Production of the antimalarial drug precursor artemisinic acid in engineered yeast

The oleaginous yeast Rhodosporidium toruloides engineered for biomass hydrolysate-derived (E)-α-bisabolene production

The oleaginous yeast Rhodosporidiumtoruloides has been exploited for many bioproducts, including several terpenes, owing to its oleaginous nature and biomass inhibitor tolerance. Here, we built upon previous (E)-α-bisabolene work by iteratively stacking the complete mevalonate pathway from Saccharomyces cerevisiae onto a multicopy bisabolene synthase parent strain. Metabolomics and proteomics verified heterologous pathway expression and identified metabolic bottlenecks at three intermediate steps, with candidate feedback-resistant mevalonate kinases screening improving titers 15%. Subtle differences in codon optimization, and preliminary attenuation of competing flux toward lipids resulted in 6-fold, 7-fold higher titers relative to controls, respectively. Media optimization led to modest improvements, with zinc identified as the most promising at 10% titer improvement. Ultimately, high-performance strains were cultivated with corn-stover biomass hydrolysate in microtiter plates at 300 g/L total sugar, achieving 20.8 g/L bisabolene, the highest reported titer in the literature. A 2 L glucose minimal medium bioreactor achieved 19.3 g/L bisabolene and a literature-high productivity of 0.11 g/L/h.

Synergistic interaction of AaMYC2 and AaMYC2-LIKE enhances artemisinin production in Artemisia annua L

Artemisinin-based combination therapies recommended by WHO marks Artemisia annua as the only natural source of artemisinin fighting deadly disease, Malaria. In this study, we isolated two transcription factors, AaMYC2 and AaMYC2-LIKE, from A. annua and investigated their role in regulating artemisinin biosynthetic pathway. Our findings depict that both AaMYC2 and AaMYC2-LIKE are transcriptionally active and, when co-transformed in yeast cells, significantly enhance β-galactosidase activity in transactivation assays as compared to their individual transformations. Furthermore, Yeast two-hybrid (Y2H) and Biomolecular fluorescence complementation assays revealed AaMYC2 physically interacts with AaMYC2-LIKE in yeast cells and in the nucleus of onion epidermal cells respectively. Generation of transient transgenic over expression and co-expression lines of AaMYC2 and AaMYC2-LIKE resulted in elevated expression of artemisinin biosynthetic genes and trichome development genes in co-expression lines as compared to individual transgenic lines and wildtype. Importantly, the glandular trichome density and artemisinin content was also significantly higher in co-transformed transgenic lines compared to individual AaMYC2 and AMYC2-LIKE transgenic lines. Conversely, artemisinin content was markedly reduced in AaMYC2-RNAi lines, underscoring the critical role of functional AaMYC2 in synergistic regulation with AaMYC2-LIKE. Altogether the above studies provide valuable insights into the regulatory networks of MYC type bHLH transcription factors in controlling economically and medically important pathway in A. annua.

CRISPR/Cas9-based iterative multi-copy integration for improved metabolite yields in Saccharomyces cerevisiae

High-copy integration of key genes offers a promising strategy for efficient biosynthesis of valuable natural products in Saccharomyces cerevisiae. However, traditional multi-copy gene integration methods meet challenges including low efficiency and labor-intensive screening processes. In this study, we developed the IMIGE (Iterative Multi-copy Integration by Gene Editing) system, a CRISPR/Cas9-based approach that exploits both δ and rDNA repetitive sequences for simultaneous multi-copy integrations in S. cerevisiae. This system combines the mixture of Cas9-sgRNA expression vectors with a split-marker strategy for efficient donor DNA assembly in vivo and enables rapid, iterative screening through growth-related phenotypes. When applied to the biosynthesis of ergothioneine and cordycepin, the IMIGE system achieved significant yield improvements, with titers of 105.31 ± 1.53 mg/L and 62.01 ± 2.4 mg/L, respectively, within just two screening cycles (5.5-6 days in total). These yields represent increases of 407.39 % and 222.13 %, respectively, compared to the strains with episomal expression. By streamlining the integration process, utilizing growth-based selection, and minimizing screening demands in both equipment and labor, the IMIGE system could provide an efficient and scalable platform for high-throughput strain engineering, facilitating enhanced microbial production of a wide range of bioproducts.

Metabolome guided treasure hunt - learning from metabolic diversity

Metabolomics is a rapidly evolving field focused on the comprehensive identification and quantification of small molecules in biological systems. As the final layer of the biological hierarchy following of the genome, transcriptome and proteome, it presents a dynamic snapshot of phenotype, influenced by genetic, environmental and physiological factors. Whilst the metabolome sits downstream of genes and proteins, there are multiple higher levels-tissues, organs, the entire organism, and interactions with other organisms, which need to be considered in order to fully comprehend organismal biology. Advances in metabolomics continue to expand its applications in plant biology, biotechnology, and natural product discovery unlocking many of nature's most beneficial colors, tastes, nutrients and medicines. Flavonoids and other specialized metabolites are essential for plant defense against oxidative stress and function as key phytonutrients for human health. Recent advancements in gene-editing and metabolic engineering have significantly improved the nutritional value and flavor of crop plants. Here we highlight how advanced metabolic analysis is driving improvements in crops uncovering genes that influence nutrient and flavor profile and plant derived compounds with medicinal potential.

