Metabolic engineering of Escherichia coli for the production of succinate from glycerol

Metabolic Engineering of Trichoderma reesei for l-Malic Acid Production

l-Malic acid has various applications in the chemical and food industries. The filamentous fungus Trichoderma reesei is known to be an efficient enzyme producer. Here, through metabolic engineering, T. reesei was constructed for the first time as an excellent cell factory for l-malic acid production. The heterologous overexpression of genes encoding the C4-dicarboxylate transporter from Aspergillus oryzae and Schizosaccharomyces pombe initiated l-malic acid production. The overexpression of pyruvate carboxylase from A. oryzae in the reductive tricarboxylic acid pathway further increased both the titer and yield of l-malic acid, resulting in the highest titer reported in a shake-flask culture. Furthermore, the deletion of malate thiokinase blocked l-malic acid degradation. Finally, the engineered T. reesei strain produced 220.5 g/L of l-malic acid in a 5 L fed-batch culture (productivity of 1.15 g/L/h). A T. reesei cell factory was created for the efficient production of l-malic acid.

Factors affecting the competitiveness of bacterial fermentation

Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of 'net zero carbon' that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproducing an increasing number of chemicals and materials, some of which have been translated to industrial-scale production. Fermentation is one of the key processes determining the overall economics of bioprocesses, but has recently been attracting less research attention. In this Review, we revisit and discuss factors affecting the competitiveness of bacterial fermentation in connection to strain development by systems metabolic engineering. Future perspectives for developing efficient fermentation processes are also discussed.

Optimizing microbial networks through metabolic bypasses

Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.

Metabolomics for the design of new metabolic engineering strategies for improving aerobic succinic acid production in Escherichia coli

INTRODUCTION

Glycerol is a byproduct from the biodiesel industry that can be biotransformed by Escherichia coli to high added-value products such as succinate under aerobic conditions. The main genetic engineering strategies to achieve this aim involve the mutation of succinate dehydrogenase (sdhA) gene and also those responsible for acetate synthesis including acetate kinase, phosphate acetyl transferase and pyruvate oxidase encoded by ackA, pta and pox genes respectively in the ΔsdhAΔack-ptaΔpox (M4) mutant. Other genetic manipulations to rewire the metabolism toward succinate consist on the activation of the glyoxylate shunt or blockage the pentose phosphate pathway (PPP) by deletion of isocitrate lyase repressor (iclR) or gluconate dehydrogenase (gnd) genes on M4-ΔiclR and M4-Δgnd mutants respectively.

OBJECTIVE

To deeply understand the effect of the blocking of the pentose phosphate pathway (PPP) or the activation of the glyoxylate shunt, metabolite profiles were analyzed on M4-Δgnd, M4-ΔiclR and M4 mutants.

METHODS

Metabolomics was performed by FT-IR and GC-MS for metabolite fingerprinting and HPLC for quantification of succinate and glycerol.

RESULTS

Most of the 65 identified metabolites showed lower relative levels in the M4-ΔiclR and M4-Δgnd mutants than those of the M4. However, fructose 1,6-biphosphate, trehalose, isovaleric acid and mannitol relative concentrations were increased in M4-ΔiclR and M4-Δgnd mutants. To further improve succinate production, the synthesis of mannitol was suppressed by deletion of mannitol dehydrogenase (mtlD) on M4-ΔgndΔmtlD mutant that increase ~ 20% respect to M4-Δgnd.

CONCLUSION

Metabolomics can serve as a holistic tool to identify bottlenecks in metabolic pathways by a non-rational design. Genetic manipulation to release these restrictions could increase the production of succinate.

Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers

The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.

