Engineering Escherichia coli for fumaric acid production from glycerol

Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells

This study investigated the potential of using steam-exploded oil palm empty fruit bunches (EFB) as a renewable feedstock for producing fumaric acid (FA), a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the fungal isolate K20. The efficiency of FA production by free and immobilized cells was compared. The maximum FA concentration (3.25 g/L), with 0.034 g/L/h productivity, was observed after incubation with the free cells for 96 h. Furthermore, the production was scaled up in a 3-L air-lift fermenter using oil palm EFB-derived glucose as the substrate. The FA concentration, yield, and productivity from 100 g/L initial oil palm EFB-derived glucose were 44 g/L, 0.39 g/g, and 0.41 g/L/h, respectively. The potential for scaling up the fermentation process indicates favorable results, which could have significant implications for industrial applications.

Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids

As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.

Conversion of acetate and glyoxylate to fumarate by a cell-free synthetic enzymatic biosystem

Fumarate is a value-added chemical that is widely used in food, medicine, material, and agriculture industries. With the rising attention to the demand for fumarate and sustainable development, many novel alternative ways that can replace the traditional petrochemical routes emerged. The in vitro cell-free multi-enzyme catalysis is an effective method to produce high value chemicals. In this study, a multi-enzyme catalytic pathway comprising three enzymes for fumarate production from low-cost substrates acetate and glyoxylate was designed. The acetyl-CoA synthase, malate synthase, and fumarase from Escherichia coli were selected and the coenzyme A achieved recyclable. The enzymatic properties and optimization of reaction system were investigated, reaching a fumarate yield of 0.34 mM with a conversion rate of 34% after 20 h of reaction. We proposed and realized the conversion of acetate and glyoxylate to fumarate in vitro using a cell-free multi-enzyme catalytic system, thus providing an alternative approach for the production of fumarate.

Fermentation optimization of surfactin production of Bacillus amyloliquefaciens HM618

This work isolated a strain named Bacillus amyloliquefaciens HM618 from the soil, which can inhibit the growths of Botrytis cinerea, Rhizoctonia solani, and Escherichia coli DH5α. Based on the results of response surface methodology, the surfactin levels of strain HM618 were elevated from 0.724 to 1.876 g/L and 0.995 to 1.888 g/L under the pure culture with the optimized medium (containing 62.39 g/L sucrose, 15.06 g/L yeast extracts, and 3.27 g/L aspartate) and under the coculture of strains HM618 and Bacillus subtilis 168 with the optimized medium (containing 50.52 g/L sucrose, 19.76 g/L yeast extracts, and 1.02 g/L glutamate), respectively. Additionally, influences of nonconstitutive amino acids involved in the biosynthesis of surfactin were also explored. The highest surfactin level reached 2.04 g/L after adding 3.0 g/L exogenous ornithine. However, the surfactin production of strain HM618 was significantly inhibited after adding the mixtures of nonconstitutive amino acids.

Recent advances and perspectives on production of value-added organic acids through metabolic engineering

Organic acids are important consumable materials with a wide range of applications in the food, biopolymer and chemical industries. The global consumer organic acids market is estimated to increase to $36.86 billion by 2026. Conventionally, organic acids are produced from the chemical catalysis process with petrochemicals as raw materials, which posts severe environmental concerns and conflicts with our sustainable development goals. Most of the commonly used organic acids can be produced from various organisms. As a state-of-the-art technology, large-scale fermentative production of important organic acids with genetically-modified microbes has become an alternative to the chemical route to meet the market demand. Despite the fact that bio-based organic acid production from renewable cheap feedstock provides a viable solution, low productivity has impeded their industrial-scale application. With our deeper understanding of strain genetics, physiology and the availability of strain engineering tools, new technologies including synthetic biology, various metabolic engineering strategies, omics-based system biology tools, and high throughput screening methods are gradually established to bridge our knowledge gap. And they were further applied to modify the cellular reaction networks of potential microbial hosts and improve the strain performance, which facilitated the commercialization of consumable organic acids. Here we present the recent advances of metabolic engineering strategies to improve the production of important organic acids including fumaric acid, citric acid, itaconic acid, adipic acid, muconic acid, and we also discuss the current challenges and future perspectives on how we can develop a cost-efficient, green and sustainable process to produce these important chemicals from low-cost feedstocks.