Unlocking the potential of Artemisia annua for artemisinin production: current insights and emerging strategies

Malaria is a deadly disease, and the best effective treatments depend on artemisinin, a sesquiterpene lactone compound isolated from the plant Artemisia annua. However, artemisinin is produced in very small amount within the plant which is insufficient to meet the global demand. Although researchers have investigated synthetic and semi-synthetic approaches, they still face significant challenges, such as high costs and low efficiency, making A. annua the most viable source. Biotechnological advances in breeding and genetic engineering have developed new A. annua varieties with higher artemisinin content, and some varieties have achieved up to 3.2% of plant dry weight. Furthermore, researchers have identified the key genes and transcription factors that can be modified to boost production further. Environmental factors, such as light and specific plant hormones, play a crucial role in regulating this pathway. Also, tissue culture, hairy root systems, and natural elicitors have shown promising results, but need further refinement. Interestingly, the use of whole plants (such as dried leaf powder) instead of purified artemisinin alone has been found to improve drug absorption in the body, improve its effectiveness, and help combat artemisinin resistance. Beyond treating malaria, A. annua also demonstrates other therapeutic potential in treating other diseases, including cancer and viral infections. These findings highlight that A. annua is not just a source of artemisinin; it is a valuable medicinal plant that deserves continued research focus, primarily through approaches that improve artemisinin production directly in the plant.

Harnessing the Power of Natural Products for Targeted Protein Degradation

Natural products have garnered significant attention due to their complex chemical structures and remarkable pharmacological activities. With inherent recognition capabilities for protein surfaces, natural products serve as ideal candidates for designing proteolysis-targeting chimeras (PROTACs). The utilization of natural products in PROTAC development offers distinct advantages, including their rich chemical diversity, multitarget activities, and sustainable sourcing. This comprehensive review explores the vast potential of harnessing natural products in PROTAC research. Moreover, the review discusses the application of natural degradant technology, which involves utilizing natural product-based compounds to selectively degrade disease-causing proteins, as well as the implementation of computer-aided drug design (CADD) technology in identifying suitable targets for degradation within the realm of natural products. By harnessing the power of natural products and leveraging computational tools, PROTACs derived from natural products have the potential to revolutionize drug discovery and provide innovative therapeutic interventions for various diseases.

Addressing semantic ambiguity in biotechnology: Proposals from the European research infrastructure IBISBA

Driven by numerous scientific discoveries in biology in the second half of the last century, biotechnology is now set to play an important role as a driver for advanced manufacturing, leveraging the power of living organisms to produce a range of goods and services. Considering this prospect, it is vital that terminology surrounding biotechnology is sufficiently clear to provide a basis for efficient regulation and public buy-in. Despite the apparent clarity of the term biotechnology, its definition is the subject of a longstanding debate and liberal interpretations. Likewise, other more recent terms such as biomanufacturing, synthetic biology and engineering biology also lack consensual definitions despite their use in both scientific and secular circles. Additionally, new terms such as precision fermentation and cellular agriculture, recently introduced in the framework of business-to-business exchanges, appear to call upon imaginaries rather than scientific facts. Herein, we examine the lexical complexity of the biotechnology field and argue that, for the sake of efficient policymaking, it is vital to harmonise the definitions of some core terms, including biotechnology, biomanufacturing, engineering biology and synthetic biology. With this aim in mind, this discussion paper is intended to be useful to policymakers and science communicators, whether in the media or in professional settings.

Dihydroartemisinic acid dehydrogenase-mediated alternative route for artemisinin biosynthesis

Dihydroartemisinic acid (DHAA) converts into antimalarial drug artemisinin (ART) by auto-oxidation. High production of artemisinic acid (AA) has been achieved by fermentation of engineered Saccharomyces cerevisiae, and AA can be converted into ART through DHAA by chemical synthesis. However, there is no enzyme reported to catalyze the conversion of AA to DHAA. Here, we report a dihydroartemisinic acid dehydrogenase (AaDHAADH) from Artemisia annua L, which catalyzes the bidirectional conversion between AA and DHAA. An optimized mutant AaDHAADH (P26L) is obtained through site-directed mutagenesis and its activity toward AA is 2.82 times that of the original gene. De novo synthesis of DHAA is achieved in S. cerevisiae using the targeted optimized gene AaDHAADH (P26L). Furthermore, 3.97 g/L of DHAA is obtained by fermentation of engineered S. cerevisiae in 5 L bioreactor. The discovery of AaDHAADH provides a more convenient and efficient alternative route for ART biosynthesis.

Combining Chemical Catalysis with Enzymatic Steps for the Synthesis of the Artemisinin Precursor Dihydroartemisinic Acid

The supply of artemisinin, the primary antimalarial drug recommended by the World Health Organization (WHO), is limited due to synthesis cost and supply constraints. This study explores novel chemo-enzymatic pathways for the efficient synthesis of dihydroartemisinic acid (DHAA), the penultimate precursor to artemisinin. The key concept here is to leverage the seamless integration of chemical and enzymatic steps for more thoroughly exploring synthesis alternatives. Using novoStoic, a biosynthetic pathway design tool, we identified previously unexplored carbon- and energy-balanced pathways for converting amorpha-4,11-diene (AMPD) to DHAA. For some of the enzymatically catalyzed steps lacking efficient enzymes, chemical catalysis alternatives were proposed and implemented, leading to a hybrid chemo-enzymatic pathway design. The proposed pathway converts AMPD directly to DHAA without going through artemisinic acid (AA), making it a shorter pathway compared with the existing synthesis routes for artemisinin. This effort paves the way for the systematic design of chemo-enzymatic pathways and provides insight into decision strategies between chemical synthesis and enzymatic synthesis steps. It serves as an example of how synthesis pathway design tools can be integrated with human intuition for accelerating retrosynthesis and how AI-based tools can identify and replace human intuitions to automate the decision processes. This can help reduce human-machine interventions and improve the development of future tools for synthesis planning.

