De Novo Production of Plant 4'-Deoxyflavones Baicalein and Oroxylin A from Ethanol in Crabtree-Negative Yeast

Novel Insights Into Naringenin: A Multifaceted Exploration of Production, Synthesis, Health Effects, Nanodelivery Systems, and Molecular Simulation

Naringenin, a flavonoid widely present in citrus fruits, has garnered considerable attention due to its diverse biological activities and health-promoting benefits. As research on naringenin advances, the application scope of naringenin has significantly expanded. This paper provides a systematic overview of the production and synthesis methods of naringenin, focusing especially on the application of green extraction techniques and the strategies for constructing microbial metabolic engineering. Naringenin not only achieves its diverse biological activities including antioxidant, antiinflammatory, and glucolipid metabolism regulation through multiple mechanisms but also modulates the balance of gut microbiota, thereby mediating synergistic health effects via the host-microbial metabolic axis. Given the low oral bioavailability of naringenin, various nanodelivery systems have been developed to improve its bioavailability. Meanwhile, molecular simulation techniques elucidate the binding conformation characteristics with receptors at the molecular level, providing novel insights into its mechanisms of action. In conclusion, this review seeks to offer a theoretical basis and future directions for further research and application of naringenin.

Engineering metabolic flux for the microbial synthesis of aromatic compounds

Microbial cell factories have emerged as a sustainable alternative to traditional chemical synthesis and plant extraction methods for producing aromatic compounds. However, achieving economically viable production of these compounds in microbial systems remains a significant challenge. This review summarizes the latest advancements in metabolic flux regulation during the microbial production of aromatic compounds, providing an overview of its applications and practical outcomes. Various strategies aimed at improving the utilization of extracellular substrates, enhancing the efficiency of synthetic pathways for target products, and rewiring intracellular metabolic networks to boost the titer, yield, and productivity of aromatic compounds are discussed. Additionally, the persistent challenges in this field and potential solutions are highlighted.

Rational design and characterization of enhanced alcohol-inducible synthetic promoters in Pichia pastoris

The C1 and C2 alcohols hold great promise as substrates for biomanufacturing due to their low cost and rich resources. Pichia pastoris is considered a preferred host for methanol and ethanol bioconversion due to its natural utilization of methanol and ethanol. However, the scarcity of strong and tightly regulated alcohol-inducible promoters limits its extended use. This study aimed to develop enhanced methanol- and ethanol-inducible promoters capable of improving gene expression in P. pastoris. Rational design strategies were employed to rewire the upstream regulatory sequence of the methanol-inducible PAOX1, generating several high-strength methanol-inducible promoters with a stringent regulatory pattern. Eleven strong promoters were identified from 36 endogenous ethanol-inducible candidates recognized from transcriptome analysis. Core promoter regions, the crucial element influencing transcriptional strength, were also characterized. Five high-activity core promoters were then combined with four upstream regulatory sequences of high-strength promoters, resulting in four groups of synthetic promoters. Ultimately, the highly active methanol-inducible PA13 and ethanol-inducible P0688 and PsynIV-5 were selected for the expression of an α-amylase and yielded enzyme activity 1.6, 2.6, and 4.5 times higher as compared to that of PAOX1. This work expands the genetic toolkit available for P. pastoris, providing more precise and efficient options for regulating gene expression. It benefits the use of P. pastoris as an efficient platform for the C1 and C2 alcohol-based biotransformation in industrial biotechnology.IMPORTANCEP. pastoris represents a preferred microbial host for the bio-utilization of C1 and C2 alcohols that are regarded as renewable carbon sources based on clean energy. However, lack of efficient and regulated expression tools highly limits the C1 and C2 alcohols based bioproduction. By exploring high-strength and strictly regulated alcohol-inducible promoters, this study expands the expression toolkit for P. pastoris on C1 and C2 alcohols. The newly developed methanol-inducible PA13 and ethanol-inducible PsynIV-5 demonstrate significantly higher expression levels than the commercial PAOX1 system. The endogenous and synthetic promoter series established in this study provides new construction references and alternative tools for expression control in P. pastoris for C1 and C2 alcohols based biomanufacturing.

