Communities of niche-optimized strains (CoNoS) – a novel concept for improving biotechnological production of small molecules

点击翻译按钮获取中文摘要

The majority of biotechnological production processes for small molecules is based on pure cultures of single, engineered production strains. These strains often possess overcapacities of central, metabolic proteins, which is a natural mechanism to cope with changing environmental conditions. In the comparably well-defined environment of a bioreactor, these unused overcapacities represent lost carbon and energy for production of the desired product. To make these overcapacities available for the production of small molecules, we plan to design synthetic communities of niche-optimized strains (CoNoS). A CoNoS consists of at least two strains of the same species, each auxotrophic for one or more amino acid. The strains are supposed to cross-feed each other and thereby saving carbon and energy by using the naturally available biosynthesis capacity for one amino acid more efficiently. Similar communities, where auxotrophic genome reduced bacteria cross-feed each other, have frequently evolved in nature, demonstrating that there must be a significant fitness advantage compared to the technically used prototrophic pure cultures. The overall aim of our project is to generate CoNoS that produce selected amino acids more efficiently than pure cultures of current best producer strains. For this purpose, we will generate novel Corynebacterium glutamicum strains carrying broad gene deletions in the selected amino acid biosynthesis pathways, starting from the recently constructed genome-reduced C. glutamicum chassis strain C1*. The performance of these strains will be quantitatively analyzed both in pure cultures with external supplementation of the respective amino acid and in reciprocal cross-feeding communities. To optimize cross feeding and growth performance of the communities, adaptive laboratory evolution (ALE) will be used, followed by a detailed molecular analysis of the mutations enriched during these experiments. Thereby we will gain a better understanding how the strains interact in such a setting. Additionally, existing information on further targets for rational engineering will be utilized to construct 2nd generation CoNoS strains, which will then enter fed-batch process development. Strains will be labelled with specific genomic markers that will allow a quantitative characterization of the synthetic mixed cultures throughout the whole production process development. The latter will also be supported by model-based analyses of CoNoS dynamics under production conditions by applying state of the art 13C/15N metabolic flux analysis. Our project requires a tight integration of molecular biologists and bioprocess engineers, an approach which is ideally represented by the Interzell program.