Targeted diversity generation by intraterrestrial archaea and archaeal viruses
Identifieur interne : 000069 ( Main/Exploration ); précédent : 000068; suivant : 000070Targeted diversity generation by intraterrestrial archaea and archaeal viruses
Auteurs : Blair G. Paul [États-Unis] ; Sarah C. Bagby [États-Unis] ; Elizabeth Czornyj [États-Unis] ; Diego Arambula [États-Unis] ; Sumit Handa [États-Unis] ; Alexander Sczyrba [Allemagne, États-Unis] ; Partho Ghosh [États-Unis] ; Jeff F. Miller [États-Unis] ; David L. Valentine [États-Unis]Source :
- Nature Communications [ 2041-1723 ] ; 2015.
Abstract
In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >1018 protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.
Url:
DOI: 10.1038/ncomms7585
PubMed: 25798780
PubMed Central: 4372165
Affiliations:
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Paul</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Marine Science Institute, University of California</institution>, Santa Barbara, California 93106,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bagby, Sarah C" sort="Bagby, Sarah C" uniqKey="Bagby S" first="Sarah C." last="Bagby">Sarah C. Bagby</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Marine Science Institute, University of California</institution>, Santa Barbara, California 93106,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Czornyj, Elizabeth" sort="Czornyj, Elizabeth" uniqKey="Czornyj E" first="Elizabeth" last="Czornyj">Elizabeth Czornyj</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Department of Microbiology, Immunology and Molecular Genetics, University of California</institution>, Los Angeles, California 90095,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Arambula, Diego" sort="Arambula, Diego" uniqKey="Arambula D" first="Diego" last="Arambula">Diego Arambula</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Department of Microbiology, Immunology and Molecular Genetics, University of California</institution>, Los Angeles, California 90095,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Handa, Sumit" sort="Handa, Sumit" uniqKey="Handa S" first="Sumit" last="Handa">Sumit Handa</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Department of Chemistry and Biochemistry, University of California San Diego</institution>, La Jolla, California 92093,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sczyrba, Alexander" sort="Sczyrba, Alexander" uniqKey="Sczyrba A" first="Alexander" last="Sczyrba">Alexander Sczyrba</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Center for Biotechnology and Faculty of Technology, Bielefeld University</institution>, 33615 Bielefeld,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a5"><institution>DOE Joint Genome Institute</institution>, Walnut Creek, California 94598,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ghosh, Partho" sort="Ghosh, Partho" uniqKey="Ghosh P" first="Partho" last="Ghosh">Partho Ghosh</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Department of Chemistry and Biochemistry, University of California San Diego</institution>, La Jolla, California 92093,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Miller, Jeff F" sort="Miller, Jeff F" uniqKey="Miller J" first="Jeff F." last="Miller">Jeff F. Miller</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Department of Microbiology, Immunology and Molecular Genetics, University of California</institution>, Los Angeles, California 90095,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a6"><institution>Molecular Biology Institute, University of California</institution>, Los Angeles, California 90095,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a7"><institution>California NanoSystems Institute, University of California</institution>, Los Angeles, California 90095,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Valentine, David L" sort="Valentine, David L" uniqKey="Valentine D" first="David L." last="Valentine">David L. Valentine</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Marine Science Institute, University of California</institution>, Santa Barbara, California 93106,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a8"><institution>Department of Earth Science, University of California Santa Barbara</institution>, Santa Barbara, California 93106<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >10<sup>18</sup> protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kallmeyer, J" uniqKey="Kallmeyer J">J. Kallmeyer</name></author><author><name sortKey="Pockalny, R" uniqKey="Pockalny R">R. Pockalny</name></author><author><name sortKey="Adhikari, R R" uniqKey="Adhikari R">R. R. Adhikari</name></author><author><name sortKey="Smith, D C" uniqKey="Smith D">D. C. Smith</name></author><author><name sortKey="Dhondt, S" uniqKey="Dhondt S">S. DHondt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lipp, J" uniqKey="Lipp J">J. Lipp</name></author><author><name sortKey="Morono, Y" uniqKey="Morono Y">Y. Morono</name></author><author><name sortKey="Inagaki, F" uniqKey="Inagaki F">F. 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J. Blaser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H. Teeling</name></author><author><name sortKey="Meyerdierks, A" uniqKey="Meyerdierks A">A. Meyerdierks</name></author><author><name sortKey="Bauer, M" uniqKey="Bauer M">M. Bauer</name></author><author><name sortKey="Amann, R" uniqKey="Amann R">R. Amann</name></author><author><name sortKey="Glockner, F O" uniqKey="Glockner F">F. O. Glöckner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dick, G J" uniqKey="Dick G">G. J. Dick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oksanen, J" uniqKey="Oksanen J">J. Oksanen</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Paul, Blair G" sort="Paul, Blair G" uniqKey="Paul B" first="Blair G." last="Paul">Blair G. Paul</name></noRegion><name sortKey="Arambula, Diego" sort="Arambula, Diego" uniqKey="Arambula D" first="Diego" last="Arambula">Diego Arambula</name><name sortKey="Bagby, Sarah C" sort="Bagby, Sarah C" uniqKey="Bagby S" first="Sarah C." last="Bagby">Sarah C. Bagby</name><name sortKey="Czornyj, Elizabeth" sort="Czornyj, Elizabeth" uniqKey="Czornyj E" first="Elizabeth" last="Czornyj">Elizabeth Czornyj</name><name sortKey="Ghosh, Partho" sort="Ghosh, Partho" uniqKey="Ghosh P" first="Partho" last="Ghosh">Partho Ghosh</name><name sortKey="Handa, Sumit" sort="Handa, Sumit" uniqKey="Handa S" first="Sumit" last="Handa">Sumit Handa</name><name sortKey="Miller, Jeff F" sort="Miller, Jeff F" uniqKey="Miller J" first="Jeff F." last="Miller">Jeff F. Miller</name><name sortKey="Miller, Jeff F" sort="Miller, Jeff F" uniqKey="Miller J" first="Jeff F." last="Miller">Jeff F. Miller</name><name sortKey="Miller, Jeff F" sort="Miller, Jeff F" uniqKey="Miller J" first="Jeff F." last="Miller">Jeff F. Miller</name><name sortKey="Sczyrba, Alexander" sort="Sczyrba, Alexander" uniqKey="Sczyrba A" first="Alexander" last="Sczyrba">Alexander Sczyrba</name><name sortKey="Valentine, David L" sort="Valentine, David L" uniqKey="Valentine D" first="David L." last="Valentine">David L. Valentine</name><name sortKey="Valentine, David L" sort="Valentine, David L" uniqKey="Valentine D" first="David L." last="Valentine">David L. Valentine</name></country><country name="Allemagne"><noRegion><name sortKey="Sczyrba, Alexander" sort="Sczyrba, Alexander" uniqKey="Sczyrba A" first="Alexander" last="Sczyrba">Alexander Sczyrba</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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