Synthesis of Bio-based monomers and polymers using microbes for a sustainable bioeconomy

As a result of environmental concerns and the depletion of biomass assets, eco-friendly, renewable biomass-based chemical extraction has recently received significant attention. Bio-based chemicals can be prepared using different renewable feedstockbio-resources through microbial fermentation. Chemicals produced from renewable feedstockscan reduce ecological consequences from improper disposal and repurpose them into valuable products. Biodegradability, biocompatibility and non-toxicity, particularly in biomedical applications, have inspired researchers towards developing novel technologies that have social benefit. Among semi-synthetic and synthetic polymeric materials, utilization of natural bio-based monomeric materials can provide opportunities for sustainable development of novel non-toxic, biodegradable and biocompatible products. The purpose of this work is to give a summary of research into the generation of natural bio-based succinic acid (SA) monomer, the development of poly(butylene succinate) (PBS) as biodegradable polymer, PBS-based nanocomposites and their innovative uses.

Bioconversion of organic wastes into value-added products: A review

Rapid urbanization has increased the demand for food, feed, and chemicals that have in turn augmented the use of fossil-based resources and generation of organic waste. Owning to the characteristics like high abundance, renewability, and ease of accessibility, valorization of organic wastes serves as a potential solution for waste management issues. Several industrial wastes, due to their organic and nutrient-rich composition, have been utilized as a resource for the production of value-added products such as biofuels, biopesticides, biohydrogen, enzymes, and bioplastics via microbial fermentation processes. The process consists of pre-treatment of the waste biomass, production of value-added product in reactors and downstream processing for product's recovery. The integration of new comprehensive technologies for organic waste utilization will also stimulate the transition towards a circular economy. Therefore, the feasibility and sustainability of the production of various value-added products from biowastes and byproduct streams will be discussed in the present review.

In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli

Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H₂ , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H₂ evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H₂ evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.

An Escherichia coli FdrA Variant Derived from Syntrophic Coculture with a Methanogen Increases Succinate Production Due to Changes in Allantoin Degradation

Wild-type Escherichia coli was adapted to syntrophic growth with Methanobacterium formicicum for glycerol fermentation over 44 weeks. Succinate production by E. coli started to increase in the early stages of syntrophic growth. Genetic analysis of the cultured E. coli population by pooled sequencing at eight time points suggests that (i) rapid evolution occurred through repeated emergence of mutators that introduced a large number of nucleotide variants and (ii) many mutators increased to high frequencies but remained polymorphic throughout the continuous cultivation. The evolved E. coli populations exhibited gains both in fitness and succinate production, but only for growth under glycerol fermentation with M. formicicum (the condition for this laboratory evolution) and not under other growth conditions. The mutant alleles of the 69 single nucleotide polymorphisms (SNPs) identified in the adapted E. coli populations were constructed individually in the ancestral wild-type E. coli. We analyzed the phenotypic changes caused by 84 variants, including 15 nonsense variants, and found that FdrA_D296Y was the most significant variant leading to increased succinate production. Transcription of fdrA was induced under anaerobic allantoin degradation conditions, and FdrA was shown to play a crucial role in oxamate production. The FdrA_D296Y variant increased glyoxylate conversion to malate by accelerating oxamate production, which promotes carbon flow through the C4 branch, leading to increased succinate production.

IMPORTANCE Here, we demonstrate the ability of E. coli to perform glycerol fermentation in coculture with the methanogen M. formicicum to produce succinate. We found that the production of succinate by E. coli significantly increased during successive cocultivation. Genomic DNA sequencing, evaluation of relative fitness, and construction of SNPs were performed, from which FdrA_D296Y was identified as the most significant variant to enable increased succinate production by E. coli. The function of FdrA is uncertain. In this study, experiments with gene expression assays and metabolic analysis showed for the first time that FdrA could be the “orphan enzyme” oxamate:carbamoyltransferase in anaerobic allantoin degradation. Furthermore, we demonstrate that the anaerobic allantoin degradation pathway is linked to succinate production via the glyoxylate pathway during glycerol fermentation.

Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability

Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO₂ and CH₄) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.

