Effects of metabolic engineering on downstream processing operational cost and energy consumption: the case of Escherichia coli's glycerol conversion to succinic acid

Abstract

BACKGROUND: Succinic acid production has been studied from a metabolic engineering or a downstream processing perspective, separately. The concentration of succinic acid and other by-products obtained after the strain design influences the production cost during the recovery and purification stage. A metabolic engineering-downstream coupling evaluation is important when selecting the metabolic targets for the strain design. In this in silico study, the metabolic engineering of an Escherichia coli strain to produce succinic acid using glycerol as a carbon source in the downstream process was evaluated in terms of operational cost and energy consumption. (0.3068, 0.0576, 0.1089 h -1 ) and succinate productivity (2.7534, 6.0772, 5.5661 mmol g -1 DW h -1 ), respectively. The results showed that the succinic acid productivity constituted a central parameter when selecting the appropriate gene targets for deletion, despite the presence of organic acids in the downstream process and the biomass growth rate. RESULTS: Three strain scenarios were selected using a bi-level linear optimization problem solved by Mixed Integer Linear Programing, and simulated in a transient fashion with dynamic flux balance analysis considering both biomass growth rate CONCLUSION: A metabolism-downstream coupled model shows that the bioproduct productivity and fermentation timeare key points when considering the operational cost and energy consumption involved in the engineering of strains for industrial-scale production.Metabolic engineering targets were obtained using OptKnock, which is a bi-level linear optimization problem solved by MILP. 33

Clostridium butyricum population balance model: Predicting dynamic metabolic flux distributions using an objective function related to extracellular glycerol content

“…We propose the dynamic model as a valid tool to predict a wide variety of scenarios that would otherwise be experimentally demanding in terms of time and resources. Future research could couple the i Cbu641 GSM model and DFBA predictions with downstream processes, allowing for the estimation of the technical-economic feasibility of a hypothetical industrial process [103, 104]. The model also could be used to design efficient automatic control systems that amortize unwanted oscillatory processes during cultures in bioreactors, as is the case of designing adequately an automatized control system of the feeding flow of fed-batch cultures [105–107].…”

From industrial by‐products to value‐added compounds: the design of efficient microbial cell factories by coupling systems metabolic engineering and bioprocesses

“…Metabolic network modeling is able to predict a great number of cell capabilities and it has been useful in predicting metabolic engineering targets. Some methods based on flux balance analysis, such as dynamic flux balance analysis, have been described in order to predict a metabolic cell behavior over time 13,39,40 . Then, it is possible to predict if a metabolic intervention would change the phenotype in terms of growth rate, carbon source utilization, yields, productivity, and by‐product generation in a dynamic state.…”

“…First, the growth medium, usually a rich complex medium, requires expensive carbon sources to reach high yield / productivities, which increases substrate requirements, price, and the separation and purification process 10,11 . Second, genetic manipulation negatively affects the growth rate demanding long culture periods and extra operational cost 12,13 . Finally, after metabolic manipulation, by‐products are generated, which result in complex and high‐cost separation and purification processes 14,15 .…”

Is Bioseparation still the limiting step in bioprocess development?

“…Finally, the research papers of this Special Issue present selected advances in the field of primary recovery, purification and bioprocess development . Examples from the primary recovery of products include: a new method to extract recombinant intracellular GFP from E. coli by using aqueous solutions of surface‐active compounds, a novel integrated bioseparation process for the in situ recovery of L‐asparaginase from fermentation broth, a stable and efficient flocculation method associated with depth filtration for continuous cell separation and an approach using ultrafiltration for whey protein separation .…”

“…As a final part of this Special Issue , three examples on bioprocess development were selected. These examples include: a metabolic, engineering‐bioseparation coupling evaluation for the production of succinic acid, an integrated process development platform at microscale, using quality by design measures for the production of a recombinant protein as inclusion bodies and the practical experiences derived from the bench‐scale implementation of a bioprocess for fucoxanthin production . This report provides the required guidelines to facilitate process scale‐up for the potential commercial production and recovery of fucoxanthin.…”