Complete biosynthesis of opioids in yeast

Mechanism and engineering of endoplasmic reticulum-localized membrane protein folding in Saccharomyces cerevisiae

Correct folding of endoplasmic reticulum (ER)-localized membrane proteins, such as cytochrome P450, endows a synthetic biology host with crucial catalytic functions, which is of vital importance in the field of metabolic engineering and synthetic biology. However, due to complexed interaction with cellular membrane environment and other proteins (e.g., molecular chaperone) regulation, a substantial proportion of heterologous membrane proteins cannot be properly folded in the ER of Saccharomyces cerevisiae, a widely used synthetic biology host. In this review, we first introduce the four steps in membrane protein folding process and the affecting factors including the amino acid sequence of membrane protein, the folding process, molecular chaperones, quality control mechanism, and lipid environment in S. cerevisiae. Then, we summarize the metabolic engineering strategies to enhance the correct folding of ER-localized membrane proteins, such as by engineering and de novel design of membrane protein, regulation of the co-translational folding process, co-expression of molecular chaperones, modulation of ER quality, and lipids engineering. Finally, we discuss the limitations of current strategies and propose future research directions to address the key issues.

Exploration and mutagenesis of the germacrene A synthase from Solidago canadensis to enhance germacrene A production in E. coli

β-elemene is an effective anti-cancer component which has been widely used in clinic. However, it still relies on the extraction from the Chinese medicine plant Curcuma wenyujin, which seriously limits its application. Synthetic biology offers a promising approach to satisfy its supply. β-elemene is derived from germacrene A (GA), which is synthesized by germacrene A synthase (GAS), through Cope rearrangement under heat condition instead of enzymatic reaction. In this study, an effective germacrene A synthase (ScGAS) was identified from Solidago canadensis which could produce GA when expressed in E. coli. By introducing the heterogeneous MVA pathway to enrich the FPP pool, the strain yielded 147 mg/L of GA in shake flasks which represented 2.98-fold improvement over the initial one. Moreover, combining molecular docking with phylogeny analysis of ScGAS largely narrowed down the category of its key residues' mutagenesis. The Y376L mutant showed the highest yield of 487 mg/L which was almost 10-fold higher than the initial yield. These results indicate that diverting the metabolism of the host and enzyme mutagenesis based on the combination of molecular docking and phylogeny analysis are of great value to constructing terpenoids chassis.

Unravelling fungal genome editing revolution: pathological and biotechnological application aspects

Fungi represent a broad and evolutionarily unique group within the eukaryotic domain, characterized by extensive ecological adaptability and metabolic versatility. Their inherent biological intricacy is evident in the diverse and dynamic relationships they establish with various hosts and environmental niches. Notably, fungi are integral to disease processes and a wide array of biotechnological innovations, highlighting their significance in medical, agricultural, and industrial domains. Recent advances in genetic engineering have revolutionized fungal research, with CRISPR/Cas emerging as the most potent and versatile genome editing platform. This technology enables precise manipulation of fungal genomes, from silencing efflux pump genes in Candida albicans (enhancing antifungal susceptibility) to targeting virulence-associated sirtuins in Aspergillus fumigatus (attenuating pathogenicity). Its applications span gene overexpression, multiplexed mutagenesis, and secondary metabolite induction, proving transformative for disease management and biotechnological innovation. CRISPR/Cas9's advantages-unmatched precision, cost-effectiveness, and therapeutic potential-are tempered by challenges like off-target effects, ethical dilemmas, and regulatory gaps. Integrating nanoparticle delivery systems and multi-omics approaches may overcome technical barriers, but responsible innovation requires addressing these limitations. CRISPR-driven fungal genome editing promises to redefine solutions for drug-resistant infections, sustainable bioproduction, and beyond as the field evolves. In conclusion, genome editing technologies have enhanced our capacity to dissect fungal biology and expanded fungi's practical applications across various scientific and industrial domains. Continued innovation in this field promises to unlock the vast potential of fungal systems further, enabling more profound understanding and transformative biotechnological progress.

Systems and synthetic biology for plant natural product pathway elucidation

Plants are one of the major reservoirs of medicinal compounds, serving as a cornerstone of both traditional and modern medicine. However, despite their importance, the complex biosynthetic pathways of many plant-derived compounds remain only partially understood, hindering their full potential in therapeutic applications. This review paper summarizes the advances in systems and synthetic biology utilized in the characterization and engineering of plant metabolic pathways. We discuss various strategies such as (1) co-expression analysis, (2) gene cluster identification, (3) metabolite profiling, (4) deep learning approaches, (5) genome-wide association studies, and (6) protein complex identification. Through case studies on several biosynthesis pathways, we highlight how these methods are applied to unravel complex pathways and enhance the production of important natural products. Finally, we discuss future directions in the context of metabolic engineering, including metabolon engineering, AI integration, and sustainable production strategies, underscoring the potential for cheaper and greener production of plant natural products.

De Novo Artificial Biosynthesis of 3-Hydroxyphloretin in Escherichia coli

3-Hydroxyphloretin (3-OH phloretin), a dihydrochalcone compound containing a catechol moiety, is naturally present in apples and exhibits potent anti-adipogenic, anti-obesity, and anticancer activities. In this study, we developed a modular co-culture platform enabling the de novo biosynthesis of 3-OH phloretin from glucose in Escherichia coli. We demonstrated that 4-coumarate 3-hydroxylase (Sam5), derived from Saccharothrix espanaensis, efficiently catalyzes the hydroxylation of phloretin to 3-OH phloretin. The engineered co-culture system comprised two functional modules: an upstream module that converts l-tyrosine to phloretic acid through the expression of tyrosine ammonia-lyase and enoate reductase genes, and a downstream module that converts phloretic acid to 3-OH phloretin via the sequential action of 4-coumarate-CoA ligase, a mutated chalcone synthase, and Sam5. Using this system, we successfully achieved the de novo production of 3-OH phloretin at a titer of 4.69 mg/L from glucose. In parallel, the artificial biosynthetic pathway also yielded phloretic acid and 3-hydroxyphloretic acid (3-OH phloretic acid) at titers of 161.7 and 176.2 mg/L, respectively, in an engineered l-tyrosine-overproducing E. coli strain. To the best of our knowledge, this study represents the first successful establishment of an artificial biosynthetic route for the production of both 3-OH phloretic acid and 3-OH phloretin directly from glucose in E. coli. This platform lays the groundwork for the microbial production of valuable dihydrochalcone compounds and holds promise for further optimization toward industrial-scale applications.

Molecular farming for the food sector

Molecular farming, initially developed to produce therapeutic proteins using genetically modified plants, gained renewed interest during the Ebola and COVID-19 outbreaks and has expanded into functional food ingredients. This article evaluates molecular farming technologies, market potential, and startups, and identifies opportunities in dairy proteins, food enzymes, collagen, and cellular agriculture.

