Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts

Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts

Minden, Steven (University of Stuttgart)
Aniolek, Maria (University of Stuttgart)
Noorman, H.J. (TU Delft BT/Bioprocess Engineering; DSM)
Takors, Ralf (University of Stuttgart)

2023

Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.

bioreactor
Ethanol Red™
Saccharomyces cerevisiae
scale-down
scale-up
stimulus–response experiment
substrate gradient
transcriptomics

http://resolver.tudelft.nl/uuid:5e615c6f-e29a-4292-aa8e-d68ea998df0b

https://doi.org/10.3390/genes14050997

2073-4425

Genes, 14 (5)

Institutional Repository

journal article

© 2023 Steven Minden, Maria Aniolek, H.J. Noorman, Ralf Takors