RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)

In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs. Previously, we characterized short- and long-term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply, while studying a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). Genes were repeatedly switched on/off when E. coli returned to the STR. Moreover, E. coli revealed highly diverging long-term transcriptional responses in ammonia compared to glucose fluctuations. The identification of target genes may help to create robust cells and processes for large-scale application. Overall design: mRNA time profiles of E. coli K12 W3110 ammonia-limited chemostat STR-PFR culture: 59 samples derived from STR or different PFR sample ports over process time including three samples derived from the reference steady state before PFR addition, in duplicate, generated using Illumina HiSeq 2500.