Switching the yeast metabolism via manipulation of sugar phosphorylation

Saccharomyces cerevisiae predominantly ferments sugar to ethanol, irrespective of the presence of oxygen, which is known as the Crabtree-effect. Traditional methods rely on static controls of glycolytic flux to make S. cerevisiae Crabtree-negative, which are not favorable for future biomanufacturing applications. Considering native metabolic pathways typically harness dynamic regulatory networks, we therefore aim to develop an alternative strategy using dynamic regulation of the yeast central metabolism to generate Crabtree-negative S. cerevisiae. We report that manipulating a single step at sugar phosphorylation can alter the mode of yeast metabolism with an attenuated Crabtree-effect. By implementing catabolite-regulated sugar phosphorylation, the diauxic shift in budding yeast was effectively reduced. The Crabtree-attenuated metabolism in the engineered yeast was confirmed by multidimensional characterizations such as cell morphology, the measurements of sugar utilization rate and ethanol production, and transcriptomics. In addition, we demonstrated that the Crabtree-attenuated metabolism could substantially improve the mitochondrial synthesis of short branched-chain fatty acids from amino acid catabolism, and allow the synthesis and accumulation of retinaldehyde. Taken together, we present for the first time that manipulation of sugar phosphorylation can alter the mode of yeast metabolism, and the synthetic Crabtree-attenuated yeast factory established here might serve as a non-fermentative biomanufacturing chassis.

Advances in the analysis and application of metabolites from tropical plants

Tropical regions are characterized by a rich diversity of plant species and unique growth environments, resulting in the production of numerous important medicinal metabolites. This review summarizes the recent progress in the analysis of metabolites from tropical plants. These plants have developed specific metabolites that aid their adaptation to challenging environments, and these compounds hold significant medicinal value. The review further examines the genetic biosynthetic pathways that contribute to the production of these compounds, providing insights into the mechanisms of their synthesis. Additionally, it discusses future prospects for the utilization of these metabolites, exploring potential advancements in biotechnological approaches to enhance their production and application. By emphasizing the significance of tropical plants as reservoirs of bioactive substances, this review aims to encourage further exploration and sustainable use of these important natural resources in the field of medicine and beyond.

Reinforced NADPH regeneration in engineered Saccharomyces cerevisiae enhances rosmarinic acid production

Rosmarinic acid (RA) is a valuable natural product for its significant antioxidative activity, which is mainly derived from plants or by chemical synthesis. With the development of biotechnology, the research on the production of RA by microbial cell factory has attracted more attention. In this study, we engineered Saccharomyces cerevisiae to produce RA by constructing a de novo RA synthesis pathway which utilized two cytochrome P450s from Salvia miltiorrhiza Bunge and Coleus scutellarioides (L.) Benth. Through reinforcing NAD(P)H regeneration by overexpression of zwf1 and integration of ARO4K229L and ARO7G141S into the genome, the engineered S. cerevisiae produced 4.92 mg/L of RA, 8.2-fold of the control, in shake flask fermentation. The titer of RA reached 11.3 mg/L by fed-batch fermentation in 5 L bioreactor. This study increased the production of RA by combination cofactor and pathway engineering, revealed the diversity of RA synthesis in S. cerevisiae, and also provided a reference for the synthesis and accumulation of other active components in yeast.

Synthetic Biology in Natural Product Biosynthesis

Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.

Analysis of the intrinsic value of life in the context of synthetic biology

The ongoing advancements in synthetic biology, employing either "bottom-up" or "top-down" approaches to construct synthetic life, are generating significant interest. However, the broad application of these scientific practices remains fraught with ethical controversies. Thus, investigating the intrinsic value associated with synthetic life is crucial for determining whether and how synthetic life should be constructed and utilized. This study draws upon and extends Ronald Sandler's theory of intrinsic value, analyzing the intrinsic subjective value of synthetic life from the perspectives of ecocentrism, human culture, and the structural properties of synthetic life itself. It examines the intrinsic objective value of synthetic life based on its natural purposes. Additionally, the study explores the inherent worth of synthetic life from three angles: biology, subjectivity, and relationships with human beings. We conclude that the intrinsic value of synthetic life increases sequentially from synthetic microorganisms to synthetic plants, synthetic invertebrates, synthetic vertebrates, and synthetic humans. All forms of synthetic life possess intrinsic subjective and objective value. However, only synthetic life above the grade of synthetic microorganisms has inherent worth; thus, humans have moral obligations towards them.

De novo biosynthesis of plant lignans by synthetic yeast consortia

Reconstructing the biosynthesis of complex natural products such as lignans in yeast is challenging and can result in metabolic promiscuity, affecting the biosynthetic efficiency. Here we divide the lignan biosynthetic pathway across a synthetic yeast consortium with obligated mutualism and use ferulic acid as a metabolic bridge. This cooperative system successfully overcomes the metabolic promiscuity and synthesizes the common precursor, coniferyl alcohol. Furthermore, combined with systematic engineering strategies, we achieve the de novo synthesis of key lignan skeletons, pinoresinol and lariciresinol, and verify the scalability of the consortium by synthesizing complex lignans, including antiviral lariciresinol diglucoside. These results provide a starting engineering platform for the heterologous synthesis of lignans. In particular, the study illustrates that the yeast consortium with obligate mutualism is a promising strategy that mimics the metabolic division of labor among multiple plant cells, thereby improving the biosynthesis of long pathways and complex natural products.

Computational biology predicts metabolic engineering targets for increased production of 103 valuable chemicals in yeast

Development of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product and microbial host of interest. Despite major advancements in the field of metabolic modeling in recent years, prediction of genetic modifications for increased production remains challenging. Here, we present a computational pipeline that leverages the concept of protein limitations in metabolism for prediction of optimal combinations of gene engineering targets for enhanced chemical bioproduction. We used our pipeline for prediction of engineering targets for 103 different chemicals using Saccharomyces cerevisiae as a host. Furthermore, we identified sets of gene targets predicted for groups of multiple chemicals, suggesting the possibility of rational model-driven design of platform strains for diversified chemical production.

Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications

The combination of artificial intelligence (AI) with microbial technology marks the start of a major transformation, improving applications throughout biotechnology, especially in healthcare. With the capability of AI to process vast amounts of biological big data, advanced microbial technology allows for a comprehensive understanding of complex biological systems, advancing disease diagnosis, treatment and the development of microbial therapeutics. This mini review explores the impact of AI-integrated microbial technologies in healthcare, highlighting advancements in microbial biomarker-based diagnosis, the development of microbial therapeutics and the microbial production of therapeutic compounds. This exploration promises significant improvements in the design and implementation of health-related solutions, steering a new era in biotechnological applications.

