Project Title
A Systems Biology approach for optimization of recombinant fermentation processes
Project Type
Nacional / Public
Funding Body
Funding Program
  • CEB: 73 107,00
  • Total: 97 707,00
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Principal Investigator

Team Members - CEB


The purpose of this project is to derive strategies for increasing the productivity of recombinant protein production processes by applying a systems biology perspective to the phenomena occurring in the recombinant cell. This will specifically involve the use of genome-scale analysis of the transcriptome, proteome and fluxome.\nEscherichia coli has been the organism of choice for the production of many recombinant proteins with high therapeutic value. However, while the research on molecular biology has allowed the development of very strong promoters, there are still two main phenomena associated with this process that hamper the full use of these technologies: aerobic acetate production associated with high specific growth rates, and the so-called stringent response that usually occurs when very high levels of heterologous protein production takes place. In both cases, productivity is affected due to a decrease in the specific growth and production rates.\nWhile there have been several studies covering the recombinant protein production process with E. coli, including genome-scale analysis of the transcriptome, proteome, fluxome or metabolome, there has been a lack of an integrative approach where genomic and physiological information is combined through the use of high-throughput analysis. Moreover, it is often very difficult to elucidate which phenomena represents the causes and which ones the consequences, most of the times the derivation of hypothesis being based on misassumptions. Finally, some of the conclusions extracted from those studies are difficult to apply directly to industrial processes, as the experiments are often run in shake flaks or batch fermentations with low cellular densities, while most industrial fermentations in this field are conducted in the fed-batch mode at very high-cell densities.\nAlso, the existence of genome-scale models that cover both stoichiometry and regulation of some pathways has not been taken into account in genome-scale data analysis and for the consequent formulation of hypothesis and development of new strategies for improving the performance of the process. \nIn this work, the high-cell density fed-batch recombinant protein production process in E. coli will be studied, giving particular relevance to acetate production and stringent response phenomena. The approach is intended to be systematic, by first compiling the existing knowledge about those phenomena, extending existing genome-scale models to accommodate that knowledge, and derive hypothesis in silico that will then be tested by using genome-scale analysis of the omes. A reliable fed-batch high-cell density fermentation process will be developed enabling to reproducibly study those phenomena in different strains, in order to reduce external variances to a minimum. This approach will improve our understanding of those important phenomena as well as allow the formulation of new strategies for improving the process performance either by genetic manipulations or fermentation strategies.