<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of pasteur-01374955</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-22T18:09:14+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability</title>
            <author role="crp">
              <persName>
                <forename type="first">Marie</forename>
                <surname>Bobay</surname>
              </persName>
              <email type="md5">e13725525bbc240586bb1026134d5348</email>
              <email type="domain">pasteur.fr</email>
              <idno type="idhal" notation="numeric">989850</idno>
              <idno type="halauthorid" notation="string">1064839-989850</idno>
              <affiliation ref="#struct-412430"/>
              <affiliation ref="#struct-222620"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Marie</forename>
                <surname>Touchon</surname>
              </persName>
              <email type="md5">be65765ba05086aec1d6513e133bdd6a</email>
              <email type="domain">pasteur.fr</email>
              <idno type="idhal" notation="string">marie-touchon</idno>
              <idno type="idhal" notation="numeric">178489</idno>
              <idno type="halauthorid" notation="string">5226-178489</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-7389-447X</idno>
              <idno type="IDREF">https://www.idref.fr/094340374</idno>
              <affiliation ref="#struct-412430"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Eduardo P. C.</forename>
                <surname>Rocha</surname>
              </persName>
              <email type="md5">81ebd616123ad6c7dc179b3b98db2e41</email>
              <email type="domain">pasteur.fr</email>
              <idno type="idhal" notation="string">epcrocha</idno>
              <idno type="idhal" notation="numeric">184966</idno>
              <idno type="halauthorid" notation="string">362566-184966</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-7704-822X</idno>
              <idno type="IDREF">https://www.idref.fr/066829178</idno>
              <affiliation ref="#struct-412430"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Rocha</forename>
                <surname>Eduardo</surname>
              </persName>
              <email type="md5">81ebd616123ad6c7dc179b3b98db2e41</email>
              <email type="domain">pasteur.fr</email>
            </editor>
            <funder ref="#projeurop-85807"/>
            <funder>This work was supported by an European Research Council starting grant [EVOMOBILOME nu 281605]; and a grant from the Ministère de l’enseignement superieur et de la recherche to LMB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript </funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2016-10-02 18:38:58</date>
              <date type="whenModified">2023-03-24 14:53:02</date>
              <date type="whenReleased">2016-10-03 10:32:23</date>
              <date type="whenProduced">2013-09-26</date>
              <date type="whenEndEmbargoed">2016-10-03</date>
              <ref type="file" target="https://pasteur.hal.science/pasteur-01374955v1/document">
                <date notBefore="2016-10-03"/>
              </ref>
              <ref type="file" subtype="publisherPaid" n="1" target="https://pasteur.hal.science/pasteur-01374955v1/file/pgen.1003825.pdf" id="file-1374955-1455475">
                <date notBefore="2016-10-03"/>
              </ref>
              <ref type="externalLink" target="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784561"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="133389">
                <persName>
                  <forename>Rocha</forename>
                  <surname>Eduardo</surname>
                </persName>
                <email type="md5">81ebd616123ad6c7dc179b3b98db2e41</email>
                <email type="domain">pasteur.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">pasteur-01374955</idno>
            <idno type="halUri">https://pasteur.hal.science/pasteur-01374955</idno>
            <idno type="halBibtex">bobay:pasteur-01374955</idno>
            <idno type="halRefHtml">&lt;i&gt;PLoS Genetics&lt;/i&gt;, 2013, 9 (9), pp.e1003825. &lt;a target="_blank" href="https://dx.doi.org/10.1371/journal.pgen.1003825.s010"&gt;&amp;#x27E8;10.1371/journal.pgen.1003825.s010&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">PLoS Genetics, 2013, 9 (9), pp.e1003825. &amp;#x27E8;10.1371/journal.pgen.1003825.s010&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-1374955-1455475"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="PASTEUR">Institut Pasteur</idno>
            <idno type="stamp" n="UPMC" corresp="SORBONNE-UNIVERSITE">Université Pierre et Marie Curie</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="OPENAIRE">OpenAIRE</idno>
            <idno type="stamp" n="SORBONNE-UNIVERSITE">Sorbonne Université</idno>
            <idno type="stamp" n="SU-MEDECINE" corresp="SORBONNE-UNIVERSITE">Faculté de Santé de Sorbonne Université</idno>
            <idno type="stamp" n="SU-MED" corresp="SORBONNE-UNIVERSITE">Médecine - Sorbonne Université</idno>
            <idno type="stamp" n="SU-TI">Sorbonne Université - Texte Intégral</idno>
            <idno type="stamp" n="ALLIANCE-SU"> Alliance Sorbonne Université</idno>
            <idno type="stamp" n="MICROBIAL-EVOLUTIONARY-GENOMICS" corresp="PASTEUR">Génomique évolutive des microbes</idno>
            <idno type="stamp" n="UMR3525" corresp="PASTEUR">Génétique des génomes</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability</title>
                <author role="crp">
                  <persName>
                    <forename type="first">Marie</forename>
                    <surname>Bobay</surname>
                  </persName>
                  <email type="md5">e13725525bbc240586bb1026134d5348</email>
                  <email type="domain">pasteur.fr</email>
                  <idno type="idhal" notation="numeric">989850</idno>
                  <idno type="halauthorid" notation="string">1064839-989850</idno>
                  <affiliation ref="#struct-412430"/>
                  <affiliation ref="#struct-222620"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Marie</forename>
                    <surname>Touchon</surname>
                  </persName>
                  <email type="md5">be65765ba05086aec1d6513e133bdd6a</email>