Elucidation and biosynthesis of tetrahydroisoquinoline alkaloids: Recent advances and prospects

Tetrahydroisoquinoline alkaloids (THIAs) are a prominent class of plant-derived compounds with various important pharmaceutical applications. Considerable progress has been made in the biosynthesis of THIAs in microorganisms due to the elucidation of their natural biosynthetic pathways and the discovery of key enzymes. In this review, we systematically summarize recent progress in elucidating the natural biosynthetic pathways of THIAs and their biosynthesis in industrial microorganisms. In addition, recent advancements in the synthesis of THIAs through the construction of artificial multi-enzyme cascades and chemoenzymatic cascades are highlighted. Finally, the current challenges in developing efficient cell factories for producing THIAs are discussed, along with proposed strategies aimed at providing insights into the industrial production of THIAs.

Creation of a eukaryotic multiplexed site-specific inversion system and its application for metabolic engineering

The site-specific recombination system is a versatile tool in genome engineering, enabling controlled DNA inversion or deletion at specific sites to generate genetic diversity. The multiplexed inversion system, which preferentially facilitates inversion at reverse-oriented sites rather than deletion at same-oriented sites, has not been found in eukaryotes. Here, we establish a multiplexed site-specific inversion system, Rci51-5/multi-sfxa101, in yeast. Firstly, we develop a high-throughput screening system based on the on/off transcriptional control of multiple markers by DNA inversion. After two rounds of progressively stringent directed evolution, a mutant Rci51-5 shows an ability of multisite inversion and a ~ 1000-fold increase in total inversion efficiency against the wild-type Rci derived from Salmonella typhimurium. Subsequently, we demonstrate that the Rci51-5/multi-sfxa101 system exhibits significantly lower deletion rate than the Cre/multi-loxP system. Using the synthetic metabolic pathway of β-carotene as an example, we illustrate that the system can effectively facilitate promoter substitution in the metabolic pathway, resulting in a more than 7-fold increase in the yield of β-carotene. In summary, we develop a multiplexed site-specific inversion system in eukaryotes, providing an approach to metabolic engineering and a tool for eukaryotic genome manipulation.

A concise enzyme cascade enables the manufacture of natural and halogenated protoberberine alkaloids

The application and drug development of plant-derived natural products are often limited by their low abundance in medicinal plants and the lack of structural complexity and diversity. Herein, we design a concise enzyme cascade to efficiently produce natural and unnatural protoberberine alkaloids from cost-effective, readily available substrates. Through enzyme discovery and engineering, along with systematic optimization of the berberine bridge enzyme to address remaining manufacturing challenges in protoberberine alkaloid biosynthesis, the high production of drug Rotundine is achieved at an impressive gram-scale titer, demonstrating its industrial potential. More importantly, this cascade also enables the efficient biosynthesis of various unnatural halogenated protoberberine alkaloids. Thus, this work not only unlocks the potential of enzyme cascades in overcoming longstanding challenges in the efficient biosynthesis of plant-derived alkaloids, but also opens avenues to introduce structural complexity and diversity into alkaloids through synthetic biology, offering significant potential for drug development.

Modeling for understanding and engineering metabolism

Metabolism is at the core of all functions of living cells as it provides Gibbs free energy and building blocks for synthesis of macromolecules, which are necessary for structures, growth, and proliferation. Metabolism is a complex network composed of thousands of reactions catalyzed by enzymes involving many co-factors and metabolites. Traditionally it has been difficult to study metabolism as a whole network and most traditional efforts were therefore focused on specific metabolic pathways, enzymes, and metabolites. By using engineering principles of mathematical modeling to analyze and study metabolism, as well as engineer it, that is, design and build, new metabolic features, it is possible to gain many new fundamental insights as well as applications in biotechnology. Here, we present the history and basic principles of engineering metabolism, as well as the newest developments in the field. We are using examples of applications in: (1) production of protein pharmaceuticals and chemicals; (2) basic studies of metabolism; and (3) impacting health care. We will end by discussing how engineering metabolism can benefit from advances in artificial intelligence (AI)-based models.

Beyond In Vivo, Pharmaceutical Molecule Production in Cell-Free Systems and the Use of Noncanonical Amino Acids Therein

Throughout history, we have looked to nature to discover and copy pharmaceutical solutions to prevent and heal diseases. Due to the advances in metabolic engineering and the production of pharmaceutical proteins in different host cells, we have moved from mimicking nature to the delicate engineering of cells and proteins. We can now produce novel drug molecules, which are fusions of small chemical drugs and proteins. Currently we are at the brink of yet another step to venture beyond nature's border with the use of unnatural amino acids and manufacturing without the use of living cells using cell-free systems. In this review, we summarize the progress and limitations of the last decades in the development of pharmaceutical protein development, production in cells, and cell-free systems. We also discuss possible future directions of the field.

Antimicrobials from endophytes as novel therapeutics to counter drug-resistant pathogens

The rapid increase in antimicrobial resistance (AMR) projects a "global emergency" and necessitates a need to discover alternative resources for combating drug-resistant pathogens or "superbugs." One of the key themes in "One Health Concept" is based on the fact that the interconnected network of humans, the environment, and animal habitats majorly contribute to the rapid selection and spread of AMR. Moreover, the injudicious and overuse of antibiotics in healthcare, the environment, and associated disciplines, further aggravates the concern. The prevalence and persistence of AMR contribute to the global economic burden and are constantly witnessing an upsurge due to fewer therapeutic options, rising mortality statistics, and expensive healthcare. The present decade has witnessed the extensive exploration and utilization of bio-based resources in harnessing antibiotics of potential efficacies. The discovery and characterization of diverse chemical entities from endophytes as potent antimicrobials define an important yet less-explored area in natural product-mediated drug discovery. Endophytes-produced antimicrobials show potent efficacies in targeting microbial pathogens and synthetic biology (SB) mediated engineering of endophytes for yield enhancement, forms a prospective area of research. In keeping with the urgent requirements for new/novel antibiotics and growing concerns about pathogenic microbes and AMR, this paper comprehensively reviews emerging trends, prospects, and challenges of antimicrobials from endophytes and their effective production via SB. This literature review would serve as the platform for further exploration of novel bioactive entities from biological organisms as "novel therapeutics" to address AMR.

