Integrated Robotic Mini Bioreactor Platform for Automated, Parallel Microbial Cultivation With Online Data Handling and Process Control

During process development, the experimental search space is defined by the number of experiments that can be performed in specific time frames but also by its sophistication (e.g., inputs, sensors, sampling frequency, analytics). High-throughput liquid-handling stations can perform a large number of automated experiments in parallel. Nevertheless, the experimental data sets that are obtained are not always relevant for development of industrial bioprocesses, leading to a high rate of failure during scale-up. We present an automated mini bioreactor platform that enables parallel cultivations in the milliliter scale with online monitoring and control, well-controlled conditions, and advanced feeding strategies similar to industrial processes. The combination of two liquid handlers allows both automated mini bioreactor operation and at-line analysis in parallel. A central database enables end-to-end data exchange and fully integrated device and process control. A model-based operation algorithm allows for the accurate performance of complex cultivations for scale-down studies and strain characterization via optimal experimental redesign, significantly increasing the reliability and transferability of data throughout process development. The platform meets the tradeoff between experimental throughput and process control and monitoring comparable to laboratory-scale bioreactors.

Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions

Alternative sigma factors control numerous aspects of bacterial life, including adaptation to physiological stresses, morphological development, persistence states and virulence. This is especially true for the physiologically complex actinobacteria. Here we report the development of a robust gene deletions system for Streptomyces lividans TK24 based on a BAC library combined with the λ-Red recombination technique. The developed system was validated by systematically deleting the most highly expressed genes encoding alternative sigma factors and several other regulatory genes within the chromosome of S. lividans TK24. To demonstrate the possibility of large scale genomic manipulations, the major part of the undecylprodigiosin gene cluster was deleted as well. The resulting mutant strains were characterized in terms of morphology, growth parameters, secondary metabolites production and response to thiol-oxidation and cell-wall stresses. Deletion of SLIV_12645 gene encoding S. coelicolor SigR1 ortholog has the most prominent phenotypic effect, resulted in overproduction of actinorhodin and coelichelin P1 and increased sensitivity to diamide. The secreted proteome analysis of SLIV_12645 mutant revealed SigR1 influence on trafficking of proteins involved in cell wall biogenesis and refactoring. The reported here gene deletion system will further facilitate work on S. lividans strain improvement as a host for either secondary metabolites or protein production and will contribute to basic research in streptomycetes physiology, morphological development, secondary metabolism. On the other hand, the systematic deletion of sigma factors encoding genes demonstrates the complexity and conservation of regulatory processes conducted by sigma factors in streptomycetes.