Abstract:Natural products, important sources of innovative drugs, food, spices and daily chemicals, are closely related to people’s healthy life. With the development and integration of modern biological and chemical technologies of natural products, the researches on biosynthesis of natural products have made great progresses in recent years. The biosynthetic pathways of a number of natural products have been analyzed. Many pathway enzymes and modifying enzymes involved in the biosynthesis of natural products have been mined and functionally characterized. Furthermore, genes encoding pathway enzymes have been introduced into chassis to construct cell factories producing natural products through synthetic biology technologies. Also, other biotechnologies including genome editing and genome mining, have been used in the biosynthesis of natural products. In order to further promote the development of researches on biosynthesis of natural products, we edited a Special Issue on the topic of “biosynthesis of natural products”, focusing on the researches progress in three aspects: the analysis of biosynthetic pathways of natural products, genome-wide mining and functional characterization of genes encoding tool enzymes, and the scale preparation of natural products by biosynthetic technology. Also included in this Special Issue was the prospect of the biosynthesis of natural products. This Special Issue can provide reference and guidance for the further development of natural product biosynthesis.

Abstract:Vitamin C is an essential vitamin for human beings. It has a huge market in the fields of food and pharmaceuticals. 2-keto-l-gulonic acid is an important precursor to produce vitamin C by microbial fermentation in industrial. In microbial fermentations, the l-sorbose pathway and the D-gluconate pathway have been the focus of research because of high yield. This article aims at stating recent research progress in dehydrogenases related to biosynthesis of vitamin C in the l-sorbose pathway and the D-gluconate pathway. The properties of dehydrogenase in terms of localization, substrate specificity, cofactors, and electron transport carrier are elaborated. And then, the main problems and strategies are reviewed in the l-sorbose pathway and in the D-gluconate pathway. Finally, future research on the dehydrogenases in the biosynthesis of vitamin C through l-sorbose pathway and D-gluconate pathway is discussed.

Abstract:Non-ribosomal peptide synthetases catalyze the biosynthesis of structurally and functionally diverse non-ribosomal peptide natural products, which have broad applications in pharmaceutical, agricultural, and industrial sectors. Engineered non-ribosomal peptide synthetases can be used to produce novel non-ribosomal peptides through combinatorial biosynthesis. This conforms to the concept of green chemistry, thus attracts increasing attention across the world. Herein, three different engineering strategies were summarized, and recent advances in this field were reviewed.

Abstract:Sucrose is a natural product occurs widely in nature. In living organisms such as plants, sucrose phosphate synthase (SPS) is the key rate-limiting enzyme for sucrose synthesis. SPS catalyzes the synthesis of sucrose-6-phosphate, which is further hydrolyzed by sucrose phosphatase to form sucrose. Researches on SPS in recent decades have been focused on the determination of enzymatic activity of SPS, the identification of the inhibitors and activators of SPS, the covalent modification of SPS, the carbohydrate distribution in plants regulated by SPS, the mechanism for promoting plant growth by SPS, the sweetness of fruit controlled by SPS, and many others. A systematic review of these aspects as well as the crystal structure and catalytic mechanism of SPS are presented.

Abstract:Methyltransferases (MTs) constitute a large group of enzymes that catalyze the transfer of a methyl moiety, most frequently from S-adenosyl-L-methionine, to their substrates. It plays an essential role in regulation of gene expression and synthesis of many natural compounds. Owing to its broad substrate spectrum, MTs make important contributions to diversify the spectrum of products through methylation modifications. Recently, great progress has been made in application of MTs for the biosynthesis of various natural products including phenylpropane compounds, fragrances, hormones and antibiotics, which is summarized in this review. Moreover, we highlighted the strategies of using MTs for efficient production and for expanding the diversity of these methylated natural products, and discussed the current challenges and future prospects in this area.

Abstract:Plant serine carboxypeptidase-like acyltransferases (SCPL-AT) have similar structural characteristics and high homology compared to the serine carboxypeptidase. They can transfer the acyl from acyl glucose esters to many natural products, participate in the acylation modification of plant secondary metabolites, enrich the structural diversity of natural products, and improve the physicochemical properties such as water solubility and stability of compounds. This review summarizes the structural characteristics, catalytic mechanism, functional characterization, and biocatalytic applications of SCPL-AT from plants. This will help to promote the functional characterization of these acyltransferase genes and the biosynthesis of useful plant secondary metabolites by synthetic biotechnology.