Production of Succinic Acid from Amino Acids in Escherichia coli

Glutamate (Glu) and aspartate (Asp) are the most abundant amino acids in various sources of protein waste, recognized as a sustainable resource. In this study, Escherichia coli was engineered to produce succinic acid (SA) from Glu and Asp. Succinate dehydrogenase involved in the tricarboxylic acid was inactivated in the Glu-utilizing strain. To grow on Asp, this mutant strain was subjected to metabolic evolution. One resulting strain capable of metabolizing Asp was further evolved to improve the growth of Glu and Asp. After the deletion of arcA, the resulting strain was employed for the aerobic production of SA. The shake-flask culture was conducted with the minimal medium containing 10 g/L Glu and 10 g/L Asp. Finally, it resulted in the SA production, with a titer, the molar yield, and productivity reaching 72.8 mM (i.e., 8.6 g/L), 0.54 (ca. 75.4% of the theoretical yield), and 0.66 g/L/h, respectively. Overall, this study opens up a new avenue of the biorefinery platform based on renewable amino acids.

In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products

Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, it is important to use tools that allow predicting gene deletions. An in silico experiment was performed to model and understand the metabolic engineering effects on the cell factory considering a second complexity level by transcriptomics data integration. In this study, a systems-based metabolic engineering target prediction was used to increase glycerol bioconversion to succinic acid based on Escherichia coli. Transcriptomics analysis suggests insights on how to increase cell glycerol utilization to further design efficient cell factories. Three E. coli models were used: a core model, a second model based on the integration of transcriptomics data obtained from growth in an optimized culture media, and a third one obtained after integration of transcriptomics data from adaptive laboratory evolution (ALE) experiments. A total of 2,402 strains were obtained with fumarase and pyruvate dehydrogenase being frequently predicted for all the models, suggesting these reactions as essential to increase succinic acid production. Finally, based on using flux balance analysis (FBA) results for all the mutants predicted, a machine learning method was developed to predict new mutants as well as to propose optimal metabolic engineering targets and mutants based on the measurement of the importance of each knockout's (feature's) contribution. Glycerol has become an interesting carbon source for industrial processes due to biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. The combination of transcriptome, systems metabolic modeling, and machine learning analyses revealed the versatility of computational models to predict key metabolic engineering targets in a less cost-, time-, and laborious-intensive process. These data provide a platform to improve the prediction of metabolic engineering targets to design efficient cell factories. Our results may also work as a guide and platform for the selection/engineering of microorganisms for the production of interesting chemical compounds.

Promising advancement in fermentative succinic acid production by yeast hosts

As a platform chemical with various applications, succinic acid (SA) is currently produced by petrochemical processing from oil-derived substrates such as maleic acid. In order to replace the environmental unsustainable hydrocarbon economy with a renewable environmentally sound carbohydrate economy, bio-based SA production process has been developed during the past two decades. In this review, recent advances in the valorization of solid organic wastes including mixed food waste, agricultural waste and textile waste for efficient, green and sustainable SA production have been reviewed. Firstly, the application, market and key global players of bio-SA are summarized. Then achievements in SA production by several promising yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica are detailed, followed by calculation and comparison of SA production costs between oil-based substrates and raw materials. Lastly, challenges in engineered microorganisms and fermentation processes are presented together with perspectives on the development of robust yeast SA producers via genome-scale metabolic optimization and application of low-cost raw materials as fermentation substrates. This review provides valuable insights for identifying useful directions for future bio-SA production improvement.

Metabolic pathway engineering: Perspectives and applications

BACKGROUND

Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering.

CONCLUSION

In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.

Enhancement of gibberellic acid production from Fusarium fujikuroi by mutation breeding and glycerol addition

Gibberellic acid (GA₃) is a natural plant growth hormone that has been widely used in agriculture and horticulture. To obtain higher GA₃ producing strains, the method of screening the strains for resistance to simvastatin was used after treatment with nitrosoguanidine (NTG) and gamma rays. The rationale for the strategy was that mutants showing simvastatin resistance were likely to be high GA₃ producers, as their activity of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase is relatively more effective. GA₃ yield of mutant S109 increased by 14.2% than that of the original strain. The GA₃ production ability in mutant S109 remained relatively stable after ten generations. With the addition of 0.4 g glycerol on the 5th day during the fermentation process in Erlenmeyer flask, maximum GA₃ production of 2.7 g/L was achieved by this mutant, exhibiting 28.6% increase compared with original strain. Furthermore, we also achieved 2.8 g/L GA₃ and had a 33.3% increase with addition 20 g glycerol on the 5th day during the fermentation process in a 5-L bioreactor. Our results indicated efficient GA₃ production could be achieved on the condition that the supply of glycerol at the suitable conditions. This study would lay a foundation for industrial production of GA₃.

