Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel
Identifieur interne : 000350 ( Main/Exploration ); précédent : 000349; suivant : 000351Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel
Auteurs : Jose Martin Pujolar [Italie] ; Ilaria Am Marino [Italie] ; Massimo Milan [Italie] ; Alessandro Coppe [Italie] ; Gregory E. Maes [Belgique] ; Fabrizio Capoccioni [Italie] ; Eleonora Ciccotti [Italie] ; Lieven Bervoets [Belgique] ; Adrian Covaci [Belgique] ; Claude Belpaire [Belgique] ; Gordon Cramb [Royaume-Uni] ; Tomaso Patarnello [Italie] ; Luca Bargelloni [Italie] ; Stefania Bortoluzzi [Italie] ; Lorenzo Zane [Italie]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Abstract
Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (
To this end, we first (i) updated the European eel transcriptome using deep sequencing data with a total of 640,040 reads assembled into 44,896 contigs (Eeelbase release 2.0), and (ii) developed a transcriptomic platform for global gene expression profiling in the critically endangered European eel of about 15,000 annotated contigs, which was applied to detect differentially expressed genes between polluted sites. Several detoxification genes related to metabolism of pollutants were upregulated in the highly polluted site, including genes that take part in phase I of the xenobiotic metabolism (CYP3A), phase II (glutathione-S-transferase) and oxidative stress (glutathione peroxidase). In addition, key genes in the mitochondrial respiratory chain and oxidative phosphorylation were down-regulated at the Tiber site relative to the Bolsena site.
Together with the induced high expression of detoxification genes, the suggested lowered expression of genes supposedly involved in metabolism suggests that pollution may also be associated with decreased respiratory and energy production.
Url:
DOI: 10.1186/1471-2164-13-507
PubMed: 23009661
PubMed Central: 3532374
Affiliations:
- Belgique, Italie, Royaume-Uni
- Latium, Province d'Anvers, Province du Brabant flamand, Région flamande
- Anvers, Louvain, Rome
- Katholieke Universiteit Leuven, Université d'Anvers
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Maes</name><affiliation wicri:level="4"><nlm:aff id="I3">Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit Leuven (KU Leuven), B-3000, Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit Leuven (KU Leuven), B-3000, Leuven</wicri:regionArea><orgName type="university">Katholieke Universiteit Leuven</orgName><placeName><settlement type="city">Louvain</settlement><region>Région flamande</region><region type="district" nuts="2">Province du Brabant flamand</region></placeName></affiliation></author><author><name sortKey="Capoccioni, Fabrizio" sort="Capoccioni, Fabrizio" uniqKey="Capoccioni F" first="Fabrizio" last="Capoccioni">Fabrizio Capoccioni</name><affiliation wicri:level="3"><nlm:aff id="I4">Department of Biology, Università Roma Tor Vergata, I-00133, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, 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d'Anvers</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="I6">Toxicological Center, University of Antwerp, B-2610, Wilrijk, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Toxicological Center, University of Antwerp, B-2610, Wilrijk</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="Belpaire, Claude" sort="Belpaire, Claude" uniqKey="Belpaire C" first="Claude" last="Belpaire">Claude Belpaire</name><affiliation wicri:level="1"><nlm:aff id="I7">Research Institute for Nature and Forest, B-1560, Groenendaal-Hoeilaart, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Research Institute for Nature and Forest, B-1560, 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of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Zane, Lorenzo" sort="Zane, Lorenzo" uniqKey="Zane L" first="Lorenzo" last="Zane">Lorenzo Zane</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23009661</idno><idno type="pmc">3532374</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532374</idno><idno type="RBID">PMC:3532374</idno><idno type="doi">10.1186/1471-2164-13-507</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000295</idno><idno type="wicri:explorRef" wicri:stream="Pmc" 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last="Pujolar">Jose Martin Pujolar</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Marino, Ilaria Am" sort="Marino, Ilaria Am" uniqKey="Marino I" first="Ilaria Am" last="Marino">Ilaria Am Marino</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Milan, Massimo" sort="Milan, Massimo" uniqKey="Milan M" first="Massimo" last="Milan">Massimo