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.

Encapsulation of select violacein pathway enzymes in the 1,2-propanediol utilization bacterial microcompartment to divert pathway flux

A continual goal in metabolic engineering is directing pathway flux to desired products and avoiding loss of pathway intermediates to competing pathways. Encapsulation of the pathway is a possible solution, as it creates a diffusion barrier between pathway intermediates and competing enzymes. It is hypothesized that bacteria use organelles known as bacterial microcompartments - proteinaceous shells encapsulating a metabolic pathway - for this purpose. We aim to determine to what degree this hypothesized benefit is conferred to encapsulated pathways. To this end, we used bacterial microcompartments to encapsulate select enzymes from the violacein pathway, which is composed of five enzymes that produce violacein as the main product and deoxyviolacein as a side product. Importantly, we studied the pathway in a cell-free context, allowing us to hold constant the concentration of unencapsulated and encapsulated enzymes and increase our control over reaction conditions. The VioE enzyme is a branch point in that it makes the precursor for both violacein and deoxyviolacein, the VioC enzyme is required for production of deoxyviolacein, and the VioD enzyme is required for violacein production. When we encapsulated VioE and VioC and left VioD unencapsulated, the product profile shifted toward deoxyviolacein and away from violacein compared to when VioC and VioD were both unencapsulated. This work provides the first fully quantitative evidence that microcompartment-based encapsulation can be used to divert pathway flux to the encapsulated pathway. It provides insight into why certain pathways are encapsulated natively and could be leveraged for metabolic engineering applications.

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.

Characterization and Engineering of a Bisabolene Synthase Reveal an Unusual Hydride Shift and Key Residues Critical for Mono-, Bi-, and Tricyclic Sesquiterpenes Formation

Sesquiterpene synthases (STSs) catalyze carbocation cascade reactions with various hydrogen shifts and cyclization patterns that generate structurally diverse sesquiterpene skeletons. However, the molecular basis for hydrogen shifts and cyclizations, which determine STS product distributions, remains enigmatic. In this study, an elusive STS SydA was identified in the biosynthesis of sydonol, which synthesized a new bisabolene-type sesquiterpene 6 with a unique saturated terminal pendant isopentane. Extensive evidence from isotope labeling experiments, crystal structures of SydA and its variant, quantum chemical calculations, and mutagenesis experiments reveal a plausible mechanism for the formation of 6 involving an unusual 1,7-hydride shift, which may be a key branchpoint for monocyclic, bicyclic, and tricyclic products. Structure-based engineering resulted in SydA variants that promote different reaction pathways, leading to the production of bicyclic α-cuprenene and (+)-β-chamigrene and tricyclic 7-epi-β-cedrene and β-microbiotene. These findings not only reveal a new bisabolene and its biosynthesis but also provide insights into the molecular basis of the hydride shifts and cyclizations, which pave the way for engineering STSs to produce complex terpenoid products.

Comprehensive evaluation of the capacities of microbial cell factories

Systems metabolic engineering is facilitating the development of high-performing microbial cell factories for producing chemicals and materials. However, constructing an efficient microbial cell factory still requires exploring and selecting various host strains, as well as identifying the best-suited metabolic engineering strategies, which demand significant time, effort, and costs. Here, we comprehensively evaluate the capacities of various microbial cell factories and propose strategies for systems metabolic engineering steps, including host strain selection, metabolic pathway reconstruction, and metabolic flux optimization. We analyze the metabolic capacities of five representative industrial microorganisms as cell factories for the production of 235 different bio-based chemicals and suggest the most suitable host strain for the corresponding chemical production. To improve the innate metabolic capacity by constructing more efficient metabolic pathways, heterologous metabolic reactions, and cofactor exchanges are systematically analyzed. Additionally, we present metabolic engineering strategies, which include up- and down-regulation target reactions, for the improved production of chemicals. Altogether, this study will serve as a comprehensive resource for the systems metabolic engineering of microorganisms in the bio-based production of chemicals.

Engineering a Yeast Cell Factory to Sustainably Biosynthesize Parthenolide

The sesquiterpene lactone parthenolide is a promising anticancer drug. Its biosynthesis via a microbial cell factory has been considered as a sustainable alternative to plant extraction. Herein, systematic metabolic engineering approaches, as well as the introduction of a novel noncanonical tricarboxylic acid (TCA) cycle, were employed to enhance the production of the key precursor germacrene A. By identifying two new dehydrogenases and controlling the expression of parthenolide synthase, we further achieved the elimination of byproducts and enhanced parthenolide production. A two-stage fermentation approach and in situ product extraction using macroreticular resin were further applied to relieve the nocuous effect of costunolide and parthenolide on the growth of yeast cell factories, ultimately achieving a titer of 549.7 mg/L for parthenolide and 972.7 mg/L for costunolide in a 10 L fermenter, which represents the highest reported titer obtained by microbial fermentation. The strategies should also contribute to the microbial cell factory-construction for other natural products exhibiting toxicity.

