Terpene biosynthesis: modularity rules

The role and mechanisms of canonical and non-canonical tailoring enzymes in bacterial terpenoid biosynthesis

Covering: up to April 2024Terpenoids represent the largest and structurally most diverse class of natural products. According to textbook knowledge, this diversity arises from a two-step biosynthetic process: first, terpene cyclases generate a vast array of mono- and polycyclic hydrocarbon scaffolds with multiple stereocenters from a limited set of achiral precursors, a process extensively studied over the past two decades. Subsequently, tailoring enzymes further modify these complex scaffolds through regio- and stereocontrolled oxidation and other functionalization reactions, a topic of increasing interest in recent years. The resulting highly functionalized terpenoids exhibit a broad spectrum of unique biological activities, making them promising candidates for drug development. Recent advances in genome sequencing technologies along with the development and application of sophisticated genome mining tools have revealed bacteria as a largely untapped resource for the discovery of complex terpenoids. Functional characterization of a limited number of bacterial terpenoid biosynthetic pathways, combined with in-depth mechanistic studies of key enzymes, has begun to reveal the versatility of bacterial enzymatic processes involved in terpenoid modification. In this review, we examine the various tailoring reactions leading to complex bacterial terpenoids. We first discuss canonical terpene-modifying enzymes, that catalyze the functionalization of unactivated C-H bonds, incorporation of diverse functional groups, and oxidative and non-oxidative rearrangements. We then explore non-canonical terpene-modifying enzymes that facilitate oxidative rearrangement, cyclization, isomerization, and dimerization reactions. The increasing number of characterized tailoring enzymes that participate in terpene hydrocarbon scaffold fomation, rather than merely decorating pre-formed scaffolds suggests that a re-evaluation of the traditional two-phase model for terpenoid biosynthesis might be warranted. Finally, we address the potential and challenges of mining bacterial genomes to identify terpene biosynthetic gene clusters and expand the bacterial terpene biosynthetic and chemical space.

Molecular insights into a distinct class of terpenoid cyclases

Terpenoid cyclases (TCs) account for the synthesis of the most widespread and diverse natural compounds. A sesquiterpene cyclase termed BcABA3 from an abscisic acid-producing fungus Botrytis cinerea that yields (2Z,4E)-α-ionylideneethane but lacks signature feature of canonical TCs represents a distinct type of TCs. Here, we report the crystal structures of BcABA3, a closely related RuABA3 from Rutstroemia sp. and a bacterial SkABA3 from Shimazuella kribbensis. These ABA3 proteins adopt an all-α-helix fold and bind pyrophosphate moiety of farnesyl pyrophosphate by Glu-chelated Mg2+ ion cluster. We conduct mutagenesis experiments to validate the role of the substrate-binding residues. SkABA3 appears to yield compounds that are distinct from (2Z,4E)-α-ionylideneethane. These results not only provide the molecular insight into ABA3 proteins that serve as an important basis to the future investigation of this class of TCs, but also reveal the existence of more uncharacterized terpenoids synthesized via dedicated machineries.

Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product

Sabinene is a plant natural product with a distinctive strained [3.1.0] bicyclic ring system that is used commercially as a spicy and pine-like fragrance with citrus undertones. This unusual monoterpene has also been studied as an antifungal and anti-inflammatory agent as well as a next-generation biofuel. In order to understand the molecular determinants of [3.1.0] bicyclic ring formation in sabinene biosynthesis, we now report three X-ray crystal structures of sabinene synthase from Western red cedar, Thuja plicata (TpSS), with open and partially closed active site conformations at 2.21-2.72 Å resolution. We additionally report the complete biochemical characterization of sabinene synthase, including steady-state kinetics, active site mutagenesis, and product array profiling. The catalytic metal ion requirement is unexpectedly broad for a class I terpene cyclase: optimal catalytic activity was measured using Mn2+ or Co2+, with more modest activity observed using Mg2+ or Ni2+. Kinetic parameters were determined for both full-length TpSS and a deletion variant lacking the putative N-terminal plastidial targeting sequence, designated ΔTpSS. Monoterpene product profiles for both indicated similar product arrays independent of the catalytic metal ion used, with sabinene comprising nearly 90% of the total products generated. Site-directed mutagenesis was utilized to probe the function of active site residues, and several mutants yielded altered product arrays. Most notably, the G458A substitution converted ΔTpSS into a high-activity α-pinene synthase. α-Pinene contains a bicyclic [3.1.1] ring system; structural and mechanistic analyses suggest a molecular rationale for the reprogrammed transannulation reaction, leading to the alternative bicyclic product.

Functional Redundancy and Dual Function of a Hypothetical Protein in the Biosynthesis of Eunicellane-Type Diterpenoids

Many complex terpenoids, predominantly isolated from plants and fungi, show drug-like physicochemical properties. Recent advances in genome mining revealed actinobacteria as an almost untouched treasure trove of terpene biosynthetic gene clusters (BGCs). In this study, we characterized a terpene BGC with an unusual architecture. The selected BGC includes, among others, genes encoding a terpene cyclase fused to a truncated reductase domain and a cytochrome P450 monooxygenase (P450) that is split over three gene fragments. Functional characterization of the BGC in a heterologous host led to the identification of several new members of the trans-eunicellane family of diterpenoids, the euthailols, that feature unique oxidation patterns. A combination of bioinformatic analyses, structural modeling studies, and heterologous expression revealed a dual function of the pathway-encoded hypothetical protein that acts as an isomerase and an oxygenase. Moreover, in the absence of other tailoring enzymes, a P450 hydroxylates the eunicellane scaffold at a position that is not modified in other eunicellanes. Surprisingly, both the modifications installed by the hypothetical protein and one of the P450s exhibit partial redundancy. Bioactivity assays revealed that some of the euthailols show growth inhibitory properties against Gram-negative ESKAPE pathogens. The characterization of the euthailol BGC in this study provides unprecedented insights into the partial functional redundancy of tailoring enzymes in complex diterpenoid biosynthesis and highlights hypothetical proteins as an important and largely overlooked family of tailoring enzymes involved in the maturation of complex terpenoids.

