{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:12:14Z","timestamp":1790745134699,"version":"4.1.0"},"reference-count":91,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2023,10,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Genome evolution, and more specifically gene duplication, is a key process shaping host\u2013microorganism interaction. The conserved paralogs usually provide an advantage to the bacterium to thrive. If not, these genes become pseudogenes and disappear. Here, we show that during the emergence of the genus\n                    <jats:italic toggle=\"yes\">Dickeya<\/jats:italic>\n                    , the gene encoding the porin OmpF was duplicated. Our results show that the\n                    <jats:italic toggle=\"yes\">ompF2<\/jats:italic>\n                    expression is deleterious to the virulence of\n                    <jats:italic toggle=\"yes\">Dickeya dadantii<\/jats:italic>\n                    , the agent causing soft rot disease. Interestingly,\n                    <jats:italic toggle=\"yes\">ompF<\/jats:italic>\n                    2 is regulated while\n                    <jats:italic toggle=\"yes\">ompF<\/jats:italic>\n                    is constitutive but activated by the EnvZ-OmpR two-component system.\n                    <jats:italic toggle=\"yes\">In vitro<\/jats:italic>\n                    , acidic pH triggers the system. The pH measured in four eudicotyledons increased from an initial pH of 5.5 to 7 within 8 h post-infection. Then, the pH decreased to 5.5 at 10 h post-infection and until full maceration of the plant tissue. Yet, the production of phenolic acids by the plant\u2019s defenses prevents the activation of the EnvZ-OmpR system to avoid the\n                    <jats:italic toggle=\"yes\">ompF2<\/jats:italic>\n                    expression even though environmental conditions should trigger this system. We highlight that gene duplication in a pathogen is not automatically an advantage for the infectious process and that, there was a need for our model organism to adapt its genetic regulatory networks to conserve these duplicated genes.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Dickeya<\/jats:italic>\n                      species cause various diseases in a wide range of crops and ornamental plants. Understanding the molecular program that allows the bacterium to colonize the plant is key to developing new pest control methods. Unlike other enterobacterial pathogens,\n                      <jats:italic toggle=\"yes\">Dickeya dadantii<\/jats:italic>\n                      , the causal agent of soft rot disease, does not require the EnvZ-OmpR system for virulence. Here, we showed that during the emergence of the genus\n                      <jats:italic toggle=\"yes\">Dickeya<\/jats:italic>\n                      , the gene encoding the porin OmpF was duplicated and that the expression of\n                      <jats:italic toggle=\"yes\">ompF2<\/jats:italic>\n                      was deleterious for virulence. We revealed that while the EnvZ-OmpR system was activated\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      by acidic pH and even though the pH was acidic when the plant is colonized, this system was repressed by phenolic acid (generated by the plant\u2019s defenses). These results provide a unique\u2014 biologically relevant\u2014perspective on the consequence of gene duplication and the adaptive nature of regulatory networks to retain the duplicated gene.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00833-23","type":"journal-article","created":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T09:00:16Z","timestamp":1693299616000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Emergence of the\n                    <i>Dickeya<\/i>\n                    genus involved duplication of the OmpF porin and the adaptation of the EnvZ-OmpR signaling network"],"prefix":"10.1128","volume":"11","author":[{"given":"Cl\u00e9mence","family":"Cochard","sequence":"first","affiliation":[{"name":"Univ. 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Lille, CNRS, UMR 8576 - UGSF - Unit\u00e9 de Glycobiologie Structurale et Fonctionnelle","place":["Lille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Marceau","sequence":"additional","affiliation":[{"name":"Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille","place":["Lille, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iulia","family":"Macavei","sequence":"additional","affiliation":[{"name":"Univ. Lyon, CNRS, Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Lemoine","sequence":"additional","affiliation":[{"name":"Univ. Lyon, CNRS, Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chrystelle","family":"Le Danvic","sequence":"additional","affiliation":[{"name":"Univ. Lille, CNRS, UMR 8576 - UGSF - Unit\u00e9 de Glycobiologie Structurale et Fonctionnelle","place":["Lille, France"]},{"name":"R&D Department, ALLICE","place":["Paris, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franck","family":"Bouchart","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Polytechnique Hauts-de-France, EA 2443 - LMCPA - Laboratoire des Mat\u00e9riaux C\u00e9ramiques et Proc\u00e9d\u00e9s Associ\u00e9s","place":["Valenciennes, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brigitte","family":"Delrue","sequence":"additional","affiliation":[{"name":"Univ. 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