Heterologous Biosynthesis of Prenylflavonoids in Escherichia coli Based on Fungus Screening of Prenyltransferases

Flavonoids are natural products with high biological activity and potential applications. Prenylation increases the lipophilicity of flavonoids, endowing them with specific functions, selectivity, and pharmacological properties. However, traditional methods of plant extraction and chemical synthesis are insufficient to meet the demand for prenylflavonoids. Heterologous biosynthesis of prenylflavonoids in microorganisms provides an alternative approach. Compared with plant prenyltransferases, microbial prenyltransferases showed broad substrate specificity, which is more conducive to the biosynthesis of diverse prenylflavonoids. In this study, we cloned 31 dimethylallyltryptophan synthase prenyltransferases from five fungal species and tested candidate substrates. The products of Ad03 and Ao01 were identified, resulting in two unnatural prenylflavonoids and four natural prenylflavonoids. We constructed the isopentenol utilization pathway in Escherichia coli to develop the efficient dimethylallyl diphosphate synthesis pathway for 6-prenylsilybin (6-PS) synthesis. By optimizing the whole cell catalysis and two-phase reaction system, the 6-PS production titer reached 176 mg/L and the yield of silybin was 88%. Our study provides an efficient method for prenylflavonoids production.

Novel cell factory for the production of 24-epi-ergosterol, an un-natural semi-synthetic precursor for the production of brassinolide in Yarrowia lipolytica

Brassinolide (BL) is the most bioactive plant growth regulator among Brassinosteroids (BRs), belonging to the sixth class of plant hormones. However, its low natural abundance limits large-scale agricultural applications. An unnatural sterol, 24-epi-ergosterol, was proposed as a semi-synthetic precursor for economic production of BL. Here, we constructed a synthetic pathway for 24-epi-ergosterol in Yarrowia lipolytica, which has abundant acetyl-CoA content and a hydrophobic intracellular environment. Initially, we introduced a mutant plant-derived Δ24(28) sterol reductase (Dwf1) into Y. lipolytica to enable 24-epi-ergosterol production. The production of 24-epi-ergosterol was subsequently enhanced by regulating sterol homeostasis, optimizing transcriptional regulators, and overexpressing key pathway genes. Next, the accumulation of 24-epi-ergosterol was further improved by increasing acetyl-CoA levels and adjusting lipid metabolism. Finally, the 24-epi-ergosterol production reached 1626.85 mg/L after optimizing the fermentation conditions and performing a fed-batch culture in a 2 L fermenter. This study represents the first successful de novo synthesis of 24-epi-ergosterol in Y. lipolytica, offering a novel approach for the industrial production of BL.

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.

Enhancing Cannabichromenic Acid Biosynthesis in Saccharomyces cerevisiae

Cannabichromene (CBC), a valuable but extremely low-abundance component of cannabinoids in Cannabis sativa L., is known for its ability to promote neurogenesis. The scarcity of CBC in natural C. sativa is primarily attributed to the inefficiency of the 1-deoxy-D-xylulose 5-phosphate/2-C-methyl-D-erythritol 4 phosphate (DOXP/MEP) and fatty acid metabolism pathways, along with the limited competitive advantage of cannabichromenic acid synthetase (CBCAS) compared to other cannabinoid synthases. In this study, we constructed Saccharomyces cerevisiae capable of biosynthesizing cannabichromenic acid (CBCA) from glucose and olivetolic acid. First, we enhanced the supply of the precursor isopentenyl diphosphate/dimethylallyl diphosphate by introducing a two-step isopentenol utilization pathway (IUP). Additionally, we increased the CBCA titer by co-overexpressing endoplasmic reticulum auxiliary protein genes. Moreover, we improved the selectivity and catalytic activity of CBCAS through rational design. By localizing the IUP to peroxisomes, geranylgeranyl pyrophosphate and CBCA titers were further increased by 1.6-fold and 28%, respectively. Notably, the yeast strain synthesized CBCA at a rate 25.8% higher than that of C. sativa. Our findings suggest that microbial synthesis offers a promising alternative to traditional C. sativa for sustainable CBCA production.

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.

Nanoencapsulation of Living Microbial Cells in Porous Covalent Organic Framework Shells

Encapsulating living cells within nanoshells offers an important approach to enhance their stability against environmental stressors and broaden their application scope. However, this often leads to impaired mass transfer at the cell biointerface. Strengthening the protective shell with well-defined, ordered transport channels is crucial to regulating molecular transport and maintaining cell viability and biofunctionality. Herein, we report the construction of covalent organic framework (COF) mesoporous shells for single-cell nanoencapsulation, providing selective permeability and comprehensive protection for living microbial cells. The COF shells ensure nutrient uptake while blocking large harmful molecules and UV-C radiation, thereby preserving cell viability and metabolic activity. Integration of such crystalline porous shells with genetically modified cell factories for metabolic production is further investigated, revealing no adverse effects, as demonstrated by riboflavin production. Moreover, the COF shell effectively shields cells, ensuring efficient bioproduction even after being treated under harsh conditions. This versatile encapsulation approach is applicable for different cell types, providing a robust platform for cell surface engineering.

New approaches to secondary metabolite discovery from anaerobic gut microbes

The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme & Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism. KEY POINTS: • Gut microbial secondary metabolites have therapeutic and biotechnological potential • Culture- and (meta)genome-based workflows drive gut anaerobe metabolite discovery • Anaerobic biofoundries enable high-throughput workflows for metabolite discovery.

Emerging trends and new developments in global research on artemisinin and its derivatives

Background

The World Health Organization recommends the use of artemisinin (ART) and its derivatives for malaria treatment. Furthermore, these compounds exhibit encouraging pharmacological effects for the treatment of several diseases. Nevertheless, ongoing antimalarial treatment efforts have been significantly hindered by the emergence of drug resistance. A systematic evaluation and analysis of relevant studies may yield insights to help resolve this dilemma and reveal options for future research.

Purpose

The objective of this study was to provide researchers with a comprehensive synopsis of the advancements made in the study of ART and its significant derivatives, as well as to visually present the data and provide insightful observations that can inform subsequent investigations in this domain.

