Heterologous biosynthesis of natural product naringenin by co-culture engineering

Pathway reconstruction and metabolic engineering for the de novo and enhancing production of monacolin J in Pichia pastoris

The statin is the primary cholesterol-lowering drug. Monacolin J (MJ) is a key intermediate in the biosynthetic pathway of statin. It was obtained in industry by the alkaline hydrolysis of lovastatin. The hydrolysis process resulted in multiple by-products and expensive cost of wastewater treatment. In this work, we used Pichia pastoris as the host to produce the MJ. The biosynthesis pathway of MJ was built in P. pastoris. The stable recombinant strain MJ2 was obtained by the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 genome-editing tool, and produced the MJ titer of 153.6 ± 2.4 mg/L. The metabolic engineering was utilized to enhance the production of MJ, and the fermentation condition was optimized. The MJ titer of 357.5 ± 5.0 mg/L was obtained from the recombinant strain MJ5-AZ with ATP-dependent citrate lyase (ACL), glucose-6-phosphate dehydrogenase (ZWF1) and four lovB genes, 132.7% higher than that from the original strain MJ2. The recombinant strain MJ5-AZ was cultured in a 7-L fermenter, and the MJ titer of 1493.0 ± 9.2 mg/L was achieved. The results suggested that increasing the gene dosage of rate-limiting step in the biosynthesis pathway of chemicals could improve the titer of production. It might be applicable to the production optimization of other polyketide metabolites.

Enhancement of polymyxin B1 production by an artificial microbial consortium of Paenibacillus polymyxa and recombinant Corynebacterium glutamicum producing precursor amino acids

Polymyxin B, produced by Paenibacillus polymyxa, is used as the last line of defense clinically. In this study, exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of P. polymyxa CJX518-AC (PPAC) from 0.15 g/L and 61.8 % to 0.33 g/L and 79.9 %, respectively. The co-culture of strain PPAC and recombinant Corynebacterium glutamicum-leu01, which produces high levels of threonine, leucine, and isoleucine, increased polymyxin B1 production to 0.64 g/L. When strains PPAC and C. glu-leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone, polymyxin B1 production was increased to 0.97 g/L. Furthermore, the polymyxin B1 production in the co-culture of strains PPAC and C. glu-leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L peptone. This study provides a new strategy to improve polymyxin B1 production.

High-Level Biosynthesis of Chlorogenic Acid from Mixed Carbon Sources of Xylose and Glucose through a Rationally Refactored Pathway Network

Chlorogenic acid (CGA) has incredible potential for various pharmaceutical, nutraceutical, and agricultural applications. However, the traditional extraction approach from plants is time-consuming, further limiting its production. Herein, we design and construct the de novo biosynthesis pathway of CGA using modular coculture engineering in Escherichia coli, which is composed of MG09 and BD07 strains. To accomplish this, the phenylalanine-deficient MG09 strain was engineered to utilize xylose preferentially and to overproduce precursor caffeic acid, while the tyrosine-deficient BD07 strain was constructed to consume glucose exclusively to enhance another precursor quinic acid availability for the biosynthesis of CGA. Further pathway modularization and balancing in the context of syntrophic cocultures resulted in additional production improvement. The coculture strategy avoids metabolic flux competition in the biosynthesis of two CGA precursors, caffeic acid and quinic acid, and allows for production improvement by balancing module proportions. Finally, the optimized coculture based on the aforementioned efforts produced 131.31 ± 7.89 mg/L CGA. Overall, the modular coculture engineering strategy in this study provides a reference for constructing microbial cell factories that can efficiently biomanufacture complex natural products.

Applications of synthetic yeast consortia for the production of native and non-native chemicals

The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.

Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production

Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of (S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization in Scheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated from Aspergillus niger facilitates shikimate translocation to the co-cultured Saccharomyces cerevisiae that converts shikimate to (S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for an S. cerevisiae monoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production.

Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production

Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.

Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis

Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.

