Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli

Combined metabolic and enzymatic engineering for de novo biosynthesis of δ-tocotrienol in Yarrowia lipolytica

δ-Tocotrienol, an isomer of vitamin E with anti-inflammatory, neuroprotective and anti-coronary arteriosclerosis properties, is widely used in health care, medicine and other fields. Microbial synthesis of δ-tocotrienol offers significant advantages over plant extraction and chemical synthesis methods, including increased efficiency, cost-effectiveness and environmental sustainability. However, limited precursor availability and low catalytic efficiency of key enzymes remain major bottlenecks in the biosynthesis of δ-tocotrienol. In this study, we assembled the complete δ-tocotrienol biosynthetic pathway in Yarrowia lipolytica and enhanced the precursor supply, resulting in a titre of 102.8 mg/L. The catalytic efficiency of the rate-limiting steps in the pathway was then enhanced through various strategies, including fusion expression of key enzymes homogentisate phytyltransferaseand and tocopherol cyclase, semi-rational design of SyHPT and multi-copy integration of pathway genes. The final a δ-tocotrienol titre in a 5 L bioreactor was 466.8 mg/L following fed-batchfermentation. This study represents the first successful de novo biosynthesis of δ-tocotrienol in Y. lipolytica, providing valuable insights into the synthesis of vitamin E-related compounds.

Improving sustainable isopropanol production in engineered Escherichia coli W via oxygen limitation

BACKGROUND

Due to ecological concerns, alternative supply lines for fuel and bulk chemicals such as isopropanol are increasingly pursued. By implementing the formation pathways from natural producers like Clostridium beijerinckii and Clostridium aurantibutyricum, isopropanol can be produced in Escherichia coli. However, developing an industrially and economically feasible microbial production process requires a robust and efficient process strategy. Therefore, this study explores microaerobic conditions in combination with lactose and sour whey as sustainable carbon source as a basis for large-scale microbial isopropanol production.

RESULTS

Different gas-liquid mass transfer regimes (affected by variations of the stirrer speed and ingas oxygen concentration) allowed the implementation of different microaerobic conditions characterized by their specific oxygen uptake rate (qO2) in cultivations with an isopropanol producing E. coli W strain on lactose. Under microaerobic conditions, the specific isopropanol production rate (qp, ipa) exhibited a direct correlation with qO2. Moreover, isopropanol production showed a pseudo growth-coupled behavior. Monitoring of the formation rates of various by-products such as acetone, lactate, acetate, pyruvate, formate and succinate allowed to identify a qO2 of 9.6 mmol g- 1 h- 1 in only slightly microaerobic cultivations as the best conditions for microbial isopropanol production. Additionally, the data suggests that a carbon bottleneck exists at the pyruvate node and the availability of the redox factor NADPH is crucial to shift the product balance from acetone to isopropanol. Finally, confirmation runs prove the effectiveness of the microaerobic production approach by yielding 8.2 g L- 1 (135.8 ± 13.3 mmol L- 1) and 20.6 g L- 1 (342.9 ± 0.4 mmol L- 1) isopropanol on lactose and whey, respectively, reaching a volumetric isopropanol formation rate of up to 2.44 g L- 1 h- 1 (40.6 mmol L- 1 h- 1).

CONCLUSIONS

This study identifies slightly microaerobic conditions (qO2 ~ 10 mmol g- 1 h- 1) as the currently best conditions for microbial isopropanol production on lactose and whey in E. coli W. In the future, optimizing the carbon flux around the pyruvate node, ensuring sufficient NADPH supply, and establishing a feedback control loop to control process variables affecting oxygen transfer to the culture, could make microbial isopropanol production feasible at an industrial scale.

Acetate production from corn stover hydrolysate using recombinant Escherichia coli BL21 (DE3) with an EP-bifido pathway

BACKGROUND

Acetate is an important chemical feedstock widely applied in the food, chemical and textile industries. It is now mainly produced from petrochemical materials through chemical processes. Conversion of lignocellulose biomass to acetate by biotechnological pathways is both environmentally beneficial and cost-effective. However, acetate production from carbohydrate in lignocellulose hydrolysate via glycolytic pathways involving pyruvate decarboxylation often suffers from the carbon loss and results in low acetate yield.