Methods

We searched the Web of Science Core Collection for relevant studies published by December 31, 2023. The research hotspots and frontiers pertinent to this field in terms of countries, institutions, authors, journals, references, and keywords were ascertained through scientometric analysis via CiteSpace software.

Results

This study included an extensive assemblage of 12,985 data points, and the findings suggest that ART and its derivatives have garnered considerable interest among scientists. Prolonged international collaboration has fostered progress in this research field. "Antimalarials," "synthesis," "drug resistance," and "Plasmodium vivax" are areas of intense research. Potential areas for future investigations may include "proliferation," "oxidative stress," "pathways," and "mechanisms."

Conclusion

This study offers a comprehensive compendium of the developments and trends in the relevant research field over the past fifty years. Since pharmaceutical drug synthesis can influence both drug efficacy and cost-effectiveness, ongoing efforts to improve drug synthesis are warranted. Although the advent of novel therapeutic approaches has partially mitigated drug resistance, further investigations into the underlying mechanisms are needed. While better treatments for malaria have been developed, the therapeutic potential of ART and its derivatives for numerous additional important diseases is also possible, and future research in this area can lead to dramatic improvements in health.

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.

Application and development of CRISPR technology in the secondary metabolic pathway of the active ingredients of phytopharmaceuticals

As an efficient gene editing tool, the CRISPR/Cas9 system has been widely employed to investigate and regulate the biosynthetic pathways of active ingredients in medicinal plants. CRISPR technology holds significant potential for enhancing both the yield and quality of active ingredients in medicinal plants. By precisely regulating the expression of key enzymes and transcription factors, CRISPR technology not only deepens our understanding of secondary metabolic pathways in medicinal plants but also opens new avenues for drug development and the modernization of traditional Chinese medicine. This article introduces the principles of CRISPR technology and its efficacy in gene editing, followed by a detailed discussion of its applications in the secondary metabolism of medicinal plants. This includes an examination of the composition of active ingredients and the implementation of CRISPR strategies within metabolic pathways, as well as the influence of Cas9 protein variants and advanced CRISPR systems in the field. In addition, this article examines the long-term impact of CRISPR technology on the progress of medicinal plant research and development. It also raises existing issues in research, including off-target effects, complexity of genome structure, low transformation efficiency, and insufficient understanding of metabolic pathways. At the same time, this article puts forward some insights in order to provide new ideas for the subsequent application of CRISPR in medicinal plants. In summary, CRISPR technology presents broad application prospects in the study of secondary metabolism in medicinal plants and is poised to facilitate further advancements in biomedicine and agricultural science. As technological advancements continue and challenges are progressively addressed, CRISPR technology is expected to play an increasingly vital role in the research of active ingredients in medicinal plants.

AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research

As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR's capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.

An independent biosynthetic route to frame a xanthanolide-type sesquiterpene lactone in Asteraceae

Xanthanolides, also described as seco-guaianolides, are unique sesquiterpene lactones (STLs) with diverse bioactivities. Most of xanthanolides are 12,8-olides based on the position of their lactone ring. The biosynthetic pathway leading to xanthanolides has hitherto been elusive, especially how nature creates the xanthane skeleton is a long-standing question. This study reports the elucidation of a complete biosynthetic pathway to the important 12,8-xanthanolide 8-epi-xanthatin. The xanthane-type backbone is directly derived from the central precursor germacrene-type sesquiterpene, germacrene A acid, via oxidative rearrangement, catalyzed by an unusual cytochrome P450. Subsequently, a 12,8-lactone ring is formed within this xanthane-type backbone resulting in xanthanolides. The biosynthetic pathway for xanthanolides contrasts with the previously unified biosynthetic route for diverse 12,6-guaianolides, in which a 12,6-lactone ring formation precedes the transformation of a germacrene-type skeleton into a guaiane-type structure. The discovery of the full biosynthetic pathway of 8-epi-xanthantin opens new opportunities for producing xanthanolides in microbial organisms using synthetic biology strategies.

Developing filamentous fungal chassis for natural product production

The growing demand for green and sustainable production of high-value chemicals has driven the interest in microbial chassis. Recent advances in synthetic biology and metabolic engineering have reinforced filamentous fungi as promising chassis cells to produce bioactive natural products. Compared to the most used model organisms, Escherichia coli and Saccharomyces cerevisiae, most filamentous fungi are natural producers of secondary metabolites and possess an inherent pre-mRNA splicing system and abundant biosynthetic precursors. In this review, we summarize recent advances in the application of filamentous fungi as chassis cells. Emphasis is placed on strategies for developing a filamentous fungal chassis, including the establishment of mature genetic manipulation and efficient genetic tools, the catalogue of regulatory elements, and the optimization of endogenous metabolism. Furthermore, we provide an outlook on the advanced techniques for further engineering and application of filamentous fungal chassis.

Dynamic transcriptomics unveils parallel transcriptional regulation in artemisinin and phenylpropanoid biosynthesis pathways under cold stress in Artemisia annua

Cold stress, a major abiotic factor, positively modulates the synthesis of artemisinin in Artemisia annua and influences the biosynthesis of other secondary metabolites. To elucidate the changes in the synthesis of secondary metabolites under low-temperature conditions, we conducted dynamic transcriptomic and metabolite quantification analyses of A. annua leaves. The accumulation of total organic carbon (TOC) in leaves under cold stress provided ample precursors for secondary metabolite synthesis. Short-term exposure to low temperature induced a transient increase in jasmonic acid synthesis, which positively regulates the artemisinin biosynthetic pathway, contributing to artemisinin accumulation. Additionally, transcripts of genes encoding key enzymes and transcription factors in both the phenylpropanoid and artemisinin biosynthetic pathways, including PAL, C4H, ADS, and DBR2, exhibited similar expression patterns, suggesting a coordinated effect between these pathways. Prolonged exposure to low temperature sustained high levels of phenylpropanoid synthesis, leading to significant increases in lignin, flavonoids, and anthocyanin. Conversely, the final stage of the artemisinin biosynthetic pathway is inhibited under these conditions, resulting in elevated levels of dihydroartemisinic acid and artemisinic acid. Collectively, our study provides insights into the parallel transcriptional regulation of artemisinin and phenylpropanoid biosynthetic pathways in A. annua under cold stress.

