SysMO Pseudomonas (Martins dos Santos)-Westerhoff

The chemical industry has been and is highly important to human society. It produces many of the substances that are used on a daily basis. Some chemical production processes are far from self-sustaining or closed; they require the input of much energy and much material, both of which are getting scarcer. In addition they may shed catalysts, waste, carbon dioxide and heat into the environment, which tends to be saturated with some of these effects, even at a global level. Certain biological processes are known to be more self-sustaining. Therefore, white biotechnology, which implements bacteria and yeasts as 'factories', is increasingly considered as a possible alternative to some chemical production processes. The design and management of a chemical factory already being difficult, the engineering and controlling of living organisms is even more so. First, living organisms do not usually thrive under conditions of the traditional chemical processes. Second, they are full of homeostatic mechanisms by which they actively resist attempts to make them do precisely what the engineer wants them to do. And third, any new biotechnological process will have to be competitive as compared to the already existing and optimized processes in the chemical industry. And then an issue that has become clear only relatively recently is the fact that the engineering of a single components of a living organism will not suffice, as organisms operate on the basis of complex, hierarchical networks of many molecules. Until recently, it has been impossible to understand the networks that steer living organisms, because they consist of hundreds of components that interact in highly complex ways. The newly developing science Systems Biology combines quantitative experimentation with mathematical approaches in order to understand the complex networks of living organisms. This project will develop a Systems Biology approach to white biotechnology in the organism Pseudomonas putida. This organism is already rather robust with respect to many types of stress, and thereby potentially a good cell factory. A large network of scientific groups from laboratories in four European countries will undertake this highly challenging research program.

White Biotechnology (the exploitation of the catalytic properties of microorganisms for industrial applications) is increasingly recognized as one of the pillars of the knowledge-base Economy that Europe is bound to drive into. The purpose of this Project is to develop the necessary knowledge base and the material and conceptual (computational) resources to establish the Gram negative soil bacterium Pseudomonas putida strain KT2440 as the vehicle for implementing biological activities into a whole range of industrially-related processes. This includes hyperproduction of enzymes for cell-free biocatalysis biopolymer and secondary metabolite production, bioremediation and even plant protection and growth promotion among others. P. putida, moreover is unusually tolerant of physico-chemical conditions relevant to industrial processes, such as solvents, hydrophobic substances/2-phase systems, low pH, low temperature, chaotropic compounds like urea, etc. Nevertheless, engineered biotechnological applications invariably impose unnatural, sometimes severe stresses on the cell that reduce performance and select compensatory changes. The specific goal of this proposal is therefore to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that achieve quantum increases in cell factory performance through a systems biology understanding of key metabolic and regulatory parameters that control cellular responses to key stresses generated during biotechnological application of this versatile bacterium.