RESULTS

Escherichia coli BL21 (DE3) was confirmed to have high tolerance to acetate in this work. Thus, it was selected from seven laboratory E. coli strains for acetate production from lignocellulose hydrolysate. The byproduct-producing genes frdA, ldhA, and adhE in E. coli BL21 (DE3) were firstly knocked out to decrease the generation of succinate, lactate, and ethanol. Then, the genes pfkA and edd were also deleted and bifunctional phosphoketolase and fructose-1,6-bisphosphatase were overexpressed to construct an EP-bifido pathway in E. coli BL21 (DE3) to increase the generation of acetate from glucose. The obtained strain E. coli 5K/pFF can produce 22.89 g/L acetate from 37.5 g/L glucose with a yield of 0.61 g/g glucose. Finally, the ptsG gene in E. coli 5K/pFF was also deleted to make the engineered strain E. coli 6K/pFF to simultaneously utilize glucose and xylose in lignocellulosic hydrolysates. E. coli 6K/pFF can produce 20.09 g/L acetate from corn stover hydrolysate with a yield of 0.52 g/g sugar.

CONCLUSION

The results presented here provide a promising alternative for acetate production with low cost substrate. Besides acetate production, other biotechnological processes might also be developed for other acetyl-CoA derivatives production with lignocellulose hydrolysate through further metabolic engineering of E. coli 6K/pFF.

Efficiency of acetate-based isopropanol synthesis in Escherichia coli W is controlled by ATP demand

BACKGROUND

Due to increasing ecological concerns, microbial production of biochemicals from sustainable carbon sources like acetate is rapidly gaining importance. However, to successfully establish large-scale production scenarios, a solid understanding of metabolic driving forces is required to inform bioprocess design. To generate such knowledge, we constructed isopropanol-producing Escherichia coli W strains.

RESULTS

Based on strain screening and metabolic considerations, a 2-stage process was designed, incorporating a growth phase followed by a nitrogen-starvation phase. This process design yielded the highest isopropanol titers on acetate to date (13.3 g L-1). Additionally, we performed shotgun and acetylated proteomics, and identified several stress conditions in the bioreactor scenarios, such as acid stress and impaired sulfur uptake. Metabolic modeling allowed for an in-depth characterization of intracellular flux distributions, uncovering cellular demand for ATP and acetyl-CoA as limiting factors for routing carbon toward the isopropanol pathway. Moreover, we asserted the importance of a balance between fluxes of the NADPH-providing isocitrate dehydrogenase (ICDH) and the product pathway.

CONCLUSIONS

Using the newly gained system-level understanding for isopropanol production from acetate, we assessed possible engineering approaches and propose process designs to maximize production. Collectively, our work contributes to the establishment and optimization of acetate-based bioproduction systems.

De novo biosynthesis of 3-hydroxy-3-methylbutyrate as anti-catabolic supplement by metabolically engineered Escherichia coli

3-Hydroxy-3-methylbutyrate (HMB) is a five-carbon branch-chain hydroxy acid currently used as a dietary supplement to treat sarcopenia and exercise training. However, its current production relies on conventional chemical processes which require toxic substances and are generally non-sustainable. While bio-based syntheses of HMB have been developed, they are dependent on biotransformation of its direct precursors which are generally costly. Therefore, in this work, we developed a synthetic de novo HMB biosynthetic pathway that enables HMB production from renewable resources. This novel HMB biosynthesis employs heterologous enzymes from mevalonate pathway and myxobacterial iso-fatty acid pathway for converting acetyl-CoA to HMB-CoA. Subsequently, HMB-CoA is hydrolyzed by a thioesterase to yield HMB. Upon expression of this pathway, our initial Escherichia coli strain produced 660 mg/L of HMB from glucose in 48 hours. Through optimization of coenzyme A removal from HMB-CoA and genetic operon structure, our final strain achieved HMB production titer of 17.7 g/L in glucose minimal media using a bench-top bioreactor. This engineered strain was further demonstrated to produce HMB from other renewable carbon sources such as xylose, glycerol, and acetate. The results from this work provided a flexible and environmentally benign method for producing HMB.

