Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities
Identifieur interne : 000168 ( Pmc/Curation ); précédent : 000167; suivant : 000169Adaptation 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
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<series><title level="j">BMC Genomics</title>
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id>
<journal-title-group><journal-title>BMC Genomics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2164</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25294412</article-id>
<article-id pub-id-type="pmc">4287501</article-id>
<article-id pub-id-type="publisher-id">6783</article-id>
<article-id pub-id-type="doi">10.1186/1471-2164-15-877</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Fernandez</surname>
<given-names>Leyden</given-names>
</name>
<address><email>leyden.fernandez@bsc.es</email>
</address>
<xref ref-type="aff" rid="Aff41"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mercader</surname>
<given-names>Josep M</given-names>
</name>
<address><email>josep.mercader@bsc.es</email>
</address>
<xref ref-type="aff" rid="Aff41"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Planas-Fèlix</surname>
<given-names>Mercè</given-names>
</name>
<address><email>merce.planas@bsc.es</email>
</address>
<xref ref-type="aff" rid="Aff41"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Torrents</surname>
<given-names>David</given-names>
</name>
<address><email>david.torrents@bsc.es</email>
</address>
<xref ref-type="aff" rid="Aff41"></xref>
<xref ref-type="aff" rid="Aff42"></xref>
</contrib>
<aff id="Aff41"><label></label>
Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona, Spain</aff>
<aff id="Aff42"><label></label>
Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg Luís Companys 23, Barcelona, 08010 USA</aff>
</contrib-group>
<pub-date pub-type="epub"><day>8</day>
<month>10</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<volume>15</volume>
<issue>1</issue>
<elocation-id>877</elocation-id>
<history><date date-type="received"><day>4</day>
<month>2</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>24</day>
<month>9</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© Fernandez et al.; licensee BioMed Central Ltd. 2014</copyright-statement>
<license license-type="open-access"><license-p>This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><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>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Adaptation</kwd>
<kwd>Environment</kwd>
<kwd>Gene regulation</kwd>
<kwd>Metagenomes</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2014</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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