Engineering caveolin-mediated endocytosis in Saccharomyces cerevisiae

As a potential substitute for fatty acids, common low-cost oils could be used to produce acetyl-CoA derivatives, which meet the needs of low-cost industrial production. However, oils are hydrophobic macromolecules and cannot be directly transported into cells. In this study, caveolin was expressed in Saccharomyces cerevisiae to absorb exogenous oils. The expression of caveolin fused with green fluorescent protein showed that caveolin mediated the formation of microvesicles in S. cerevisiae and the addition of 5,6-carboxyfluorescein showed that caveolae had the ability to transport exogenous substances into cells. The intracellular and extracellular triacylglycerol levels were then detected after the addition of soybean oil pre-stained with Nile Red, which proved that caveolae had the ability to absorb the exogenous oils. Lastly, caveolin for oils absorption and lipase from Bacillus pumilus for oil hydrolysis were co-expressed in the naringenin-producing Saccharomyces cerevisiae strain, resulting in naringenin production increasing from 222 mg/g DCW (dry cell weight) (231 mg/L) to 269 mg/g DCW (241 mg/L). These results suggested that the caveolin-mediated transporter independent oil transport system would provide a promising strategy for the transport of hydrophobic substrates.

Microbial production of valuable chemicals by modular co-culture strategy

Nowadays, microbial synthesis has become a common way for producing valuable chemicals. Traditionally, microbial production of valuable chemicals is accomplished by a single strain. For the purpose of increasing the production titer and yield of a recombinant strain, complicated pathways and regulation layers should be fine-tuned, which also brings a heavy metabolic burden to the host. In addition, utilization of various complex and mixed substrates further interferes with the normal growth of the host strain and increases the complexity of strain engineering. As a result, modular co-culture technology, which aims to divide a target complex pathway into separate modules located at different single strains, poses an alternative solution for microbial production. Recently, modular co-culture strategy has been employed for the synthesis of different natural products. Therefore, in this review, various chemicals produced with application of co-cultivation technology are summarized, including co-culture with same species or different species, and regulation of population composition between the co-culture members. In addition, development prospects and challenges of this promising field are also addressed, and possible solution for these issues were also provided.

Engineered biosynthesis of plant polyketides by type III polyketide synthases in microorganisms

Plant specialized metabolites occupy unique therapeutic niches in human medicine. A large family of plant specialized metabolites, namely plant polyketides, exhibit diverse and remarkable pharmaceutical properties and thereby great biomanufacturing potential. A growing body of studies has focused on plant polyketide synthesis using plant type III polyketide synthases (PKSs), such as flavonoids, stilbenes, benzalacetones, curcuminoids, chromones, acridones, xanthones, and pyrones. Microbial expression of plant type III PKSs and related biosynthetic pathways in workhorse microorganisms, such as Saccharomyces cerevisiae, Escherichia coli, and Yarrowia lipolytica, have led to the complete biosynthesis of multiple plant polyketides, such as flavonoids and stilbenes, from simple carbohydrates using different metabolic engineering approaches. Additionally, advanced biosynthesis techniques led to the biosynthesis of novel and complex plant polyketides synthesized by diversified type III PKSs. This review will summarize efforts in the past 10 years in type III PKS-catalyzed natural product biosynthesis in microorganisms, especially the complete biosynthesis strategies and achievements.

De Novo Production of Hydroxytyrosol by Saccharomyces cerevisiae-Escherichia coli Coculture Engineering

Hydroxytyrosol is a valuable plant-derived phenolic compound with excellent pharmacological activities for application in the food and health care industries. Microbial biosynthesis provides a promising approach for sustainable production of hydroxytyrosol via metabolic engineering. However, its efficient production is limited by the machinery and resources available in the commonly used individual microbial platform, for example, Escherichia coli, Saccharomyces cerevisiae. In this study, a S. cerevisiae-E. coli coculture system was designed for de novo biosynthesis of hydroxytyrosol by taking advantage of their inherent metabolic properties, whereby S. cerevisiae was engineered for de novo production of tyrosol based on an endogenous Ehrlich pathway, and E. coli was dedicated to converting tyrosol to hydroxytyrosol by use of native hydroxyphenylacetate 3-monooxygenase (EcHpaBC). To enhance hydroxytyrosol production, intra- and intermodule engineering was employed in this microbial consortium: (I) in the upstream S. cerevisiae strain, multipath regulations combining with a glucose-sensitive GAL regulation system were engineered to enhance the precursor supply, resulting in significant increase of tyrosol production (from 17.60 mg/L to 461.07 mg/L); (II) Echpabc was overexpressed in the downstream E. coli strain, improving the conversion rate of tyrosol to hydroxytyrosol from 0.03% to 86.02%; (III) and last, intermodule engineering with this coculture system was performed by optimization of the initial inoculation ratio of each population and fermentation conditions, achieving 435.32 mg/L of hydroxytyrosol. This S. cerevisiae-E. coli coculture strategy provides a new opportunity for de novo production of hydroxytyrosol from inexpensive feedstock.