Engineering cellular dephosphorylation boosts (+)-borneol production in yeast

(+)-Borneol, the main component of "Natural Borneol" in the Chinese Pharmacopoeia, is a high-end spice and precious medicine. Plant extraction cannot meet the increasing demand for (+)-borneol, while microbial biosynthesis offers a sustainable supply route. However, its production was extremely low compared with other monoterpenes, even with extensively optimizing the mevalonate pathway. We found that the key challenge is the complex and unusual dephosphorylation reaction of bornyl diphosphate (BPP), which suffers the side-reaction and the competition from the cellular dephosphorylation process, especially lipid metabolism, thus limiting (+)-borneol synthesis. Here, we systematically optimized the dephosphorylation process by identifying, characterizing phosphatases, and balancing cellular dephosphorylation metabolism. For the first time, we identified two endogenous phosphatases and seven heterologous phosphatases, which significantly increased (+)-borneol production by up to 152%. By engineering BPP dephosphorylation and optimizing the MVA pathway, the production of (+)-borneol was increased by 33.8-fold, which enabled the production of 753 mg/L under fed-batch fermentation in shake flasks, so far the highest reported in the literature. This study showed that rewiring dephosphorylation metabolism was essential for high-level production of (+)-borneol in Saccharomyces cerevisiae, and balancing cellular dephosphorylation is also helpful for efficient biosynthesis of other terpenoids since all whose biosynthesis involves the dephosphorylation procedure.

Advances in the biosynthesis of naturally occurring benzylisoquinoline alkaloids

Benzylisoquinoline alkaloids (BIAs) are a prominent class of plant metabolites with significant pharmaceutical and industrial significance that have garnered substantial attention from researchers worldwide. BIAs exhibit several pharmacological activities and have been used extensively. Examples include analgesics such as morphine, tetrahydropalmatine, antimicrobials such as berberine, and antineoplastic agents including cepharanthine. Most BIAs are derived and isolated from medicinal plants; however, these plants are predominantly wild resources that are scarce. Their high environmental impact, slow growth rate, scarcity of resources, and expensive direct extraction costs pose a significant challenge. Certain BIAs are present in trace amounts in medicinal plants; moreover, they have complex chemical structures and unstable properties. Designing chemical synthesis routes and processes is challenging. Thus, a major obstacle in developing and utilizing these natural products in the pharmaceutical industry lies in their low abundance in nature. Consequently, the limited supply of these molecules fails to meet high research and market demands. In recent years, biosynthesis approaches have emerged as a novel and efficient method to obtain BIAs. In this review, recent progress in the field of enzymes related to the elucidation of biosynthetic pathways and the biosynthesis of BIAs are discussed, and future perspectives for designing viable strategies for their targeted manipulation are presented.

Codeine 3-O-demethylase catalyzed biotransformation of morphinan alkaloids in Escherichia coli: site directed mutagenesis of terminal residues improves enzyme expression, stability and biotransformation yield

The cultivation of opium poppy is the only commercially viable source of most morphinan alkaloids. Bioproduction of morphinan alkaloids in recombinant whole-cell systems provides a promising alternate source of these valuable compounds. The enzyme codeine 3-O-demethylase can transform morphinan alkaloids by O-demethylation and has been applied in single step biotransformation reactions or as part of larger biosynthetic cascade, however, the productivity for these reactions remains low and suboptimal enzyme properties could be improved. This mutagenesis study targeted non-conserved N-and C-terminal residues, which were replaced with the equivalent residues from enzyme thebaine 6-O-demethylase. Whole cell biotransformation performance was significantly improved in Escherichia coli expressing codeine 3-O-demethylase mutants, with a ~ 2.8-fold increase in the production of oripavine from thebaine and ~ 1.3-fold increase in the production of morphine from codeine. Statistical analysis of biotransformation yield, enzyme expression and stability, predicted using changes in Gibbs free energy (ΔΔG) with deep-learning-based model DDmut, suggested that altered enzyme stability and/or expression of soluble protein may contribute to the observed improvements in biotransformation. This approach could be beneficial for screening future codeine 3-O-demethylase mutations and for other enzymes.

Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes

T7 RNA polymerase (RNAP) has enabled orthogonal control of gene expression and recombinant protein production across diverse prokaryotic host chassis organisms for decades. However, the absence of 5' methyl guanosine caps on T7 RNAP-derived transcripts has severely limited its utility and widespread adoption in eukaryotic systems. To address this shortcoming, we evolved a fusion enzyme combining T7 RNAP with the single subunit capping enzyme from African swine fever virus using Saccharomyces cerevisiae. We isolated highly active variants of this fusion enzyme, which exhibited roughly two orders of magnitude higher protein expression compared to the wild-type enzyme. We demonstrate the programmable control of gene expression using T7 RNAP-based genetic circuits in yeast and validate enhanced performance of these engineered variants in mammalian cells. This study presents a robust, orthogonal gene regulatory system applicable across diverse eukaryotic hosts, enhancing the versatility and efficiency of synthetic biology applications.

Effects of typical plant growth regulator chlormequat chloride on alkaloidal compounds in Corydalis yanhusuo and molecular mechanisms

The effects of chlormequat chloride, a typical plant growth regulator, on the medicinal herb Corydalis yanhusuo were investigated. A standardized field experiment was conducted to investigate the molecular mechanisms and variations in active compounds resulting from chlormequat chloride treatment. Samples of C. yanhusuo were collected under controlled conditions and at varying doses of chlormequat chloride. The differential compounds identified in both control and treated groups of C. yanhusuo were primarily alkaloids, as determined by non-targeted metabolomics analysis. The metabolite content was determined through the precise quantification of 12 enriched alkaloidal compounds across various categories of C. yanhusuo using targeted metabolomics. A comprehensive metabolomics evaluation method was developed that focuses on pharmacodynamically active compounds. Transcriptomic analysis also facilitates the identification of differential genes and enzymes associated with alkaloid production between the two groups. Chlormequat chloride significantly increased the yield of C. yanhusuo, but the content of the quantitatively abundant alkaloids decreased. It was suggested that the level of cytochrome P450 enzymes, primarily involved in the biosynthesis of benzylisoquinoline alkaloids, was inhibited by chlormequat chloride. In conclusion, this study revealed a dose-dependent effect of chlormequat chloride on C. yanhusuo and its associated molecular mechanisms as determined by omics analysis.

Engineering Saccharomyces cerevisiae for medical applications

BACKGROUND

During the last decades, the advancements in synthetic biology opened the doors for a profusion of cost-effective, fast, and ecologically friendly medical applications priorly unimaginable. Following the trend, the genetic engineering of the baker's yeast, Saccharomyces cerevisiae, propelled its status from an instrumental ally in the food industry to a therapy and prophylaxis aid.

MAIN TEXT

In this review, we scrutinize the main applications of engineered S. cerevisiae in the medical field focusing on its use as a cell factory for pharmaceuticals and vaccines, a biosensor for diagnostic and biomimetic assays, and as a live biotherapeutic product for the smart in situ treatment of intestinal ailments. An extensive view of these fields' academic and commercial developments as well as main hindrances is presented.

CONCLUSION

Although the field still faces challenges, the development of yeast-based medical applications is often considered a success story. The rapid advances in synthetic biology strongly support the case for a future where engineered yeasts play an important role in medicine.

