The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

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dc.contributor.authorOoi, Wen Fongen
dc.contributor.authorOng, Catherineen
dc.contributor.authorNandi, Tannistgaen
dc.contributor.authorKreisberg, Jason F.en
dc.contributor.authorChua, Hui Hoonen
dc.contributor.authorSun, Guangwenen
dc.contributor.authorChen, Yahuaen
dc.contributor.authorMueller, Claudiaen
dc.contributor.authorConejero, Lauraen
dc.contributor.authorEshaghi, Majiden
dc.contributor.authorAng, Roy Moh Liken
dc.contributor.authorLiu, Jianhuaen
dc.contributor.authorSobral, Brunoen
dc.contributor.authorKorbsrisate, Suneeen
dc.contributor.authorGen, Yunn Hwenen
dc.contributor.authorTitball, Richard W.en
dc.contributor.authorBancroft, Gregory J.en
dc.contributor.authorValade, Ericen
dc.contributor.authorTan, Patricken
dc.date.accessed2014-05-06en
dc.date.accessioned2014-06-17T20:12:10Zen
dc.date.available2014-06-17T20:12:10Zen
dc.date.issued2013-09-12en
dc.description.abstractBurkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes — Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes — quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an “accidental pathogen”, where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.en
dc.description.sponsorshipThis work was funded by a core grant provided by the Agency for Science, Technology and Research to the Genome Institute of Singapore, and funding from the Defence Medical and Environmental Research Institute, Singapore. This work was supported in part through NIAID contract HHSN266200400035C to BWS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.identifier.citationOoi WF, Ong C, Nandi T, Kreisberg JF, Chua HH, et al. (2013) The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei. PLoS Genet 9(9): e1003795.en
dc.identifier.doihttps://doi.org/10.1371/journal.pgen.1003795en
dc.identifier.issn1553-7404en
dc.identifier.urihttp://hdl.handle.net/10919/49013en
dc.identifier.urlhttp://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003795en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectBacterial genomicsen
dc.subjectCromosomesen
dc.subjectDNA transcriptionen
dc.subjectGene expressionen
dc.subjectGenetic networksen
dc.subjectGenome evolutionen
dc.subjectOperonsen
dc.subjectSequence motif analysisen
dc.titleThe Condition-Dependent Transcriptional Landscape of Burkholderia pseudomalleien
dc.title.serialPlos Geneticsen
dc.typeArticle - Refereeden

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