Genetic engineering for enhanced productivity in bioelectrochemical systems

A shift from petrochemical processes toward a bio-based economy is one of the most advocated developments for a sustainable future. To achieve this will require the biotechnological production of platform chemicals that can be further processed by chemical engineering. Bioelectrochemical systems (BESs) are a novel tool within the biotechnology field. In BESs, microbes serve as biocatalysts for the production of biofuels and value-added compounds, as well as for the production of electricity. Although the general feasibility of bioelectrochemical processes has been demonstrated in recent years, much research has been conducted to develop biocatalysts better suited to meet industrial demands. Initially, mainly natural exoelectrogenic organisms were investigated for their performance in BESs. Driven by possibilities of recent developments in genetic engineering and synthetic biology, the spectrum of microbial catalysts and their versatility (substrate and product range) have expanded significantly. Despite these developments, there is still a tremendous gap between currently achievable space-time yields and current densities on the one hand and the theoretical limits of BESs on the other. It will be necessary to move the performance of the biocatalysts closer to the theoretical possibilities in order to establish viable production routines. This review summarizes the status quo of engineering microbial biocatalysts for anode-applications with high space-time yields. Furthermore, we will address some of the theoretical limitations of these processes exemplarily and discuss which of the present strategies might be combined to achieve highly synergistic effects and, thus, meet industrial demands.

High-Level Production of Succinic Acid from Crude Glycerol by a Wild Type Organism

With the transition to the bio-based economy, it is becoming increasingly important for the chemical industry to obtain basic chemicals from renewable raw materials. Succinic acid, one of the most important bio-based building block chemicals, is used in the food and pharmaceutical industries, as well as in the field of bio-based plastics. An alternative process for the bio-based production of succinic acid was the main objective of this study, focusing on the biotechnological production of succinic acid using a newly isolated organism. Pure glycerol compared to crude glycerol, at the lowest purity, directly from a biodiesel plant side stream, was successfully converted. A maximum final titer of 117 g L−1 succinic acid and a yield of 1.3 g g−1 were achieved using pure glycerol and 86.9 g L−1 succinic acid and a yield of 0.9 g g−1 using crude glycerol. Finally, the succinic acid was crystallized, achieving maximum yield of 95% and a purity of up to 99%.

Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hyper-SA producing M. succiniciproducens by introducing the best MDH. Corynebacterium glutamicum MDH (CgMDH) shows the highest specific activity and least substrate inhibition, whereas M. succiniciproducens MDH (MsMDH) shows low specific activity at physiological pH and strong uncompetitive inhibition toward oxaloacetate (ki of 67.4 and 588.9 μM for MsMDH and CgMDH, respectively). Structural comparison of the two MDHs reveals a key residue influencing the specific activity and susceptibility to substrate inhibition. A high-inoculum fed-batch fermentation of the final strain expressing cgmdh produces 134.25 g L-1 of SA with the maximum productivity of 21.3 g L-1 h-1, demonstrating the importance of enzyme optimization in strain development.