Overproduction of Cucurbitadienol through Modular Metabolic Engineering and Fermentation Optimization in Saccharomyces cerevisiae

Cucurbitadienol is a key intermediate in the biosynthesis of cucurbitane-type compounds and serves as a precursor for mogrosides, cucurbitacins, and other valuable natural products of potential biological and food importance. However, microbial fermentation for cucurbitadienol production remains inefficient, limiting its potential for further industrial application. This study achieved the efficient synthesis of cucurbitadienol through a multimodular strategy. First, an N-degron tag was used to direct metabolic flux toward cucurbitadienol synthesis without compromising cell growth. Second, enzyme engineering strategies were employed to improve the utilization efficiency of intermediate metabolites. Finally, to increase precursor availability, the transcription factor UPC2-1 was introduced, which upregulated the expression of ERGs in the pre-squalene pathway. After eliminating nitrogen supplementation and optimizing fermentation conditions, cucurbitadienol accumulation in the 5 L bioreactor increased to 6.1 g/L, representing the highest titer reported to date. These findings provide a solid foundation for the industrial-scale production of cucurbitadienol and its derivatives.

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes. KEY POINTS: • Transcriptomics revealed further insights into the photobiology of X. dendrorhous, specifically metabolic nodes that are transcriptionally regulated by light. • A modular genetic part collection was developed, including 26 constitutive and regulated promoters derived from the transcriptomics of X. dendrorhous. • Omics-to-parts can be applied to nonconventional microbes for rapid "onboarding".

De Novo Production of the Bioactive Phenylpropanoid Artepillin C Using Membrane-Bound Prenyltransferase in Komagataella phaffii

Artepillin C is a diprenylated phenylpropanoid with various pharmacological benefits for human health. Its natural occurrence is limited to a few Asteraceae plants, such as Baccharis species, necessitating a stable supply through synthetic biology. In Saccharomyces cerevisiae, the utilization of aromatic substrates within the cell was limited, resulting in very low production of artepillin C. In this study, we used AcPT1, a p-coumaric acid (p-CA)-specific diprenyltransferase, in Komagataella phaffii to produce artepillin C. Detailed studies revealed that the critical bottleneck in K. phaffii was the supply of prenyl diphosphates, not phenylpropanoid flux. By enhancing the prenyl substrate pathway through overexpression of isopentenyl diphosphate isomerase and a truncated HMG-CoA reductase, we achieved a strong increase in artepillin C production. A major part of artepillin C was accumulated in yeast cells. One of the advantages of K. phaffii is its superior growth and ability to achieve high cell density cultivation compared to that of S. cerevisiae. Therefore, fed-batch cultivation with glycerol was performed. As a result, the dry cell weight (DCW) reached 61.0 g/L, and the intracellular amount of de novo produced artepillin C reached 187.3 μg/DCW. Analysis of intermediates revealed that the supply of p-CA constituted a bottleneck in artepillin C production in the engineered strain. By enhancing the p-CA supply, the intracellular accumulation of artepillin C reached 1200 μg/DCW even in batch cultivation. Moreover, the total intra- and extracellular amounts of artepillin C reached 12.5 mg/L, marking the highest de novo synthesis amount of artepillin C reported thus far, even under batch cultivation conditions.

Advancements in Microbial Cell Engineering for Benzylisoquinoline Alkaloid Production

Benzylisoquinoline alkaloids (BIAs) are a class of natural compounds found in plants of the Ranunculaceae family, known for their diverse pharmacological activities. However, the extraction yields of BIAs from plants are limited, and the cost of chemical synthesis is prohibitively high. Recent advancements in systems metabolic engineering and genomics have made it feasible to use microbes as bioreactors for BIAs production. This review explores recent progress in enhancing the production and yields of BIAs in two microbial systems: Escherichia coli and Saccharomyces cerevisiae. It covers various BIAs, including (S)-reticuline, morphinane, protoberberine, and aporphine alkaloids. The review provides strategies and technologies for BIAs synthesis, analyzes current challenges in BIAs research, and offers recommendations for future research directions.

Bioinformatics deciphers the thebaine biosynthesis pathway in opium poppy: Hub genes, network analysis, and miRNA regulation

Thebaine, a vital precursor in the codeine and morphine pathway, shows promise in addiction treatment. We conducted a comprehensive study on the thebaine biosynthesis pathway in opium poppy, utilizing bioinformatics tools. The dataset comprising the thirteen genes associated with the thebaine biosynthesis pathway was compiled from an extensive review of published literature and validated using the NCBI BLAST tool. Utilizing STRING and Cytoscape, we analyzed gene interactions and visualized the molecular interaction network, respectively. To identify hub proteins, CytoHubba was administered. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) at STRING were used for the enrichment analysis of the hub genes. CytoCluster was used to analyze the network in clusters. Promoter regions of hub genes and potential miRNAs were explored using MEME and the psRNATarget database. Hub genes crucial to thebaine biosynthesis were identified, contributing to essential cellular functions like growth, development, stress response, and signal transduction. Metabolic processes emerged as pivotal for thebaine production, indicating a broader role for the thebaine pathway gene network beyond primary metabolite production. Cell component subnetwork genes demonstrated associations with anatomical units, indicating involvement in plant defense responses. Dominant molecular functions drove plant defense responses. KEGG pathway analysis highlighted the significance of metabolic pathways and biosynthesis of secondary metabolites. Cluster analysis emphasized the relevance of the biosynthesis of amino acids, confirming the link between primary and secondary metabolites. Promoter analysis suggested the potential involvement of signal transduction in thebaine production. Hub genes were targeted by 40 miRNAs, suggesting potential novel biomarkers or target genes within the thebaine biosynthesis pathway. Based on the role of miRNAs identified in connection with the hub genes of the thebaine production process, the secondary metabolite pathway of thebaine appears to be associated with several key plant pathways, e.g. growth, development and stress response. However, these findings, based on bioinformatics analysis, warrant further experimental validation and promise to advance our understanding of the biosynthesis of thebaine and its interactions with other genes and metabolic pathways that influence the production of metabolites.

Biosynthesis of plant-derived triterpenoid asiatic acid in Saccharomyces cerevisiae cell factories

Asiatic acid, a bioactive component of Centella asiatica (L.) Urban, exhibits plentiful valuable pharmacological properties. Herein, we engineered Saccharomyces cerevisiae to produce asiatic acid. Initially, asiatic acid was synthesized by expressing the Centella asiatica cytochrome P450 monooxygenases CYP714E19 and CYP716C11 in a Saccharomyces cerevisiae strain optimized for ursolic acid production. The engineered strain yielded 0.42 ± 0.01 mg/L and 0.067 ± 0.0013 mg/g dry cell weight (DCW) of asiatic acid. Subsequently, a suitable cytochrome P450 reductase was screened, and key enzymes were overexpressed to effectively convert ursolic acid to asiatic acid. Strengthening heme biosynthesis, promoting endoplasmic reticulum (ER) expansion, and enhancing the cofactor supply were implemented to improve P450 catalytic activity. Additionally, a PDZ-PDZlig-mediated protein self-assembly strategy was used to improve the efficiency of the CYP714E19 and CYP716C11 catalytic cascade. Finally, the highest production was achieved (30.09 ± 0.15 mg/L, 4.09 ± 0.01 mg/g DCW) in microbial cell factories. This work establishes a foundation for efficient production of asiatic acid.

Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design

Constructing efficient cell factories requires the rational design of metabolic pathways, yet quantitatively predicting the potential pathway for breaking stoichiometric yield limit in hosts remains challenging. This leaves it uncertain whether the pathway yield of various products can be enhanced to surpass the stoichiometric yield limit and whether common strategies exist. Here, a high-quality cross-species metabolic network model (CSMN) and a quantitative heterologous pathway design algorithm (QHEPath) are developed to address this challenge. Through systematic calculations using CSMN and QHEPath, 12,000 biosynthetic scenarios are evaluated across 300 products and 4 substrates in 5 industrial organisms, revealing that over 70% of product pathway yields can be improved by introducing appropriate heterologous reactions. Thirteen engineering strategies, categorized as carbon-conserving and energy-conserving, are identified, with 5 strategies effective for over 100 products. A user-friendly web server is developed to quantitatively calculate and visualize the product yields and pathways, which successfully predicts biologically plausible strategies validated in literature for multiple products.

Engineering enzyme conformation within liquid-solid hybrid microreactors for enhanced continuous-flow biocatalysis

The artificial engineering of an enzyme's structural conformation and dynamic properties to promote its catalytic activity and stability outside cellular environments is highly pursued in industrial biotechnology. Here, we describe an elegant strategy of combining the rationally designed liquid-solid hybrid microreactor with a tailor-made polyethylene glycol functional ionic liquid (PEG-IL) microenvironment to exercise a high level of control over the configuration of enzymes for practical continuous-flow biocatalysis. As exemplified by a lipase driven kinetic resolution reaction, the obtained system exhibits a 2.70 to 30.35-fold activity enhancement compared to their batch or traditional IL-based counterparts. Also, our results demonstrate that the thermal stability of encapsulated lipase can be significantly strengthened in the presence of PEG groups, showcasing a long-term continuous-flow stability even up to 1000 h at evaluated temperature of 60 oC. Through systematic experiment and molecular dynamics simulation studies, the conformational changes of the active site cavity in the modified lipases are correlated with enzymatic properties alteration, and the pronounced effects of PEG-groups in stabilizing enzyme's secondary structures by delaying unfolding at elevated temperatures are identified. We believe that this study will guide the design of high-performance enzymatic systems, promoting their utilization in real-world biocatalysis applications.

Tuning architectural organization of eukaryotic P450 system to boost bioproduction in Escherichia coli

Eukaryotic cytochrome P450 enzymes, generally colocalizing with their redox partner cytochrome P450 reductase (CPR) on the cytoplasmic surface of organelle membranes, often perform poorly in prokaryotic cells, whether expressed with CPR as a tandem chimera or free-floating individuals, causing a low titer of heterologous chemicals. To improve their biosynthetic performance in Escherichia coli, here, we architecturally design self-assembled alternatives of eukaryotic P450 system using reconstructed P450 and CPR, and create a set of N-termini-bridged P450-CPR heterodimers as the counterparts of eukaryotic P450 system with N-terminus-guided colocalization. The covalent counterparts show superior and robust biosynthetic performance, and the N-termini-bridged architecture is validated to improve the biosynthetic performance of both plant and human P450 systems. Furthermore, the architectural configuration of protein assemblies has an inherent effect on the biosynthetic performance of N-termini-bridged P450-CPR heterodimers. The results suggest that spatial architecture-guided protein assembly could serve as an efficient strategy for improving the biosynthetic performance of protein complexes, particularly those related to eukaryotic membranes, in prokaryotic and even eukaryotic hosts.

Structural diversity, evolutionary origin, and metabolic engineering of plant specialized benzylisoquinoline alkaloids

Covering: up to June 2024Benzylisoquinoline alkaloids (BIAs) represent a diverse class of plant specialized metabolites derived from L-tyrosine, exhibiting significant pharmacological properties such as anti-microbial, anti-spasmodic, anti-cancer, cardiovascular protection, and analgesic effects. The industrial production of valuable BIAs relies on extraction from plants; however, challenges concerning their low concentration and efficiency hinder drug development. Hence, alternative approaches, including biosynthesis and chemoenzymatic synthesis, have been explored. Model species like Papaver somniferum and Coptis japonica have played a key role in unraveling the biosynthetic pathways of BIAs; however, many aspects, particularly modified steps like oxidation and methylation, remain unclear. Critical enzymes, e.g., CYP450s and methyltransferases, play a substantial role in BIA backbone formation and modification, which is essential for understanding the origin and adaptive evolution of these plant specialized metabolites. This review comprehensively analyzes the structural diversity of reported BIAs and their distribution in plant lineages. In addition, the progress in understanding biosynthesis, evolution, and catalytic mechanisms underlying BIA biosynthesis is summarized. Finally, we discuss the progress and challenges in metabolic engineering, providing valuable insights into BIA drug development and the sustainable utilization of BIA-producing plants.

Isolation, biological activity, and synthesis of isoquinoline alkaloids

Covering: 2019 to 2023Isoquinoline alkaloids, an important class of N-based heterocyclic compounds, have attracted considerable attention from researchers worldwide. To follow up on our prior review (covering 2014-2018) and present the progress of this class of compounds, this review summarizes and provides updated literature on novel isoquinoline alkaloids isolated during the period of 2019-2023, together with their biological activity and underlying mechanisms of action. Moreover, with the rapid development of synthetic modification strategies, the synthesis strategies of isoquinoline alkaloids have been continuously optimized, and the total synthesis of these classes of natural products is reviewed critically herein. Over 250 molecules with a broad range of bioactivities, including antitumor, antibacterial, cardioprotective, anti-inflammatory, neuroprotective and other activities, are isolated and discussed. The total synthesis of more than nine classes of isoquinoline alkaloids is presented, and thirteen compounds constitute the first total synthesis. This survey provides new indications or possibilities for the discovery of new drugs from the original naturally occurring isoquinoline alkaloids.