Abstract:Quercetin 3-O-glycosides (Q3Gs) are important members of quercetin glycosides with excellent pharmacological activities such as anti-oxidation, anti-inflammation, anti-cancer and anti-virus. Two representatives of Q3Gs, rutin and troxerutin, have been developed into clinical drugs, demonstrating Q3Gs have become one of the important sources of innovative drugs. However, the applications of Q3Gs in food and pharmaceutical industries are hampered by its poor bioavailability. Of the known means, selective acylation modification of Q3Gs through enzymatic catalysis to obtain Q3G esters is one of the effective ways to improve its bioavailability. Herein, the enzyme-mediated acylation of Q3Gs were reviewed in details, focusing on the four tool enzymes (acyltransferases, lipases, proteases and esterases) and the whole-cell mediated biotransformation, as well as the effect of acylations on the biological activities of Q3Gs. Furthermore, the highly efficient synthesis and diversification of acylated site for Q3G esters were also discussed. Taken together, this review provides a new perspective for further structural modifications of Q3Gs towards drug development.

Abstract:Glycosidases are widely used in food and pharmaceutical industries due to its ability to hydrolyze the glycosidic bonds of various sugar-containing compounds including glycosides, oligosaccharides and polysaccharides to generate derivatives with important physiological and pharmacological activity. While glycosidases often need to be used under high temperature to improve reaction efficiency and reduce contamination, most glycosidases are mesophilic enzymes with low activity under industrial production conditions. It is therefore critical to improve the thermo-stability of glycosidases. This review summarizes the recent advances achieved in engineering the thermo-stability of glycosidases using strategies such as directed evolution, rational design and semi-rational design. We also compared the pros and cons of various techniques and discussed the future prospects in this area.

Abstract:Medicinal natural products derived from plants are usually of low content and difficult to extract and isolate. Moreover, these compounds are structurally complex, making it difficult to obtain them by environmental unfriendly chemical synthesis. Biosynthesis of medicinal natural products through synthetic biology is a novel, environment-friendly and sustainable approach. Taking terpenoids (ginsenosides, paclitaxel, artemisinin, tanshinones), alkaloids (vincristine and morphine), and flavonoids (breviscapine) as examples, this review summarizes the advances of the biosynthetic pathways and synthetic biology strategies of plant-derived medicinal natural products. Moreover, we introduce the key technologies and methods of synthetic biology used in the research of medicinal natural products, and provide future prospects in this area.

Abstract:Cadinanes are a class of bicyclic sesquiterpenes with complex stereochemistry and broad pharmacological activities, such as antibacterial, anti-inflammatory, and hypoglycemic activities. To date, structurally diverse and bioactive cadinane sesquiterpenes have been isolated and identified from a variety of plants and microorganisms. Moreover, deeper understandings on cadinane sesquiterpene synthases have been made. This article categorized the 124 new cadinanes which were published in the literatures in the past four years (2017–2020) into five structural types, and presented their pharmacological activities. We also illustrated the elucidation of the biosynthetic pathways for typical cadinanes, summarized the research progress on cadinane sesquiterpene synthases. Finally, current challenges and future prospects were proposed and discussed.

Abstract:Phytocannabinoids are bioactive terpenoids that are exclusive to Cannabis sativa L. The main pharmacologically active phytocannabinoids are Δ9-tetrahydrocannabinol and cannabidiol, both target endogenous cannabinoid receptors. Δ9-tetrahydrocannabinol and cannabidiol have extensive therapeutic potential due to their participation in many physiological and pathological processes in human body by activating the endocannabinoid system. At present, Δ9-tetrahydrocannabinol, cannabidiol and their analogues or combination preparations are used to treat epilepsy, vomiting in patients with cancer chemotherapy, spasticity in multiple sclerosis and relieve neuropathic pain and pain in patients with advanced cancer. With the further exploration of the application value of Δ9-tetrahydrocannabinol and cannabidiol as well as the increasing demand for standardization of pharmaceutical preparations, it is imminent to achieve large-scale production of Δ9-tetrahydrocannabinol and cannabidiol in the pharmaceutical industry. In this article, pharmacological research progress of phytocannabinoids in recent years, biosynthetic pathways of phytocannabinoids and the mechanism of key enzymes as well as various product development strategies of cannabinoids in pharmaceutical industry are reviewed. By exploring the potential of synthetic biology as an alternative strategy for the source of phytocannabinoids, it will provide a theoretical basis for the research and development of microbial engineering for cannabinoids synthesis, and promote the large-scale production of medicinal cannabinoids.