Engineering the glyoxylate cycle for chemical bioproduction

With growing concerns about environmental issues and sustainable economy, bioproduction of chemicals utilizing microbial cell factories provides an eco-friendly alternative to current petro-based processes. Creating high-performance strains (with high titer, yield, and productivity) through metabolic engineering strategies is critical for cost-competitive production. Commonly, it is inevitable to fine-tuning or rewire the endogenous or heterologous pathways in such processes. As an important pathway involved in the synthesis of many kinds of chemicals, the potential of the glyoxylate cycle in metabolic engineering has been studied extensively these years. Here, we review the metabolic regulation of the glyoxylate cycle and summarize recent achievements in microbial production of chemicals through tuning of the glyoxylate cycle, with a focus on studies implemented in model microorganisms. Also, future prospects for bioproduction of glyoxylate cycle-related chemicals are discussed.

Production of polyhydroxyalkanoates containing monomers conferring amorphous and elastomeric properties from renewable resources: Current status and future perspectives

Petrochemical-based plastics cause environmental pollution and threaten humans and ecosystems. Polyhydroxyalkanoate (PHA) is considered a promising alternative to nondegradable plastics since it is eco-friendly and biodegradable polymer having similar properties to conventional plastics. PHA's material properties are generally determined by composition and type of monomers in PHA. PHA can be designed in tailor-made manner for their suitable application areas. Among many monomers in PHAs, ω-hydroxalkanoates such as 3-hydroxypropionate (3HP), 4-hydroxybutyrate (4HB), 5-hydroxyvalerate (5HV), and 6-hydroxyhexanoate (6HHx) and medium-chain-length 3-hydroxyalkanoate such as 3-hydroxyhexanoate (3HHx) and 4-hydroxyvalerate (4HV), have been examined as potential monomers able to confer amorphous and elastomer properties when these are incorporated as comonomer in poly(3-hydroxybutyrate) copolymer that has 3HB as main monomer along with comonomers in different monomer fraction. Herein, recent advances in production of PHAs designed to have amorphous and elastomeric properties from renewable sources such as lignocellulose, levulinic acid, crude glycerol, and waste oil are discussed.

Fumaric acid: fermentative production, applications and future perspectives

The rising prices of petroleum-based chemicals and the growing apprehension about food safety and dairy supplements have reignited interest in fermentation process to produce fumaric acid. This article reviews the main issues associated with industrial production of fumaric acid. Different approaches such as strain modulation, morphological control, selection of substrate and fermentative separation have been addressed and discussed followed by their potential towards production of fumaric acid at industrial scale is highlighted. The employment of biodegradable wastes as substrates for the microorganisms involved in fumaric acid synthesis has opened an economic and green route for production of the later on a commercial scale. Additionally, the commercial potential and technological approaches to the augmented fumaric acid derivatives have been discussed. Conclusion of the current review reveals future possibilities for microbial fumaric acid synthesis.

Recovery and Purification of Fumaric Acid from Fermented Oil Palm Empty Fruit Bunches Using a Simple Two-Stage Precipitation Procedure

Oil palm empty fruit bunches (EFBs) are an attractive lignocellulosic material that can be used as a cheap renewable feedstock to produce organic acids and many other value-added products. This research is aimed at investigating the potential of steam-exploded oil palm EFBs for the production of fumaric acid, a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the selected fungal isolate Rhizopus oryzae K20. To develop an efficient method for the recovery and purification of fumaric acid from fermented oil palm EFBs, a two-stage precipitation protocol was employed, followed by an activated carbon-mediated polishing step to remove contaminants. After these two processes were accomplished, a recovery yield of 81.2% and a purity of 83.5% were achieved.