Trace impurities in sodium phosphate influences the physiological activity of Escherichia coli in M9 minimal medium

In the field of applied microbiology, reproducibility and experimental variability are important factors that influence both basic research as well as process development for industrial applications. Experimental reproducibility and accuracy depend not only on culture conditions such as temperature and aeration but also on raw materials and procedures used for media preparation. The M9 minimal medium is one of the most common synthetic media for culturing Escherichia coli and other bacteria. This synthetic medium can be used to observe and evaluate the physiological activity of microbes under minimal nutritional requirements and determine the limiting factor for the desired phenotype. Although one of the advantages using the M9 medium is that its composition can be modulated, it is difficult to control presence of trace components and impurities from the reagents for preparing this medium. Herein, we showed that trace ingredients present in the reagents used for M9 media preparation affect the bacterial physiological activities (e.g., cell growth, substrate consumption, and byproduct formation). Additionally, we systematically identified the trace ingredient that influenced phenotypic differences. Our results showed that the selection of reagents and accuracy during reagent preparation is important for experimental reproducibility in the field of bio-engineering and systems biology focused on the systematic and continuous development of biomolecular systems (e.g., biorefinery, metabolic engineering, and synthetic biology).

Local metabolic response of Escherichia coli to the module genetic perturbations in l-methionine biosynthetic pathway

l-Methionine biosynthesis is through multilevel regulated and multibranched biosynthetic pathway (MRMBP). Because of the complex regulatory mechanism and the imbalanced metabolic flux between branched pathways, microbial production of l-methionine has not been commercialized. In this study, local metabolic response in MRMBP of l-methionine was investigated and various crucial genes in branched pathways were determined. In l-serine pathway, the crucial gene was serABC. In O-succinyl homoserine (OSH) pathway, which was the C4 backbone of l-methionine, metB and metL controlled the metabolic flux jointly. In l-cysteine pathway, the crucial gene cysE^fbr could disturb the flux distribution of local network in l-methionine biosynthesis. However, no crucial gene for l-methionine production in 5-methyl tetrahydrofolate (CH₃-THF) pathway was found. The relation between these pathways was also researched. l-Serine pathway, as the upstream pathway of l-cysteine and CH₃-THF, played a crucial role in l-methionine biosynthesis. l-Cysteine pathway showed the strongest controlling force of the metabolic flux, and OSH pathway was second to l-cysteine pathway. In contrast, CH₃-THF pathway was the weakest, which was probably the mainly limited steps at present and had great potential in further research. In addition, constructed W3110 IJAHFEBC/pA∗HAmL was able to produce 2.62 g/L l-methionine in flask. This study is instructive for l-methionine biosynthesis and provides a new research method of biosynthesizing other metabolic products in MRMBPs.

A tunable metabolic valve for precise growth control and increased product formation in Pseudomonas putida

Metabolic engineering of microorganisms aims to design strains capable of producing valuable compounds under relevant industrial conditions and in an economically competitive manner. From this perspective, and beyond the need for a catalyst, biomass is essentially a cost-intensive, abundant by-product of a microbial conversion. Yet, few broadly applicable strategies focus on the optimal balance between product and biomass formation. Here, we present a genetic control module that can be used to precisely modulate growth of the industrial bacterial chassis Pseudomonas putida KT2440. The strategy is based on the controllable expression of the key metabolic enzyme complex pyruvate dehydrogenase (PDH) which functions as a metabolic valve. By tuning the PDH activity, we accurately controlled biomass formation, resulting in six distinct growth rates with parallel overproduction of excess pyruvate. We deployed this strategy to identify optimal growth patterns that improved the production yield of 2-ketoisovalerate and lycopene by 2.5- and 1.38-fold, respectively. This ability to dynamically steer fluxes to balance growth and production substantially enhances the potential of this remarkable microbial chassis for a wide range of industrial applications.

The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca

The aerobic, thermophilic Actinobacterium, Thermobifida fusca has been proposed as an organism to be used for the efficient conversion of plant biomass to fatty acid-derived precursors of biofuels or biorenewable chemicals. Despite the potential of T. fusca to catabolize plant biomass, there is remarkably little data available concerning the natural ability of this organism to produce fatty acids. Therefore, we determined the fatty acids that T. fusca produces when it is grown on different carbon sources (i.e., glucose, cellobiose, cellulose and avicel) and at two different growth temperatures, namely at the optimal growth temperature of 50°C and at a suboptimal temperature of 37°C. These analyses establish that T. fusca produces a combination of linear and branched chain fatty acids (BCFAs), including iso-, anteiso-, and 10-methyl BCFAs that range between 14- and 18-carbons in length. Although different carbon sources and growth temperatures both quantitatively and qualitatively affect the fatty acid profiles produced by T. fusca, growth temperature is the greater modifier of these traits. Additionally, genome scanning enabled the identification of many of the fatty acid biosynthetic genes encoded by T. fusca.