                  <email type="domain">pasteur.fr</email>
                  <idno type="idhal" notation="string">marie-touchon</idno>
                  <idno type="idhal" notation="numeric">178489</idno>
                  <idno type="halauthorid" notation="string">5226-178489</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-7389-447X</idno>
                  <idno type="IDREF">https://www.idref.fr/094340374</idno>
                  <affiliation ref="#struct-412430"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Eduardo P. C.</forename>
                    <surname>Rocha</surname>
                  </persName>
                  <email type="md5">81ebd616123ad6c7dc179b3b98db2e41</email>
                  <email type="domain">pasteur.fr</email>
                  <idno type="idhal" notation="string">epcrocha</idno>
                  <idno type="idhal" notation="numeric">184966</idno>
                  <idno type="halauthorid" notation="string">362566-184966</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-7704-822X</idno>
                  <idno type="IDREF">https://www.idref.fr/066829178</idno>
                  <affiliation ref="#struct-412430"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">1957</idno>
                <idno type="issn">1553-7390</idno>
                <idno type="eissn">1553-7404</idno>
                <title level="j">PLoS Genetics</title>
                <imprint>
                  <publisher>Public Library of Science</publisher>
                  <biblScope unit="volume">9</biblScope>
                  <biblScope unit="issue">9</biblScope>
                  <biblScope unit="pp">e1003825</biblScope>
                  <date type="datePub">2013-09-26</date>
                  <date type="dateEpub">2013-09-26</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1371/journal.pgen.1003825.s010</idno>
              <idno type="pubmed">24086157</idno>
              <idno type="pubmedcentral">PMC3784561</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="sdv.bibs">Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]</classCode>
              <classCode scheme="halDomain" n="sdv.gen.gpo">Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Phages, like many parasites, tend to have small genomes and may encode autonomous functions or manipulate those of their hosts'. Recombination functions are essential for phage replication and diversification. They are also nearly ubiquitous in bacteria. The E. coli genome encodes many copies of an octamer (Chi) motif that upon recognition by RecBCD favors repair of double strand breaks by homologous recombination. This might allow self from non-self discrimination because RecBCD degrades DNA lacking Chi. Bacteriophage Lambda, an E. coli parasite, lacks Chi motifs, but escapes degradation by inhibiting RecBCD and encoding its own autonomous recombination machinery. We found that only half of 275 lambdoid genomes encode recombinases, the remaining relying on the host's machinery. Unexpectedly, we found that some lambdoid phages contain extremely high numbers of Chi motifs concentrated between the phage origin of replication and the packaging site. This suggests a tight association between replication, packaging and RecBCD-mediated recombination in these phages. Indeed, phages lacking recombinases strongly over-represent Chi motifs. Conversely, phages encoding recombinases and inhibiting host recombination machinery select for the absence of Chi motifs. Host and phage recombinases use different mechanisms and the latter are more tolerant to sequence divergence. Accordingly, we show that phages encoding their own recombination machinery have more mosaic genomes resulting from recent recombination events and have more diverse gene repertoires, i.e. larger pan genomes. We discuss the costs and benefits of superseding or manipulating host recombination functions and how this decision shapes phage genome structure and evolvability.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-412430" status="OLD">
          <idno type="RNSR">201321776T</idno>
          <orgName>Génomique évolutive des Microbes / Microbial Evolutionary Genomics</orgName>
          <date type="end">2021-07-21</date>
          <desc>
            <address>
              <addrLine>Département Génomes et Génétique - 25-28 rue du docteur Roux, F-75724 Paris Cedex 15</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://research.pasteur.fr/fr/team/microbial-evolutionary-genomics/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300027" type="direct"/>
            <relation name="UMR3525" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-222620" status="OLD">
          <orgName>Cellule Pasteur UPMC</orgName>
          <desc>
            <address>
              <addrLine>25-28, rue du Docteur Roux 75724 Paris cedex 15</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-93591" type="direct"/>
            <relation active="#struct-300027" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300027" status="VALID">
          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <idno type="ROR">https://ror.org/0495fxg12</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <orgName type="acronym">IP</orgName>
          <date type="start">1887-06-04</date>
          <desc>
            <address>
              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-93591" status="OLD">
          <idno type="ROR">https://ror.org/02en5vm52</idno>
          <orgName>Université Pierre et Marie Curie - Paris 6</orgName>
          <orgName type="acronym">UPMC</orgName>
          <date type="end">2017-12-31</date>
          <desc>
            <address>
              <addrLine>4 place Jussieu - 75005 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.upmc.fr/</ref>
          </desc>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="europeanProject" xml:id="projeurop-85807" status="VALID">
          <idno type="number">281605</idno>
          <idno type="program">ERC-2011-StG_20101109</idno>
          <idno type="call">ERC-2011-StG_20101109</idno>
          <orgName>EVOMOBILOME</orgName>
          <desc>Evolution of gene mobility: how mobile elements shape the function and sociality of microbial communities</desc>
          <date type="start">2012-01-07</date>
          <date type="end">2017-12-31</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>