State of the Art on the Microbial Production of Industrially Relevant Organic Acids

The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by many cells. They are the products, by-products or co-products of many primary metabolic processes of microbial cells. Thanks to the potential of microbial cell factories and to the development of industrial biotechnology, from the last decades of the previous century, the microbial-based production of these molecules has started to approach the market. This was possible because of a joint effort of microbial biotechnologists and biochemical and process engineers that boosted natural production up to the titer, yield and productivity needed to be industrially competitive. More recently, the possibility to utilize renewable residual biomasses as feedstock not only for biofuels, but also for organic acids production is further augmenting the sustainability of their production, in a logic of circular bioeconomy. In this review, we briefly present the latest updates regarding the production of some industrially relevant organic acids (citric fumaric, itaconic, lactic and succinic acid), discussing the challenges and possible future developments of successful production.

The challenges and prospects of Escherichia coli as an organic acid production host under acid stress

OBJECTIVE

Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production.

IMPORTANCE

However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment.

ELABORATION

This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application.

IMPLICATION

At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value.

KEY POINTS

• E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.

GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level

Motivation

Large-scale metabolic models are widely used to design metabolic engineering strategies for diverse biotechnological applications. However, the existing computational approaches focus on alteration of reaction fluxes and often neglect the manipulations of gene expression to implement these strategies.

Results

Here, we find that the association of genes with multiple reactions leads to infeasibility of engineering strategies at the flux level, since they require contradicting manipulations of gene expression. Moreover, we identify that all of the existing approaches to design gene knockout strategies do not ensure that the resulting design may also require other gene alterations, such as up- or downregulations, to match the desired flux distribution. To address these issues, we propose a constraint-based approach, termed GeneReg, that facilitates the design of feasible metabolic engineering strategies at the gene level and that is readily applicable to large-scale metabolic networks. We show that GeneReg can identify feasible strategies to overproduce ethanol in Escherichia coli and lactate in Saccharomyces cerevisiae, but overproduction of the TCA cycle intermediates is not feasible in five organisms used as cell factories under default growth conditions. Therefore, GeneReg points at the need to couple gene regulation and metabolism to design rational metabolic engineering strategies.

Availability and implementation

https://github.com/MonaRazaghi/GeneReg

Supplementary information

Supplementary data are available at Bioinformatics online.

Microbial engineering for the production of C2-C6 organic acids

Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C₂-C₆ organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.

Enhanced O-succinyl-l-homoserine production by recombinant Escherichia coli ΔIJBB*TrcmetL/pTrc-metAfbr -Trc-thrAfbr -yjeH via multilevel fermentation optimization

AIMS

Constructing a strain with high yield of O-succinyl-l-homoserine (OSH) and improving the titre through multilevel fermentation optimization.

METHODS AND RESULTS

OSH high-yielding strain was first constructed by deleting the thrB gene to block the threonine biosynthesis. Single-factor experiment was carried out, where a Plackett-Burman design was used to screen out three factors (glucose, yeast and threonine) from the original 11 factors that affected the titre of OSH. The Box-Behnken response surface method was used to optimize the fermentation conditions. Through gene editing and medium optimization, the titre of OSH increased from 7·20 to 8·70 g l^-1 in 500 ml flask. Furthermore, the fermentation process and fed-batch fermentation conditions including pH, temperature, feeding strategy and feeding medium were investigated and optimized. Under the optimal conditions, the titre of OSH reached 102·5 g l^-1 , which is 5·6 times higher than before (15·6 g l^-1 ).

CONCLUSIONS

O-succinyl-l-homoserine fermentation process was established and the combination of response surface methodology and metabolic pathway analysis effectively improved the titre of OSH.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this study, the titre of OSH reached the needs for industrial production and the metabolic pathway of OSH was demonstrated for further optimization.

Engineering the transmission efficiency of the noncyclic glyoxylate pathway for fumarate production in Escherichia coli

BACKGROUND

Fumarate is a multifunctional dicarboxylic acid in the tricarboxylic acid cycle, but microbial engineering for fumarate production is limited by the transmission efficiency of its biosynthetic pathway.

RESULTS

Here, pathway engineering was used to construct the noncyclic glyoxylate pathway for fumarate production. To improve the transmission efficiency of intermediate metabolites, pathway optimization was conducted by fluctuating gene expression levels to identify potential bottlenecks and then remove them, resulting in a large increase in fumarate production from 8.7 to 16.2 g/L. To further enhance its transmission efficiency of targeted metabolites, transporter engineering was used by screening the C₄-dicarboxylate transporters and then strengthening the capacity of fumarate export, leading to fumarate production up to 18.9 g/L. Finally, the engineered strain E. coli W3110△4-P_(H)CAI_(H)SC produced 22.4 g/L fumarate in a 5-L fed-batch bioreactor.

