Cell biology and Biotechnology

Regulatory mechanisms of gene expression in pollutant-degrading bacteria


Many bacteria have the ability to degrade a variety of environmental pollutants and use them as growth substrates, making them a powerful tool for removing dangerous pollutants that are causing irreversible damage to the biosphere.

Far from controlled conditions in the laboratory, microbial survival in natural habitats is often threatened by constantly fluctuating environmental conditions. Bacteria have learned to adapt to these stressful situations by adjusting their transcriptional profile and optimising gene expression. We study gene regulation and regulatory mechanisms (regulatory proteins, regulatory RNAs, induced gene function, etc.) that allow environmental pollutant-degrading bacteria to trigger the appropriate physiological and metabolic response to each environmental condition.

We focus on two aspects of regulation and also in Bioremediation.
  • The General Stress Response (GSR) of Sphingopyxis granuli TFA. TFA is an Alphaproteobacterium capable of growing with the organic solvent tetralin (1,2,3,4-tetrahydronaphthalene) as its sole carbon and energy source. GSR is a global bacterial protective response against a wide variety of stresses. This response is controlled by two sigma factors of extracytoplasmic function (ECFG1-ECFG2). The regulatory cascade involves in addition to ECFs, the anti-sigma proteins NepR1-NepR2 and the anti-anti-sigma proteins PhyR1-PhyR2.
  • The regulation of anaerobic metabolism in Sphingopyxis granuli TFA. TFA is the only Sphingopyxis described with the ability to grow under anaerobic conditions by respiring nitrate. This new metabolism makes it particularly interesting as it allows it to inhabit new ecological niches. As part of this response, we are working on the identification and characterisation of small regulatory RNAs in anaerobiosis and the regulation of flagellar genes to oxygen availability. 
  • Functional metagenomics for the identification of new enzymes and the development of biocatalysts of environmental interestThe astonishing genetic diversity of the microbial world offers an extraordinary array of functions that have the potential to contribute to the development of industrial applications in many different fields. However, the vast majority of bacteria in natural ecosystems (more than 99%) cannot be cultured in the laboratory. This means that we are losing an enormous amount of information and its potential application using traditional techniques. Functional metagenomics allows access to all the genetic material of microorganisms in an environmental sample by direct extraction, without the need for prior cultivation of the microorganisms. Functional metagenomics involves extraction of DNA from a particular environment, creation of a metagenomic DNA library, expression of the library in the appropriate host and finally identification of an activity of interest in an enzymatic assay or growth on selective media. In this project we use metagenomic libraries to identify new enzymes in the area of by-product revalorisation (use of lignocellulosic waste for biofuel production and other biotechnological processes) and in the degradation of environmental pollutants such as plastics. 

CABD - Centro Andaluz de Biología del Desarrollo

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