Advances in Flavonoid and Derivative Biosynthesis: Systematic Strategies for the Construction of Yeast Cell Factories

Flavonoids, a significant group of natural polyphenolic compounds, possess a broad spectrum of pharmacological effects. Recent advances in the systematic metabolic engineering of yeast cell factories (YCFs) provide new opportunities for enhanced flavonoid production. Herein, we outline the latest research progress on typical flavonoid products in YCFs. Advanced engineering strategies involved in flavonoid biosynthesis are discussed in detail, including enhancing precursor supply, cofactor engineering, optimizing core pathways, eliminating competitive pathways, relieving transport limitations, and dynamic regulation. Additionally, we highlight the existing problems in the biosynthesis of flavonoid glucosides in yeast, such as endogenous degradation of flavonoid glycosides, substrate promiscuity of UDP-glycosyltransferases, and an insufficient supply of UDP-sugars, with summaries on the corresponding solutions. Discussions also cover other typical postmodifications like prenylation and methylation, and the recent biosynthesis of complex flavonoid compounds in yeast. Finally, a series of advanced technologies are envisioned, i.e., semirational enzyme engineering, ML/DL algorithn, and systems biology, with the aspiration of achieving large-scale industrial production of flavonoid compounds in the future.

Microbial conversion of ethanol to high-value products: progress and challenges

Industrial biotechnology heavily relies on the microbial conversion of carbohydrate substrates derived from sugar- or starch-rich crops. This dependency poses significant challenges in the face of a rising population and food scarcity. Consequently, exploring renewable, non-competing carbon sources for sustainable bioprocessing becomes increasingly important. Ethanol, a key C2 feedstock, presents a promising alternative, especially for producing acetyl-CoA derivatives. In this review, we offer an in-depth analysis of ethanol's potential as an alternative carbon source, summarizing its distinctive characteristics when utilized by microbes, microbial ethanol metabolism pathway, and microbial responses and tolerance mechanisms to ethanol stress. We provide an update on recent progress in ethanol-based biomanufacturing and ethanol biosynthesis, discuss current challenges, and outline potential research directions to guide future advancements in this field. The insights presented here could serve as valuable theoretical support for researchers and industry professionals seeking to harness ethanol's potential for the production of high-value products.

Programmable Biosynthesis of Plant-Derived 4'-Deoxyflavone Glycosides by an Unconventional Yeast Consortium

Previous data established 4'-deoxyflavone glycosides (4'-DFGs) as important pharmaceutical components in the roots of rare medical plants like Scutellaria baicalensis Georgi. Extracting these compounds from plants involves land occupation and is environmentally unfriendly. Therefore, a modular ("plug-and-play") yeast-consortium platform is developed to synthesize diverse 4'-DFGs de novo. By codon-optimizing glycosyltransferase genes from different organisms for Pichia pastoris, six site-specific glycosylation chassis are generated to be capable of biosynthesizing 18 different 4'-DFGs. Cellular factories showed increased 4'-DFG production (up to 18.6-fold) due to strengthened synthesis of UDP-sugar precursors and blocked hydrolysis of endogenous glycosides. Co-culturing upstream flavone-synthesis-module cells with downstream glycoside-transformation-module cells alleviated the toxicity of 4'-deoxyflavones and enabled high-level de novo synthesis of 4'-DFGs. Baicalin is produced at the highest level (1290.0 mg L-1) in a bioreactor by controlling the consortium through carbon-source shifting. These results provide a valuable reference for biosynthesizing plant-derived 4'-DFGs and other glycosides with potential therapeutic applications.

Upcycling CO2 into succinic acid via electrochemical and engineered Escherichia coli

Converting CO2 into value-added chemicals still remains a grand challenge. Succinic acid has long been considered as one of the top building block chemicals. This study reported efficiently upcycling CO2 into succinic acid by combining between electrochemical and engineered Escherichia coli. In this process, the Cu-organic framework catalyst was synthesized for electrocatalytic CO2-to-ethanol conversion with high Faradaic efficiency (FE, 84.7 %) and relative purity (RP, 95 wt%). Subsequently, an engineered E. coli with efficiently assimilating CO2-derived ethanol to produce succinic acid was constructed by combining computational design and metabolic engineering, and the succinic acid titer reached 53.8 mM with the yield of 0.41 mol/mol, which is 82 % of the theoretical yield. This study effort to link the two processes of efficient ethanol synthesis by electrocatalytic CO2 and succinic acid production from CO2-derived ethanol, paving a way for the production of succinic acid and other value-added chemicals by converting CO2 into ethanol.

