Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities

BMC Genomics

David Torrents²  Mercè Planas-Fèlix¹  Josep M Mercader¹  Leyden Fernandez¹ 

[1]Joint IRB-BSC program on Computational Biology. BSC, Jordi Girona, 29, 08034 Barcelona, Spain

[2]Institució Catalana de Recerca i Estudis Avançats (ICREA) Pg Luís Companys 23, Barcelona 08010, USA

关键词: Metagenomes;    Gene regulation;    Environment;    Adaptation;   

Others  :  1128482
DOI  :  10.1186/1471-2164-15-877

 received in 2014-02-04, accepted in 2014-09-24,  发布年份 2014

【 摘 要 】

Background

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.

【 授权许可】

   
2014 Fernandez et al.; licensee BioMed Central Ltd.

【 图 表 】

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