From Cyclopropene to Housane Derivatives Via Intramolecular Cyclopropanation

The synthesis of housane derivatives from cyclopropenes is described. Under rhodium(II) catalysis, cyclopropenylvinyl carbinols can regioselectively generate a carbene intermediate which undergoes an intramolecular cyclopropanation to form a housane, a skeleton with similar ring strain as the cyclopropene precursor. The procedure shows a remarkable broad scope and efficiency. Moreover, the method served to prepare man-made housane-containing terpene derivatives, which are not accessible by Nature.

Bifunctional Sesquiterpene/Diterpene Synthase Agr2 from Cyclocybe aegerita Gives Rise to the Novel Diterpene Cyclocybene

Cyclocybe aegerita is a model mushroom belonging to the fungal phylum Basidiomycota. Among others, C. aegerita is known for its diverse terpenome, containing various volatile and nonvolatile terpenes and terpenoids. Here, we deepen the knowledge on their biosynthetic pathways by studying the terpene synthase Agr2 in detail. In contrast to previous studies, the heterologous production of Agr2 in the agaric host Coprinopsis cinerea revealed the production of two terpenes, one of which was the already known sesquiterpene viridiflorene. The other one was a so far unknown diterpene that had to be isolated and purified by means of preparative RP-HPLC for structure elucidation. 1D- and 2D-NMR experiments revealed the compound as the novel diterpene cyclocybene, pointing to the bifunctionality of Agr2 to produce both a sesquiterpene and a diterpene.

Recent advancements in mogrosides: A review on biological activities, synthetic biology, and applications in the food industry

Mogrosides are low-calorie, biologically active sweeteners that face high production costs due to strict cultivation requirements and the low yield of monk fruit. The rapid advancement in synthetic biology holds the potential to overcome this challenge. This review presents mogrosides exhibiting antioxidant, anti-inflammatory, anti-cancer, anti-diabetic, and liver protective activities, with their efficacy in diabetes treatment surpassing that of Xiaoke pills (a Chinese diabetes medication). It also discusses the latest elucidated biosynthesis pathways of mogrosides, highlighting the challenges and research gaps in this field. The critical and most challenging step in this pathway is the transformation of mogrol into a variety of mogrosides by different UDP-glucosyltransferases (UGTs), primarily hindered by the poor substrate selectivity, product specificity, and low catalytic efficiency of current UGTs. Finally, the applications of mogrosides in the current food industry and the challenges they face are discussed.

Effect of Hemp Extraction Procedures on Cannabinoid and Terpenoid Composition

A variety of techniques have been developed to extract hemp phytochemicals for research and consumption. Some of the most common processes in the industry include supercritical CO2 extraction, hydrodistillation, and solvent-based (ethanol) extractions. Each of these processes has the potential to differentially extract various phytochemicals, which would impact their efficacy, tolerability, and safety. However, despite these differences, there has been no direct comparison of the methods and the resulting phytochemical composition. This work aimed to compare cannabinoid and terpene profiles using the three primary commercial procedures, using hemp inflorescence from a CBD/CBG dominant Cannabis sativa L. cultivar. Extracts were then evaluated for their terpene and cannabinoid content using GC-MS and LC-MS/MS, respectively. Hydrodistilled extracts contained the most variety and abundance of terpenes with β-caryophyllene to be the most concentrated terpene (25-42 mg/g). Supercritical CO2 extracts displayed a minimal variety of terpenes, but the most variety and abundance of cannabinoids with CBD ranging from 12.8-20.6 mg/g. Ethanol extracts contained the most acidic cannabinoids with 3.2-4.1 mg/g of CBDA along with minor terpene levels. The resulting extracts demonstrated substantially different chemical profiles and highlight how the process used to extract hemp can play a large role in product composition and potential biological effects.

Plant-Derived Antimicrobials and Their Crucial Role in Combating Antimicrobial Resistance

Antibiotic resistance emerged shortly after the discovery of the first antibiotic and has remained a critical public health issue ever since. Managing antibiotic resistance in clinical settings continues to be challenging, particularly with the rise of superbugs, or bacteria resistant to multiple antibiotics, known as multidrug-resistant (MDR) bacteria. This rapid development of resistance has compelled researchers to continuously seek new antimicrobial agents to curb resistance, despite a shrinking pipeline of new drugs. Recently, the focus of antimicrobial discovery has shifted to plants, fungi, lichens, endophytes, and various marine sources, such as seaweeds, corals, and other microorganisms, due to their promising properties. For this review, an extensive search was conducted across multiple scientific databases, including PubMed, Elsevier, ResearchGate, Scopus, and Google Scholar, encompassing publications from 1929 to 2024. This review provides a concise overview of the mechanisms employed by bacteria to develop antibiotic resistance, followed by an in-depth exploration of plant secondary metabolites as a potential solution to MDR pathogens. In recent years, the interest in plant-based medicines has surged, driven by their advantageous properties. However, additional research is essential to fully understand the mechanisms of action and verify the safety of antimicrobial phytochemicals. Future prospects for enhancing the use of plant secondary metabolites in combating antibiotic-resistant pathogens will also be discussed.

Simulation-Guided Engineering Enables a Functional Switch in Selinadiene Synthase toward Hydroxylation

Engineering sesquiterpene synthases to form predefined alternative products is a major challenge due to their diversity in cyclization mechanisms and our limited understanding of how amino acid changes affect the steering of these mechanisms. Here, we use a combination of atomistic simulation and site-directed mutagenesis to engineer a selina-4(15),7(11)-diene synthase (SdS) such that its final reactive carbocation is quenched by trapped active site water, resulting in the formation of a complex hydroxylated sesquiterpene (selin-7(11)-en-4-ol). Initially, the SdS G305E variant produced 20% selin-7(11)-en-4-ol. As suggested by modeling of the enzyme-carbocation complex, selin-7(11)-en-4-ol production could be further improved by varying the pH, resulting in selin-7(11)-en-4-ol becoming the major product (48%) at pH 6.0. We incorporated the SdS G305E variant along with genes from the mevalonate pathway into bacterial BL21(DE3) cells and demonstrated the production of selin-7(11)-en-4-ol at a scale of 10 mg/L in batch fermentation. These results highlight opportunities for the simulation-guided engineering of terpene synthases to produce predefined complex hydroxylated sesquiterpenes.

