Trade-off Between Resistance and Persistence in High Cell DensityEscherichia ColiCultures

Abstract

Microbes experience high cell density in many environments that come with diverse resource limitations and stresses. However, high density physiology remains poorly understood. We utilized well-controlled culturing systems to grow wild-type and metabolically engineered Escherichia coli strains into high cell densities (50-80 g Cdry cell weight L-1) and explore the associated transcriptional dynamics. Knowledge-enriched machine-learning-based analytics reveal distinct stress-related gene expression patterns that are consistent with a fundamental trade-off between resistance and persistence. We suggest that this trade-off explains observed growth arrests in high-density cultures and that it results from the disruption of cellular homeostasis, due to reallocation of limited cellular resources from resistance functions towards maintenance requirements of engineered production pathways. This study deepens our understanding of high-density physiology and demonstrates its importance to fundamental biomanufacturing challenges.

Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing

“…Although these benefits did not translate to increased melatonin titer in the batch fermentation tests, the mutations are believed to offer potential robustness advantages in larger bioreactors where these ROS and acid stresses are more pronounced. 58 These results also demonstrate how mutations in different genes involved in E. coli ’s iron utilization in response to oxidative stress can result in different phenotypes…”

“…This enhancement may also be less burdensome than that of oxyR mutations. Although these benefits did not translate to increased melatonin titer in the batch fermentation tests, the mutations are believed to offer potential robustness advantages in larger bioreactors where these ROS and acid stresses are more pronounced . These results also demonstrate how mutations in different genes involved in E.…”

“…HPLC was performed as described previously . The medium for batch fermentation was described before . Dry cell weight (DCW, g/L) was calculated by multiplying the final manually measured optical density (600 nm) by a conversion factor of 0.341 (Abs/g DCW /L) determined using strain BW25113.…”