De novo synthesis of 1-phenethylisoquinoline in engineered Escherichia coli

Phenylethylisoquinoline alkaloids (PIAs) are medicinally important natural products derived from the 1-phenylethylisoquinoline precursor. Heterologous production of the PIAs remains challenging due to the incomplete elucidation of biosynthetic pathway and the lack of proper microbial cell factory designed for precursor enhancement. In this work, an artificial pathway composed of eight enzymes from different species was established for de novo 1-phenylethylisoquinoline biosynthesis in engineered Escherichia coli. The yield of the intermediate 4-hydroxydihydrocinnamaldehyde was optimized through screening various NADP+-dependent 2-alkenal reductases, cofactor regeneration and the site-directed mutagenesis of key residues in ChAER1. Subsequently, incorporation of the modified dopamine pathway into an endogenous reductase-deficient E. coli with high tyrosine yield boosted the production of 1-phenylethylisoquinoline, reaching 402.58 mg/L in a 5L fermenter. Our work lays a foundation for the future large-scale production of high value-added 1-phenylethylisoquinoline-related alkaloids.

TRYing to evaluate production costs in microbial biotechnology

Microbial fermentations offer the opportunity to produce a wide range of chemicals in a sustainable fashion, but it is important to carefully evaluate the production costs. This can be done on the basis of evaluation of the titer, rate, and yield (TRY) of the fermentation process. Here we describe how the three TRY metrics impact the technoeconomics of a microbial fermentation process, and we illustrate the use of these for evaluation of different processes in the production of two commodity chemicals, 1,3-propanediol (PDO) and ethanol, as well as for the fine chemical penicillin. On the basis of our discussions, we provide some recommendations on how the TRY metrics should be reported when new processes are described.

Two ubiquitous aldo-keto reductases in the genus Papaver support a patchwork model for morphine pathway evolution

The evolution of morphinan alkaloid biosynthesis in plants of the genus Papaver includes permutation of several processes including gene duplication, fusion, neofunctionalization, and deletion resulting in the present chemotaxonomy. A critical gene fusion event resulting in the key bifunctional enzyme reticuline epimerase (REPI), which catalyzes the stereochemical inversion of (S)-reticuline, was suggested to precede neofunctionalization of downstream enzymes leading to morphine biosynthesis in opium poppy (Papaver somniferum). The ancestrally related aldo-keto reductases 1,2-dehydroreticuline reductase (DRR), which occurs in some species as a component of REPI, and codeinone reductase (COR) catalyze the second and penultimate steps, respectively, in the pathway converting (S)-reticuline to morphine. Orthologs for each enzyme isolated from the transcriptomes of 12 Papaver species were shown to catalyze their respective reactions in species that capture states of the metabolic pathway prior to key evolutionary events, including the gene fusion event leading to REPI, thus suggesting a patchwork model for pathway evolution. Analysis of the structure and substrate preferences of DRR orthologs in comparison with COR orthologs revealed structure-function relationships underpinning the functional latency of DRR and COR orthologs in the genus Papaver, thus providing insights into the molecular events leading to the evolution of the pathway.

Not all cytochrome b5s are created equal: How a specific CytB5 boosts forskolin biosynthesis in Saccharomyces cerevisiae

Cytochrome B5s, or CytB5s, are small heme-binding proteins, ubiquitous across all kingdoms of life that serve mainly as electron donors to enzymes engaged in oxidative reactions. They often function as redox partners of the cytochrome P450s (CYPs), a superfamily of enzymes participating in multiple biochemical processes. In plants, CYPs catalyze key reactions in the biosynthesis of plant specialized metabolites with their activity dependent on electron donation often from cytochrome P450 oxidoreductases (CPRs or PORs). In eukaryotic microsomal CYPs, CytB5s frequently participate in the electron transfer process although their exact role remains understudied, especially in plant systems. In this study, we assess the role of CytB5s in the heterologous biotechnological production of plant specialized metabolites in yeast. For this, we used as a case-study the biosynthesis of forskolin - a bioactive diterpenoid produced exclusively from the plant Coleus forskohlii. The complete biosynthetic pathway for forskolin is known and includes three CYP enzymes. We reconstructed the entire forskolin pathway in the yeast Saccharomyces cerevisiae, and upon co-expression of the three CytB5s - identified in C. forskohlii transcriptomes - alleviation of a CYP-related bottleneck step was noticed only when a specific CytB5, CfCytB5A, was used. Co-expression of CfCytB5A in yeast, in combination with forskolin pathway engineering, resulted in forskolin production at titers of 1.81 g/L in a bioreactor. Our findings demonstrate that CytB5s not only play an important role in plant specialized metabolism but also, they can interact with precision with specific CYPs, indicating that the properties of CytB5s are far from understood. Moreover, our work highlights how CytB5s may act as indispensable components in the sustainable microbial production of plant metabolites, when their biosynthetic pathways involve CYP enzymes.

Engineering the L-tryptophan metabolism for efficient de novo biosynthesis of tryptophol in Saccharomyces cerevisiae

Tryptophol (IET) is a metabolite derived from L-tryptophan that can be isolated from plants, bacteria, and fungi and has a wide range of biological activities in living systems. Despite the fact that IET biosynthesis pathways exist naturally in living organisms, industrial-scale production of IET and its derivatives is solely based on environmentally unfriendly chemical conversion. With diminishing petroleum reserves and a significant increase in global demand in all major commercial segments, it becomes essential to develop new technologies to produce chemicals from renewable resources and under mild conditions, such as microbial fermentation. Here we characterized and engineered the less-studied L-tryptophan pathway and IET biosynthesis in the baker's yeast Saccharomyces cerevisiae, with the goal of investigating microbial fermentation as an alternative/green strategy to produce IET. In detail, we divided the aromatic amino acids (AAAs) metabolism related to IET synthesis into the shikimate pathway, the L-tryptophan pathway, the competing L-tyrosine/L-phenylalanine pathways, and the Ehrlich pathway based on a modular engineering concept. Through stepwise engineering of these modules, we obtained a yeast mutant capable of producing IET up to 1.04 g/L through fed-batch fermentation, a ~ 650-fold improvement over the wild-type strain. Besides, our engineering process also revealed many insights about the regulation of AAAs metabolism in S. cerevisiae. Finally, during our engineering process, we also discovered yeast mutants that accumulate anthranilate and L-tryptophan, both of which are precursors of various valuable secondary metabolites from fungi and plants. These strains could be developed to the chassis for natural product biosynthesis upon introducing heterologous pathways.

A novel plasmid-based experimental system in Saccharomyces cerevisiae that enables the introduction of 10 different plasmids into cells

The budding yeast Saccharomyces cerevisiae is commonly used as an expression platform for the production of valuable compounds. Yeast-based genetic research can uniquely utilize auxotrophy in transformant selection: auxotrophic complementation by an auxotrophic marker gene on exogenous DNA (such as plasmids). However, the number of required auxotrophic nutrients restricts the number of plasmids maintained by the cells. We, therefore, developed novel Δ10 strains that are auxotrophic for 10 different nutrients and new plasmids with two multiple cloning sites and auxotrophic markers for use in Δ10 strains. We confirmed that Δ10 strains were able to maintain 10 types of plasmids. Using plasmids encoding model proteins, we detected the co-expression of 17 different genes in Δ10 cell lines. We also constructed Δ9 strains that exhibited auxotrophy for nine nutrients and increased growth compared to Δ10. This study opens a new avenue for the co-expression of a large number of genes in eukaryotic cells.