Coatings Based on Essential Oils for Combating Antibiotic Resistance

In the current era of widespread antimicrobial resistance, the utilization of essential oils (EOs) derived from plants has emerged as a promising alternative in combating pathogens that have developed resistance to antibiotics. This review explores the therapeutic potential of essential oils as valuable tools in restoring the efficacy of antibiotics, highlighting their unique ability to affect bacteria in multiple ways and target various cellular systems. Despite the challenge of elucidating their precise mode of action, EOs have shown remarkable results in rigorous testing against a diverse range of bacteria. This review explores the multifaceted role of EOs in combating bacterial microorganisms, emphasizing their extraction methods, mechanisms of action, and comparative efficacy against synthetic antibiotics. Key findings underscore the unique strategies EOs deploy to counter bacteria, highlighting significant differences from conventional antibiotics. The review extends to advanced coating solutions for medical devices, exploring the integration of EO formulations into these coatings. Challenges in developing effective EO coatings are addressed, along with various innovative approaches for their implementation. An evaluation of these EO coatings reveals their potential as formidable alternatives to traditional antibacterial agents in medical device applications. This renaissance in exploring natural remedies emphasizes the need to combine traditional wisdom with modern scientific advancements to address the urgent need for effective antimicrobial solutions in the post-antibiotic era.

Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase

cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.

Unlocking the genomic potential of Red Sea coral probiotics

The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.

Genomic analysis based on chromosome-level genome assembly reveals Myrtaceae evolution and terpene biosynthesis of rose myrtle

BACKGROUND

Rose myrtle (Rhodomyrtus tomentosa (Ait.) Hassk), is an evergreen shrub species belonging to the family Myrtaceae, which is enriched with bioactive volatiles (α-pinene and β-caryophyllene) with medicinal and industrial applications. However, the mechanism underlying the volatile accumulation in the rose myrtle is still unclear.

RESULTS

Here, we present a chromosome-level genomic assembly of rose myrtle (genome size = 466 Mb, scaffold N50 = 43.7 Mb) with 35,554 protein-coding genes predicted. Through comparative genomic analysis, we found that gene expansion and duplication had a potential contribution to the accumulation of volatile substances. We proposed that the action of positive selection was significantly involved in volatile accumulation. We identified 43 TPS genes in R. tomentosa. Further transcriptomic and TPS gene family analyses demonstrated that the distinct gene subgroups of TPS may contribute greatly to the biosynthesis and accumulation of different volatiles in the Myrtle family of shrubs and trees. The results suggested that the diversity of TPS-a subgroups led to the accumulation of special sesquiterpenes in different plants of the Myrtaceae family.

CONCLUSIONS

The high quality chromosome-level rose myrtle genome and the comparative analysis of TPS gene family open new avenues for obtaining a higher commercial value of essential oils in medical plants.

A comprehensive review of the molecular and genetic mechanisms underlying gum and resin synthesis in Ferula species

Ferula spp. are plants that produce oleo-gum-resins (OGRs), which are plant exudates with various colors. These OGRs have various industrial applications in pharmacology, perfumery, and food. The main constituents of these OGRs are terpenoids, a diverse group of organic compounds with different structures and functions. The biosynthesis of OGRs in Ferula spp., particularly galbanum, holds considerable economic and ecological importance. However, the molecular and genetic underpinnings of this biosynthetic pathway remain largely enigmatic. This review provides an overview of the current state of knowledge on the biosynthesis of OGRs in Ferula spp., highlighting the major enzymes, genes, and pathways involved in the synthesis of different terpenoid classes, such as monoterpenes, sesquiterpenes, and triterpenes. It also examines the potential of using omics techniques, such as transcriptomics and metabolomics, and genome editing tools, such as CRISPR/Cas, to increase the yield and quality of Ferula OGRs, as well as to create novel bioactive compounds with enhanced properties. Moreover, this review addresses the current challenges and opportunities of applying gene editing in Ferula spp., and suggests some directions for future research and development.

Gas Chromatography-Mass Spectrometry Metabolites and Transcriptome Profiling Reveal Molecular Mechanisms and Differences in Terpene Biosynthesis in Two Torrya grandis Cultivars during Postharvest Ripening

Terpene aroma compounds are key quality attributes of postharvest Torreya grandis nuts, contributing to their commercial value. However, terpene biosynthesis and regulatory networks in different T. grandis cvs. are still poorly understood. Here, chief cvs. 'Xi Fei' and 'Xiangya Fei' were investigated for their differences in terpene biosynthesis and gene expression levels during postharvest ripening using headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) and transcriptomic datasets. A total of 28 and 22 aroma compounds were identified in 'Xi Fei' and 'Xiangya Fei', respectively. Interestingly, differences in aroma composition between the two cvs. were mostly attributed to D-limonene and α-pinene levels as key determinants in Torreya nuts' flavor. Further, transcriptome profiling, correlation analysis, and RT-qPCR annotated two novel genes, TgTPS1 in 'Xi Fei' and TgTPS2 in 'Xiangya Fei', involved in terpene biosynthesis. In addition, six transcription factors (TFs) with comparable expression patterns to TgTPS1 and four TFs to TgTPS2 were identified via correlation analysis of a volatile and transcriptome dataset to be involved in terpene biosynthesis. Our study provides novel insight into terpene biosynthesis and its regulation at the molecular level in T. grandis nut and presents a valuable reference for metabolic engineering and aroma improvement in this less explored nut.