De Novo Synthesis of Chrysin in Saccharomyces cerevisiae

Chrysin, a flavonoid, has been found to have been widely used in the health food field. But at present, chrysin production is hindered by the low availability of precursors and the lack of catalytic enzymes with high activity. Therefore, ZmPAL was initially screened to synthesize trans-cinnamic acid with high catalytic activity and specificity. To enhance the supply of precursors, the shikimic acid and chorismic acid pathway genes were overexpressed. Besides, the expression of the intracellular and mitochondrial carbon metabolism genes CIT, MAC1/3, CTP1, YHM2, RtME, and MDH was enhanced to increase the intracellular acetyl-CoA content. Chrysin was synthesized through a novel gene combination of ScCPR-EbFNSI-1 and PcFNSI. Finally, de novo synthesis of chrysin was achieved, reaching 41.9 mg/L, which is the highest reported concentration to date. In summary, we identified efficient enzymes for chrysin production and increased it by regulating acetyl-CoA metabolism in mitochondria and the cytoplasm, laying a foundation for future large-scale production.

Advances in pharmacology, biosynthesis, and metabolic engineering of Scutellaria-specialized metabolites

Scutellaria Linn., which belongs to the family Lamiaceae, is a commonly used medicinal plant for heat clearing and detoxification. In particular, the roots of S. baicalensis and the entire herb of S. barbata have been widely used in traditional medicine for thousands of years. The main active components of Scutellaria, including: baicalein, wogonin, norwogonin, scutellarein, and their glycosides have potential or existing drug usage. However, the wild resources of Scutellaria plants have been overexploited, and degenerated germplasm resources cannot fulfill the requirements of chemical extraction and clinical usage. Metabolic engineering and green production via microorganisms provide alternative strategies for greater efficiency in the production of natural products. Here, we review the progress of: pharmacological investigations, multi-omics, biosynthetic pathways, and metabolic engineering of various Scutellaria species and their active compounds. In addition, based on multi-omics data, we systematically analyze the phylogenetic relationships of Scutellaria and predict candidate transcription factors related to the regulation of active flavonoids. Finally, we propose the prospects of directed evolution of core enzymes and genome-assisted breeding to alleviate the shortage of plant resources of Scutellaria. This review provides important insights into the sustainable utilization and development of Scutellaria resources.

Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production

Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.

Genetic tools for metabolic engineering of Pichia pastoris

The methylotrophic yeast Pichia pastoris (also known as Komagataella phaffii) is widely used as a yeast cell factory for producing heterologous proteins. Recently, it has gained attention for its potential in producing chemicals from inexpensive feedstocks, which requires efficient genetic engineering platforms. This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P. pastoris. The topics cover promoters, terminators, plasmids, genome integration sites, and genetic editing systems, with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools. Additionally, this review highlights the prospects of multiplex genome integration, fine-tuning gene expression, and single-base editing systems. Overall, the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P. pastoris.

Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories

Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.

Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level

Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.

Biotransformation to synthesize the methylated derivatives of baicalein using engineered Escherichia coli

Oroxylin A and negletein are flavonoid compounds existing in plants, with excellent pharmacological activities such as anti-inflammatory, anti-viropexis, and anti-cancer. Nevertheless, the natural abundance of these compounds in plants is extremely low. Here, a biotransformation pathway was developed in engineered strains to synthesize oroxylin A and negletein from baicalin by using the crude extract of Scutellaria baicalensis as the substrate. Briefly, the precursor baicalin in this crude extract was hydrolyzed by a β-glucuronidase to form the intermediate baicalein, then O-methyltransferases utilize this intermediate to synthesize oroxylin A and negletein. Through screening strains and carbon sources, regulating intercellular S-adenosyl L-methionine synthesis, and optimizing culture conditions, the titers of the target products increased gradually, with 188.0 mg/L for oroxylin A and 222.7 mg/L for negletein finally. The study illustrates a convenient method to synthesize oroxylin A and negletein from a low-cost substrate, paving the way for the mass acquisition and further bioactivities development and utilization of these rare and high-value compounds.

