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Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting &amp;gt;100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular \u03b1-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.<\/jats:p>","DOI":"10.1038\/ismej.2016.23","type":"journal-article","created":{"date-parts":[[2016,3,8]],"date-time":"2016-03-08T15:03:51Z","timestamp":1457449431000},"page":"2129-2144","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum"],"prefix":"10.1093","volume":"10","author":[{"given":"Marie","family":"de Barsy","sequence":"first","affiliation":[{"name":"Institute of Microbiology, University Hospital Center, University of Lausanne , Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Frandi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ga\u00ebl","family":"Panis","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Th\u00e9raulaz","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trestan","family":"Pillonel","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University Hospital Center, University of Lausanne , Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilbert","family":"Greub","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University Hospital Center, University of Lausanne , Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick H","family":"Viollier","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva , Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,3,8]]},"reference":[{"key":"2024011819104430400_CR1","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1093\/nar\/gkp1032","article-title":"Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome","volume":"38","author":"Albrecht","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2024011819104430400_CR2","doi-asserted-by":"crossref","first-page":"R98","DOI":"10.1186\/gb-2011-12-10-r98","article-title":"The transcriptional landscape of Chlamydia pneumoniae","volume":"12","author":"Albrecht","year":"2011","journal-title":"Genome Biol"},{"key":"2024011819104430400_CR3","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1128\/aem.63.1.115-121.1997","article-title":"Obligate intracellular bacterial parasites of acanthamoebae related to Chlamydia spp","volume":"63","author":"Amann","year":"1997","journal-title":"Appl Environ 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