Traditional Uses, Phytochemistry, and Pharmacological Activities of Vernonia cinerea (L.) Less.: An Updated Review

Vernonia cinerea (L.) Less. is a perennial herbaceous plant found mainly in tropical areas, particularly in Southeast Asia, South America, and India. Various parts of V. cinerea have traditionally been used in folk medicine to treat several diseases, such as malaria, fever, and liver diseases. V. cinerea has so far yielded about 92 secondary metabolites. The majority of these are sesquiterpene lactones, but triterpenes, flavonoids, steroids, phenolics, and other compounds are present as well. V. cinerea crude extracts reportedly exhibit anti-inflammatory, antiprotozoal, antidiabetic, anticancer, antimicrobial, antioxidant, and renoprotective activities. This study aims to provide the latest up-to-date information on the botanical characterization, distribution, traditional uses, phytochemistry, and pharmacological activity of V. cinerea. Information on V. cinerea was thoroughly reviewed. The literature published between 1950 and 2024 was compiled through online bibliographic databases, including SciFinder, Web of Science, Google Scholar, PubMed, ScienceDirect, Springer Link, Wiley, and the MDPI online library. The keywords used for the literature search included Vernonia cinerea (L.) Less. and the synonyms Cyanthillium cinereum (L.) H.Rob., Conyza cinerea L., and various others.

Ancestral terpene cyclases: From fundamental science to applications in biosynthesis

Terpenes constitute one of the largest family of natural products with potent applications as renewable platform chemicals and medicines. The low activity, selectivity and stability displayed by terpene biosynthetic machineries can constitute an obstacle towards achieving expedient biosynthesis of terpenoids in processes that adhere to the 12 principles of green chemistry. Accordingly, engineering of terpene synthase enzymes is a prerequisite for industrial biotechnology applications, but obstructed by their complex catalysis that depend on reactive carbocationic intermediates that are prone to undergo bifurcation mechanisms. Rational redesign of terpene synthases can be tedious and requires high-resolution structural information, which is not always available. Furthermore, it has proven difficult to link sequence space of terpene synthase enzymes to specific product profiles. Herein, the author shows how ancestral sequence reconstruction (ASR) can favorably be used as a protein engineering tool in the redesign of terpene synthases without the need of a structure, and without excessive screening. A detailed workflow of ASR is presented along with associated limitations, with a focus on applying this methodology on terpene synthases. From selected examples of both class I and II enzymes, the author advocates that ancestral terpene cyclases constitute valuable assets to shed light on terpene-synthase catalysis and in enabling accelerated biosynthesis.

Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique

Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.

Climbing the Oxidase Phase Ladder by Using Dioxygen as the Sole Oxidant: The Case Study of Costunolide

Natural sesquiterpenoid lactones are prominent scaffolds in drug discovery. Despite the progress made in their synthesis, their extensive oxidative decoration makes their chemo- and stereoselective syntheses highly challenging. Herein, we report our effort to mimic part of the oxidase phase used in the costunolide pathway to achieve the protecting-group-free total synthesis of santamarine, dehydrocostus lactone, estafiatin, and nine more related natural sesquiterpenoid lactones by using dioxygen as the sole oxidant.

Functional and Mechanistic Characterization of the 4,5-diepi-Isoishwarane Synthase from the Liverwort Radula lindenbergiana

The microbial type sesquiterpene synthase RlMTPSL4 from the liverwort Radula lindenbergiana was investigated for its products, showing the formation of several sesquiterpene hydrocarbons. The main product was structurally characterized as the new compound 4,5-diepi-isoishwarane, while the side products included the known hydrocarbons germacrene A, α-selinene, eremophilene and 4,5-diepi-aristolochene. The cyclization mechanism towards 4,5-diepi-isoishwarane catalyzed by RlMTPSL4 was investigated through isotopic labeling experiments, revealing the stereochemical course for the deprotonation step to the neutral intermediate germacrene A, a reprotonation for its further cyclization, and a 1,2-hydride shift along the cascade. The absolute configuration of 4,5-diepi-isoishwarane was determined using a stereoselective deuteration approach, revealing an absolute configuration typically observed for a microbial type sesquiterpene.

Class II terpene cyclases: structures, mechanisms, and engineering

Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.

Deciphering magnesium binding site and structure-function insights in a class II sesquiterpene cyclase

Magnesium ions (Mg2+) are crucial in class II terpene cyclases that utilize substrates with diphosphate groups. Interestingly, these enzymes catalyze reactions without cleaving the diphosphate group, instead initiating the reaction through protonation. In our recent research, we discovered a novel class II sesquiterpene cyclase in Streptomyces showdoensis. Notably, we determined its crystal structure and identified Mg2+ within its active site. This finding has shed light on the previously elusive question of Mg2+ binding in class II terpene cyclases. In this chapter, we outline our methods for discovering this novel enzyme, including steps for its purification, crystallization, and kinetic analysis.

Evaluation of spontaneous exploratory and anxiety-related behaviors of mice treated with gymnopilins obtained from the mushroom Gymnopilus imperialis (Agaricomycetes, Basidiomycota)

Gymnopilins are long chain oligoisoprenoids produced through the condensation of isoprene units from MEV and MEP biosynthetic pathways. In Gymnopilus, these carotenoid-like molecules are recognized as major compounds in some species. In the present study, oligoisoprenoids derived from gymnopilins were dereplicated from Gymnopilus imperialis, a mushroom-forming basidiomycete, using liquid chromatographic coupled with high-resolution mass spectrometry (tandem LC-HRMS/MS) and GNPS. From the dichloromethane extract (Gym-DCM) of G. imperialis we annotated 3 oligoisoprenoids from the GNPS molecular library spectra and 15 analogs from the curation of the molecular networking. Data from NMR spectroscopic of the extract confirmed the annotation of the metabolites. Based on the literature data suggesting the neurotoxic effect of gymnopilins, we investigated the effects of the administering different doses of gymnopilin extracts (1, 4 or 10 mg/kg) and diazepam (4 mg/kg) on the acquisition of object recognition memory (ORM) in mice. By studying novel object recognition memory (ORM), a type of non-aversive memory. ORM was assessed based on the total time of spontaneous exploration of both objects, the discrimination index (DI), and the frequency of contact with both objects. Our present findings reveal, for the first time, that gymnopilins treatment before training modulates ORM in a dose-dependent manner. It is also suggested that differential effects on memory might be related to differential effects on GABAA receptors but do not exclude its effects in other neurotransmitter systems. Another class of secondary metabolites, alkaloids, might modulate AChR, which is essential for maintaining object recognition memory over time.

