Pseudomonas putida is a particularly attractive microorganism for biocatalysis purposes. However, some of the Pseudomonas-based applications are still in an early stage of progress largely due to a lack of knowledge of the genotype/phenotype relationships in this bacterium, mainly under conditions relevant for both industrial and environmental endeavors. The general objective of my research project is to increase the current understanding of metabolic pathways regulation in P. putida by applying systems and synthetic biology methods to assist in elucidating and quantifying metabolic properties of the cells.

Ilaria placa 1

The TOL (pWW0) catabolic plasmid of P. putida mt-2 encodes the upper and lower (ormeta) pathways needed for mineralization of aromatic compounds, namely toluene and xylenes. While models of regulatory circuits controlling expression of involved genes are available, little is known about the actual metabolic state of the cells. A currently accepted tenet is that what we know as phenotype in a clonal population is the macroscopic result of an average of two or more metabolic states. I will attempt to address this issue in P. putida cells growing on aromatic compounds (and other carbon sources) by using not only experimental data from the whole population, but also by studyingmetabolic traits at the single-cell level.

I am also interested in re-factoring large metabolic blocks in P. putida. With a focus on diversity rather than efficiency, the central metabolism of this bacterium is geared for the catabolism of a large variety of substrates, especially organic acids. It would be rather useful to have strains that efficiently use substrates of industrial interest (i.a., glucose), and also able to grow under different conditions of oxygen availability. In order to re-design these relevant properties, the very central metabolic core of P. putida has to be streamlined. I will attempt to detach both small and large metabolic modules from the rest of the metabolic network (i.e., orthogonalization) and to re-direct key metabolic intermediates into alternative native and heterologous pathways.

Besides these main research subjects, I am involved in developing new synthetic biology tools to facilitate the manipulation of microorganisms for metabolic engineering endeavors (see figure below).