CONCLUSIONS

In this study, we offered rational metabolic engineering and flux optimization strategies for efficient production of fumarate. These strategies have great potential in developing efficient microbial cell factories for production of high-value added chemicals.

Fermentative production of the unnatural amino acid L-2-aminobutyric acid based on metabolic engineering

Background

l-2-aminobutyric acid (l-ABA) is an unnatural amino acid that is a key intermediate for the synthesis of several important pharmaceuticals. To make the biosynthesis of l-ABA environmental friendly and more suitable for the industrial-scale production. We expand the nature metabolic network of Escherichia coli using metabolic engineering approach for the production of l-ABA.

Results

In this study, Escherichia coli THR strain with a modified pathway for threonine-hyperproduction was engineered via deletion of the rhtA gene from the chromosome. To redirect carbon flux from 2-ketobutyrate (2-KB) to l-ABA, the ilvIH gene was deleted to block the l-isoleucine pathway. Furthermore, the ilvA gene from Escherichia coli W3110 and the leuDH gene from Thermoactinomyces intermedius were amplified and co-overexpressed. The promoter was altered to regulate the expression strength of ilvA* and leuDH. The final engineered strain E. coli THR ΔrhtAΔilvIH/Gap-ilvA*-Pbs-leuDH was able to produce 9.33 g/L of l-ABA with a yield of 0.19 g/L/h by fed-batch fermentation in a 5 L bioreactor.

Conclusions

This novel metabolically tailored strain offers a promising approach to fulfill industrial requirements for production of l-ABA.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1095-z) contains supplementary material, which is available to authorized users.

Fumaric acid: production and separation

Fumaric acid is a valuable compound used in foods, beverages, detergents, animal feed, pharmaceuticals and miscellaneous industrial products. It is produced on a large scale by the petrochemical route but the current tendency is towards implementing "green production" and environmental friendly technologies like biotechnological production of fumaric acid using low-cost raw materials. In this context, numerous studies focus on improving the fermentation process not only by using renewable raw material and genetically modified microorganisms, but also by developing and applying different downstream techniques for easy recovery of fumaric acid from the fermented broth. This review presents the main methods for production and separation of fumaric acid, highlighting the advantages and disadvantages of these and the potential economic impact in industry.

Genetic manipulation of Escherichia coli central carbon metabolism for efficient production of fumaric acid

Fumaric acid is one of the top 12-biomass building-block chemicals. In this study, we reported manipulation of E. coli central carbon metabolism with the aim to decrease the by-products and improve fumaric acid production. PEP-dependent glucose phosphotransferase system was replaced with a galactose translocation system to minimize the consumption of phosphoenolpyruvate. Engineering anaplerotic pathway (phosphoenolpyruvate carboxylase) was employed to redistribute carbon flux from glycolysis to Krebs cycle. Deletion of malate dehydrogenase and overexpression of acetyl-CoA synthase could decrease the byproducts malic acid and acetic acid. The combined strategies led to fumaric acid yield up to 1.53 g/g dry cell weight, a 50% increase compared with the parental strain. The result demonstrated that these genetic modifications were effective strategies for improving the production of fumaric acid and the engineered strain may serve a platform microbial cell factory for efficient production of fumaric acid or other dicarboxylic acids.

Engineered Microorganisms for the Production of Food Additives Approved by the European Union-A Systematic Analysis