Mechanistic characterisation of a sesquiterpene synthase for asterisca-1,6-diene from the liverwort Radula lindenbergiana and implications for pentalenene biosynthesis

A sesquiterpene synthase from the liverwort Radula lindenbergiana was characterised and shown to produce the new sesquiterpene hydrocarbon (3R,9R)-asterisca-1,6-diene, besides small amounts of pentalenene. The biosynthesis of asterisca-1,6-diene was studied through isotopic labelling experiments, giving additional insights into the long discussed biosynthesis of pentalenene.

The Promiscuity of Squalene Synthase-Like Enzyme: Dehydrosqualene Synthase, a Natural Squalene Hyperproducer?

Dehydrosqualene synthase (CrtM), as a squalene synthase-like enzyme from Staphylococcus aureus, can naturally utilize farnesyl diphosphate to produce dehydrosqualene (C30H48). However, no study has documented the natural production of squalene (C30H50) by CrtM. Here, based on an HPLC-Q-Orbitrap-MS/MS study, we report that the expression of crtM in vitro or in Bacillus subtilis 168 both results in the output of squalene, dehydrosqualene, and phytoene (C40H64). Notably, wild-type CrtM exhibits a significantly higher squalene yield compared to squalene synthase (SQS) from Bacillus megaterium with an approximately 2.4-fold increase. Moreover, the examination of presqualene diphosphate's stereostructures in both CrtM and SQS enzymes provides further understanding into the presence of multiple identified terpenoids. In summary, this study not only provides insights into the promiscuity demonstrated by squalene synthase-like enzymes but also highlights a new strategy of utilizing CrtM as a potential replacement for SQS in cell factories, thereby enhancing squalene production.

Use of Essential Oils to Counteract the Phenomena of Antimicrobial Resistance in Livestock Species

Antimicrobial resistance is an increasingly widespread phenomenon that is of particular concern because of the possible consequences in the years to come. The dynamics leading to the resistance of microbial strains are diverse, but certainly include the incorrect use of veterinary drugs both in terms of dosage and timing of administration. Moreover, the drug is often administered in the absence of a diagnosis. Many active ingredients in pharmaceutical formulations are, therefore, losing their efficacy. In this situation, it is imperative to seek alternative treatment solutions. Essential oils are mixtures of compounds with different pharmacological properties. They have been shown to possess the antibacterial, anti-parasitic, antiviral, and regulatory properties of numerous metabolic processes. The abundance of molecules they contain makes it difficult for treated microbial species to develop pharmacological resistance. Given their natural origin, they are environmentally friendly and show little or no toxicity to higher animals. There are several published studies on the use of essential oils as antimicrobials, but the present literature has not been adequately summarized in a manuscript. This review aims to shed light on the results achieved by the scientific community regarding the use of essential oils to treat the main agents of bacterial infection of veterinary interest in livestock. The Google Scholar, PubMed, SciELO, and SCOPUS databases were used for the search and selection of studies. The manuscript aims to lay the foundations for a new strategy of veterinary drug use that is more environmentally friendly and less prone to the emergence of drug resistance phenomena.

Characterization of a Unique Pair of Ferredoxin and Ferredoxin NADP+ Reductase Isoforms That Operates in Non-Photosynthetic Glandular Trichomes

Our recent investigations indicated that isoforms of ferredoxin (Fd) and ferredoxin NADP+ reductase (FNR) play essential roles for the reductive steps of the 2C-methyl-D-erythritol 4-phosphate (MEP) pathway of terpenoid biosynthesis in peppermint glandular trichomes (GTs). Based on an analysis of several transcriptome data sets, we demonstrated the presence of transcripts for a leaf-type FNR (L-FNR), a leaf-type Fd (Fd I), a root-type FNR (R-FNR), and two root-type Fds (Fd II and Fd III) in several members of the mint family (Lamiaceae). The present study reports on the biochemical characterization of all Fd and FNR isoforms of peppermint (Mentha × piperita L.). The redox potentials of Fd and FNR isoforms were determined using photoreduction methods. Based on a diaphorase assay, peppermint R-FNR had a substantially higher specificity constant (kcat/Km) for NADPH than L-FNR. Similar results were obtained with ferricyanide as an electron acceptor. When assayed for NADPH-cytochrome c reductase activity, the specificity constant with the Fd II and Fd III isoforms (when compared to Fd I) was slightly higher for L-FNR and substantially higher for R-FNR. Based on real-time quantitative PCR assays with samples representing various peppermint organs and cell types, the Fd II gene was expressed very highly in metabolically active GTs (but also present at lower levels in roots), whereas Fd III was expressed at low levels in both roots and GTs. Our data provide evidence that high transcript levels of Fd II, and not differences in the biochemical properties of the encoded enzyme when compared to those of Fd III, are likely to support the formation of copious amounts of monoterpene via the MEP pathway in peppermint GTs. This work has laid the foundation for follow-up studies to further investigate the roles of a unique R-FNR-Fd II pair in non-photosynthetic GTs of the Lamiaceae.

Methods for the preparation and analysis of a bifunctional class II diterpene synthase, copalyl diphosphate synthase from Penicillium fellutanum

Terpenes comprise the largest class of natural products and are used in applications spanning the areas of medicine, cosmetics, fuels, flavorings, and more. Copalyl diphosphate synthase from the Penicillium genus is the first bifunctional terpene synthase identified to have both prenyltransferase and class II cyclase activities within the same polypeptide chain. Prior studies of bifunctional terpene synthases reveal that these systems achieve greater catalytic efficiency by channeling geranylgeranyl diphosphate between the prenyltransferase and cyclase domains. A molecular-level understanding of substrate transit phenomena in these systems is highly desirable, but a long disordered polypeptide segment connecting the prenyltranferase and cyclase domains thwarts the crystallization of full-length enzymes. Accordingly, these systems are excellent candidates for structural analysis using cryo-electron microscopy (cryo-EM). Notably, these systems form hexameric or octameric oligomers, so the quaternary structure of the full-length enzyme may influence substrate transit between catalytic domains. Here, we describe methods for the preparation of bifunctional hexameric copalyl diphosphate synthase from Penicillium fellutanum (PfCPS). We also outline approaches for the preparation of cryo-EM grids, data collection, and data processing to yield two-dimensional and three-dimensional reconstructions.