Expanding the use of ethanol as a feedstock for cell-free synthetic biochemistry by implementing acetyl-CoA and ATP generating pathways

Ethanol is a widely available carbon compound that can be increasingly produced with a net negative carbon balance. Carbon-negative ethanol might therefore provide a feedstock for building a wider range of sustainable chemicals. Here we show how ethanol can be converted with a cell free system into acetyl-CoA, a central precursor for myriad biochemicals, and how we can use the energy stored in ethanol to generate ATP, another key molecule important for powering biochemical pathways. The ATP generator produces acetone as a value-added side product. Our ATP generator reached titers of 27 ± 6 mM ATP and 59 ± 15 mM acetone with maximum ATP synthesis rate of 2.8 ± 0.6 mM/h and acetone of 7.8 ± 0.8 mM/h. We illustrated how the ATP generating module can power cell-free biochemical pathways by converting mevalonate into isoprenol at a titer of 12.5 ± 0.8 mM and a maximum productivity of 1.0 ± 0.05 mM/h. These proof-of-principle demonstrations may ultimately find their way to the manufacture of diverse chemicals from ethanol and other simple carbon compounds.

Dynamic metabolic engineering of Escherichia coli improves fermentation for the production of pyruvate and its derivatives

Pyruvate is a key intermediate that is involved in various synthetic metabolic pathways for microbial chemical and fuel production. It is widely used in the food, chemical, and pharmaceutical industries. However, the microbial production of pyruvate and its derivatives compete with microbial cell growth, as pyruvate is an important metabolic intermediate that serves as a hub for various endogenous metabolic pathways, including gluconeogenesis, amino acid synthesis, TCA cycle, and fatty acid biosynthesis. To achieve a more efficient bioprocess for the production of pyruvate and its derivatives, it is necessary to reduce the metabolic imbalance between cell growth and target chemical production. For this purpose, we devised a dynamic metabolic engineering strategy within an Escherichia coli model, in which a metabolic toggle switch (MTS) was employed to redirect metabolic flux from the endogenous pathway toward the target synthetic pathway. Through a combination of TCA cycle interruption through MTS and reduction of pyruvate consumption in endogenous pathways, we achieved a drastic improvement (163 mM, 26-fold) in pyruvate production. In addition, we demonstrated the redirection of metabolic flux from excess pyruvate toward isobutanol production. The final isobutanol production titer of the strain harboring MTS was 26% improved compared with that of the control strain.

Quantitative metabolomics for dynamic metabolic engineering using stable isotope labeled internal standards mixture (SILIS)

The production of chemicals and fuels from renewable resources using engineered microbes is an attractive alternative for current fossil-dependent industries. Metabolic engineering has contributed to pathway engineering for the production of chemicals and fuels by various microorganisms. Recently, dynamic metabolic engineering harnessing synthetic biological tools has become a next-generation strategy in this field. The dynamic regulation of metabolic flux during fermentation optimizes metabolic states according to each fermentation stage such as cell growth phase and compound production phase. However, it is necessary to repeat the evaluation and redesign of the dynamic regulation system to achieve the practical use of engineered microbes. In this study, we performed quantitative metabolome analysis to investigate the effects of dynamic metabolic flux regulation on engineered Escherichia coli for γ-amino butyrate (GABA) fermentation. We prepared a stable isotope-labeled internal standard mixture (SILIS) for the stable isotope dilution method (SIDM), a mass spectrometry-based quantitative metabolome analysis method. We found multiple candidate bottlenecks for GABA production. Some metabolic reactions in the GABA production pathway should be engineered for further improvement in the direct GABA fermentation with dynamic metabolic engineering strategy.