Biochemical conversion of biodiesel by-product into malic acid: A way towards sustainability

Crude glycerol, one of the ever-growing by-product of biodiesel industry and is receiving the closest review in recent times because direct disposal of crude glycerol may emerge ecological issues. The renewability, bioavailability and typical structure of glycerol, therefore, discover conceivable application in serving the role of carbon and energy source for microbial biosynthesis of high value products. This conceivable arrangement could find exploitation of crude glycerol as a renewable building block for bio-refineries as it is economically as well as environmentally profitable. In this review, we summarize the uptake and catabolism of crude glycerol by different wild and recombinant microorganism. The chemical and biochemical transformation of crude glycerol into high esteem malic acid by various microbial pathways is also additionally discussed. An extensive investigation in the synthesis of high-value malic acid production from various feed stock which finds applications in cosmeceutical and chemical industries, food and beverages, and to some extent in the field of medical science is also likewise studied. Finally, the open doors for unrefined crude glycerol in serving as a promising abundant energy source for malic acid production in near future have been highlighted.

Metabolic engineering of Escherichia coli to produce succinate from woody hydrolysate under anaerobic conditions

It is of great economic interest to produce succinate from low-grade carbon sources, e.g., lignocellulosic biomass hydrolysate, which mainly contains glucose and xylose. Inactivation of the glucose uptake system PtsG was evaluated for succinate production from xylose-rich feedstocks. Strains with integration of succinate production modules into the chromosome of Escherichia coli were then constructed. These strains have better succinate production performance from xylose-rich feedstocks than strain FZ560 harboring pHL413KF1. Glucose utilization was enhanced in FZ661T by manipulation of the gal operon to allow efficient use of the high-concentration glucose in woody biomass hydrolysate. Up to 906.7 mM (107.0 g/L) succinate was produced from mixed sugars in fed-batch fermentation and more than 461.7 mM (54.5 g/L) succinate was produced from woody hydrolysate in a batch fermentation. In this study, FZ661T was able to produce succinate from woody hydrolysate in minimal medium efficiently, making it attractive for industrial applications in succinate production.

Enhanced Production of 2-Hydroxyphenazine from Glycerol by a Two-Stage Fermentation Strategy in Pseudomonas chlororaphis GP72AN

2-Hydroxyphenazine (2-OH-PHZ) is an effective biocontrol antibiotic secreted by Pseudomonas chlororaphis GP72AN and is transformed from phenazine-1-carboxylic acid (PCA). PCA is the main component of the recently registered biopesticide "Shenqinmycin". Previous research showed that 2-OH-PHZ was better in controlling wheat take-all disease than PCA; however, 2-OH-PHZ production was low under natural conditions. Herein, we confirmed that PCA induced reactive oxygen species in its host P. chlororaphis GP72AN and that the addition of DTT improved PCA production by 1.8-fold, whereas the supplementation of K₃[Fe(CN)₆] and H₂O₂ increased the conversion rate of PCA to 2-OH-PHZ. Finally, a two-stage fermentation strategy combining the addition of DTT at 12 h and H₂O₂ at 24 h enhanced 2-OH-PHZ production. Taken together, the two-stage fermentation strategy was designed to enhance 2-OH-PHZ production for the first time, and it provided a valuable reference for the fermentation of other antibiotics.

Advances in microbial production of medium-chain dicarboxylic acids for nylon materials

Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.

Rewiring glycerol metabolism for enhanced production of poly-γ-glutamic acid in Bacillus licheniformis

BACKGROUND

Poly-γ-glutamic acid (γ-PGA) is a natural polymer with great potential applications in areas of agriculture, industry, and pharmaceutical. The biodiesel-derived glycerol can be used as an attractive feedstock for γ-PGA production due to its availability and low price; however, insufficient production of γ-PGA from glycerol is limitation.

RESULTS

The metabolic pathway of Bacillus licheniformis WX-02 was rewired to improve the efficiency of glycerol assimilation and the supply of NADPH for γ-PGA synthesis. GlpK, GlpX, Zwf, and Tkt1 were found to be the key enzymes for γ-PGA synthesis using glycerol as a feedstock. Through combinational expression of these key enzymes, the γ-PGA titer increased to 19.20 ± 1.57 g/L, which was 1.50-fold of that of the wild-type strain. Then, we studied the flux distributions, gene expression, and intracellular metabolites in WX-02 and the recombinant strain BC4 (over-expression of the above quadruple enzymes). Our results indicated that over-expression of the quadruple enzymes redistributed metabolic flux to γ-PGA synthesis. Furthermore, using crude glycerol as carbon source, the BC4 strain showed a high productivity of 0.38 g/L/h, and produced 18.41 g/L γ-PGA, with a high yield of 0.46 g γ-PGA/g glycerol.