Characterization and Molecular Engineering of a N-Methyltransferase from Edible Nelumbo nucifera Leaves Involved in Nuciferine Biosynthesis

Lotus leaf, traditionally used as both edible tea and herbal medicine in Asia, contains nuciferine, a lipid-lowering and weight-loss compoud. The biosynthetic pathways of nuciferine in Nelumbo nucifera remain unclear. We characterized a specific N-methyltransferase, NnNMT, which had a novel function and catalyzed only nuciferine synthesis from the aporphine-type alkaloid N-nornuciferine. The expression profile of NnNMT was in agreement with BIA accumulation patterns in four tissues from three varieties, suggesting that NnNMT is involved in nucleiferine biosynthesis in Nelumbo nucifera. Protein engineering based on molecular docking and dynamic simulations revealed key residues (Y98, H208, F256, Y81, F329, G260, P76, and H80) crucial for NnNMT activity, with the F257A mutant showing increased efficiency. These findings enhance our understanding of aporphine alkaloid biosynthesis and support the development of lotus-based functional foods and medicinal applications.

QM/MM Study of the Reaction Mechanism of L-Tyrosine Hydroxylation Catalyzed by the Enzyme CYP76AD1

We have studied the hydroxylation mechanism of l-Tyr by the heme-dependent enzyme CYP76AD1 from the sugar beet (Beta vulgaris). This enzyme has a promising biotechnological application in modified yeast strains to produce medicinal alkaloids, an alternative to the traditional opium poppy harvest. A generative machine learning software based on AlphaFold was used to build the structure of CYP76AD1 since there are no structural data for this specific enzyme. After model validation, l-Tyr was docked in the active site of CYP76AD1 to assemble the reactive complex, whose catalytic distances remained stable throughout the 100 ns of MD simulation. Subsequent QM/MM calculations elucidated that l-Tyr hydroxylation occurs in two steps: hydrogen abstraction from l-Tyr by CpdI, forming an l-Tyr radical, and subsequent radical rebound, corresponding to a rate-limiting step of 16.0 kcal·mol-1. Our calculations suggest that the hydrogen abstraction step should occur in the doublet state, while the radical rebound should happen in the quartet state. The clarification of the reaction mechanism of CYP76AD1 provides insights into the rational optimization of the biosynthesis of alkaloids to eliminate the use of opium poppy.

Celastrol: A century-long journey from the isolation to the biotechnological production and the development of an antiobesity drug

Celastrol, a triterpenoid found in the root of the traditional medicinal plant Tripterygium wilfordii, is a potent anti-inflammatory and antiobesity agent. However, pharmacological exploitation of celastrol has been hindered by the limited accessibility of plant material, the co-existence of other toxic compounds in the same plant tissue, and the lack of an efficient chemical synthesis method. In this review, we highlight recent progress in elucidating celastrol biosynthesis and discuss how this knowledge can facilitate its scalable bioproduction using cell factories and its further development as an antiobesity and anti-inflammatory drug.

Integration of co-culture and transport engineering for enhanced metabolite production

Microbial production of valuable plant metabolites is feasible. However, constructing all pathways in a single cell is a formidable challenge, and the extended biosynthetic pathways within cells often result in reduced productivity. To address these challenges, a co-culture system that divides biosynthetic pathways into several host cells and co-cultures has been developed. Various combinations of host cells, along with the optimal conditions for each co-culture, have been documented, leading to the successful production of valuable metabolites. In addition, efficient biosynthesis frequently involves metabolite movement, encompassing substrate uptake, intracellular intermediate transport, and end-product efflux. Recent advances in plant transporters of specialized metabolites have enhanced productivity by harnessing these transporters. This review summarizes the latest findings on co-culture systems and transport engineering and provides insights into the future of valuable metabolite production through the integration of co-culture and transport engineering.

Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes

T7 RNA polymerase has enabled orthogonal control of gene expression and recombinant protein production across diverse prokaryotic host chassis organisms for decades. However, the absence of 5' methyl guanosine caps on T7 RNAP derived transcripts has severely limited its utility and widespread adoption in eukaryotic systems. To address this shortcoming, we evolved a fusion enzyme combining T7 RNAP with the single subunit capping enzyme from African swine fever virus using Saccharomyces cerevisiae. We isolated highly active variants of this fusion enzyme, which exhibited roughly two orders of magnitude higher protein expression compared to the wild-type enzyme. We demonstrate the programmable control of gene expression using T7 RNAP-based genetic circuits in yeast and validate enhanced performance of these engineered variants in mammalian cells. This study presents a robust, orthogonal gene regulatory system applicable across diverse eukaryotic hosts, enhancing the versatility and efficiency of synthetic biology applications.

Integrated metabolite profiling and transcriptome analysis reveal candidate genes involved in the biosynthesis of benzylisoquinoline alkaloids in Corydalis solida

Structurally diverse benzylisoquinoline alkaloids (BIAs) are found in specific plant families, some of which are desirable for their efficient production because of their strong biological activities. Corydalis plants (e.g., Corydalis yanhusuo) of the family Papaveraceae also produce various BIAs; thus, they have been used in traditional Chinese medicine. Because metabolic engineering and synthetic biology using microorganisms are promising technologies for the effective production of useful metabolites, elucidation of the biosynthetic pathway of each BIA is indispensable. Although several enzyme genes involved in the biosynthesis of Corydalis BIAs have recently been isolated, many remain unknown, such as the protoberberine alkaloid C-methyltransferase involved in the biosynthesis of corydaline, one of the main BIAs found in the tubers of Corydalis plants. In this study, we performed transcriptome analysis combined with metabolite profiling of different tissues of Corydalis solida. Based on the high accumulation of several BIAs, including protopine, allocryptopine, and corydaline, genes encoding putative biosynthetic enzymes, including cytochrome P450, methyltransferase, and oxidase proteins, that were highly expressed in the tubers were screened. Two OMT genes, CsOMT1 and CsOMT2, were highly expressed in the tuber, and further characterization using crude enzyme preparations demonstrated that CsOMT1 showed 7-O-methylation activity against reticuline, whereas CsOMT2 catalyzed 9-O-methylation of scoulerine, followed by 2-O-methylation of tetrahydrocolumbamine. Our findings provide valuable information for the isolation of novel biosynthetic enzyme genes in Corydalis species.