Recent advances in microbial co-culture for production of value-added compounds

Micro-organisms have often been used to produce bioactive compounds as antibiotics, antifungals, and anti-tumors, etc. due to their easy and applicable culture, genetic manipulation, and extraction, etc. Mainly, microbial mono-cultures have been applied to produce value-added compounds and gotten numerous valuable results. However, mono-culture also has several complicated problems, such as metabolic burdens affecting the growth and development of the host, leading to a decrease in titer of the target compound. To circumvent those limitations, microbial co-culture has been technically developed and gained much interest compared to mono-culture. For example, co-culture simplifies the design of artificial biosynthetic pathways and restricts the recombinant host's metabolic burden, causing increased titer of desired compounds. This paper summarizes the recent advanced progress in applying microbial platform co-culture to produce natural products, such as flavonoid, terpenoid, alkaloid, etc. Furthermore, importantly different strategies for enhancing production, overcoming the metabolic burdens, building autonomous modulation of cell growth rate and culture composition in response to a quorum-sensing signal, etc., were also described in detail.

Compendium of naringenin: potential sources, analytical aspects, chemistry, nutraceutical potentials and pharmacological profile

Naringenin is flavorless, water insoluble active principle belonging to flavanone subclass. It exhibits a diverse pharmacological profile as well as divine nutraceutical values. Although several researchers have explored this phytoconstituent to evaluate its promising properties, still it has not gained recognition at therapeutic levels and more clinical investigations are still required. Also the neutraceutical potential has limited marketed formulations. This compilation includes the description of reported therapeutic potentials of naringenin in variety of pathological conditions alongwith the underlying mechanisms. Details of various analytical investigations carried on this molecule have been provided along with brief description of chemistry and structural activity relationship. In the end, various patents filed and clinical trial data has been provided. Naringenin has revealed promising pharmacological activities including cardiovascular diseases, neuroprotection, anti-diabetic, anticancer, antimicrobial, antiviral, antioxidant, anti-inflammatory and anti-platelet activity. It has been marketed in the form of nanoformulations, co-crystals, solid dispersions, tablets, capsules and inclusion complexes. It is also available in various herbal formulations as nutraceutical supplement. There are some pharmacokinetic issue with naringenin like poor absorption and low dissolution rate. Although these issues have been sorted out upto certain extent still further research to investigate the bioavailability of naringenin from herbal supplements and its clinical efficacy is essential.

Biotechnological advances for improving natural pigment production: a state-of-the-art review

In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.

Optogenetic approaches in biotechnology and biomaterials

Advances in genetic engineering, combined with the development of optical technologies, have allowed optogenetics to broaden its area of possible applications in recent years. However, the application of optogenetic tools in industry, including biotechnology and the production of biomaterials, is still limited, because each practical task requires the engineering of a specific optogenetic system. In this review, we discuss recent advances in the use of optogenetic tools in the production of biofuels and valuable chemicals, the synthesis of biomedical and polymer materials, and plant agrobiology. We also offer a comprehensive analysis of the properties and industrial applicability of light-controlled and other smart biomaterials. These data allow us to outline the prospects for the future use of optogenetics in bioindustry.