CONCLUSIONS

The approach to rewiring of metabolic pathways enables B. licheniformis to efficiently synthesize γ-PGA from glycerol. The γ-PGA productivity reported in this work is the highest obtained in glutamate-free medium. The present study demonstrates that the recombinant B. licheniformis strain shows significant potential to produce valuable compounds from crude glycerol.

Long-term adaptation of Escherichia coli to methanogenic co-culture enhanced succinate production from crude glycerol

Escherichia coli can hardly grow anaerobically on glycerol without exogenous electron acceptor. The formate-consuming methanogen Methanobacterium formicicum plays a role as a living electron acceptor in glycerol fermentation of E. coli. Wild-type and mutant E. coli strains were screened for succinate production using glycerol in a co-culture with M. formicicum. Subsequently, E. coli was adapted to glycerol fermentation over 39 rounds (273 days) by successive co-culture with M. formicicum. The adapted E. coli (19.9 mM) produced twice as much succinate as non-adapted E. coli (9.7 mM) and 62% more methane. This study demonstrated improved succinate production from waste glycerol using an adapted wild-type strain of E. coli with wild-type M. formicicum, which is more useful than genetically modified strains. Crude glycerol, an economical feedstock, was used for the cultivation. Furthermore, the increase in methane production by M. formicicum during co-culture with adapted E. coli illustrated the possibility of energy-saving effects for the fermentation process.

Recent advances in the production of value added chemicals and lipids utilizing biodiesel industry generated crude glycerol as a substrate - Metabolic aspects, challenges and possibilities: An overview

One of the major ecological concerns associated with biodiesel production is the generation of waste/crude glycerol during the trans-esterification process. Purification of this crude glycerol is not economically viable. In this context, the development of an efficient and economically viable strategy would be biotransformation reactions converting the biodiesel derived crude glycerol into value added chemicals. Hence the process ensures the sustainability and waste management in biodiesel industry, paving a path to integrated biorefineries. This review addresses a waste to wealth approach for utilization of crude glycerol in the production of value added chemicals, current trends, challenges, future perspectives, metabolic approaches and the genetic tools developed for the improved synthesis over wild type microorganisms were described.

Biosensor-Based Evolution and Elucidation of a Biosynthetic Pathway in Escherichia coli

The successful evolution of metabolite-producing microbes requires a high-throughput screening method to obtain the desired properties within a short time. In this study, we developed a transcription-factor-driven device that combines a metabolite-responsive element and a selection module. This device was able to specifically sense intracellular l-phenylalanine (l-Phe) and convert this signal into an observable phenotype. Applying this device, we successfully improved l-Phe production by screening hyperproducing phenotypes from a ribonucleotide binding site library and a random mutagenesis library. In addition, several site mutations introduced by random mutagenesis were identified and elucidated to facilitate the improvement of l-Phe production. Our results present a paradigm for screening of compounds that are not easily observable to raise the yield of targeted compounds from a large candidate library. This approach may guide further applications in rewiring metabolic circuits and facilitate the directed evolution of recombinant strains.

Efficient anaerobic production of succinate from glycerol in engineered Escherichia coli by using dual carbon sources and limiting oxygen supply in preceding aerobic culture

Glycerol is an important resource for production of value-added bioproducts due to its large availability from the biodiesel industry as a by-product. In this study, two metabolic regulation strategies were applied in the aerobic stage of a two-stage fermentation to achieve high metabolic capacities of the pflB ldhA double mutant Escherichia coli strain overexpressing phosphoenolpyruvate carboxykinase (PCK) in the subsequent anaerobic stage: use of acetate as a co-carbon source of glycerol and restriction of oxygen supply in the PCK induction period. The succinate concentration achieved 926.7mM with a yield of 0.91mol/mol during the anaerobic stage of fermentation in a 1.5-L reactor. qRT-PCR indicated that the two strategies enhanced transcription of genes related with glycerol metabolism and succinate production. Our results showed this metabolically engineered E. coli strain has a great potential in producing succinate using glycerol as carbon source.