Abstract:Since synthetic pigments are potentially harmful to human health, natural ones such as bixin, one of the carotenoids, are favored. As the second widely used natural pigment in the world, there is significant interest in the biosynthetic pathway of bixin which has not been fully elucidated. This review summarizes the chemical properties, extraction methods, biosynthetic pathway and application of bixin. In addition, we compared the difference between traditional extraction methods and new extraction techniques. Moreover, we described the genes involved in the biosynthetic pathway of bixin and the effects of abiotic stress on the biosynthesis of bixin, and discussed the application of bixin in food, pharmaceutical and chemical industries. However, the researches on bixin biosynthesis pathway are mostly carried out at the transcriptome level and most of the gene functions have not been elucidated. Therefore, we propose to characterize the entire bixin biosynthetic pathway using techniques of genomics, bioinformatics, and phytochemistry. This will help facilitate the synthetic biology research of bixin and development of bixin into new drugs.

Abstract:Aromatic compounds make up a large part of fragrances and are traditionally produced by chemical synthesis and direct extraction from plants. Chemical synthesis depends on petroleum resources and has disadvantages such as causing environment pollutions and harsh reaction conditions. Due to the low content of aromatic compounds in plants and the low yield of direct extraction, plant extractions require large amounts of plant resources that occupy arable land. In recent years, with the development of metabolic engineering and synthetic biology, microbial synthesis of aromatic compounds from renewable resources has become a promising alternative approach to traditional methods. This review describes the research progress on the synthesis of aromatic fragrances by model microorganisms such as Escherichia coli or yeast, including the synthesis of vanillin through shikimic acid pathway and the synthesis of raspberry ketone through polyketide pathway. Moreover, this review highlights the elucidation of native biosynthesis pathways, the construction of synthetic pathways and metabolic regulation for the production of aromatic fragrances by microbial fermentation.

Abstract:Plant-derived aromatic natural products have important medicinal value and can be made into pharmaceutical and healthcare products with antibacterial, anti-inflammatory, analgesic, anti-oxidative, insecticidal and anthelmintic, expectorant and cough suppressant, tranquilizer and antitumor effects. However, the low content of aromatic natural products in plants and the difficulty and high costs in extraction and purification hampered its large-scale production and application. Recent advances in synthetic biology and metabolic engineering have enabled the tailor-made production of aromatic natural products using engineered microbial cell factories. This review summarizes the categories, the synthetic pathways, the key enzymes and the synthetic biology strategies for production of aromatic natural products, and discusses the challenges and opportunities in this area.

Abstract:Podophyllotoxin (PTOX) is an aryl-tetralin lignan of plant origin found in some species of Podophyllum such as Dysosma versipellis, Diphylleia sinensis, and Sinopodophyllum hexandrum. Etoposide and teniposide are produced semisynthetically from PTOX and used clinically to treat several forms of cancer. As a typical representative of new drug discovery from natural products, the production of PTOX solely depends on extraction from plants, resulting in severe contradiction between supply and demand. With the advantages of unconstrained resources and eco-friendly reaction conditions, biosynthesis method has become a trend in the production of PTOX and its derivatives. In this review, we summarize the research progress of PTOX biosynthesis in plants and expound the functions of the key enzymes as well as their subcellular location. The synthetic biology for production of PTOX intermediates in a tobacco chassis is also introduced. Finally, the heterologous expression and biotransformation of PTOX in microorganisms is summarized, which sets the foundation for the efficient microbial production of PTOX using cell factories.

Abstract:Triptolide has wide clinical applications due to its anti-inflammatory, anti-tumor and immunosuppressive activities. In this study, we investigated the effect of blocking isopentenyl pyrophosphate (IPP) translocation on the biosynthesis of triptolide by exogenously adding d,l-glyceraldehyde (DLG) to the suspension cells of Ttripterygium wilfordii at different stages (7 d, 14 d). Subsequently, the cell viability, biomass accumulation, triptolide contents, as well as the profiles of the key enzyme genes involved in the upstream pathway of triptolide biosynthesis, were analyzed. The results showed that IPP translocation is involved in the biosynthesis of triptolide. IPP is mainly translocated from the plastid (containing the MEP pathway) to the cytoplasm (containing the MVA pathway) in the early stage of the culture, but reversed in the late stage. Blocking the translocation of IPP affected the expression of key enzyme genes involved in the upstream pathway of triptolide, which in turn affected the accumulation of triptolide. Understanding the characteristics and mechanism of IPP translocation provides a theoretical basis for further promoting triptolide biosynthesis through synthetic biology.

