" last="Rouy">Zoe Rouy</name>
<name sortKey="Rouy, Zoe" sort="Rouy, Zoe" uniqKey="Rouy Z" first="Zoe" last="Rouy">Zoe Rouy</name>
<name sortKey="Rouy, Zoe" sort="Rouy, Zoe" uniqKey="Rouy Z" first="Zoe" last="Rouy">Zoe Rouy</name>
<name sortKey="Sabaty, Monique" sort="Sabaty, Monique" uniqKey="Sabaty M" first="Monique" last="Sabaty">Monique Sabaty</name>
<name sortKey="Talla, Emmanuel" sort="Talla, Emmanuel" uniqKey="Talla E" first="Emmanuel" last="Talla">Emmanuel Talla</name>
<name sortKey="Talla, Emmanuel" sort="Talla, Emmanuel" uniqKey="Talla E" first="Emmanuel" last="Talla">Emmanuel Talla</name>
<name sortKey="Wu, Long Ei" sort="Wu, Long Ei" uniqKey="Wu L" first="Long-Fei" last="Wu">Long-Fei Wu</name>
<name sortKey="Wu, Long Ei" sort="Wu, Long Ei" uniqKey="Wu L" first="Long-Fei" last="Wu">Long-Fei Wu</name>
<name sortKey="Xiao, Tian" sort="Xiao, Tian" uniqKey="Xiao T" first="Tian" last="Xiao">Tian Xiao</name>
<name sortKey="Yang, Jing" sort="Yang, Jing" uniqKey="Yang J" first="Jing" last="Yang">Jing Yang</name>
<name sortKey="Zhang, Lichen" sort="Zhang, Lichen" uniqKey="Zhang L" first="Lichen" last="Zhang">Lichen Zhang</name>
<name sortKey="Zhang, Sheng A" sort="Zhang, Sheng A" uniqKey="Zhang S" first="Sheng-Da" last="Zhang">Sheng-Da Zhang</name>
<name sortKey="Zhang, Wei Ia" sort="Zhang, Wei Ia" uniqKey="Zhang W" first="Wei-Jia" last="Zhang">Wei-Jia Zhang</name>
</country>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Zhang, Wei Ia" sort="Zhang, Wei Ia" uniqKey="Zhang W" first="Wei-Jia" last="Zhang">Wei-Jia Zhang</name>
</noRegion>
<name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name>
<name sortKey="Pan, Hongmiao" sort="Pan, Hongmiao" uniqKey="Pan H" first="Hongmiao" last="Pan">Hongmiao Pan</name>
<name sortKey="Tian, Jiesheng" sort="Tian, Jiesheng" uniqKey="Tian J" first="Jiesheng" last="Tian">Jiesheng Tian</name>
<name sortKey="Xiao, Tian" sort="Xiao, Tian" uniqKey="Xiao T" first="Tian" last="Xiao">Tian Xiao</name>
<name sortKey="Yang, Jing" sort="Yang, Jing" uniqKey="Yang J" first="Jing" last="Yang">Jing Yang</name>
<name sortKey="Zhang, Wei Ia" sort="Zhang, Wei Ia" uniqKey="Zhang W" first="Wei-Jia" last="Zhang">Wei-Jia Zhang</name>
<name sortKey="Zhang, Wenyan" sort="Zhang, Wenyan" uniqKey="Zhang W" first="Wenyan" last="Zhang">Wenyan Zhang</name>
</country>
</tree>
</affiliations>
</record>

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