Construction of acetyl-CoA and DBAT hybrid metabolic pathway for acetylation of 10-deacetylbaccatin III to baccatin III

10-Deacetylbaccatin III (10-DAB) C10 acetylation is an indispensable procedure for Taxol semi-synthesis, which often requires harsh conditions. 10-Deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) catalyzes the acetylation but acetyl-CoA supply remains a key limiting factor. Here we refactored the innate biosynthetic pathway of acetyl-CoA in Escherichia coli and obtained a chassis with acetyl-CoA productivity over three times higher than that of the host cell. Then, we constructed a microbial cell factory by introducing DBAT gene into this chassis for efficiently converting 10-DAB into baccatin III. We found that baccatin III could be efficiently deacetylated into 10-DAB by DBAT with CoASH and K⁺ under alkaline condition. Thus, we fed acetic acid to the engineered strain both for serving as a substrate of acetyl-CoA biosynthesis and for alleviating the deacetylation of baccatin III. The fermentation conditions were optimized and the baccatin III titers reached 2, 3 and 4.6 g/L, respectively, in a 3-L bioreactor culture when 2, 3 and 6 g/L of 10-DAB were supplied. Our study provides an environment-friendly approach for the large scale 10-DAB acetylation without addition of acetyl-CoA in the industrial Taxol semi-synthesis. The finding of DBAT deacetylase activity may broaden its application in the structural modification of pharmaceutically important lead compounds.

Recent advances in metabolic engineering-integration of in silico design and experimental analysis of metabolic pathways

Microorganisms are widely used to produce valuable compounds. Because thousands of metabolic reactions occur simultaneously and many metabolic reactions are related to target production and cell growth, the development of a rational design method for metabolic pathway modification to optimize target production is needed. In this paper, recent advances in metabolic engineering are reviewed, specifically considering computational pathway modification design and experimental evaluation of metabolic fluxes by ¹³C-metabolic flux analysis. Computational tools for seeking effective gene deletion targets and recruiting heterologous genes are described in flux balance analysis approaches. A kinetic model and adaptive laboratory evolution were applied to identify and eliminate the rate-limiting step in metabolic pathways. Data science-based approaches for process monitoring and control are described to maximize the performance of engineered cells in bioreactors.

Designing an irreversible metabolic switch for scalable induction of microbial chemical production

Bacteria can be harnessed to synthesise high-value chemicals. A promising strategy for increasing productivity uses inducible control systems to switch metabolism from growth to chemical synthesis once a large population of cell factories are generated. However, use of expensive chemical inducers limits scalability of this approach for biotechnological applications. Switching using cheap nutrients is an appealing alternative, but their tightly regulated uptake and consumption again limits scalability. Here, using mathematical models of fatty acid uptake in E. coli as an exemplary case study, we unravel how the cell's native regulation and program of induction can be engineered to minimise inducer usage. We show that integrating positive feedback loops into the circuitry creates an irreversible metabolic switch, which, requiring only temporary induction, drastically reduces inducer usage. Our proposed switch should be widely applicable, irrespective of the product of interest, and brings closer the realization of scalable and sustainable microbial chemical production.

Metabolic Detoxification of 2-Oxobutyrate by Remodeling Escherichia coli Acetate Bypass

2-Oxobutyrate (2-OBA), as a toxic metabolic intermediate, generally arrests the cell growth of most microorganisms and blocks the biosynthesis of target metabolites. In this study, we demonstrated that using the acetate bypass to replace the pyruvate dehydrogenase complex (PDHc) in Escherichia coli could recharge the intracellular acetyl-CoA pool to alleviate the metabolic toxicity of 2-OBA. Furthermore, based on the crystal structure of pyruvate oxidase (PoxB), two candidate residues in the substrate-binding pocket of PoxB were predicted by computational simulation. Site-directed saturation mutagenesis was performed to attenuate 2-OBA-binding affinity, and one of the variants, PoxB^F112W, exhibited a 20-fold activity ratio of pyruvate/2-OBA in substrate selectivity. PoxB^F112W was employed to remodel the acetate bypass in E. coli, resulting in l-threonine (a precursor of 2-OBA) biosynthesis with minimal inhibition from 2-OBA. After metabolic detoxification of 2-OBA, the supplies of intracellular acetyl-CoA and NADPH (nicotinamide adenine dinucleotide phosphate) used for l-threonine biosynthesis were restored. Therefore, 2-OBA is the substitute for pyruvate to engage in enzymatic reactions and disturbs pyruvate metabolism. Our study makes a straightforward explanation of the 2-OBA toxicity mechanism and gives an effective approach for its metabolic detoxification.

