Cell-free synthesis of industrial chemicals and biofuels from carbon feedstocks

Design of a synthetic enzyme cascade for the in vitro fixation of formaldehyde to acetoin

Formaldehyde (FALD) has gained prominence as an essential C1 building block in the synthesis of valuable chemicals. However, there are still challenges in converting FALD into commodities. Recently, cell-free biocatalysis has emerged as a popular approach for producing such commodities. Acetoin, also known as 3-hydroxy-2-butanone, has been widely used in food, cosmetic, agricultural and the chemical industry. It is valuable to develop a process to produce acetoin from FALD. In this study, a cell-free multi-enzyme catalytic system for the production of acetoin using FALD as the substrate was designed and constructed. It included three scales: FALD utilization pathway, glycolysis pathway and acetoin synthesis pathway. After the optimization of the reaction system, 20.17 mM acetoin was produced from 122 mM FALD, with a yield of 0.165 mol/mol, reaching 99.0% of the theoretical yield. The pathway provides a new approach for high-yield acetoin production from FALD, which consolidates the foundation for the production of high value-added chemicals using cheap one-carbon compounds.

Structure-guided engineering of branched-chain α-keto acid decarboxylase for improved 1,2,4-butanetriol production by in vitro synthetic enzymatic biosystem

Efficient synthetic routes for biomanufacturing chemicals often require the overcoming of pathway bottlenecks by tailoring enzymes to improve the catalytic efficiency or even implement non-native activities. 1,2,4-butanetriol (BTO), a valuable commodity chemical, is currently biosynthesized from D-xylose via a four-enzyme reaction cascade, with the ThDP-dependent α-keto acid decarboxylase (KdcA) identified as the potential bottleneck. Here, to further enhance the catalytic activity of KdcA toward the non-native substrate α-keto-3-deoxy-xylonate (KDX), in silico screening and structure-guided evolution were performed. The best mutants, S286L/G402P and V461K, exhibited a 1.8- and 2.5-fold higher enzymatic activity in the conversion of KDX to 3,4-dihydroxybutanal when compared to KdcA, respectively. MD simulations revealed that the two sets of mutations reshaped the substrate binding pocket, thereby increasing the binding affinity for KDX and promoting interactions between KDX and cofactor ThDP. Then, when the V461K mutant instead of wild type KdcA was integrated into the enzyme cascade, a 1.9-fold increase in BTO titer was observed. After optimization of the reaction conditions, the enzyme cocktail contained V461K converted 60 g/L D-xylose to 22.1 g/L BTO with a yield of 52.1 %. This work illustrated that protein engineering is a powerful tool for modifying the output of metabolic pathway.

Modular bioengineering of whole-cell catalysis for sialo-oligosaccharide production: coordinated co-expression of CMP-sialic acid synthetase and sialyltransferase

BACKGROUND

In whole-cell bio-catalysis, the biosystems engineering paradigm shifts from the global reconfiguration of cellular metabolism as in fermentation to a more focused, and more easily modularized, optimization of comparably short cascade reactions. Human milk oligosaccharides (HMO) constitute an important field for the synthetic application of cascade bio-catalysis in resting or non-living cells. Here, we analyzed the central catalytic module for synthesis of HMO-type sialo-oligosaccharides, comprised of CMP-sialic acid synthetase (CSS) and sialyltransferase (SiaT), with the specific aim of coordinated enzyme co-expression in E. coli for reaction flux optimization in whole cell conversions producing 3'-sialyllactose (3SL).

RESULTS

Difference in enzyme specific activity (CSS from Neisseria meningitidis: 36 U/mg; α2,3-SiaT from Pasteurella dagmatis: 5.7 U/mg) was compensated by differential protein co-expression from tailored plasmid constructs, giving balance between the individual activities at a high level of both (α2,3-SiaT: 9.4 × 102 U/g cell dry mass; CSS: 3.4 × 102 U/g cell dry mass). Finally, plasmid selection was guided by kinetic modeling of the coupled CSS-SiaT reactions in combination with comprehensive analytical tracking of the multistep conversion (lactose, N-acetyl neuraminic acid (Neu5Ac), cytidine 5'-triphosphate; each up to 100 mM). The half-life of SiaT in permeabilized cells (≤ 4 h) determined the efficiency of 3SL production at 37 °C. Reaction at 25 °C gave 3SL (40 ± 4 g/L) in ∼ 70% yield within 3 h, reaching a cell dry mass-specific productivity of ∼ 3 g/(g h) and avoiding intermediary CMP-Neu5Ac accumulation.

CONCLUSIONS

Collectively, balanced co-expression of CSS and SiaT yields an efficient (high-flux) sialylation module to support flexible development of E. coli whole-cell catalysts for sialo-oligosaccharide production.

Integrating Carbohydrate and C1 Utilization for Chemicals Production

In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO₂ and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO₂ and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L^-1 ethanol or 2 g L^-1 isobutanol from 7.5 g L^-1 xylose and 1.6 g L^-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO₂ and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO₂ or sugars.