Coordination of metabolic pathways: Enhanced carbon conservation in 1,3-propanediol production by coupling with optically pure lactate biosynthesis

Metabolic engineering has emerged as a powerful tool for bioproduction of both fine and bulk chemicals. The natural coordination among different metabolic pathways contributes to the complexity of metabolic modification, which hampers the development of biorefineries. Herein, the coordination between the oxidative and reductive branches of glycerol metabolism was rearranged in Klebsiella oxytoca to improve the 1,3-propanediol production. After deliberating on the product value, carbon conservation, redox balance, biological compatibility and downstream processing, the lactate-producing pathway was chosen for coupling with the 1,3-propanediol-producing pathway. Then, the other pathways of 2,3-butanediol, ethanol, acetate, and succinate were blocked in sequence, leading to improved d-lactate biosynthesis, which as return drove the 1,3-propanediol production. Meanwhile, efficient co-production of 1,3-propanediol and l-lactate was also achieved by replacing ldhD with ldhL from Bacillus coagulans. The engineered strains PDL-5 and PLL co-produced over 70g/L 1,3-propanediol and over 100g/L optically pure d-lactate and l-lactate, respectively, with high conversion yields of over 0.95mol/mol from glycerol.

Glycerol Production and Transformation: A Critical Review with Particular Emphasis on Glycerol Reforming Reaction for Producing Hydrogen in Conventional and Membrane Reactors

Glycerol represents an emerging renewable bio-derived feedstock, which could be used as a source for producing hydrogen through steam reforming reaction. In this review, the state-of-the-art about glycerol production processes is reviewed, with particular focus on glycerol reforming reactions and on the main catalysts under development. Furthermore, the use of membrane catalytic reactors instead of conventional reactors for steam reforming is discussed. Finally, the review describes the utilization of the Pd-based membrane reactor technology, pointing out the ability of these alternative fuel processors to simultaneously extract high purity hydrogen and enhance the whole performances of the reaction system in terms of glycerol conversion and hydrogen yield.

Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production

The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse features of its application in biotechnology and protein production.

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

The metabolic byproducts secreted by growing cells can be easily measured and provide a window into the state of a cell; they have been essential to the development of microbiology, cancer biology, and biotechnology. Progress in computational modeling of cells has made it possible to predict metabolic byproduct secretion with bottom-up reconstructions of metabolic networks. However, owing to a lack of data, it has not been possible to validate these predictions across a wide range of strains and conditions. Through literature mining, we were able to generate a database of Escherichia coli strains and their experimentally measured byproduct secretions. We simulated these strains in six historical genome-scale models of E. coli, and we report that the predictive power of the models has increased as they have expanded in size and scope. The latest genome-scale model of metabolism correctly predicts byproduct secretion for 35/89 (39%) of designs. The next-generation genome-scale model of metabolism and gene expression (ME-model) correctly predicts byproduct secretion for 40/89 (45%) of designs, and we show that ME-model predictions could be further improved through kinetic parameterization. We analyze the failure modes of these simulations and discuss opportunities to improve prediction of byproduct secretion.

Production of Succinate from Acetate by Metabolically Engineered Escherichia coli

Acetate, a major component of industrial biological wastewater and of lignocellulosic biomass hydrolysate, could potentially be a less costly alternative carbon source. Here we engineered Escherichia coli MG1655 strain for succinate production from acetate as the sole carbon source. Strategies of metabolic engineering included the blockage of the TCA cycle, redirection of the gluconeogenesis pathway, and enhancement of the glyoxylate shunt. The engineered strain MG03 featuring the deletion of genes: succinate dehydrogenase (sdhAB), isocitrate lyase regulator (iclR), and malic enzymes (maeB) accumulated 6.86 mM of succinate in 72 h. MG03(pTrc99a-gltA) overexpressing citrate synthase (gltA) accumulated 16.45 mM of succinate and the yield reached 0.46 mol/mol, about 92% of the maximum theoretical yield. Resting-cell was adopted for the conversion of acetate to succinate, and the highest concentration of succinate achieved 61.7 mM.

