Site-specific integration and constitutive expression of key genes into Escherichia coli chromosome increases shikimic acid yields

Metabolic network rewiring and temperature-dependent regulation for enhanced 3-dehydroshikimate production in Escherichia coli

The cyclohexane organic acid 3-dehydroshikimate (DHS) has potent antioxidant activity and is widely utilised in chemical and pharmaceutical industries. However, its production requires a long fermentation with a suboptimal yield and low productivity, and a disproportionate growth-to-production ratio impedes the upscaling of DHS synthesis in microbial cell factories. To overcome these limitations, competing and degradation pathways were knocked-out and key enzymes were balanced in an engineered Escherichia coli production strain, resulting in 12.2 g/L DHS. Furthermore, to achieve equilibrium between cell growth and DHS production, a CRISPRi-based temperature-responsive multi-component repressor system was developed to dynamically control the expression of critical genes (pykF and aroE), resulting in a 30-fold increase in DHS titer. After 33 h fermentation in 5 L bioreactor, the DHS titer, productivity and yield reached 94.2 g/L, 2.8 g/L/h and 55 % glucose conversion, respectively. The results provided valuable insight into the production of DHS and its derivatives.

Microbial engineering for shikimate biosynthesis

Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.

Multiple Metabolic Engineering Strategies to Improve Shikimate Titer in Escherichia coli

Shikimate is a valuable chiral precursor for synthesizing oseltamivir (Tamiflu^®) and other chemicals. High production of shikimate via microbial fermentation has attracted increasing attention to overcome the unstable and expensive supply of shikimate extracted from plant resources. The current cost of microbial production of shikimate via engineered strains is still unsatisfactory, and thus more metabolic strategies need to be investigated to further increase the production efficiency. In this study, we first constructed a shikimate E. coli producer through the application of the non-phosphoenolpyruvate: carbohydrate phosphotransferase system (non-PTS) glucose uptake pathway, the attenuation of the shikimate degradation metabolism, and the introduction of a mutant of feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase. Inspired by the natural presence of bifunctional 3-dehydroquinate dehydratase (DHD)-shikimate dehydrogenase (SDH) enzyme in plants, we then designed an artificial fusion protein of DHD-SDH to decrease the accumulation of the byproduct 3-dehydroshikimate (DHS). Subsequently, a repressed shikimate kinase (SK) mutant was selected to promote shikimate accumulation without the supplementation of expensive aromatic substances. Furthermore, EsaR-based quorum sensing (QS) circuits were employed to regulate the metabolic flux distribution between cell growth and product synthesis. The final engineered strain dSA10 produced 60.31 g/L shikimate with a yield of 0.30 g/g glucose in a 5 L bioreactor.

Shikimic acid biosynthesis in microorganisms: Current status and future direction

Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.

Systems engineering of Escherichia coli for high-level shikimate production

To further increase the production efficiency of microbial shikimate, a valuable compound widely used in the pharmaceutical and chemical industries, ten key target genes contributing to shikimate production were identified by exploiting the enzyme constraint model ec_iML1515, and subsequently used for promoting metabolic flux towards shikimate biosynthesis in the tryptophan-overproducing strain Escherichia coli TRP0. The engineered E. coli SA05 produced 78.4 g/L shikimate via fed-batch fermentation. Deletion of quinate dehydrogenase and introduction of the hydroaromatic equilibration-alleviating shikimate dehydrogenase mutant AroE^T61W/L241I reduced the contents of byproducts quinate (7.5 g/L) and 3-dehydroshikimic acid (21.4 g/L) by 89.1% and 52.1%, respectively. Furthermore, a high concentration shikimate responsive promoter P_rpoS was recruited to dynamically regulate the expression of the tolerance target ProV to enhance shikimate productivity by 23.2% (to 2 g/L/h). Finally, the shikimate titer was increased to 126.4 g/L, with a yield of 0.50 g/g glucose and productivity of 2.63 g/L/h, using a 30-L fermenter and the engineered strain E. coli SA09. This is, to the best of our knowledge, the highest reported shikimate titer and productivity in E. coli.

Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production

As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.

Engineering Escherichia coli to improve tryptophan production via genetic manipulation of precursor and cofactor pathways

Optimizing the supply of biosynthetic precursors and cofactors is usually an effective metabolic strategy to improve the production of target compounds. Here, the combination of optimizing precursor synthesis and balancing cofactor metabolism was adopted to improve tryptophan production in Escherichia coli. First, glutamine synthesis was improved by expressing heterologous glutamine synthetase from Bacillus subtilis and Bacillus megaterium in the engineered Escherichia coli strain KW001, resulting in the best candidate strain TS-1. Then icd and gdhA were overexpressed in TS-1, which led to the accumulation of 1.060 g/L tryptophan. Subsequently, one more copy of prs was introduced on the chromosome to increase the flux of 5-phospho-α-d-ribose 1-diphosphate followed by the expression of mutated serA and thrA to increase the precursor supply of serine, resulting in the accumulation of 1.380 g/L tryptophan. Finally, to maintain cofactor balance, sthA and pntAB, encoding transhydrogenase, were overexpressed. With sufficient amounts of precursors and balanced cofactors, the engineered strain could produce 1.710 g/L tryptophan after 48 h of shake-flask fermentation, which was 2.76-times higher than the titer of the parent strain. Taken together, our results demonstrate that the combination of optimizing precursor supply and regulating cofactor metabolism is an effective approach for high-level production of tryptophan. Similar strategies could be applied to the production of other amino acids or related derivatives.

Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway

The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.

Cell Factory Design and Culture Process Optimization for Dehydroshikimate Biosynthesis in Escherichia coli

3-Dehydroshikimate (DHS) is a useful starting metabolite for the biosynthesis of muconic acid (MA) and shikimic acid (SA), which are precursors of various valuable polymers and drugs. Although DHS biosynthesis has been previously reported in several bacteria, the engineered strains were far from satisfactory, due to their low DHS titers. Here, we created an engineered Escherichia coli cell factory to produce a high titer of DHS as well as an efficient system for the conversion DHS into MA. First, the genes showing negative effects on DHS accumulation in E. coli, such as tyrR (tyrosine dependent transcriptional regulator), ptsG (glucose specific sugar: phosphoenolpyruvate phosphotransferase), and pykA (pyruvate kinase 2), were disrupted. In addition, the genes involved in DHS biosynthesis, such as aroB (DHQ synthase), aroD (DHQ dehydratase), ppsA (phosphoenolpyruvate synthase), galP (D-galactose transporter), aroG (DAHP synthase), and aroF (DAHP synthase), were overexpressed to increase the glucose uptake and flux of intermediates. The redesigned DHS-overproducing E. coli strain grown in an optimized medium produced ~117 g/L DHS in 7-L fed-batch fermentation, which is the highest level of DHS production demonstrated in E. coli. To accomplish the DHS-to-MA conversion, which is originally absent in E. coli, a codon-optimized heterologous gene cassette containing asbF, aroY, and catA was expressed as a single operon under a strong promoter in a DHS-overproducing E. coli strain. This redesigned E. coli grown in an optimized medium produced about 64.5 g/L MA in 7-L fed-batch fermentation, suggesting that the rational cell factory design of DHS and MA biosynthesis could be a feasible way to complement petrochemical-based chemical processes.

Production and Synthetic Modifications of Shikimic Acid

Shikimic acid is a natural product of industrial importance utilized as a precursor of the antiviral Tamiflu. It is nowadays produced in multihundred ton amounts from the extraction of star anise ( Illicium verum) or by fermentation processes. Apart from the production of Tamiflu, shikimic acid has gathered particular notoriety as its useful carbon backbone and inherent chirality provide extensive use as a versatile chiral precursor in organic synthesis. This review provides an overview of the main synthetic and microbial methods for production of shikimic acid and highlights selected methods for isolation from available plant sources. Furthermore, we have attempted to demonstrate the synthetic utility of shikimic acid by covering the most important synthetic modifications and related applications, namely, synthesis of Tamiflu and derivatives, synthetic manipulations of the main functional groups, and its use as biorenewable material and in total synthesis. Given its rich chemistry and availability, shikimic acid is undoubtedly a promising platform molecule for further exploration. Therefore, in the end, we outline some challenges and promising future directions.

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments

Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.

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".

Novel technologies combined with traditional metabolic engineering strategies facilitate the construction of shikimate-producing Escherichia coli

Shikimate is an important intermediate in the aromatic amino acid pathway, which can be used as a promising building block for the synthesis of biological compounds, such as neuraminidase inhibitor Oseltamivir (Tamiflu^®). Compared with traditional methods, microbial production of shikimate has the advantages of environmental friendliness, low cost, feed stock renewability, and product selectivity and diversity, thus receiving more and more attentions. The development of metabolic engineering allows for high-efficiency production of shikimate of Escherichia coli by improving the intracellular level of precursors, blocking downstream pathway, releasing negative regulation factors, and overexpressing rate-limiting enzymes. In addition, novel technologies derived from systems and synthetic biology have opened a new avenue towards construction of shikimate-producing strains. This review summarized successful and applicable strategies derived from traditional metabolic engineering and novel technologies for increasing accumulation of shikimate in E. coli.

Tunable switch mediated shikimate biosynthesis in an engineered non-auxotrophic Escherichia coli

Shikimate is a key intermediate in the synthesis of neuraminidase inhibitors. Compared with traditional methods, microbial production of shikimate has the advantages of environmental friendliness, low cost, feed stock renewability, and product selectivity and diversity. Despite these advantages, shikimate kinase I and II respectively encoded by aroK and aroL are inactivated in most shikimate microbial producers, thus requiring the addition of aromatic compounds during the fermentation process. To overcome this problem, we constructed a non-auxotrophic, shikimate-synthesising strain of Escherichia coli. By inactivation of repressor proteins, blocking of competitive pathways and overexpression of key enzymes, we increased the shikimate production of wild-type E. coli BW25113 to 1.73 g/L. We then designed a tunable switch that can conditionally decrease gene expression and substituted it for the original aroK promoters. Expression of aroK in the resulting P-9 strain was maintained at a high level during the growth phase and then reduced at a suitable time by addition of an optimal concentration of inducer. In 5-L fed-batch fermentation, strain P-9 produced 13.15 g/L shikimate without the addition of any aromatic compounds. The tunable switch developed in this study is an efficient tool for regulating indispensable genes involved in critical metabolic pathways.