Abstract:Plant polyphenols are phenylpropanoid derivatives including phenolic acids, stilbenes, curcumins and flavonoids. These compounds display a variety of biological and pharmacological activities such as antioxidation, vasorelaxation, anti-coagulation, anti-inflammation, anti-tumor and anti-virus, conferring a huge application potential in the sectors of drugs, foods, cosmetics, and chemicals. Microorganisms have become important hosts for heterologous synthesis of natural products due to the advantages of fast growth, easiness of culture and industrial operation. In recent years, the development of synthetic biology has boosted the microbial synthesis of plant natural products, achieving substantial progress. In this review, we summarize the synthesis of plant polyphenols in engineered Escherichia coli, Saccharomyces cerevisiae and other microorganisms equipped with the designed biosynthetic pathways of polyphenols. We also discuss the optimization strategies such as precursor engineering, dynamic regulation, and co-cultivation to improve the production of polyphenols and propose future prospects for polyphenol pathway engineering.

Abstract:Curcumin is exclusively isolated from Zingiberaceae plants with a broad spectrum of bioactivities. In the present study, we used the diketide-CoA synthase (DCS) and curcumin synthase (CURS) genes to construct a non-natural fusion gene encoding diketide-CoA synthase::curcumin synthase (DCS::CURS). This fusion protein, together with the acetyl coenzyme A carboxylase (ACC) and the 4-coumarate coenzyme A ligase (4CL), were introduced into Escherichia coli for the production of curcumin from ferulic acid. The process is divided into two stages, the growth stage using LB medium and the fermentation stage using the modified M9 medium. The yield of curcumin reached 386.8 mg/L by optimizing the induction of protein expression in the growth stage, and optimizing the inoculum volume, medium composition and fermentation time in the fermentation stage, as well as the addition of macroporous resin AB-8 into the second medium to attenuate the toxicity of the end product. The exploitation of the non-natural fusion protein DCS::CURS for the production of curcumin provides a new alternative to further promoting the production of curcumin and the related analogues.

Abstract:Terpenoids are a group of structurally diverse compounds with good biological activities and versatile functions such as anti-cancer and immunity-enhancing effects, and are widely used in food, healthcare and medical industries. Facilitated by the increasing understandings on the natural biosynthetic pathways of terpenoids in recent years, Saccharomyces cerevisiae has been engineered into high-yield strains for production of a variety of terpenoids, some of which have reached or become close to the level required by industrial production. In this connection, synthetic biology driven biotechnological production of terpenoids has become a promising alternative to chemical synthesis and traditional extraction approaches. This article summarizes the recent process in engineering S. cerevisiae for terpenoids biosynthesis, highlighting the effect of synthetic biology strategies by taking a couple of typical terpenoids as examples.

Abstract:Triterpenoids are a class of natural products of great commercial value that are widely used in pharmaceutical, health care and cosmetic industries. The biosynthesis of triterpenoids relies on the efficient synthesis of squalene epoxide, which is synthesized from the NADPH dependent oxidation of squalene catalyzed by squalene epoxidase. We screened squalene epoxidases derived from different species, and found the truncated squalene epoxidase from Rattus norvegicus (RnSETC) showed the highest activity in engineered Escherichia coli. Further examination of the effect of endogenous cytochrome P450 reductase like (CPRL) proteins showed that overexpression of NADH: quinone oxidoreductase (WrbA) under Lac promoter in a medium-copy number plasmid increased the production of squalene epoxide by nearly 2.5 folds. These results demonstrated that the constructed pathway led to the production of squalene epoxide, an important precursor for the biosynthesis of triterpenoids.

