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Ganoderic triterpenoid (GT) is a promising anti-tumour constituent of Ganoderma lucidum. GT accumulation occurs following stressors that include various elicitors or signalling molecules. Understanding the signal transduction pathways underlying elicitor-induced GT production will be helpful for commercial GT production. In this study, the activation of GT biosynthetic genes and GT accumulation mediated by biotic and abiotic elicitors will be investigated. Jasmonic acid (JA) is a well-known signalling molecule that is primarily involved in GT accumulation. Ca2+ spiking and reactive oxygen species (ROS), nitric oxide (NO) and cAMP production are other messengers that mediate GT production. This review highlights the elicitation strategies for GT production based on the principle of putative signal transduction pathways and the fundamental role of JA, ROS, NO, Ca2+, cAMP and their crosstalk in G. lucidum cells. In the future, elucidating the regulatory networks that control the secondary metabolite biosynthesis is therefore an important goal to manipulate the accumulation of GT.

Summary Vegetable oils extracted from oilseeds are an important component of foods, but are also used in a range of high value oleochemical applications. Despite being biodegradable, nontoxic and renewable current plant oils suffer from the presence of residual polyunsaturated fatty acids that are prone to free radical formation that limit their oxidative stability, and consequently shelf life and functionality. Many decades of plant breeding have been successful in raising the oleic content to ~90%, but have come at the expense of overall field performance, including poor yields. Here, we engineer superhigh oleic (SHO) safflower producing a seed oil with 93% oleic generated from seed produced in multisite field trials spanning five generations. SHO safflower oil is the result of seed‐specific hairpin‐based RNA interference of two safflower lipid biosynthetic genes, FAD2.2 and FATB, producing seed oil containing less than 1.5% polyunsaturates and only 4% saturates but with no impact on lipid profiles of leaves and roots. Transgenic SHO events were compared to non‐GM safflower in multisite trial plots with a wide range of growing season conditions, which showed no evidence of impact on seed yield. The oxidative stability of the field‐grown SHO oil produced from various sites was 50 h at 110°C compared to 13 h for conventional ~80% oleic safflower oils. SHO safflower produces a uniquely stable vegetable oil across different field conditions that can provide the scale of production that is required for meeting the global demands for high stability oils in food and the oleochemical industry.

Sunlight influences many morphological, biochemical and molecular changes in fruits and the most important is color change associated with the development of pigments. The exposure to sunlight influences the anthocyanin content of the fruit peel. With the aim to understand the influence of bagging of fruits on the mango peel color, anthocyanin and expression of anthocyanin biosynthetic genes, an experiment was conducted by covering fruits of red colored cv. ‘Lily’ with muslin cloth. The observations were recorded for fruits of control (non-bagged) and fruits developing in shade. In bagged fruits, the color of peel changed towards lightness and yellowness. The reduction in anthocyanin was observed up to 17 times in bagged and shaded fruits. We also observed the down-regulation of all anthocyanin biosynthetic genes in fruits under bagged and shaded conditions. This study reports the influence of bagging and shade on anthocyanin biosynthetic genes and subsequent change in the color of fruit peel.

Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the secondary metabolites in plants may have distinct advantages over microbial production platforms, and thus propose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels: introducing biosynthetic genes, using transcription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.

Microorganisms mainly fungi considered the most natural inhabitants of diverse environments exhibit enormous interactions capabilities to produce active molecules. However, these substances are typically produced only in limited amounts by their native hosts. The native organisms may also be difficult to cultivate and genetically engineer, and some can produce undesirable toxic bio-products. The biologically active secondary metabolites from endophytic fungi showed several kinds of bioactivities, comprising antimicrobial, anti-tumor, anti-inflammatory, immunomodulatory and anti-diabetes, developing functional constipation activities. Particularly, the novel biotechnological procedures including co-cultivation and various fermentation strategies to enhance fungal biomass and subsequently increasing valuable active products with maximum yields, have been paid more and more attention by scientists and researchers, but most endophytic fungi appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely invisible through regulatory silencing of biosynthetic genes for secondary metabolites production. This review introduced the biologically active metabolites and their main classes from fungi through artificial manipulation methods, effects and substrates, in recent years, and then the relationships between active molecules and their bio activity effects were also discussed.

