Our group has extensive experience in the characterisation of the global response and adaptation to nutrient availability of environmental microorganisms. The bacterium Pseudomonas putida KT2440 has been used as a model system in the regulation of nitrogen-limiting conditions (two-component system NtrBC) as well as carbon limitation (CbrAB system). The genus Pseudomonas within the gamma-Proteobacteria is known for its wide metabolic versatility and genetic plasticity, as well as its widespread ubiquity, which reflects a highly developed ability to adapt to contaminated environments with different and continuously changing physico-chemical conditions.
The extensive characterisation of both regulatory systems using transcriptomics, proteomics and metabolomics has provided a precise map that allows the integration of a complex regulatory cascade in which a large collection of control systems interact, including catabolic repression processes, the participation of small RNAs (sRNA), alternative sigma factors (ECF) or strict response mechanisms.
In addition, we have also deepened in the signalling cascade that allows P. putida to activate the CbrAB system via the interaction of the histidine kinase CbrA with a signal molecule yet to be determined. CbrA phosphorylates and activates CbrB, which acts as a transcriptional regulator of a whole battery of genes that allow the bacterium to activate response mechanisms in response to carbon limitation. The structure of CbrA places it in a peculiar category of sensor element within the histidine kinase families, where a solute transporter and a histidine kinase domain are combined in a single molecule.
We have recently started a research line that studies the biodegradation of emerging pollutants by bacterial consortia, in which we analyse the microbiome of environmental sites that contain considerable concentrations of emerging pollutants. Within these pollutants, we focus on widely used hospital drugs (such as some anti-inflammatory drugs, antibiotics and others), as well as some plastic polymers of complex formulation (PET or PU, among others). The aim of this study is not only to isolate and characterise the microbial populations that, as a whole, are capable of using emerging pollutants as a source of carbon and energy, but also to carry out a meta-transcriptomic approach to identify which of the metabolic activities involved in the biodegradation process are being expressed at any given moment, and to which microorganism they correspond. The ultimate goal is to design tailor-made expression systems containing genes from different sources, for use in bioremediation processes.