Metabolic Engineering for Squalene Production: Advances and Perspectives

Squalene is a linear polyunsaturated triterpene which has multiple physiological functions including anticancer, antioxidant, and skin-care. It has been widely used in the food, medicine, and cosmetics sectors and also serves as a precursor of triterpenes and steroids. Recently, the production of squalene by microbial cell hosts has drawn much attention due to its sustainability, environmental friendliness, and great efficiency. In this review, we first introduce the recent developments in the production of squalene by employing microbial cell factories, especially yeasts. Next, we underscore the primary metabolic strategies, including the biosynthetic pathway engineering, precursor manipulation, cofactor engineering, and organelle engineering. In addition to traditional metabolic engineering strategies, we also discuss some prospective metabolic regulation approaches, including regulation of lipid synthesis, identifying and manipulating related transcription factors, dynamic regulation of the metabolic pathway, and secretion engineering of membrane-impermeable terpenoids. These approaches provide insights for further metabolic engineering of squalene and related terpenoids.

Engineering Nicotiana benthamiana for chrysoeriol production using synthetic biology approaches

Flavonoids are prevalent plant secondary metabolites with a broad range of biological activities. Their antioxidant, anti-inflammatory, and anti-cancer activities make flavonoids widely useful in a variety of industries, including the pharmaceutical and health food industries. However, many flavonoids occur at only low concentrations in plants, and they are difficult to synthesize chemically due to their structural complexity. To address these difficulties, new technologies have been employed to enhance the production of flavonoids in vivo. In this study, we used synthetic biology techniques to produce the methylated flavone chrysoeriol in Nicotiana benthamiana leaves. The chrysoeriol biosynthetic pathway consists of eight catalytic steps. However, using an Agrobacterium-mediated transient expression assay to examine the in planta activities of genes of interest, we shortened this pathway to four steps catalyzed by five enzymes. Co-expression of these five enzymes in N. benthamiana leaves resulted in de novo chrysoeriol production. Chrysoeriol production was unaffected by the Agrobacterium cell density used for agroinfiltration and increased over time, peaking at 10 days after infiltration. Chrysoeriol accumulation in agroinfiltrated N. benthamiana leaves was associated with increased antioxidant activity, a typical property of flavones. Taken together, our results demonstrate that synthetic biology represents a practical method for engineering plants to produce substantial amounts of flavonoids and flavonoid derivatives without the need for exogenous substrates.

Single Point Mutation Abolishes Water Capture in Germacradien-4-ol Synthase

The high-fidelity sesquiterpene cyclase (-)-germacradien-4-ol synthase (GdolS) converts farnesyl diphosphate into the macrocyclic alcohol (-)-germacradien-4-ol. Site-directed mutagenesis was used to decipher the role of key residues in the water control mechanism. Replacement of Ala176, located in the G1/2 helix, with non-polar aliphatic residues of increasing size (valine, leucine, isoleucine and methionine) resulted in the accumulation of the non-hydroxylated products germacrene A and germacrene D. In contrast, hydroxylation was maintained when the polar residues threonine, glutamine or aspartate replaced Ala176. Additionally, although a contribution of His150 to the nucleophilic water addition could be ruled out, the imidazole ring of His150 appears to assist carbocation stabilisation. The results presented here shed light on how hydroxylating sesquiterpene synthases can be engineered to design modified sesquiterpene synthases to reduce the need for further steps in the biocatalytic production of oxygenated sesquiterpenoids.

A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 2: Non-DSM compounds

Malaria remains a severe global health concern, with 249 million cases reported in 2022, according to the World Health Organization (WHO) [1]. PfDHODH is an essential enzyme in malaria parasites that helps to synthesize certain building blocks for their growth and development. It has been confirmed that targeting Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme could lead to new and effective antimalarial drugs. Inhibitors of PfDHODH have shown potential for slowing down parasite growth during both the blood and liver stages. Over the last two decades, many species selective PfDHODH inhibitors have been designed, including DSM compounds and other non-DSM compounds. In the first chapter [2] of this review, we have reviewed all synthetic schemes and structure-activity relationship (SAR) studies of DSM compounds. In this second chapter, we have compiled all the other non-DSM PfDHODH inhibitors based on dihydrothiophenones, thiazoles, hydroxyazoles, and N-alkyl-thiophene-2-carboxamides. The review not only offers an insightful overview of the synthetic methods employed but also explores into alternative routes and innovative strategies involving different catalysts and chemical reagents. A critical aspect covered in the review is the SAR studies, which provide a comprehensive understanding of how structural modifications impact the efficacy of PfDHODH inhibitors and challenges related to the discovery of PfDHODH inhibitors. This information is invaluable for scientists engaged in the development of new antimalarial drugs, offering insights into the most promising scaffolds and their synthetic techniques.