Cotton seeds are important for the yield of fiber, oil, and protein. Previous studies have shown that phytosterols play important roles in fiber growth. However, the functions of phytosterols in cotton seed development remain to be elucidated. In this study, we detected the phytosterol content of cotton seeds at various developmental stages by gas chromatography–mass spectrometry (GC–MS). We found that the contents of sitosterol and campesterol were higher in the stages from 5 to 25 days post-anthesis (DPA) and decreased rapidly after 25 DPA. Moreover, the ratio of campesterol to sitosterol was low before 15 DPA and high at 20 and 25 DPA. During the early developmental stages of cotton seeds, sitosterol and campesterol are the predominant phytosterols, and the sitosterol content is much higher than that of campesterol. In addition, we found that most phytosterol biosynthetic genes were highly expressed in 10-DPA and/or 20-DPA seeds by qRT-PCR, which was consistent with the phytosterol content in cotton seeds. When the cotton bud was treated with the sterol biosynthesis inhibitors tridemorph and fenpropimorph, the growth of cotton seeds was retarded. Moreover, overexpression of the phytosterol biosynthetic gene GhSMT2−1 significantly increased the size and weight of cotton seeds. These results indicate that phytosterols indeed participate in the regulation of cotton seed development.

Echinacea species are important medicinal plants with significant therapeutic potential and are widely used in the pharmaceutical industry. Different Echinacea species exhibit various chemical compositions and bioactivities. In the present study, the chemical differences, antioxidant ingredients, and diversity mechanisms of Echinacea species were studied. The aerial parts and roots of six different Echinacea species (E. purpurea (L.) Moench; E. pallida (Nutt.) Nutt.; E. angustifolia DC.; E. atrorubens (Nutt.) Nutt.; E. paradoxa (Norton) Britton var. paradoxa; E. sanguinea Nutt.) were collected for investigation. Through non-target metabolomics following targeted quantitative analysis, chicoric acid, caftaric acid, and echinacoside were found to be the main different components of Echinacea species. Coincidentally, these three chemicals were also the dominant antioxidant ingredients of Echinacea extracts, as determined by correlation analysis between chemical contents and in vitro antioxidant activities. Based on the cloning, sequencing, and measurement of the identified chicoric acid biosynthetic genes, the diversity of chicoric acid and caftaric acid among Echinacea species was determined by the precursor content, as well as by the expression levels of key biosynthetic genes. Overall, these results clarified the chemical differences and the possible mechanisms, as well as the bioactive ingredients, in Echinacea species and can guide the selection of Echinacea species for different industrial applications.

A new series comprising phenylacetyl-homoserine lactones (HSLs), caffeoyl-HSL and feruloyl-HSL, was biologically synthesized using an artificial de novo biosynthetic pathway. We developed an Escherichia coli system containing artificial biosynthetic pathways that yield phenylacetyl-HSLs from simple carbon sources. These artificial biosynthetic pathways contained the LuxI-type synthase gene (rpaI) in addition to caffeoyl-CoA and feruloyl-CoA biosynthetic genes, respectively. Finally, the yields for caffeoyl-HSL and feruloyl-HSL were 97.1 ± 10.3 and 65.2 ± 5.7 mg/l, respectively, by tyrosine-overproducing E. coli with a L-methionine feeding strategy. In a quorum sensing (QS) competition assay, feruloyl-HSL and p-coumaroyl-HSL antagonized the QS receptor TraR in Agrobacterium tumefaciens NT1, whereas caffeoyl-HSL did not.

Twenty Aspergillus niger strains were isolated from peanuts and 14 strains were able to completely inhibit AFB1 production with co-cultivation. By using a Spin-X centrifuge system, it was confirmed that there are some soluble signal molecules or antibiotics involved in the inhibition by A. niger, although they are absent during the initial 24h of A. flavus growth when it is sensitive to inhibition. In A. flavus, 19 of 20 aflatoxin biosynthetic genes were down-regulated by A. niger. Importantly, the expression of aflS was significantly down-regulated, resulting in a reduction of AflS/AflR ratio. The results suggest that A. niger could directly inhibit AFB1 biosynthesis through reducing the abundance of aflS to aflR mRNAs. Interestingly, atoxigenic A. flavus JZ2 and GZ15 effectively degrade AFB1. Two new metabolites were identified and the key toxic lactone and furofuran rings both were destroyed and hydrogenated, meaning that lactonase and reductase might be involved in the degradation process.