Milan</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro</wicri:regionArea><wicri:noRegion>Legnaro</wicri:noRegion></affiliation></author><author><name sortKey="Coppe, Alessandro" sort="Coppe, Alessandro" uniqKey="Coppe A" first="Alessandro" last="Coppe">Alessandro Coppe</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Maes, Gregory E" sort="Maes, Gregory E" uniqKey="Maes G" first="Gregory E" last="Maes">Gregory E. Maes</name><affiliation wicri:level="4"><nlm:aff id="I3">Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit Leuven (KU Leuven), B-3000, Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit Leuven (KU Leuven), B-3000, Leuven</wicri:regionArea><orgName type="university">Katholieke Universiteit Leuven</orgName><placeName><settlement type="city">Louvain</settlement><region>Région flamande</region><region type="district" nuts="2">Province du Brabant flamand</region></placeName></affiliation></author><author><name sortKey="Capoccioni, Fabrizio" sort="Capoccioni, Fabrizio" uniqKey="Capoccioni F" first="Fabrizio" last="Capoccioni">Fabrizio Capoccioni</name><affiliation wicri:level="3"><nlm:aff id="I4">Department of Biology, Università Roma Tor Vergata, I-00133, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, Università Roma Tor Vergata, I-00133, Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Ciccotti, Eleonora" sort="Ciccotti, Eleonora" uniqKey="Ciccotti E" first="Eleonora" last="Ciccotti">Eleonora Ciccotti</name><affiliation wicri:level="3"><nlm:aff id="I4">Department of Biology, Università Roma Tor Vergata, I-00133, Rome, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, Università Roma Tor Vergata, I-00133, Rome</wicri:regionArea><placeName><settlement type="city">Rome</settlement><region nuts="2">Latium</region></placeName></affiliation></author><author><name sortKey="Bervoets, Lieven" sort="Bervoets, Lieven" uniqKey="Bervoets L" first="Lieven" last="Bervoets">Lieven Bervoets</name><affiliation wicri:level="4"><nlm:aff id="I5">Department of Biology, University of Antwerp, B-2020, Antwerpen, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biology, University of Antwerp, B-2020, Antwerpen</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="Covaci, Adrian" sort="Covaci, Adrian" uniqKey="Covaci A" first="Adrian" last="Covaci">Adrian Covaci</name><affiliation wicri:level="4"><nlm:aff id="I5">Department of Biology, University of Antwerp, B-2020, Antwerpen, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biology, University of Antwerp, B-2020, Antwerpen</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="I6">Toxicological Center, University of Antwerp, B-2610, Wilrijk, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Toxicological Center, University of Antwerp, B-2610, Wilrijk</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="Belpaire, Claude" sort="Belpaire, Claude" uniqKey="Belpaire C" first="Claude" last="Belpaire">Claude Belpaire</name><affiliation wicri:level="1"><nlm:aff id="I7">Research Institute for Nature and Forest, B-1560, Groenendaal-Hoeilaart, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Research Institute for Nature and Forest, B-1560, Groenendaal-Hoeilaart</wicri:regionArea><wicri:noRegion>Groenendaal-Hoeilaart</wicri:noRegion></affiliation></author><author><name sortKey="Cramb, Gordon" sort="Cramb, Gordon" uniqKey="Cramb G" first="Gordon" last="Cramb">Gordon Cramb</name><affiliation wicri:level="1"><nlm:aff id="I8">School of Medicine, University of St. Andrews, KY16 9TF, Fife, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Medicine, University of St. Andrews, KY16 9TF, Fife</wicri:regionArea><wicri:noRegion>Fife</wicri:noRegion></affiliation></author><author><name sortKey="Patarnello, Tomaso" sort="Patarnello, Tomaso" uniqKey="Patarnello T" first="Tomaso" last="Patarnello">Tomaso Patarnello</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro</wicri:regionArea><wicri:noRegion>Legnaro</wicri:noRegion></affiliation></author><author><name sortKey="Bargelloni, Luca" sort="Bargelloni, Luca" uniqKey="Bargelloni L" first="Luca" last="Bargelloni">Luca Bargelloni</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Comparative Biomedicine and Food Science, University of Padova, I-35020, Legnaro</wicri:regionArea><wicri:noRegion>Legnaro</wicri:noRegion></affiliation></author><author><name sortKey="Bortoluzzi, Stefania" sort="Bortoluzzi, Stefania" uniqKey="Bortoluzzi S" first="Stefania" last="Bortoluzzi">Stefania Bortoluzzi</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Zane, Lorenzo" sort="Zane, Lorenzo" uniqKey="Zane L" first="Lorenzo" last="Zane">Lorenzo Zane</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, University of