Integrative metabolome and transcriptome analyses reveal the differences in flavonoid and terpenoid synthesis between Glycyrrhiza uralensis (licorice) leaves and roots

Licorice from Glycyrrhiza uralensis roots is used in foods and medicines. Although we are aware that licorice roots and leaves have distinct material compositions, the specific reasons for these differences remain unknown. Comparison of the metabolomes and transcriptomes between the leaves and roots revealed flavonoids and triterpenoid saponins were significantly different. Isoflavones were enriched in roots because of upregulation of genes encoding chalcone isomerase and flavone synthase, which are involved in isoflavone synthesis. Six triterpenoid saponins were significantly enriched only in the roots. The leaves did not accumulate glycyrrhetinic acid because of low expression levels of genes involved in its synthesis. A gene encoding a UDP glycosyltransferase, which likely catalyzes the key step in the transformation of glycyrrhetinic acid to glycyrrhizin, was screened. Our results provide information about the differences in flavonoid and triterpenoid synthesis between roots and leaves, and highlight targets for genetic engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01467-y.

Methods for the preparation and analysis of the diterpene cyclase fusicoccadiene synthase

Prenyltransferases are terpene synthases that combine 5-carbon precursor molecules into linear isoprenoids of varying length that serve as substrates for terpene cyclases, enzymes that catalyze fascinating cyclization reactions to form diverse terpene natural products. Terpenes and their derivatives comprise the largest class of natural products and have myriad functions in nature and diverse commercial uses. An emerging class of bifunctional terpene synthases contains both prenyltransferase and cyclase domains connected by a disordered linker in a single polypeptide chain. Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is one of the most well-characterized members of this subclass and serves as a model system for the exploration of structure-function relationships. PaFS has been structurally characterized using a variety of biophysical techniques. The enzyme oligomerizes to form a stable core of six or eight prenyltransferase domains that produce a 20-carbon linear isoprenoid, geranylgeranyl diphosphate (GGPP), which then transits to the cyclase domains for the generation of fusicoccadiene. Cyclase domains are in dynamic equilibrium between randomly splayed-out and prenyltransferase-associated positions; cluster channeling is implicated for GGPP transit from the prenyltransferase core to the cyclase domains. In this chapter, we outline the methods we are developing to interrogate the nature of cluster channeling in PaFS, including enzyme activity and product analysis assays, approaches for engineering the linker segment connecting the prenyltransferase and cyclase domains, and structural analysis by cryo-EM.

Comparative Genome analysis of the Genus Curvibacter and the Description of Curvibacter microcysteis sp. nov. and Curvibacter cyanobacteriorum sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43T, HBC28, and HBC61T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43T, HBC28, and HBC61T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43T and HBC61T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43T =KCTC 92793T=LMG 32714T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61T =KCTC 92794T =LMG 32713T) are proposed.

Nucleophilic aromatization of monoterpenes from isoprene under nickel/iodine cascade catalysis

As a large number of organic compounds possessing two isoprene units, monoterpenes and monoterpenoids play important roles in pharmaceutical, cosmetic, agricultural, and food industries. In nature, monoterpenes are constructed from geranyl pyrophosphate (C10) via various transformations. Herein, the bulk C5 chemical-isoprene, is used for the creation of various monoterpenoids via a nucleophilic aromatization of monoterpenes under cascade catalysis of nickel and iodine. Drugs and oil mixtures from conifer and lemon can be convergently transformed to the desired monoterpenoid. Preliminary mechanistic studies are conducted to get insights about reaction pathway. Two types of cyclic monoterpenes can be respectively introduced onto two similar heterocycles via orthogonal C-H functionalization. And various hybrid terpenyl indoles are programmatically assembled from abundant C5 or C10 blocks. This work not only contributes a high chemo-, regio-, and redox-selective transformation of isoprene, but also provides a complementary approach for the creation of unnatural monoterpenoids.

An overview of food lipids toward food lipidomics

Increasing evidence regarding lipids' beneficial effects on human health has changed the common perception of consumers and dietary officials about the role(s) of food lipids in a healthy diet. However, lipids are a wide group of molecules with specific nutritional and bioactive properties. To understand their true nutritional and functional value, robust methods are needed for accurate identification and quantification. Specific analytical strategies are crucial to target specific classes, especially the ones present in trace amounts. Finding a unique and comprehensive methodology to cover the full lipidome of each foodstuff is still a challenge. This review presents an overview of the lipids nutritionally relevant in foods and new trends in food lipid analysis for each type/class of lipids. Food lipid classes are described following the LipidMaps classification, fatty acids, endocannabinoids, waxes, C8 compounds, glycerophospholipids, glycerolipids (i.e., glycolipids, betaine lipids, and triglycerides), sphingolipids, sterols, sercosterols (vitamin D), isoprenoids (i.e., carotenoids and retinoids (vitamin A)), quinones (i.e., coenzyme Q, vitamin K, and vitamin E), terpenes, oxidized lipids, and oxylipin are highlighted. The uniqueness of each food group: oil-, protein-, and starch-rich, as well as marine foods, fruits, and vegetables (water-rich) regarding its lipid composition, is included. The effect of cooking, food processing, and storage, in addition to the importance of lipidomics in food quality and authenticity, are also discussed. A critical review of challenges and future trends of the analytical approaches and computational methods in global food lipidomics as the basis to increase consumer awareness of the significant role of lipids in food quality and food security worldwide is presented.