Inducible Expression Systems Based on Xenogeneic Silencing and Counter-Silencing and Design of a Metabolic Toggle Switch

Inducible expression systems represent key modules in regulatory circuit design and metabolic engineering approaches. However, established systems are often limited in terms of applications due to high background expression levels and inducer toxicity. In bacteria, xenogeneic silencing (XS) proteins are involved in the tight control of horizontally acquired, AT-rich DNA. The action of XS proteins may be opposed by interference with a specific transcription factor, resulting in the phenomenon of counter-silencing, thereby activating gene expression. In this study, we harnessed this principle for the construction of a synthetic promoter library consisting of phage promoters targeted by the Lsr2-like XS protein CgpS of Corynebacterium glutamicum. Counter-silencing was achieved by inserting the operator sequence of the gluconate-responsive transcription factor GntR. The GntR-dependent promoter library is comprised of 28 activated and 16 repressed regulatory elements featuring effector-dependent tunability. For selected candidates, background expression levels were confirmed to be significantly reduced in comparison to established heterologous expression systems. Finally, a GntR-dependent metabolic toggle switch was implemented in a C. glutamicum l-valine production strain allowing the dynamic redirection of carbon flux between biomass and product formation.

Metabolic manipulation through CRISPRi and gene deletion to enhance cadaverine production in Escherichia coli

Due to the limiting natural resources, greenhouse effect and global warming crisis, the bio-based chemicals which are environmentally friendly materials have gradually become urgent and important. Cadaverine, a 1,5-diaminopentane (DAP), is widely used as block chemicals for synthesis of biopolymer, which can be produced from lysine by lysine decarboxylase (EC 4.1.1.18) in Escherichia coli. However, the DAP will be further utilized into by-products through downstream genes of speE, puuA, speG and ygjG, which decrease the amount of product. In this study, two approaches including Lambda-Red system for gene knockout, and clustered regularly interspaced short palindromic repeats interference (CRISPRi) for gene knockdown; are explored to manipulate the metabolic flux among 26 genetic E. coli. As a result, CadA driven by inducible T7 promoter accumulated more DAP from CRISPRi targeted on single-gene repressive strains such as BT7AiE, BT7AiP, BT7AiG and BT7AiY. The highest DAP titer and productivity was obtained to 38 g/L and 2.67 g/L/h in BT7AiY (repression of ygjG). We also investigated the co-factor pyridoxal 5'-phosphate (PLP) effect on lysine consumption and DAP production from different E. coli derivatives. In contrast to CRISPRi-mediated strains, 4 genes knockout strain (BT7AdEPGY) deal with 98% lysine consumption and achieved 37.45 g/L DAP and 3.17 g/L/h DAP productivity. The metabolic regulation by CRISPRi is a simple strategy and the results are consistent with gene knockout to manipulate the pathway for DAP production.

Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2-C6 Bioalcohol Production

Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.

Primary metabolites from overproducing microbial system using sustainable substrates

Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high production cost of metabolites is a big challenge for most of the bioprocess industries and commercial production needs to be achieved. This issue can be solved to some extent by screening and developing the engineered microbial systems via reconstruction of the genome-scale metabolic model. The predicted genetic modification is applied for an increased flux in biosynthesis pathways toward the desired product. Wherein the resulting microbial strain is capable of converting a large amount of carbon substrate to the expected product with minimum by-product formation in the optimal operating conditions. Metabolic engineering efforts have also resulted in significant improvement of metabolite yields, depending on the nature of the products, microbial cell factory modification, and the types of substrate used. The objective of this review is to comprehend the state of art for the production of various primary metabolites by microbial strains system, focusing on the selection of efficient strain and genetic or pathway modifications, applied during strain engineering.

Metabolic Engineering Design Strategies for Increasing Acetyl-CoA Flux

Acetyl-CoA is a key metabolite precursor for the biosynthesis of lipids, polyketides, isoprenoids, amino acids, and numerous other bioproducts which are used in various industries. Metabolic engineering efforts aim to increase carbon flux towards acetyl-CoA in order to achieve higher productivities of its downstream products. In this review, we summarize the strategies that have been implemented for increasing acetyl-CoA flux and concentration, and discuss their effects. Furthermore, recent works have developed synthetic acetyl-CoA biosynthesis routes that achieve higher stoichiometric yield of acetyl-CoA from glycolytic substrates.

