Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities
Identifieur interne : 000568 ( Ncbi/Checkpoint ); précédent : 000567; suivant : 000569Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities
Auteurs : Leyden Fernandez [Espagne] ; Josep M. Mercader [Espagne] ; Mercè Planas-Fèlix [Espagne] ; David Torrents [Espagne, États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2014.
Abstract
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.
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.
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.
The online version of this article (doi:10.1186/1471-2164-15-877) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-877
PubMed: 25294412
PubMed Central: 4287501
Affiliations:
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BSC, Jordi Girona, 29, 08034 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation></author><author><name sortKey="Mercader, Josep M" sort="Mercader, Josep M" uniqKey="Mercader J" first="Josep M" last="Mercader">Josep M. Mercader</name><affiliation wicri:level="2"><nlm:aff id="Aff41">Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation></author><author><name sortKey="Planas Felix, Merce" sort="Planas Felix, Merce" uniqKey="Planas Felix M" first="Mercè" last="Planas-Fèlix">Mercè Planas-Fèlix</name><affiliation wicri:level="2"><nlm:aff id="Aff41">Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation></author><author><name sortKey="Torrents, David" sort="Torrents, David" uniqKey="Torrents D" first="David" last="Torrents">David Torrents</name><affiliation wicri:level="2"><nlm:aff id="Aff41">Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff42">Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg Luís Companys 23, Barcelona, 08010 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg Luís Companys 23, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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.</p></sec><sec><title>Results</title><p>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.</p></sec><sec><title>Conclusions</title><p>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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-877) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tringe, 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uniqKey="Nawrocki E">EP Nawrocki</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author><author><name sortKey="Gardner, Pp" uniqKey="Gardner P">PP Gardner</name></author><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hyatt, D" uniqKey="Hyatt D">D Hyatt</name></author><author><name sortKey="Chen, Gl" uniqKey="Chen G">GL Chen</name></author><author><name sortKey="Locascio, Pf" uniqKey="Locascio P">PF LoCascio</name></author><author><name sortKey="Land, Ml" uniqKey="Land M">ML Land</name></author><author><name sortKey="Larimer, Fw" uniqKey="Larimer F">FW Larimer</name></author><author><name sortKey="Hauser, Lj" uniqKey="Hauser L">LJ Hauser</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li><li>États-Unis</li></country><region><li>Catalogne</li></region><settlement><li>Barcelone</li></settlement></list><tree><country name="Espagne"><region name="Catalogne"><name sortKey="Fernandez, Leyden" sort="Fernandez, Leyden" uniqKey="Fernandez L" first="Leyden" last="Fernandez">Leyden Fernandez</name></region><name sortKey="Mercader, Josep M" sort="Mercader, Josep M" uniqKey="Mercader J" first="Josep M" last="Mercader">Josep M. Mercader</name><name sortKey="Planas Felix, Merce" sort="Planas Felix, Merce" uniqKey="Planas Felix M" first="Mercè" last="Planas-Fèlix">Mercè Planas-Fèlix</name><name sortKey="Torrents, David" sort="Torrents, David" uniqKey="Torrents D" first="David" last="Torrents">David Torrents</name></country><country name="États-Unis"><region name="Catalogne"><name sortKey="Torrents, David" sort="Torrents, David" uniqKey="Torrents D" first="David" last="Torrents">David Torrents</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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