In the 1950s, the idea of a single harmonized list of food additives for the European Union arose. Already in 1962, the E-classification system, a robust food safety system intended to protect consumers from possible food-related risks, was introduced. Initially, it was restricted to colorants, but at later stages also preservatives, antioxidants, emulsifiers, stabilizers, thickeners, gelling agents, sweeteners, and flavorings were included. Currently, the list of substances authorized by the European Food Safety Authority (EFSA) (referred to as "E numbers") comprises 316 natural or artificial substances including small organic molecules, metals, salts, but also more complex compounds such as plant extracts and polymers. Low overall concentrations of such compounds in natural producers due to inherent regulation mechanisms or production processes based on non-regenerative carbon sources led to an increasing interest in establishing more reliable and sustainable production platforms. In this context, microorganisms have received significant attention as alternative sources providing access to these compounds. Scientific advancements in the fields of molecular biology and genetic engineering opened the door toward using engineered microorganisms for overproduction of metabolites of their carbon metabolism such as carboxylic acids and amino acids. In addition, entire pathways, e.g., of plant origin, were functionally introduced into microorganisms, which holds the promise to get access to an even broader range of accessible products. The aim of this review article is to give a systematic overview on current efforts during construction and application of microbial cell factories for the production of food additives listed in the EU "E numbers" catalog. The review is focused on metabolic engineering strategies of industrially relevant production hosts also discussing current bottlenecks in the underlying metabolic pathways and how they can be addressed in the future.

Metabolic engineering of E. coli for the production of O-succinyl-l-homoserine with high yield

O-succinyl-l-homoserine (OSH) is a promising platform chemical for the production of C4 chemicals with huge market potential which can be produced by fermentation from glucose. To construct a strain capable of producing OSH with high yield, the metJ (encodes transcriptional repressor) and metI (encodes a subunit of dl-methionine transporter) were deleted in Escherichia coli W3110 to obtain a strain E. coli ∆JI. Then, overexpression of metL (encodes bifunctional aspartate kinase/homoserine dehydrogenase II) and inactivation of metB (encodes cystathionine γ-synthase) were implemented in one step, and the OSH titer of the resulting strain E. coli ∆JIB^* TrcmetL was dramatically increased to 7.30 g/L. The feedback regulation was further relieved by progressively overexpressing metA^fbr (encodes homoserine O-succinyltransferase), yjeH (encodes l-methionine exporter), and thrA^fbr (encodes bifunctional aspartate kinase/homoserine dehydrogenase I) to increase the metabolic flux from aspartate to OSH. The 100% rationally designed strain E. coli ∆JIB^* TrcmetL/pTrc-metA^fbr -Trc-thrA^fbr -yjeH produced 9.31 g/L OSH from 20 g/L glucose (0.466 g/g glucose) in batch fermentation, which represents the highest OSH yield from glucose reported to date. The culture profiles of the newly constructed strains were recorded to investigate their productive properties. The effects of l-methionine addition on the fermentation process of the optimal strain were also studied. Our results demonstrate that tuning the expression level of metL, inactivation of metB, and attenuation of feedback resistance of the crucial enzymes in the biosynthetic pathway are the key factors that impact the OSH production in E. coli.

Increasing L-threonine production in Escherichia coli by engineering the glyoxylate shunt and the L-threonine biosynthesis pathway

L-threonine is an important amino acid that can be added in food, medicine, or feed. Here, the influence of glyoxylate shunt on an L-threonine producing strain Escherichia coli TWF001 has been studied. The gene iclR was deleted, and the native promoter of the aceBA operon was replaced by the trc promoter in the chromosome of TWF001, the resulting strainTWF004 could produce 0.39 g L-threonine from1 g glucose after 36-h flask cultivation. Further replacing the native promoter of aspC by the trc promoter in the chromosome of TWF004 resulted in the strain TWF006. TWF006 could produce 0.42 g L-threonine from 1 g glucose after 36-h flask cultivation. Three key genes in the biosynthetic pathway of L-threonine, thrA ^* (a mutated thrA), thrB, and thrC were overexpressed in TWF006, resulting the strain TWF006/pFW01-thrA ^* BC. TWF006/pFW01-thrA ^* BC could produce 0.49 g L-threonine from 1 g glucose after 36-h flask cultivation. Next, the genes asd, rhtA, rhtC, or thrE were inserted into the plasmid TWF006/pFW01-thrA ^* BC, and TWF006 was transformed with these plasmids, resulting the strains TWF006/pFW01-thrA ^* BC-asd, TWF006/pFW01-thrA ^* BC-rhtA, TWF006/pFW01-thrA ^* BC-rhtC, and TWF006/pFW01-thrA ^* BC-thrE, respectively. These four strains could produce more L-threonine than the control strain, and the highest yield was produced by TWF006/pFW01-thrA ^* BC-asd; after 36-h flask cultivation, TWF006/pFW01-thrA ^* BC-asd could produce 15.85 g/l L-threonine, i.e., 0.53 g L-threonine per 1 g glucose, which is a 70% increase relative to the control strain TWF001. The results suggested that the combined engineering of glyoxylate shunt and L-threonine biosynthesis pathway could significantly increase the L-threonine production in E. coli.