Unravelling the Secrets of α-Pyrones from Aspergillus Fungi: A Comprehensive Review of Their Natural Sources, Biosynthesis, and Biological Activities

Aspergillus, one of the most product-rich and genetically robust genera, contains a diverse range of species with potential economic and ecological implications. Chemically, Aspergillus is one of the essential sources of polyketides, alkaloids, diphenyl ethers, diketopiperazines, and other miscellaneous compounds, displaying a variety of pharmacological activities. The α-pyrones are unsaturated six-membered lactones. Although α-pyrone has a small structure, it is responsible for the structural diversity of several natural and synthetic compounds and multiple biological activities. In this review, we have summarized approximately 178 α-pyrone containing metabolites derivatives identified/reported from terrestrial, marine, endophytic, and filamentous Aspergillus species, including their sources, biological properties, and biosynthetic pathways until mid-2023, for the first time. This review is the first to compile and analyze the available data on α-pyrone metabolites from Aspergillus, which could facilitate further research and innovation in this field. Additionally, it offers a valuable source of scaffolds for future bioactive drug development, as some of these metabolites have shown potent antimicrobial, anti-inflammatory, and anticancer effects. Therefore, this review has significant implications for the advancement of natural product chemistry, pharmacology, biotechnology, and medicine.

Secondary Metabolites and Their Role in Strawberry Defense

Strawberry is a high-value commercial crop and a model for the economically important Rosaceae family. Strawberry is vulnerable to attack by many pathogens that can affect different parts of the plant, including the shoot, root, flowers, and berries. To restrict pathogen growth, strawberry produce a repertoire of secondary metabolites that have an important role in defense against diseases. Terpenes, allergen-like pathogenesis-related proteins, and flavonoids are three of the most important metabolites involved in strawberry defense. Genes involved in the biosynthesis of secondary metabolites are induced upon pathogen attack in strawberry, suggesting their transcriptional activation leads to a higher accumulation of the final compounds. The production of secondary metabolites is also influenced by the beneficial microbes associated with the plant and its environmental factors. Given the importance of the secondary metabolite pathways in strawberry defense, we provide a comprehensive overview of their literature and their role in the defense responses of strawberry. We focus on terpenoids, allergens, and flavonoids, and discuss their involvement in the strawberry microbiome in the context of defense responses. We discuss how the biosynthetic genes of these metabolites could be potential targets for gene editing through CRISPR-Cas9 techniques for strawberry crop improvement.

Novosphingobium cyanobacteriorum sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, HBC54T, was isolated from periphyton during a Microcystis bloom. Based on the results of the 16S rRNA gene sequence analysis, strain HBC54T was closely related to Novosphingobium aerophilum 4Y4T (98.36 %), Novosphingobium aromaticivorans DSM 12444T (98.08 %), Novosphingobium huizhouense c7T (97.94 %), Novosphingobium percolationis c1T (97.65 %), Novosphingobium subterraneum DSM 12447T (97.58 %), Novosphingobium olei TW-4T (97.58 %) and Novosphingobium flavum UCT-28T (97.37 %). The average nucleotide identity and digital DNA-DNA hybridization values between HBC54T and its related type stains were below 78.97 and 23.7 %, which are lower than the threshold values for species delineation. The major fatty acids (>10.0 %) were identified as C14 : 0 2-OH, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and the respiratory quinone was ubiquinone Q-10. The main polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and three unidentified phospholipids. The genomic DNA G+C content was 64.8 mol%. Strain HBC54T is considered to represent a novel species within the genus Novosphingobium, for which the name Novosphingobium cyanobacteriorum sp. nov. is proposed. The type strain is HBC54T (=KCTC 92033T=LMG 32427T).

The Diversity of Gut Microbiota at Weaning Is Altered in Prolactin Receptor-Null Mice

Maternal milk supports offspring development by providing microbiota, macronutrients, micronutrients, immune factors, and hormones. The hormone prolactin (PRL) is an important milk component with protective effects against metabolic diseases. Because maternal milk regulates microbiota composition and adequate microbiota protect against the development of metabolic diseases, we aimed to investigate whether PRL/PRL receptor signaling regulates gut microbiota composition in newborn mice at weaning. 16SrRNA sequencing of feces and bioinformatics analysis was performed to evaluate gut microbiota in PRL receptor-null mice (Prlr-KO) at weaning (postnatal day 21). The normalized colon and cecal weights were higher and lower, respectively, in the Prlr-KO mice relative to the wild-type mice (Prlr-WT). Relative abundances (Simpson Evenness Index), phylogenetic diversity, and bacterial concentrations were lower in the Prlr-KO mice. Eleven bacteria species out of 470 differed between the Prlr-KO and Prlr-WT mice, with two genera (Anaerotruncus and Lachnospiraceae) related to metabolic disease development being the most common in the Prlr-KO mice. A higher metabolism of terpenoids and polyketides was predicted in the Prlr-KO mice compared to the Prlr-WT mice, and these metabolites had antimicrobial properties and were present in microbe-associated pathogenicity. We concluded that the absence of the PRL receptor altered gut microbiota, resulting in lower abundance and richness, which could contribute to metabolic disease development.

Photoredox-catalyzed diastereoselective dearomative prenylation and reverse-prenylation of electron-deficient indole derivatives

Prenylated and reverse-prenylated indolines are privileged scaffolds in numerous naturally occurring indole alkaloids with a broad spectrum of important biological properties. Development of straightforward and stereoselective methods to enable the synthesis of structurally diverse prenylated and reverse-prenylated indoline derivatives is highly desirable and challenging. In this context, the most direct approaches to achieve this goal generally rely on transition-metal-catalyzed dearomative allylic alkylation of electron-rich indoles. However, the electron-deficient indoles are much less explored, probably due to their diminished nucleophilicity. Herein, a photoredox-catalyzed tandem Giese radical addition/Ireland-Claisen rearrangement is disclosed. Diastereoselective dearomative prenylation and reverse-prenylation of electron-deficient indoles proceed smoothly under mild conditions. An array of tertiary α-silylamines as radical precursors is readily incorporated in 2,3-disubstituted indolines with high functional compatibility and excellent diastereoselectivity (>20:1 d.r.). The corresponding transformations of the secondary α-silylamines provide the biologically important lactam-fused indolines in one-pot synthesis. Subsequently, a plausible photoredox pathway is proposed based on control experiments. The preliminary bioactivity study reveals a potential anticancer property of these structurally appealing indolines.