Cell-free enzyme cascades - application and transition from development to industrial implementation

In the vision to realize a circular economy aiming for net carbon neutrality or even negativity, cell-free bioconversion of sustainable and renewable resources emerged as a promising strategy. The potential of in vitro systems is enormous, delivering technological, ecological, and ethical added values. Innovative concepts arose in cell-free enzymatic conversions to reduce process waste production and preserve fossil resources, as well as to redirect and assimilate released industrial pollutions back into the production cycle again. However, the great challenge in the near future will be the jump from a concept to an industrial application. The transition process in industrial implementation also requires economic aspects such as productivity, scalability, and cost-effectiveness. Here, we briefly review the latest proof-of-concept cascades using carbon dioxide and other C1 or lignocellulose-derived chemicals as blueprints to efficiently recycle greenhouse gases, as well as cutting-edge technologies to maturate these concepts to industrial pilot plants.

Investigating ethanol production using the Zymomonas mobilis crude extract

Cell-free systems have become valuable investigating tools for metabolic engineering research due to their easy access to metabolism without the interference of the membrane. Therefore, we applied Zymomonas mobilis cell-free system to investigate whether ethanol production is controlled by the genes of the metabolic pathway or is limited by cofactors. Initially, different glucose concentrations were added to the extract to determine the crude extract's capability to produce ethanol. Then, we investigated the genes of the metabolic pathway to find the limiting step in the ethanol production pathway. Next, to identify the bottleneck gene, a systemic approach was applied based on the integration of gene expression data on a cell-free metabolic model. ZMO1696 was determined as the bottleneck gene and an activator for its enzyme was added to the extract to experimentally assess its effect on ethanol production. Then the effect of NAD+ addition at the high concentration of glucose (1 M) was evaluated, which indicates no improvement in efficiency. Finally, the imbalance ratio of ADP/ATP was found as the controlling factor by measuring ATP levels in the extract. Furthermore, sodium gluconate as a carbon source was utilized to investigate the expansion of substrate consumption by the extract. 100% of the maximum theoretical yield was obtained at 0.01 M of sodium gluconate while it cannot be consumed by Z. mobilis. This research demonstrated the challenges and advantages of using Z. mobilis crude extract for overproduction.

Cell-free metabolic engineering enables selective biotransformation of fatty acids to value-added chemicals

Fatty acid-derived products such as alkanes, fatty aldehydes, and fatty alcohols have many applications in the chemical industry. These products are predominately produced from fossil resources, but their production processes are often not environmentally friendly. While microbes like Escherichia coli have been engineered to convert fatty acids to corresponding products, the design and optimization of metabolic pathways in cells for high productivity is challenging due to low mass transfer, heavy metabolic burden, and intermediate/product toxicity. Here, we describe an E. coli-based cell-free protein synthesis (CFPS) platform for in vitro conversion of long-chain fatty acids to value-added chemicals with product selectivity, which can also avoid the above issues when using microbial production systems. We achieve the selective biotransformation by cell-free expression of different enzymes and the use of different conditions (e.g., light and heating) to drive the biocatalysis toward different final products. Specifically, in response to blue light, cell-free expressed fatty acid photodecarboxylase (CvFAP, a photoenzyme) was able to convert fatty acids to alkanes with approximately 90% conversion. When the expressed enzyme was switched to carboxylic acid reductase (CAR), fatty acids were reduced to corresponding fatty aldehydes, which, however, could be further reduced to fatty alcohols by endogenous reductases in the cell-free system. By using a thermostable CAR and a heating treatment, the endogenous reductases were deactivated and fatty aldehydes could be selectively accumulated (>97% in the product mixture) without over-reduction to alcohols. Overall, our cell-free platform provides a new strategy to convert fatty acids to valuable chemicals with notable properties of operation flexibility, reaction controllability, and product selectivity.

Toward bioproduction of oxo chemicals from C1 feedstocks using isobutyraldehyde as an example

Oxo chemicals are valuable chemicals for synthesizing a wide array of industrial and consumer products. However, producing of oxo chemicals is predominately through the chemical process called hydroformylation, which requires petroleum-sourced materials and generates abundant greenhouse gas. Current concerns on global climate change have renewed the interest in reducing greenhouse gas emissions and recycling the plentiful greenhouse gas. A carbon–neutral manner in this regard is producing oxo chemicals biotechnologically using greenhouse gas as C1 feedstocks. Exemplifying isobutyraldehyde, this review demonstrates the significance of using greenhouse gas for oxo chemicals production. We highlight the current state and the potential of isobutyraldehyde synthesis with a special focus on the in vivo and in vitro scheme of C1-based biomanufacturing. Specifically, perspectives and scenarios toward carbon– and nitrogen–neutral isobutyraldehyde production are proposed. In addition, key challenges and promising approaches for enhancing isobutyraldehyde bioproduction are thoroughly discussed. This study will serve as a reference case in exploring the biotechnological potential and advancing oxo chemicals production derived from C1 feedstocks.