Metabolic engineering of E. coli for improving mevalonate production to promote NADPH regeneration and enhance acetyl-CoA supply

Microbial production of mevalonate from renewable feedstock is a promising and sustainable approach for the production of value-added chemicals. We describe the metabolic engineering of Escherichia coli to enhance mevalonate production from glucose and cellobiose. First, the mevalonate-producing pathway was introduced into E. coli and the expression of the gene atoB, which encodes the gene for acetoacetyl-CoA synthetase, was increased. Then, the deletion of the pgi gene, which encodes phosphoglucose isomerase, increased the NADPH/NADP⁺ ratio in the cells but did not improve mevalonate production. Alternatively, to reduce flux toward the tricarboxylic acid cycle, gltA, which encodes citrate synthetase, was disrupted. The resultant strain, MGΔgltA-MV, increased levels of intracellular acetyl-CoA up to sevenfold higher than the wild-type strain. This strain produced 8.0 g/L of mevalonate from 20 g/L of glucose. We also engineered the sugar supply by displaying β-glucosidase (BGL) on the cell surface. When cellobiose was used as carbon source, the strain lacking gnd displaying BGL efficiently consumed cellobiose and produced mevalonate at 5.7 g/L. The yield of mevalonate was 0.25 g/g glucose (1 g of cellobiose corresponds to 1.1 g of glucose). These results demonstrate the feasibility of producing mevalonate from cellobiose or cellooligosaccharides using an engineered E. coli strain.

Construction of a switchable synthetic Escherichia coli for aromatic amino acids by a tunable switch

Escherichia coli, a model microorganism for which convenient metabolic engineering tools are available and that grows quickly in cheap media, has been widely used in the production of valuable chemicals, including aromatic amino acids. As the three aromatic amino acids, L-tryptophan, L-tyrosine, and L-phenylalanine, share the same precursors, to increase the titer of a specific aromatic amino acid, the branch pathways to the others are usually permanently inactivated, which leads to the generation of auxotrophic strains. In this study, a tunable switch that can toggle between different states was constructed. Then, a switchable and non-auxotrophic E. coli strain for synthesis of aromatic amino acids was constructed using this tunable switch. By adding different inducers to cultures, three different production patterns of aromatic amino acids by the engineered strain could be observed. This tunable switch can also be applied in regulating other branch pathways and in other bacteria.

Molecular parts and genetic circuits for metabolic engineering of microorganisms

Microbial conversion of biomass into value-added biochemicals is a highly sustainable process compared to petroleum-based production. In this regard, microorganisms have been engineered via simple overexpression or deletion of metabolic genes to facilitate the production. However, the producer microorganisms require complex regulatory circuits to maximize productivity and performance. To address this issue, diverse genetic circuits have been developed that allow cells to minimize their metabolic burden, overcome metabolic imbalances and respond to a dynamically changing environment. In this review, we briefly explain the basic strategy for constructing genetic circuits by assembling molecular parts such as input, operation and output modules. Next, we describe recent applications of the circuits in the metabolic engineering of microorganisms to improve biochemical production. Beyond those achievements, genetic circuits will facilitate more innovative approaches to future strain development through mining and engineering new genetic elements and improving the complexity of genetic circuit design.

Enhancement of acetyl-CoA flux for photosynthetic chemical production by pyruvate dehydrogenase complex overexpression in Synechococcus elongatus PCC 7942

Genetic manipulation in cyanobacteria enables the direct production of valuable chemicals from carbon dioxide. However, there are still very few reports of the production of highly effective photosynthetic chemicals. Several synthetic metabolic pathways (e.g., isopropanol, acetone, isoprene, and fatty acids) have been constructed by branching from acetyl-CoA and malonyl-CoA, which are key intermediates for photosynthetic chemical production downstream of pyruvate decarboxylation. Recent reports of the absolute determination of cellular metabolites in Synechococcus elongatus PCC 7942 have shown that its acetyl-CoA levels corresponded to about one hundredth of the pyruvate levels. In short, one of the reasons for lower photosynthetic chemical production from acetyl-CoA and malonyl-CoA was the smaller flux to acetyl-CoA. Pyruvate decarboxylation is a primary pathway for acetyl-CoA synthesis from pyruvate and is mainly catalyzed by the pyruvate dehydrogenase complex (PDHc). In this study, we tried to enhance the flux toward acetyl-CoA from pyruvate by overexpressing PDH genes and, thus, catalyzing the conversion of pyruvate to acetyl-CoA via NADH generation. The overexpression of PDH genes cloned from S. elongatus PCC 7942 significantly increased PDHc enzymatic activity and intracellular acetyl-CoA levels in the crude cell extract. Although growth defects were observed in overexpressing strains of PDH genes, the combinational overexpression of PDH genes with the synthetic metabolic pathway for acetate or isopropanol resulted in about 7-fold to 9-fold improvement in its production titer, respectively (9.9 mM, 594.5 mg/L acetate, 4.9 mM, 294.5 mg/L isopropanol). PDH genes overexpression would, therefore, be useful not only for the production of these model chemicals, but also for the production of other chemicals that require acetyl-CoA as a key precursor.

