Engineering Robust Production Microbes for Large-Scale Cultivation

Abstract

Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in largescale production. Challenges during Industrial Scale-up Highlights Strain engineering in the laboratory often does not consider process requirements in larger-scale bioreactors. Systems and synthetic biology can be applied to design microbial strains that allow reliable and robust production on a large scale. Commercial microbial platforms should be selected and developed based on their relevance to final process goals.

Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products inR. toruloidesto include non-ribosomal peptides

“…One of the greatest challenges in the deployment of any bioproduct into the market, native or non-native to the production host, is engineering the host to produce at high titer, rate, and yield (TRY) in industrial settings. 13,14 Strain development of a production host for industrial applications typically involves many years of costly research and resources. 15 Therefore, selection of a host organism that naturally has the ability to produce high TRY of a class of bioproducts in industrially relevant settings would be of great economic and environmental value.…”

Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

“…While previous studies used rich media and small-scale batch fermentations to produce isoprenol, further improvements in yield and productivity using inexpensive media in larger volumes are required in order to derisk trials at commercial scale (Balan, 2014;Hollinshead et al, 2014;Wehrs et al, 2019). In this study we optimize the IPPbypass mevalonate pathway for production of isoprenol in E. coli using several HMGR, HMGS and MK variants as well as engineered PMD mutants to provide optimal levels of the pathway intermediates.…”

Contemporary Tools for Regulating Gene Expression in Bacteria

“…A future challenge is how to best apply these tools to enhance the transition of novel bioprocesses from proof-of-concept to industrial scale [122,137]. To engineer robust systems, we must select the optimal regulatory mechanism, with the final process in mind, by selecting parts and devices that are robust to the types of environmental and genetic variation faced during industrial bioprocesses.…”

“…Heterogeneous growth during large-scale bioprocesses can lead to suboptimal conditions due to gas transfer effects and nutrient availability. In turn, this can lead to local metabolic stress, phenotypic and ultimately genotypic drift (recently reviewed in [122]). Feedback systems that respond to these stresses may help minimise the formation of genotypically heterogeneous populations, which ultimately lead to mutagenic escape, by redirecting metabolic flux away from the production pathway, allowing the cellular subpopulation to better cope with stress conditions.…”