Metabolic analysis to characterise and optimize an industrial enzyme production process

Metabolic analysis to characterise and optimize an industrial enzyme production process. Some microbial species are excellent candidates for industrial microbial bioprocesses, as their genomes present a large number of gene clusters encoding for enzymes involved in the biosynthesis of a wide variety of products and metabolites. Approximately half of the enzyme production bioprocesses worldwide involve species of the genus Bacillus or closely related genera, as they synthesise enzymes with good stability over a wide range of pH and temperature. Developing the ability to enhance, manipulate and/or exploit these organisms will have a significant positive impact on industrial microbial bioprocesses.

Historically, improved industrial strains were obtained by classical selection strategies, but recently genetically manipulated strains have been created to obtain not only higher productivities but also enhanced 'processability'. However, these manipulations often cause metabolic burdens in the host organism, resulting in reduced yields when the production processes are scaled up. Furthermore, some mutations may cause requirements for extra nutrients or precursors, or generate further steps for the removal of undesired proteins, affecting the bioprocess or the downstream operations.

This project deals with the study of an industrial strain which overproduces an enzyme of interest for the animal feed industry. The strain was recently described but has not been fully characterised. Knowledge of its metabolism and physiology is essential to understand the bioprocess and to design optimization strategies to obtain predictable processes, with low variability, better yields and higher productivities, with the overall objective of an improved long-term commercial viability.

The hypothesis underpinning this research project is that the overexpression of the enzyme generates metabolic limitations and physiological effects, and that the synthesis of the enzyme may be controlled by a mechanism similar to quorum-sensing. We will characterise the wild type and mutant strains to understand the metabolic impact and its effect on enzyme production, and to develop culture strategies to overcome those metabolic limiting factors.

We will construct genome scale metabolic networks of the wild type and mutant strains, using genome sequence information and experimental data to identify the metabolic limitations responsible for low yields or low productivities and to predict the response to metabolic alterations in silico.

The general objective of the project is the design of a viable platform bioprocess, accompanied by full metabolic and genetic characterisation of the chassis host strain, which is predictable, reproducible and with low variability, able to be scaled-up. Importantly, this platform process can be used for production of a range of enzymes in the same chassis host.

The outputs of this project will help to optimise industrial processes for the production of enzymes, directly benefiting the industrial partner. Academic benefits of this project will be the understanding of metabolism of the producer strain, the construction of a robust metabolic model, and the generation of data, tools, and models that can be applied in related projects.