Padova, I-35131, Padova, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, I-35131, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Genomic and transcriptomic approaches have the potential for unveiling the genome-wide response to environmental perturbations. The abundance of the catadromous European eel (<italic>Anguilla anguilla</italic>) stock has been declining since the 1980s probably due to a combination of anthropogenic and climatic factors. In this paper, we explore the transcriptomic dynamics between individuals from high (river Tiber, Italy) and low pollution (lake Bolsena, Italy) environments, which were measured for 36 PCBs, several organochlorine pesticides and brominated flame retardants and nine metals.</p></sec><sec><title>Results</title><p>To this end, we first (i) updated the European eel transcriptome using deep sequencing data with a total of 640,040 reads assembled into 44,896 contigs (Eeelbase release 2.0), and (ii) developed a transcriptomic platform for global gene expression profiling in the critically endangered European eel of about 15,000 annotated contigs, which was applied to detect differentially expressed genes between polluted sites. Several detoxification genes related to metabolism of pollutants were upregulated in the highly polluted site, including genes that take part in phase I of the xenobiotic metabolism (CYP3A), phase II (glutathione-S-transferase) and oxidative stress (glutathione peroxidase). In addition, key genes in the mitochondrial respiratory chain and oxidative phosphorylation were down-regulated at the Tiber site relative to the Bolsena site.</p></sec><sec><title>Conclusions</title><p>Together with the induced high expression of detoxification genes, the suggested lowered expression of genes supposedly involved in metabolism suggests that pollution may also be associated with decreased respiratory and energy production.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Thomas, Ma" uniqKey="Thomas M">MA Thomas</name></author><author><name sortKey="Klaper, R" uniqKey="Klaper R">R Klaper</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Travers, Se" uniqKey="Travers S">SE Travers</name></author><author><name sortKey="Smith, Md" uniqKey="Smith M">MD Smith</name></author><author><name sortKey="Bai, J" uniqKey="Bai J">J Bai</name></author><author><name sortKey="Hulbert, Sh" 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uniqKey="Pujolar J" first="Jose Martin" last="Pujolar">Jose Martin Pujolar</name></noRegion><name sortKey="Bargelloni, Luca" sort="Bargelloni, Luca" uniqKey="Bargelloni L" first="Luca" last="Bargelloni">Luca Bargelloni</name><name sortKey="Bortoluzzi, Stefania" sort="Bortoluzzi, Stefania" uniqKey="Bortoluzzi S" first="Stefania" last="Bortoluzzi">Stefania Bortoluzzi</name><name sortKey="Capoccioni, Fabrizio" sort="Capoccioni, Fabrizio" uniqKey="Capoccioni F" first="Fabrizio" last="Capoccioni">Fabrizio Capoccioni</name><name sortKey="Ciccotti, Eleonora" sort="Ciccotti, Eleonora" uniqKey="Ciccotti E" first="Eleonora" last="Ciccotti">Eleonora Ciccotti</name><name sortKey="Coppe, Alessandro" sort="Coppe, Alessandro" uniqKey="Coppe A" first="Alessandro" last="Coppe">Alessandro Coppe</name><name sortKey="Marino, Ilaria Am" sort="Marino, Ilaria Am" uniqKey="Marino I" first="Ilaria Am" last="Marino">Ilaria Am Marino</name><name sortKey="Milan, Massimo" sort="Milan, Massimo" uniqKey="Milan M" first="Massimo" last="Milan">Massimo Milan</name><name sortKey="Patarnello, Tomaso" sort="Patarnello, Tomaso" uniqKey="Patarnello T" first="Tomaso" last="Patarnello">Tomaso Patarnello</name><name sortKey="Zane, Lorenzo" sort="Zane, Lorenzo" uniqKey="Zane L" first="Lorenzo" last="Zane">Lorenzo Zane</name></country><country name="Belgique"><region name="Région flamande"><name sortKey="Maes, Gregory E" sort="Maes, Gregory E" uniqKey="Maes G" first="Gregory E" last="Maes">Gregory E. Maes</name></region><name sortKey="Belpaire, Claude" sort="Belpaire, Claude" uniqKey="Belpaire C" first="Claude" last="Belpaire">Claude Belpaire</name><name sortKey="Bervoets, Lieven" sort="Bervoets, Lieven" uniqKey="Bervoets L" first="Lieven" last="Bervoets">Lieven Bervoets</name><name sortKey="Covaci, Adrian" sort="Covaci, Adrian" uniqKey="Covaci A" first="Adrian" last="Covaci">Adrian Covaci</name><name sortKey="Covaci, Adrian" sort="Covaci, Adrian" uniqKey="Covaci A" first="Adrian" last="Covaci">Adrian Covaci</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Cramb, Gordon" sort="Cramb, Gordon" uniqKey="Cramb G" first="Gordon" last="Cramb">Gordon Cramb</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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