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Production of the antimalarial drug precursor amorphadiene by microbial terpene synthase-like from the moss Sanionia uncinata

MAIN CONCLUSION

The microbial terpene synthase-like of the moss Sanionia uncinata displays the convergent evolution of a rare plant metabolite amorpha-4,11-diene synthesis. Despite increasing demand for the exploration of biological resources, the diversity of natural compounds synthesized by organisms inhabiting various climates remains largely unexplored. This study focuses on the moss Sanionia uncinata, known as a predominant species within the polar climates of the Antarctic Peninsula, to systematically explore its metabolic profile both in-field and in controlled environments. We here report a diverse array of moss-derived terpene volatiles, including the identification of amorpha-4,11-diene, a rare sesquiterpene compound that is a precursor for antimalarial drugs. Phylogenetic reconstruction and functional validation in planta and in vitro identified a moss terpene synthase, S. uncinata microbial terpene synthase-like 2 (SuMTPSL2), which is associated with amorpha-4,11-diene production. We demonstrate that expressing SuMTPSL2 in various heterologous systems is sufficient to produce amorpha-4,11-diene. These results highlight the metabolic diversity in Antarctica, but also provide insights into the convergent evolution leading to the synthesis of a rare plant metabolite.

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.

Plant sesquiterpene lactones

Sesquiterpene lactones (STLs) are a prominent group of plant secondary metabolites predominantly found in the Asteraceae family and have multiple ecological roles and medicinal applications. This review describes the evolutionary and ecological significance of STLs, highlighting their roles in plant defence mechanisms against herbivory and as phytotoxins, alongside their function as environmental signalling molecules. We also cover the substantial role of STLs in medicine and their mode of action in health and disease. We discuss the biosynthetic pathways and the various modifications that make STLs one of the most diverse groups of metabolites. Finally, we discuss methods for identifying and predicting STL biosynthesis pathways. This article is part of the theme issue 'The evolution of plant metabolism'.

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.

Syntheses of deuterium-labeled dihydroartemisinic acid (DHAA) isotopologues and mechanistic studies focused on elucidating the conversion of DHAA to artemisinin

Dihydroartemisinic acid (DHAA), a sesquiterpenoid natural product from Artemisia annua, converts to artemisinin, an anti-malarial natural product that contains an endoperoxide bridge. The endoperoxide moiety is responsible for the biological activity of artemisinin. Therefore, understanding the biosynthesis of this functional group could lead to the optimization of the process to produce this medicine. DHAA converts to artemisinin through the incorporation of two molecules of oxygen in a four-step process. The reaction is a spontaneous cascade process that involves (i) the initial incorporation of a molecule of oxygen through the reaction of an allylic C-H bond of DHAA, (ii) followed by the cleavage of a C-C bond, (iii) the incorporation of a second molecule of oxygen, and (iv) polycyclization to yield artemisinin. This manuscript is focused on describing the chemical syntheses of regioselectively polydeuterated DHAA isotopologues at C3 and C15, in addition to research efforts related to clarifying how the endoperoxide-forming process of artemisinin occurs.

New insights into the roles of fungi and bacteria in the development of medicinal plant

BACKGROUND

The interaction between microorganisms and medicinal plants is a popular topic. Previous studies consistently reported that microorganisms were mainly considered pathogens or contaminants. However, with the development of microbial detection technology, it has been demonstrated that fungi and bacteria affect beneficially the medicinal plant production chain.

AIM OF REVIEW

Microorganisms greatly affect medicinal plants, with microbial biosynthesis a high regarded topic in medicinal plant-microbial interactions. However, it lacks a systematic review discussing this relationship. Current microbial detection technologies also have certain advantages and disadvantages, it is essential to compare the characteristics of various technologies.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review first illustrates the role of fungi and bacteria in various medicinal plant production procedures, discusses the development of microbial detection and identification technologies in recent years, and concludes with microbial biosynthesis of natural products. The relationship between fungi, bacteria, and medicinal plants is discussed comprehensively. We also propose a future research model and direction for further studies.

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron-oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

Synthesis of Natural Products Using Engineered Plants and Microorganisms

Microorganisms and plants, particularly medicinal herbs, are abundant sources of diverse natural products, many of which are bioactive molecules with significant pharmaceutical or health benefits, and include artemisinin [...].

Recent Trends in Malaria Vaccine Research Globally: A Bibliometric Analysis From 2005 to 2022

Aim: Malaria vaccine is one of the critical areas in tropical health research, considering the success recorded in other vaccine-preventable diseases. This study is aimed at reviewing recent trends in global malaria vaccine research from 2005 to 2022. Method: A validated search strategy was undertaken to identify scientific literature on the malaria vaccine in the Scopus database. Bibliometric indicators identified include a pattern of publication growth and citations over the study period; top authors, countries, funding organizations, and journals; keywords, including different malarial parasite species, and the overall research themes. Result: A total of 6457 documents were found from 2005 to 2022, published in 160 journals/sources in 189 countries/territories. Malaria Journal published the highest number of research outputs (478, 7.4%) within the study period, and the highest number of documents (468, 7.3%) were published in 2021. There were 214,323 total citations, with 33.2 average citations per document and 167 documents' h-index. The United States, United Kingdom, and Australia combined produced more than 60% of the publication output, with most collaboration with African countries such as Kenya. Plasmodium falciparum is the most occurring parasite species keyword (754, 11.7%), with a growing interest in Plasmodium knowlesi (30, 0.5%). Merozoite surface protein, characterization, trials, infant/children, traveler, and research/review were the six themes that emerged from the studies. Conclusion: The last one and half decades have seen a significant increase in malaria vaccine research and citations, mainly targeting vaccine development, safety, and efficacy in Africa. This necessitates more international efforts to improve the vaccines' effectiveness considering different Plasmodium species.