Optogenetic Control of Microbial Consortia Populations for Chemical Production

Microbial co-culture fermentations can improve chemical production from complex biosynthetic pathways over monocultures by distributing enzymes across multiple strains, thereby reducing metabolic burden, overcoming endogenous regulatory mechanisms, or exploiting natural traits of different microbial species. However, stabilizing and optimizing microbial subpopulations for maximal chemical production remains a major obstacle in the field. In this study, we demonstrate that optogenetics is an effective strategy to dynamically control populations in microbial co-cultures. Using a new optogenetic circuit we call OptoTA, we regulate an endogenous toxin-antitoxin system, enabling tunability of Escherichia coli growth using only blue light. With this system we can control the population composition of co-cultures of E. coli and Saccharomyces cerevisiae. When introducing in each strain different metabolic modules of biosynthetic pathways for isobutyl acetate or naringenin, we found that the productivity of co-cultures increases by adjusting the population ratios with specific light duty cycles. This study shows the feasibility of using optogenetics to control microbial consortia populations and the advantages of using light to control their chemical production.

Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review

Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, pharmaceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review.

Modular optimization in metabolic engineering

There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional approaches such as DNA, RNA, and protein-level modularity of intercellular machinery, by optimizing metabolic pathways for enhanced production. While research into these traditional approaches continues, limitations such as scale-up and time cost hold them back from wider use, while at the same time there is a shift to more novel methods, such as moving from episomal expression to chromosomal integration. Recently, nontraditional approaches such as co-culture systems and cell-free metabolic engineering (CFME) are being investigated for modular optimization. Co-culture modularity looks to optimally divide the metabolic burden between different hosts. CFME seeks to modularly optimize metabolic pathways in vitro, both speeding up the design of such systems and eliminating the issues associated with live hosts. In this review we will examine both traditional and nontraditional approaches for modular optimization, examining recent developments and discussing issues and emerging solutions for future research in metabolic engineering.

Optimum chalcone synthase for flavonoid biosynthesis in microorganisms

Chalcones and the subsequently generated flavonoids, as well as flavonoid derivatives, have been proven to have a variety of physiological activities and are widely used in: the pharmaceutical, food, feed, and cosmetic industries. As the content of chalcones and downstream products in native plants is low, the production of these compounds by microorganisms has gained the attention of many researchers and has a history of more than 20 years. The mining and engineering of chalcone synthase (CHS) could be one of the most important ways to achieve more efficient production of chalcones and downstream products in microorganisms. CHS has a broad spectrum of substrates, and its enzyme activity and expression level can significantly affect the efficiency of the biosynthesis of flavonoids. This review summarizes the recent advances in the: structure, mechanism, evolution, substrate spectrum, transformation, and expression regulation in the flavonoid biosynthesis of this vital enzyme. Future development directions were also suggested. The findings may further promote the research and development of flavonoids and health products, making them vital in the fields of human diet and health.

Engineering rhizobacteria for sustainable agriculture

Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.

Microbial co-culturing strategies for the production high value compounds, a reliable framework towards sustainable biorefinery implementation - an overview

The microbial co-cultures or consortia are a natural set of microorganisms formed from different species or the same species but different strains, in which members can interact with each other. The co-culture systems have wide variety of technological applications such as the production of foods, treatment of wastewater, removal of toxic substances, environmental recovery, and all these without the need to work in sterile conditions. Therefore, the need of understanding communication mechanisms between cell-to-cell within co-culture will allow to construct and to program their biological behavior from the use of complex substrates to produce biocompounds. The technology of co-culture systems enables the development of biorefinery platforms to obtain biofuels, and high value compounds through biomass transformation by sustainable process. This review focuses on understanding the roles of consortia microbial to design and built co-culture systems to produce high value compounds in terms a sustainable biorefinery.

Potential application of CHS and 4CL genes from grape endophytic fungus in production of naringenin and resveratrol and the improvement of polyphenol profiles and flavour of wine

4-Coumaroyl-CoA ligase (Al4CL) and chalcone synthase (AlCHS) genes were found in grape endophyte Alternaria sp. MG1, but were not functional verified. A cross-validation method was used in Saccharomyces cerevisiae to identify their functions. AlCHS was identified to synthesize both naringenin and resveratrol, while Al4CL synthesized p-coumaroyl CoA. Co-culture of S. cerevisiae strains separately containing AlCHS and Al4CL resulted in the simultaneous production of naringenin (18.5 mg/L) and resveratrol (113.2 μg/L). Strain S. cerevisiae containing Al4CL was used in winemaking and the chemical and aroma compounds in wine were detected by HPLC and SPME-GC-MS. Results showed that the total contents of polyphenols, anthocyanins, flavonol, ethyl esters and fatty acids significantly increased, while the 4-vinylphenol content decreased, and the fruit and cheese flavour increased but the green aroma declined. This study indicated the potential application of Al4CL and AlCHS genes from Alternaria sp. MG1 for improvement of wine nutrients and flavour.

