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dc.contributor.authorFernandez, Leyden
dc.contributor.authorMercader, Josep M.
dc.contributor.authorPlanas-Fèlix, Mercè
dc.contributor.authorTorrents, David
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-02-24T14:16:54Z
dc.date.available2016-02-24T14:16:54Z
dc.date.issued2014-10-08
dc.identifier.citationFernandez, Leyden [et al.]. Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities. "BMC Genomics", 08 Octubre 2014, vol. 15, núm. 877.
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/2117/83398
dc.description.abstractBackground: It has been shown in a number of metagenomic studies that the addition and removal of specific genes have allowed microbiomes to adapt to specific environmental conditions by losing and gaining specific functions. But it is not known whether and how the regulation of gene expression also contributes to adaptation. Results: We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. For this, we have developed a computational protocol to extract regulatory regions and their corresponding transcription factors binding sites directly from metagenomic reads and applied it to three well known environments: Acid Mine, Whale Fall, and Waseca Farm. Taking the density of regulatory sites in promoters as a measure of the potential and complexity of gene regulation, we found it to be quantitatively the same in all three environments, despite their different physico-chemical conditions and species composition. However, we found that each environment distributes their regulatory potential differently across their functional space. Among the functions with highest regulatory potential in each niche, we found significant enrichment of processes related to sensing and buffering external variable factors specific to each environment, like for example, the availability of co-factors in deep sea, of oligosaccharides in soil and the regulation of pH in the acid mine. Conclusions: These results highlight the potential impact of gene regulation in the adaptation of bacteria to the different habitats through the distribution of their regulatory potential among specific functions, and point to critical environmental factors that challenge the growth of any microbial community.
dc.format.extent12 p.
dc.language.isoeng
dc.publisherBioMed Central
dc.rightsAttribution 4.0 International License
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectÀrees temàtiques de la UPC::Ciències de la salut
dc.subject.lcshGene regulation
dc.subject.otherAdaptation
dc.subject.otherEnvironment
dc.subject.otherGene regulation
dc.subject.otherMetagenomes
dc.titleAdaptation to environmental factors shapes the organization of regulatory regions in microbial communities
dc.typeArticle
dc.subject.lemacGenètica -- Regulació
dc.identifier.doi10.1186/1471-2164-15-877
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-877
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/ES/5PN/BIO2006-15036
upcommons.citation.publishedtrue
upcommons.citation.publicationNameBMC Genomics
upcommons.citation.volume15
upcommons.citation.number877
dc.identifier.pmid25294412


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