Biochemical Characterization of a Flavone Synthase I from Daucus carota and its Application for Bioconversion of Flavanones to Flavones

In this study, we studied the biochemical characterization of flavone synthase I from Daucus carota (DcFNS I) and applied it with flavonoid 6-hydroxylase from Scutellaria baicalensis (SbCYP) to convert flavanones to flavones. The recombinant DcFNS I was expressed in the form of the glutathione-S-transferase fusion protein. Rather than taxifolin, naringenin, pinocembrin, and eriodictyol were accepted as substrates. The optimal temperature and pH for reaction in vitro were 35 °C and 7.5, respectively, and 2-oxoglutarate was essential in the assay system. Co²⁺, Cu²⁺, Mn²⁺, Ni²⁺, and Zn²⁺ were not substitutes for Fe²⁺. EDTA and pyruvic acid inhibited the activity, except for Fe³⁺. Kinetic analysis revealed that the V_max and k_cat values of the recombinant DcFNS I against naringenin were 0.183 nmol mg^-1 s^-1 and 0.0121 s^-1, and 0.175 nmol mg^-1 s^-1 and 0.0116 s^-1 against pinocembrin. However, the recombinant DcFNS I had a higher affinity for naringenin than pinocembrin, with k_M values for each of 0.076 mM and 0.174 mM respectively. Thus, it catalyzed naringenin more efficiently than pinocembrin. Subsequently, using an Escherichia coli and Saccharomyces cerevisiae co-culture system, we successfully converted naringenin and pinocembrin to scutellarein and baicalein respectively. In a synthetic complete medium, the titers of scutellarein and baicalein reached 5.63 mg/L and 0.78 mg/L from 200 mg/L precursors.

Optimization of Pinocembrin Biosynthesis in Saccharomyces cerevisiae

The flavonoid pinocembrin and its derivatives have gained increasing interest for their benefits on human health. While pinocembrin and its derivatives can be produced in engineered Saccharomyces cerevisiae, yields remain low. Here, we describe novel strategies for improved de novo biosynthesis of pinocembrin from glucose based on overcoming existing limitations in S. cerevisiae. First, we identified cinnamic acid as an inhibitor of pinocembrin synthesis. Second, by screening for more efficient enzymes and optimizing the expression of downstream genes, we reduced cinnamic acid accumulation. Third, we addressed other limiting factors by boosting the availability of the precursor malonyl-CoA, while eliminating the undesired byproduct 2',4',6'-trihydroxy dihydrochalcone. After optimizing cultivation conditions, 80 mg/L pinocembrin was obtained in a shake flask, the highest yield reported for S. cerevisiae. Finally, we demonstrated that pinocembrin-producing strains could be further engineered to generate 25 mg/L chrysin, another interesting flavone. The strains generated in this study will facilitate the production of flavonoids through the pinocembrin biosynthetic pathway.

Efficient biosynthesis of 3-hydroxypropionic acid from ethanol in metabolically engineered Escherichia coli

Engineering microbial cell factories to convert CO₂-based feedstock into chemicals and fuels provide a feasible carbon-neutral route for the third-generation biorefineries. Ethanol became one of the major products of syngas fermentation by engineered acetogens. The key building block chemical 3-hydroxypropionic acid (3-HP) can be synthesized from ethanol by the malonyl-CoA pathway with CO₂ fixation. In this study, the effect of two ethanol consumption pathways on 3-HP synthesis were studied as well as the effect of TCA cycle, gluconeogenesis pathway, and transhydrogenase. And the 3-HP synthesis pathway was also optimized. The engineered strain synthesized 1.66 g/L of 3-HP with a yield of 0.24 g/g. Furthermore, the titer and the yield of 3-HP increased to 13.17 g/L and 0.57 g/g in the whole-cell biocatalysis system. This study indicated that ethanol as feedstock had the potential to synthesize 3-HP, which provided an alternative route for future biorefinery.

Microbial cell factories for the production of flavonoids-barriers and opportunities

Flavonoids are natural plant products with important nutritional value, health-promoting benefits, and therapeutic potential. The use of microbial cell factories to generate flavonoids is an appealing option. The microbial biosynthesis of flavonoids is compared to the classic plant extract approach in this review, and the pharmaceutical applications were presented. This paper summarize approaches for effective flavonoid biosynthesis from microorganisms, and discuss the challenges and prospects of microbial flavonoid biosynthesis. Finally, the barriers and strategies for industrial bio-production of flavonoids are highlighted. This review offers guidance on how to create robust microbial cell factories for producing flavonoids and other relevant chemicals.