Co-fermentation of glycerol and glucose by a co-culture system of engineered Escherichia coli strains for 1,3-propanediol production without vitamin B12 supplementation

The necessity of costly co-enzyme B₁₂ for the activity of glycerol dehydratase (GDHt) is considered as a major bottleneck in sustainable bioproduction of 1,3-propanediol (1,3-PD) from glycerol. Here, an E. coil Rosetta-dhaB1-dhaB2 strain was constructed by overexpressing a B₁₂-independent GDHt (dhaB1) and its activating factor (dhaB2) from Clostridium butyricum. Subsequently, it was used in designing a co-culture with E. coli BL21-dhaT that overexpressed 1,3-PD oxidoreductase (dhaT), to produce 1,3-PD during co-fermentation of glycerol and glucose. The optimum initial ratio of BL21-dhaT to Rosetta-dhaB1-dhaB2 strains in the co-culture was 1.5. Compared to the fermentation of glycerol alone, co-fermentation approach provided 1.3-folds higher 1,3-PD. Finally, co-fermentation was done in a 10 L bioreactor that produced 41.65 g/L 1,3-PD, which corresponded to 0.69 g/L/h productivity and 0.67 mol/mol yield of 1,3-PD. Hence, the developed co-culture could produce 1,3-PD cost-effectively without requiring vitamin B₁₂.

Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids

Coronavirus-related disease 2019 (COVID-19) became a pandemic in February 2020, and worldwide researchers try to tackle the disease with approved drugs of all kinds, or to develop novel compounds inhibiting viral spreading. Flavonoids, already investigated as antivirals in general, also might bear activities specific for the viral agent causing COVID-19, SARS-CoV-2. Microbial biotechnology and especially synthetic biology may help to produce flavonoids, which are exclusive plant secondary metabolites, at a larger scale or indeed to find novel pharmaceutically active flavonoids. Here, we review the state of the art in (i) antiviral activity of flavonoids specific for coronaviruses and (ii) results derived from computational studies, mostly docking studies mainly inhibiting specific coronaviral proteins such as the 3CL (main) protease, the spike protein or the RNA-dependent RNA polymerase. In the end, we strive towards a synthetic biology pipeline making the fast and tailored production of valuable antiviral flavonoids possible by applying the last concepts of division of labour through co-cultivation/microbial community approaches to the DBTL (Design, Build, Test, Learn) principle.

Metabolic modelling approaches for describing and engineering microbial communities

Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to growing awareness of their influence on a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications involving microorganisms, both in vivo and in silico, have been developed in the context of isolated microbes. In vivo microbial consortia development is extremely difficult and costly because it implies replicating suitable environments in the wet-lab. Computational approaches are thus a good, cost-effective alternative to study microbial communities, mainly via descriptive modelling, but also via engineering modelling. In this review we provide a detailed compilation of examples of engineered microbial communities and a comprehensive, historical revision of available computational metabolic modelling methods to better understand, and rationally engineer wild and synthetic microbial communities.

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly

Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.

Fermentation and Metabolic Pathway Optimization to De Novo Synthesize (2S)-Naringenin in Escherichia coli

Flavonoids have diverse biological functions in human health. All flavonoids contain a common 2-phenyl chromone structure (C6-C3-C6) as a scaffold. Hence, in using such a scaffold, plenty of highvalue-added flavonoids can be synthesized by chemical or biological catalyzation approaches. (2S)-Naringenin is one of the most commonly used flavonoid scaffolds. However, biosynthesizing (2S)-naringenin has been restricted not only by low production but also by the expensive precursors and inducers that are used. Herein, we established an induction-free system to de novo biosynthesize (2S)-naringenin in Escherichia coli. The tyrosine synthesis pathway was enhanced by overexpressing feedback inhibition-resistant genes (aroG^fbr and tyrA^fbr) and knocking out a repressor gene (tyrR). After optimizing the fermentation medium and conditions, we found that glycerol, glucose, fatty acids, potassium acetate, temperature, and initial pH are important for producing (2S)-naringenin. Using the optimum fermentation medium and conditions, our best strain, Nar-17LM1, could produce 588 mg/l (2S)-naringenin from glucose in a 5-L bioreactor, the highest titer reported to date in E. coli.