Biosynthesis and Pharmacological Activities of Flavonoids, Triterpene Saponins and Polysaccharides Derived from Astragalus membranaceus

Astragalus membranaceus (A. membranaceus), a well-known traditional herbal medicine, has been widely used in ailments for more than 2000 years. The main bioactive compounds including flavonoids, triterpene saponins and polysaccharides obtained from A. membranaceus have shown a wide range of biological activities and pharmacological effects. These bioactive compounds have a significant role in protecting the liver, immunomodulation, anticancer, antidiabetic, antiviral, antiinflammatory, antioxidant and anti-cardiovascular activities. The flavonoids are initially synthesized through the phenylpropanoid pathway, followed by catalysis with corresponding enzymes, while the triterpenoid saponins, especially astragalosides, are synthesized through the universal upstream pathways of mevalonate (MVA) and methylerythritol phosphate (MEP), and the downstream pathway of triterpenoid skeleton formation and modification. Moreover, the Astragalus polysaccharide (APS) possesses multiple pharmacological activities. In this review, we comprehensively discussed the biosynthesis pathway of flavonoids and triterpenoid saponins, and the structural features of polysaccharides in A. membranaceus. We further systematically summarized the pharmacological effects of bioactive ingredients in A. membranaceus, which laid the foundation for the development of clinical candidate agents. Finally, we proposed potential strategies of heterologous biosynthesis to improve the industrialized production and sustainable supply of natural products with pharmacological activities from A. membranaceus, thereby providing an important guide for their future development trend.

Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance

Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.

The Potential of Allelochemicals from Microalgae for Biopesticides

Improvements in agricultural productivity are required to meet the demand of a growing world population. Phytopathogens, weeds, and insects are challenges to agricultural production. The toxicity and widespread application of persistent synthetic pesticides poses a major threat to human and ecosystem health. Therefore, sustainable strategies to control pests are essential for agricultural systems to enhance productivity within a green paradigm. Allelochemicals are a less persistent, safer, and friendly alternative to efficient pest management, as they tend to be less toxic to non-target organisms and more easily degradable. Microalgae produce a great variety of allelopathic substances whose biocontrol potential against weeds, insects, and phytopathogenic fungi and bacteria has received much attention. This review provides up-to-date information and a critical perspective on allelochemicals from microalgae and their potential as biopesticides.

Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species

Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.

Antioxidant and Anti-Inflammatory Properties of Phytochemicals Found in the Yucca Genus

The Yucca genus encompasses about 50 species native to North America. Species within the Yucca genus have been used in traditional medicine to treat pathologies related to inflammation. Despite its historical use and the popular notion of its antioxidant and anti-inflammatory properties, there is a limited amount of research on this genus. To better understand these properties, this work aimed to analyze phytochemical composition through documentary research. This will provide a better understanding of the molecules and the mechanisms of action that confer such antioxidant and anti-inflammatory properties. About 92 phytochemicals present within the genus have reported antioxidant or anti-inflammatory effects. It has been suggested that the antioxidant and anti-inflammatory properties are mainly generated through its free radical scavenging activity, the inhibition of arachidonic acid metabolism, the decrease in TNF-α (Tumor necrosis factor-α), IL-6 (Interleukin-6), iNOS (Inducible nitric oxide synthase), and IL-1β (Interleukin 1β) concentration, the increase of GPx (Glutathione peroxidase), CAT (Catalase), and SOD (Superoxide dismutase) concentration, and the inhibition of the MAPK (Mitogen-Activated Protein Kinase), and NF-κB (Nuclear factor kappa B), and the activation of the Nrf2 (Nuclear factor erythroid 2-related factor) signaling pathway. These studies provide evidence of its use in traditional medicine against pathologies related to inflammation. However, more models and studies are needed to properly understand the activity of most plants within the genus, its potency, and the feasibility of its use to help manage or treat chronic inflammation.

Persicamidines-Unprecedented Sesquarterpenoids with Potent Antiviral Bioactivity against Coronaviruses

A new family of highly unusual sesquarterpenoids (persicamidines A-E) exhibiting significant antiviral activity was isolated from a newly discovered actinobacterial strain, Kibdelosporangium persicum sp. nov., collected from a hot desert in Iran. Extensive NMR analysis unraveled a hexacyclic terpenoid molecule with a modified sugar moiety on one side and a highly unusual isourea moiety fused to the terpenoid structure. The structures of the five analogues differed only in the aminoalkyl side chain attached to the isourea moiety. Persicamidines A-E showed potent activity against hCoV-229E and SARS-CoV-2 viruses in the nanomolar range together with very good selectivity indices, making persicamidines promising as starting points for drug development.

CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.

In Silico Prediction of Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Streptomyces thinghirensis HM3 Isolated from Arid Soil

Natural products produced by microorganisms are considered an important resource of bioactive secondary metabolites, such as anticancer, antifungal, antibiotic, and immunosuppressive molecules. Streptomyces are the richest source of bioactive natural products via possessing a wide number of secondary metabolite biosynthetic gene clusters (SM-BGCs). Based on rapid development in sequencing technologies with advances in genome mining, exploring the newly isolated Streptomyces species for possible new secondary metabolites is mandatory to find novel natural products. The isolated Streptomyces thinghirensis strain HM3 from arid and sandy texture soil in Qassim, SA, exerted inhibition activity against tested animal pathogenic Gram-positive bacteria and pathogenic fungal species. In this study, we report the draft genome of S. thinghirensis strain HM3, which consists of 7,139,324 base pairs (bp), with an average G+C content of 71.49%, predicting 7949 open reading frames, 12 rRNA operons (5S, 16S, 23S) and 60 tRNAs. An in silico analysis of strain HM3 genome by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase (PKS), two non-ribosomal peptide synthetase (NRPS) cluster)/NRPS-like fragment, two RiPP/RiPP-like (ribosomally synthesised and post-translationally modified peptide product), two butyrolactone, one CDPS (tRNA-dependent cyclodipeptide synthases), and one other (cluster containing a secondary metabolite-related protein that does not fit into any other category) BGC. The presented BGCs inside the genome, along with antibacterial and antifungal activity, indicate that HM3 may represent an invaluable source for new secondary metabolites.