Metabolic engineering of the thermophilic filamentous fungus Myceliophthora thermophila to produce fumaric acid

BACKGROUND

Fumaric acid is widely used in food and pharmaceutical industries and is recognized as a versatile industrial chemical feedstock. Increasing concerns about energy and environmental problems have resulted in a focus on fumaric acid production by microbial fermentation via bioconversion of renewable feedstocks. Filamentous fungi are the predominant microorganisms used to produce organic acids, including fumaric acid, and most studies to date have focused on Rhizopus species. Thermophilic filamentous fungi have many advantages for the production of compounds by industrial fermentation. However, no previous studies have focused on fumaric acid production by thermophilic fungi.

RESULTS

We explored the feasibility of producing fumarate by metabolically engineering Myceliophthora thermophila using the CRISPR/Cas9 system. Screening of fumarases suggested that the fumarase from Candida krusei was the most suitable for efficient production of fumaric acid in M. thermophila. Introducing the C. krusei fumarase into M. thermophila increased the titer of fumaric acid by threefold. To further increase fumarate production, the intracellular fumarate digestion pathway was disrupted. After deletion of the two fumarate reductase and the mitochondrial fumarase genes of M. thermophila, the resulting strain exhibited a 2.33-fold increase in fumarate titer. Increasing the pool size of malate, the precursor of fumaric acid, significantly increased the final fumaric acid titer. Finally, disruption of the malate-aspartate shuttle increased the intracellular malate content by 2.16-fold and extracellular fumaric acid titer by 42%, compared with that of the parental strain. The strategic metabolic engineering of multiple genes resulted in a final strain that could produce up to 17 g/L fumaric acid from glucose in a fed-batch fermentation process.

CONCLUSIONS

This is the first metabolic engineering study on the production of fumaric acid by the thermophilic filamentous fungus M. thermophila. This cellulolytic fungal platform provides a promising method for the sustainable and efficient-cost production of fumaric acid from lignocellulose-derived carbon sources in the future.

Protein and metabolic engineering for the production of organic acids

Organic acids are natural metabolites of living organisms. They have been widely applied in the food, pharmaceutical, and bio-based materials industries. In recent years, biotechnological routes to organic acids production from renewable raw materials have been regarded as very promising approaches. In this review, we provide an overview of current developments in the production of organic acids using protein and metabolic engineering strategies. The organic acids include propionic acid, pyruvate, itaconic acid, succinic acid, fumaric acid, malic acid and citric acid. We also expect that rapid developments in the fields of systems biology and synthetic biology will accelerate protein and metabolic engineering for microbial organic acid production in the future.

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood. We set out to increase the knowledge about fumarate accumulation in R. delemar. To this end, we combined a transcriptomics and proteomics approach to identify key metabolic pathways involved in fumarate production in R. delemar, and propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism.

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.

Synthesis of chemicals by metabolic engineering of microbes

Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.

Engineering Scheffersomyces stipitis for fumaric acid production from xylose

In this work, Scheffersomyces stipitis, the yeast with excellent xylose-utilizing ability, was firstly engineered for fumaric acid production from xylose with the heterologous reductive pathway from Rhizopus oryzae FM19, and 1.86g/L fumaric acid was produced by the initial strain PSRPMF under the oxygen-limited condition. Furthermore, three strategies were performed to improve the fumaric acid production, including increasing the reductive pathway activity by codon optimization, blocking the fumaric acid conversion in tricarboxylic acid cycle by knocking out the native fumarases, and improving the fumaric acid transportation by overexpressing heterologous transporter. Finally, the strain PSYPMFfS was obtained and the fumaric acid titer reached to 4.67g/L, significantly increased by 37.92-fold than that of the control strain PSPYSS. It was indicated that the S. stipitis was a promising platform for fumaric acid production from xylose.