Abstract:Carrimycin (CAM) is a new antibiotics with isovalerylspiramycins (ISP) as its major components. It is produced by Streptomyces spiramyceticus integrated with a heterogenous 4″-O-isovaleryltransferase gene (ist). However, the present CAM producing strain carries two resistant gene markers, which makes it difficult for further genetic manipulation. In addition, isovalerylation of spiramycin (SP) could be of low efficiency as the ist gene is located far from the SP biosynthesis gene cluster. In this study, ist and its positive regulatory gene acyB2 were inserted into the downstream of orf54 gene neighboring to SP biosynthetic gene cluster in Streptomyces spiramyceticus 1941 by using the CRISPR-Cas9 technique. Two new markerless CAM producing strains, 54IA-1 and 54IA-2, were obtained from the homologous recombination and plasmid drop-out. Interestingly, the yield of ISP in strain 54IA-2 was much higher than that in strain 54IA-1. Quantitative real-time PCR assay showed that the ist, acyB2 and some genes associated with SP biosynthesis exhibited higher expression levels in strain 54IA-2. Subsequently, strain 54IA-2 was subjected to rifampicin (RFP) resistance selection for obtaining high-yield CAM mutants by ribosome engineering. The yield of ISP in mutants resistant to 40 μg/mL RFP increased significantly, with the highest up to 842.9 μg/mL, which was about 6 times higher than that of strain 54IA-2. Analysis of the sequences of the rpoB gene of these 7 mutants revealed that the serine at position 576 was mutated to alanine existed in each sequenced mutant. Among the mutants carrying other missense mutations, strain RFP40-6-8 which carries a mutation of glutamine (424) to leucine showed the highest yield of ISP. In conclusion, two markerless novel CAM producing strains, 54IA-1 and 54IA-2, were successfully developed by using CRISPR-Cas9 technique. Furthermore, a novel CAM high-yielding strain RFP40-6-8 was obtained through ribosome engineering. This study thus demonstrated a useful combinatory approach for improving the production of CAM.

Abstract:Streptomyces are major sources of bioactive natural products. Genome sequencing reveals that Streptomyces have great biosynthetic potential, with an average of 20–40 biosynthetic gene clusters each strain. However, most natural products from Streptomyces are produced in low yields under regular laboratory cultivation conditions, which hamper their further study and drug development. The production of natural products in Streptomyces is controlled by the intricate regulation mechanisms. Manipulation of the regulatory systems that govern secondary metabolite production will strongly facilitate the discovery and development of natural products of Streptomyces origin. In this review, we summarize progresses in pathway-specific regulators from Streptomyces in the last five years and highlight their role in improving the yields of corresponding natural products.

Abstract:Angucyclines/angucyclinones are a large group of polycyclic aromatic polyketides and their producers are widely distributed in nature. This family of natural products attracts great attention because of their diverse biological activities and unique chemical structures. With the development of synthetic biology and the exploitation of the actinomycetes from previously unexplored environments, angucyclines/angucyclinones-like natural products with new skeletons were continuously discovered, thus enriching the structural diversity of this family. In this review we summarize the new angucyclines/angucyclinones analogues discovered in the last decade (2010–2020) by using different strategies, such as changing cultivation conditions, genetic modification, genome mining, bioactivity-guided compound isolation, and fermentation of actinomycetes from underexplored environments. We also discuss the role of synthetic biology in the discovery and development of new compounds of the angucycline/angucyclinone family.

Abstract:Bioactive peptides play important roles in promoting human health, such as lowering blood pressure, blood sugar and blood lipid, anti-obesity, and anti-cancer. Thus, exploring functional bioactive peptides and developing efficient production technologies are of crucial importance. Herein, we review the development of function discovery and production technology for natural bioactive peptides. Presently, the top-down and bottom-up approaches are mainly used for the function discovery and production of natural active peptides. The top-down approach includes the direct extraction and identification for functional discovery, and the direct extraction, enzymatic hydrolysis and microbial fermentation for production. The bottom-up approach includes the polypeptide modification and database mining for functional discovery, and the chemical synthesis, enzyme synthesis, recombinant expression and cell-free synthesis for production. The top-down approach is usually associated with complicated process, lower efficiency, higher cost, harder quality control, and uncertain functionality, while the bottom-up approach is more suitable for the development of peptide drugs but difficult to be used for functional foods. With the technology development of sequencing and mass spectrometry, it is easier to obtain the proteomic information of various organisms at the molecular level. Based on the proteomic information, the top-down and bottom-up approaches can be combined to overcome the disadvantages of using these two approaches alone, thus providing a new strategy for the rapid development and production of natural active peptides.