Optimization of Culture Conditions for the Efficient Biosynthesis of Trilobatin from Phloretin by Engineered Escherichia coli Harboring the Apple Phloretin-4'-O-glycosyltransferase

Trilobatin, a dihydrochalcone glucoside and natural sweetener, has diverse biological and therapeutic properties. In the present study, we developed a microbial system to produce trilobatin from phloretin using Escherichia coli (E. coli) overexpressing the phloretin-4'-O-glycosyltransferase from Malus x domestica Borkh. Various optimization strategies were employed for the efficient production of trilobatin using a one-factor-at-a-time method. The effect of UDP-glucose supplementation, substrate, and inducer concentrations, time of substrate feeding as well as protein induction, and different culture media combinations were evaluated and optimized to enhance the production of trilobatin. As a result, the highest trilobatin production, 246.83 μM (107.64 mg L-1), was obtained with an LB-TB medium combination, 22 h of induction with 0.1 mM IPTG followed by 4 h of feeding with 250 μM phloretin and without extracellular UDP-glucose supplementation. These results demonstrate the efficient production of trilobatin and constitute a promising foundation for large-scale production of the dihydrochalcone glycosides in engineered E. coli.

Metabolic Engineering of Microorganisms for the Production of Flavonoids

Flavonoids are a class of secondary metabolites found in plant and fungus. They have been widely used in food, pharmaceutical, and nutraceutical industries owing to their significant biological activities, such as antiaging, antioxidant, anti-inflammatory, and anticancer. However, the traditional approaches for the production of flavonoids including chemical synthesis and plant extraction involved hazardous materials and complicated processes and also suffered from low product titer and yield. Microbial synthesis of flavonoids from renewable biomass such as glucose and xylose has been considered as a sustainable and environmentally friendly method for large-scale production of flavonoids. Recently, construction of microbial cell factories for efficient biosynthesis of flavonoids has gained much attention. In this article, we summarize the recent advances in microbial synthesis of flavonoids including flavanones, flavones, isoflavones, flavonols, flavanols, and anthocyanins. We put emphasis on developing pathway construction and optimization strategies to biosynthesize flavonoids and to improve their titer and yield. Then, we discuss the current challenges and future perspectives on successful strain development for large-scale production of flavonoids in an industrial level.

Metabolic Engineering of Escherichia coli for de Novo Production of Betaxanthins

Betalains are emerging natural pigments with high tinctorial strength and stability, physiological activities, and fluorescent properties for potential application in food, cosmetic, and pharmaceutical industries. Betalains including yellow betaxanthins and red betacyanins are mainly restricted in the Caryophyllales plants. To expand the availability of individual betaxanthins, here, we constructed an Escherichia coli BTA6 for de novo biosynthesis of betalamic acid. Using this strain as a monoculture platform, 14 yellow and 2 red betaxanthins were produced by feeding amino acids and amines. Furthermore, we constructed an l-histidine overproducing strain using chromosome engineering to deattenuate regulation and established a coculture system. After optimization of the initial inoculation ratios and fermentation conditions, the compatible and robust coculture system produced 287.69 mg/L of histidine-betaxanthin. This is the first report on de novo production of betaxanthins in engineered E. coli using glucose as a carbon source. Our work highlights the feasibility of microbial cell factories to produce individual betalains.

Majority sensing in synthetic microbial consortia

As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop a two-strain gene circuit that senses and responds to which strain is in the majority. This involves a co-repressive system in which each strain produces a signaling molecule that signals the other strain to down-regulate production of its own, orthogonal signaling molecule. This co-repressive consortium links gene expression to ratio of the strains rather than population size. Further, we control the cross-over point for majority via external induction. We elucidate the mechanisms driving these dynamics by developing a mathematical model that captures consortia response as strain fractions and external induction are varied. These results show that simple gene circuits can be used within multicellular synthetic systems to sense and respond to the state of the population.