Engineering of Escherichia coli for direct and modulated biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer using unrelated carbon sources

While poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] is a biodegradable commodity plastic with broad applications, its microbial synthesis is hindered by high production costs primarily associated with the supplementation of related carbon substrates (e.g. propionate or valerate). Here we report construction of engineered Escherichia coli strains for direct synthesis of P(3HB-co-3HV) from an unrelated carbon source (e.g. glucose or glycerol). First, an E. coli strain with an activated sleeping beauty mutase (Sbm) operon was used to generate propionyl-CoA as a precursor. Next, two acetyl-CoA moieties or acetyl-CoA and propionyl-CoA were condensed to form acetoacetyl-CoA and 3-ketovaleryl-CoA, respectively, by functional expression of β-ketothiolases from Cupriavidus necator (i.e. PhaA and BktB). The resulting thioester intermediates were channeled into the polyhydroxyalkanoate (PHA) biosynthetic pathway through functional expression of acetoacetyl-CoA reductase (PhaB) for thioester reduction and PHA synthase (PhaC) for subsequent polymerization. Metabolic engineering of E. coli host strains was further conducted to enhance total PHA content and the 3-hydroxyvaleryl (3HV) monomer fraction in the copolymer. Using a selection of engineered E. coli strains for batch cultivation with an unrelated carbon source, we achieved high-level P(3HB-co-3HV) production with the 3HV monomer fraction ranging from 3 to 19 mol%, demonstrating the potential industrial applicability of these whole-cell biocatalysts.

Metabolic engineering of cyanobacteria for the photosynthetic production of succinate

Succinate is an important commodity chemical currently used in the food, pharmaceutical, and polymer industries. It can also be chemically converted into other major industrial chemicals such as 1,4-butanediol, butadiene, and tetrahydrofuran. Here we metabolically engineered a model cyanobacterium Synechococcus elongatus PCC 7942 to photosynthetically produce succinate. We expressed the genes encoding for α-ketoglutarate decarboxylase and succinate semialdehyde dehydrogenase in S. elongatus PCC 7942, resulting in a strain capable of producing 120mg/L of succinate. However, this recombinant strain exhibited severe growth retardation upon induction of the genes encoding for the succinate producing pathway, potentially due to the depletion of α-ketoglutarate. To replenish α-ketoglutarate, we expressed the genes encoding for phosphoenolpyruvate carboxylase and citrate synthase from Corynebacterium glutamicum into the succinate producing strain. The resulting strain successfully restored the growth phenotype and produced succinate with a titer of 430mg/L in 8 days. These results demonstrated the possibility of photoautotrophic succinate production.

Enhanced succinate production from glycerol by engineered Escherichia coli strains

In this study, an engineered strain Escherichia coli MLB (ldhA(-)pflB(-)) was constructed for production of succinate from glycerol. The succinate yield was 0.37mol/mol in anaerobic culture, however, the growth and glycerol consumption rates were very slow, resulting in a low succinate level. Two-stage fermentation was performed in flasks, and the succinate yield reached 0.93mol/mol, but the succinate titer was still low. Hence, overexpression of malate dehydrogenase, malic enzyme, phosphoenolpyruvate (PEP) carboxylase and PEP carboxykinase (PCK) from E. coli, and pyruvate carboxylase from Corynebacterium glutamicum in MLB was investigated for improving succinate production. Overexpression of PCK resulted in remarkable enhancement of glycerol consumption and succinate production. In flask experiments, the succinate concentration reached 118.1mM, and in a 1.5-L bioreactor the succinate concentration further increased to 360.2mM. The highest succinate yield achieved 0.93mol/mol, which was 93% of the theoretical yield, in the anaerobic stage.