Two-stage carbon distribution and cofactor generation for improving l-threonine production of Escherichia coli

L-Threonine, a kind of essential amino acid, has numerous applications in food, pharmaceutical, and aquaculture industries. Fermentative l-threonine production from glucose has been achieved in Escherichia coli. However, there are still several limiting factors hindering further improvement of l-threonine productivity, such as the conflict between cell growth and production, byproduct accumulation, and insufficient availability of cofactors (adenosine triphosphate, NADH, and NADPH). Here, a metabolic modification strategy of two-stage carbon distribution and cofactor generation was proposed to address the above challenges in E. coli THRD, an l-threonine producing strain. The glycolytic fluxes towards tricarboxylic acid cycle were increased in growth stage through heterologous expression of pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and citrate synthase, leading to improved glucose utilization and growth performance. In the production stage, the carbon flux was redirected into l-threonine synthetic pathway via a synthetic genetic circuit. Meanwhile, to sustain the transaminase reaction for l-threonine production, we developed an l-glutamate and NADPH generation system through overexpression of glutamate dehydrogenase, formate dehydrogenase, and pyridine nucleotide transhydrogenase. This strategy not only exhibited 2.02- and 1.21-fold increase in l-threonine production in shake flask and bioreactor fermentation, respectively, but had potential to be applied in the production of many other desired oxaloacetate derivatives, especially those involving cofactor reactions.

Genetic tool development and systemic regulation in biosynthetic technology

With the increased development in research, innovation, and policy interest in recent years, biosynthetic technology has developed rapidly, which combines engineering, electronics, computer science, mathematics, and other disciplines based on classical genetic engineering and metabolic engineering. It gives a wider perspective and a deeper level to perceive the nature of life via cell mechanism, regulatory networks, or biological evolution. Currently, synthetic biology has made great breakthrough in energy, chemical industry, and medicine industries, particularly in the programmable genetic control at multiple levels of regulation to perform designed goals. In this review, the most advanced and comprehensive developments achieved in biosynthetic technology were represented, including genetic engineering as well as synthetic genomics. In addition, the superiority together with the limitations of the current genome-editing tools were summarized.

Introduction of an acetyl-CoA carboxylation bypass into Escherichia coli for enhanced free fatty acid production

This study investigated the effect of the methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii on production of free fatty acid (FFA) in Escherichia coli. Overexpression of the MMC exhibited a 44% increase in FFA titer. Co-overexpression of MMC and phosphoenolpyruvate carboxylase (PPC), which supplies the MMC precursor, further improved the titer by 40%. Expression of malic enzyme (MaeB) led to a 23% increase in FFA titer in the acetyl-CoA carboxylase (ACC)-overexpressing cells, but no increase in the MMC-overexpressing cells. The highest FFA production in the MMC-overexpressing strain was achieved through the addition of aspartic acid, which can be converted into oxaloacetate (OAA), resulting in a 120% increased titer compared with that in the ACC-overexpressing strain. These findings demonstrate that MMC provides an alternative pathway for malonyl-CoA synthesis and increases fatty acid production.

Engineering metabolic pathways in Escherichia coli for constructing a "microbial chassis" for biochemical production

The present work reviews literature describing the re-design of the metabolic pathways of a microbial host using sophisticated genetic tools, yielding strains for producing value-added chemicals including fuels, building-block chemicals, pharmaceuticals, and derivatives. This work employed Escherichia coli, a well-studied microorganism that has been successfully engineered to produce various chemicals. E. coli has several advantages compared with other microorganisms, including robustness, and handling. To achieve efficient productivities of target compounds, an engineered E. coli should accumulate metabolic precursors of target compounds. Multiple researchers have reported the use of pathway engineering to generate strains capable of accumulating various metabolic precursors, including pyruvate, acetyl-CoA, malonyl-CoA, mevalonate and shikimate. The aim of this review provides a promising guideline for designing E. coli strains capable of producing a variety of useful chemicals. Herein, the present work reviews their common and unique strategies, treating metabolically engineered E. coli as a "microbial chassis".