Constructing E. coli Co-Cultures for De Novo Biosynthesis of Natural Product Acacetin

Modular co-culture engineering is an emerging approach for biosynthesis of complex natural products. In this study, microbial co-cultures composed of two and three Escherichia coli strains, respectively, are constructed for de novo biosynthesis of flavonoid acacetin, a value-added natural compound possessing numerous demonstrated biological activities, from simple carbon substrate glucose. To this end, the heterologous biosynthetic pathway is divided into different modules, each of which is accommodated in a dedicated E. coli strain for functional expression. After the optimization of the inoculation ratio between the constituent strains, the engineered co-cultures show a 4.83-fold improvement in production comparing to the mono-culture controls. Importantly, cultivation of the three-strain co-culture in shake flasks result in the production of 20.3 mg L^-1 acacetin after 48 h. To the authors' knowledge, this is the first report on acacetin de novo biosynthesis in a heterologous microbial host. The results of this work confirm the effectiveness of modular co-culture engineering for complex flavonoid biosynthesis.

Developing E. coli-E. coli co-cultures to overcome barriers of heterologous tryptamine biosynthesis

Tryptamine is an alkaloid compound with demonstrated bioactivities and is also a precursor molecule to many important hormones and neurotransmitters. The high efficiency biosynthesis of tryptamine from inexpensive and renewable carbon substrates is of great research and application significance. In the present study, a tryptamine biosynthesis pathway was established in a metabolically engineered E. coli-E. coli co-culture. The upstream and downstream strains of the co-culture were dedicated to tryptophan provision and conversion to tryptamine, respectively. The constructed co-culture was cultivated using either glucose or glycerol as carbon source for de novo production of tryptamine. The manipulation of the co-culture strains' inoculation ratio was adapted to balance the biosynthetic strengths of the pathway modules for bioproduction optimization. Moreover, a biosensor-assisted cell selection strategy was adapted to improve the pathway intermediate tryptophan provision by the upstream strain, which further enhanced the tryptamine biosynthesis. The resulting biosensor-assisted modular co-culture produced 194 ​mg/L tryptamine with a yield of 0.02 ​g/g glucose using shake flask cultivation. The findings of this work demonstrate that the biosensor-assisted modular co-culture engineering offers a new perspective for conducting microbial biosynthesis.

De novo biosynthesis of complex natural product sakuranetin using modular co-culture engineering

Flavonoids are a large family of plant and fungal natural products, among which many have been found to possess outstanding biological activities. Utilization of engineered microbes as surrogate hosts for heterologous biosynthesis of flavonoids has been investigated extensively. However, current microbial biosynthesis strategies mostly rely on using one microbial strain to accommodate the long and complicated flavonoid pathways, which presents a major challenge for production optimization. Here, we adapt the emerging modular co-culture engineering approach to rationally design, establish and optimize an Escherichia coli co-culture for de novo biosynthesis of flavonoid sakuranetin from simple carbon substrate glucose. Specifically, two E. coli strains were employed to accommodate the sakuranetin biosynthesis pathway. The upstream strain was engineered for pathway intermediate p-coumaric acid production, whereas the downstream strain converted p-coumaric acid to sakuranetin. Through step-wise optimization of the co-culture system, we were able to produce 29.7 mg/L sakuranetin from 5 g/L glucose within 48 h, which is significantly higher than the production by the conventional monoculture-based approach. The co-culture biosynthesis was successfully scaled up in a fed-batch bioreactor, resulting in the production of 79.0 mg/L sakuranetin. To our knowledge, this is the highest bioproduction concentration reported so far for de novo sakuranetin biosynthesis using the heterologous host E. coli. The findings of this work expand the applicability of modular co-culture engineering for addressing the challenges associated with heterologous biosynthesis of complex natural products. KEY POINTS: • De novo biosynthesis of sakuranetin was achieved using E. coli-E. coli co-cultures. • Sakuranetin production by co-cultures was significantly higher than the mono-culture controls. • The co-culture system was optimized by multiple metabolic engineering strategies. • The co-culture biosynthesis was scaled up in fed-batch bioreactor.

Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System

As synthetic biology and metabolic engineering tools improve, it is feasible to construct more complex microbial synthesis systems that may be limited by the machinery and resources available in an individual cell. Coculture fermentation is a promising strategy for overcoming these constraints by distributing objectives between subpopulations, but the primary method for controlling the composition of the coculture of production systems has been limited to control of the inoculum composition. We have developed a quorum sensing (QS)-based growth-regulation circuit that provides an additional parameter for regulating the composition of a coculture over the course of the fermentation. Implementation of this tool in a naringenin-producing coculture resulted in a 60% titer increase over a system that was optimized by varying inoculation ratios only. We additionally demonstrated that the growth control circuit can be implemented in combination with a communication module that couples transcription in one subpopulation to the cell-density of the other population for coordination of behavior, resulting in an additional 60% improvement in naringenin titer.

Microbial Coculture for Flavonoid Synthesis

Flavonoids are plant-derived natural products with human health-promoting benefits. The modularity and complexity of the flavonoid biosynthetic pathway allow us to leverage the metabolic characteristics of distinct microbial hosts and install structural functionalities beyond what monocultures can achieve. We discuss the promising future of applying microbial cocultures to improve the cost-efficiency and diversity of flavonoid biosynthesis.

Synthetic microbial consortia for small molecule production

Microbial consortia were designed for the production of small molecules with 'labor' being divided between two or more microorganisms. Examples of linear designs are substrate conversion preceding target molecule production or subdivision of two consecutive steps of target molecule production. Here, we review synthetic biology design approaches for microbial consortia based on ecological principles and microbial interactions that is, mutualism, and commensalism. Besides highlighting the technical challenges regarding industrial application of synthetic microbial consortia, we forecast the extension of the concept from binary linear to ternary linear and more complex microbial consortia in biotechnological applications. Microbial consortia are here reviewed and proposed as a rational solution toward feedstock accessibility as it has been shown for production of l-lysine, l-pipecolic acid and cadaverine from starch or production of fumarate from microcrystalline cellulose and alkaline pre-treated corn, or alternatively to establish new multi-step pathway for the production of rosmarinic acid from xylose and glucose.

Recent advances in modular co-culture engineering for synthesis of natural products

The microbial production of natural products has been traditionally accomplished in a single organism engineered to accommodate target biosynthetic pathways. Often times, such approaches result in large metabolic burdens as key cofactors, precursor metabolites and energy are channeled to pathways of structurally complex chemicals. Recently, modular co-culture engineering has emerged as a new approach to efficiently conduct heterologous biosynthesis and greatly enhance the production of natural products. This review highlights recent advances that leverage Escherichia coli-based modular co-culture engineering for making natural products. Potential future perspectives for studies in this promising field are addressed as well.

Balancing the non-linear rosmarinic acid biosynthetic pathway by modular co-culture engineering

Pathway balancing is a critical and common challenge for microbial biosynthesis using metabolic engineering approaches. Non-linear biosynthetic pathways, such as diverging and converging pathways, are particularly difficult for bioproduction optimization, because they require delicate balancing between all interconnected constituent pathway modules. The emergence of modular co-culture engineering offers a new perspective for biosynthetic pathways modularization and balancing, as the biosynthetic capabilities of individual pathway modules can be coordinated by flexible adjustment of the subpopulation ratio of the co-culture strains carrying the designated modules. This study developed microbial co-cultures composed of multiple metabolically engineered E. coli strains for heterologous biosynthesis of complex natural product rosmarinic acid (RA) whose biosynthesis involves a complex diverging-converging pathway. Our results showed that, compared with the conventional mono-culture strategy, the engineered two-strain co-cultures significantly improved the RA production. Further pathway modularization and balancing in the context of three-strain co-cultures resulted in additional production improvement. Moreover, metabolically engineered co-culture strains utilizing different carbon substrates were recruited to improve the three-strain co-culture stability. The optimized co-culture based on these efforts produced 172 mg/L RA, exhibiting 38-fold biosynthesis improvement over the parent strain used in mono-culture biosynthesis. The findings of this work demonstrate the strong potentials of modular co-culture engineering for overcoming the challenges of complex natural product biosynthesis involving non-linear pathways.