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.

Microbial Cell Factories in the Bioeconomy Era: From Discovery to Creation

Microbial cell factories (MCFs) are extensively used to produce a wide array of bioproducts, such as bioenergy, biochemical, food, nutrients, and pharmaceuticals, and have been regarded as the "chips" of biomanufacturing that will fuel the emerging bioeconomy era. Biotechnology advances have led to the screening, investigation, and engineering of an increasing number of microorganisms as diverse MCFs, which are the workhorses of biomanufacturing and help develop the bioeconomy. This review briefly summarizes the progress and strategies in the development of robust and efficient MCFs for sustainable and economic biomanufacturing. First, a comprehensive understanding of microbial chassis cells, including accurate genome sequences and corresponding annotations; metabolic and regulatory networks governing substances, energy, physiology, and information; and their similarity and uniqueness compared with those of other microorganisms, is needed. Moreover, the development and application of effective and efficient tools is crucial for engineering both model and nonmodel microbial chassis cells into efficient MCFs, including the identification and characterization of biological parts, as well as the design, synthesis, assembly, editing, and regulation of genes, circuits, and pathways. This review also highlights the necessity of integrating automation and artificial intelligence (AI) with biotechnology to facilitate the development of future customized artificial synthetic MCFs to expedite the industrialization process of biomanufacturing and the bioeconomy.

Identifying sesterterpenoids via feature-based molecular networking and small-scale fermentation

Terpenoids are known for their diverse structures and broad bioactivities with significant potential in pharmaceutical applications. However, natural products with low yields are usually ignored in traditional chemical analysis. Feature-based molecular networking (FBMN) was developed recently to cluster compounds with similar skeletons, which can highlight trace amounts of unknown compounds. Fusoxypene A is a sesterterpene synthesized by Fusarium oxysporum fusoxypene synthase (FoFS) with a unique 5/6/7/3/5 ring system. In this study, the FoFS-containing biosynthetic gene cluster was identified from F. oxysporum FO14005, and an efficient FBMN-based strategy was established to characterize four new sesterterpenoids, fusoxyordienoid A-D (1-4), based on a small-scale fermentation strategy. A cytochrome P450 monooxygenase, FusB, was found to be involved in the functionalization of fusoxypene A at C-17 and C-24 and responsible for the hydroxylation of fusoxyordienoid A at C-1 and C-8. This study highlights the potential of FBMN as a powerful tool for the discovery and characterization of natural compounds with low abundance. KEY POINTS: Combined small-scale fermentation and FBMN for rapid discovery of fusoxyordienoids Characterization of four new fusoxyordienoids with 5/6/7/3/5 ring system Biosynthetic pathway elucidation via tandem expression and substrate feeding.

Versatile filamentous fungal host highly-producing heterologous natural products developed by genome editing-mediated engineering of multiple metabolic pathways

Natural secondary metabolites are medically, agriculturally, and industrially beneficial to humans. For mass production, a heterologous production system is required, and various metabolic engineering trials have been reported in Escherichia coli and Saccharomyces cerevisiae to increase their production levels. Recently, filamentous fungi, especially Aspergillus oryzae, have been expected to be excellent hosts for the heterologous production of natural products; however, large-scale metabolic engineering has hardly been reported. Here, we elucidated candidate metabolic pathways to be modified for increased model terpene production by RNA-seq and metabolome analyses in A. oryzae and selected pathways such as ethanol fermentation, cytosolic acetyl-CoA production from citrate, and the mevalonate pathway. We performed metabolic modifications targeting these pathways using CRISPR/Cas9 genome editing and demonstrated their effectiveness in heterologous terpene production. Finally, a strain containing 13 metabolic modifications was generated, which showed enhanced heterologous production of pleuromutilin (8.5-fold), aphidicolin (65.6-fold), and ophiobolin C (28.5-fold) compared to the unmodified A. oryzae strain. Therefore, the strain generated by engineering multiple metabolic pathways can be employed as a versatile highly-producing host for a wide variety of terpenes.

Biosynthesis of bridged tricyclic sesquiterpenes in Inula lineariifolia

Presilphiperfolane-type sesquiterpenes represent a unique group of atypical sesquiterpenoids characterized by their distinctive tricyclic structure. They have significant potential as lead compounds for pharmaceutical and agrochemical development. Herein, we utilized a transcriptomic approach to identify a terpene synthase (TPS) gene responsible for the biosynthesis of rare presilphiperfolane-type sesquiterpenes in Inula lineariifolia, designated as IlTPS1. Through phylogenetic analysis, we have identified the evolutionary conservation of key motifs, including RR(x)8W, DDxxD, and NSE/DTE in IlTPS1, which are shared with other tricyclic sesquiterpene synthases in the TPS-a subfamily of Asteraceae plants. Subsequent biochemical characterization of recombinant IlTPS1 revealed it to be a multiproduct enzyme responsible for the synthesis of various tricyclic sesquiterpene alcohols from farnesyl diphosphate (FPP), resulting in production of seven distinct sesquiterpenes. Mass spectrometry and nuclear magnetic resonance (NMR) spectrometry identified presilphiperfolan-8β-ol and presilphiperfol-7-ene as predominant products. Furthermore, biological activity assays revealed that the products from IlTPS1 exhibited a potent antifungal activity against Nigrospora oryzae. Our study represents a significant advancement as it not only functionally identifies the first step enzyme in presilphiperfolane biosynthesis but also establishes the heterologous bioproduction of these unique sesquiterpenes.

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.