In the present study, efforts were made to determine effect of different light wavelengths on carotenoid biosynthesis in Scutellaria baicalensis, a promising traditional herbal medicine used in North America and Asia. The variation in the transcriptional level of carotenoid biosynthesis genes and carotenoid contents in the callus was analyzed after exposure to light from red (wavelength, 660 nm), blue (wavelength, 470 nm), or white (wavelength, 380 nm) light-emitting diodes. The transcription levels of phytoene synthase (SbPSY), ξ-carotene desaturase (SbZDS), β-ring carotene hydroxylase (SbCHXB), and zeaxanthin epoxidase (SbZEP) were upregulated on exposure to all three lights, with the greatest increase in expression observed upon exposure to blue light. In contrast, the transcriptional levels of two carotenoid cleavage dioxygenases (SbCCD1 and SbCCD4) decreased under all three light treatments. Increased production of zeaxanthin, β-carotene, and 9-cis-β-carotene was observed on exposure to all 3 lights. The total carotenoid production rose by 27.35% under blue light treatment, while the white and red lights did not have any considerable effect. Our findings may establish new approaches for increasing carotenoid production in S. baicalensis as well as in other plants.

Autoregulators are low-molecular-weight signaling compounds that control the production of many secondary metabolites in actinomycetes and have been referred to as 'Streptomyces hormones'. Here, potential producers of Streptomyces hormones were investigated in 40 Streptomyces and 11 endophytic actinomycetes. Production of γ-butyrolactone-type (IM-2, VB) and butenolide-type (avenolide) Streptomyces hormones was screened using Streptomyces lavendulae FRI-5 (ΔfarX), Streptomyces virginiae (ΔbarX) and Streptomyces avermitilis (Δaco), respectively. In these strains, essential biosynthetic genes for Streptomyces hormones were disrupted, enabling them to respond solely to the externally added hormones. The results showed that 20% of each of the investigated strains produced IM-2 and VB, confirming that γ-butyrolactone-type Streptomyces hormones are the most common in actinomycetes. Unlike the γ-butyrolactone type, butenolide-type Streptomyces hormones have been discovered in recent years, but their distribution has been unclear. Our finding that 24% of actinomycetes (12 of 51 strains) showed avenolide activity revealed for the first time that the butenolide-type Streptomyces hormone is also common in actinomycetes.

This review analyzes the advances in understanding the natural signaling pathways and environmental factors regulating stilbene biosynthesis. We also discuss the studies reporting on stilbene content and repertoire in plants. Stilbenes, including the most-studied stilbene resveratrol, are a family of phenolic plant secondary metabolites that have been the subject of intensive research due to their valuable pharmaceutical effects and contribution to plant disease resistance. Understanding the natural mechanisms regulating stilbene biosynthesis in plants could be useful for both the development of new plant protection strategies and for commercial stilbene production. In this review, we focus on the environmental factors and cell signaling pathways regulating stilbene biosynthesis in plants and make a comparison with the regulation of flavonoid biosynthesis. This review also analyzes the recent data on stilbene biosynthetic genes and summarizes the available studies reporting on both stilbene content and stilbene composition in different plant families.

Prosperous development in marine-based tourism has raised increasing concerns over the sanitary quality of coastal waters with potential microbial contamination. The World Health Organization has set stringent standards over a list of pathogenic microorganisms posing potential threats to people with frequent coastal water exposure and has asked for efficient detection procedures for pathogen facile identification. Inspection of survey events regarding the occurrence of marine pathogens in recreational beaches in recent years has reinforced the need for the development of a rapid identification procedure. In this review, we examine the possibility of recruiting uniform molecular assays to identify different marine pathogens and the feasibility of appropriate biomarkers, including enterochelin biosynthetic genes, for general toxicity assays. The focus is not only on bacterial pathogens but also on other groups of infectious pathogens. The ultimate goal is the development of a handy method to more efficiently and rapidly detect marine pathogens.

Vitamin E refers to four tocopherols and four tocotrienols that are exclusively synthesized by photosynthetic organisms. While α-tocopherol is the most potent vitamin E compound, it is not the main form consumed since the composition of most major crops is dominated by γ-tocopherol. Nutritional studies show that populations of developed countries do not consume enough vitamin E and that a large proportion of individuals exhibit plasma α-tocopherol deficiency. Following the identification of vitamin E biosynthetic genes, several strategies including metabolic engineering, classic breeding and mutation breeding, have been undertaken to improve the vitamin E content of crops. In addition to providing crops in which vitamin E content is enhanced, these studies are revealing the bottlenecks limiting its biosynthesis.

Filamentous fungi produce a wide range of natural products that are commonly used in various industrial contexts (e.g., pharmaceuticals and insecticides). Meroterpenoids are natural products of interest because of their various biological activities. Among the meroterpenoids, there is a group of insecticidal compounds known as the austinoids. These compounds have also been studied because of their intriguing spiro-lactone ring formation along with various modifications. Here, we present an extension of the original austinol/dehydroaustinol biosynthesis pathway from Aspergillus nidulans in the recently identified filamentous fungus Aspergillus calidoustus. Besides the discovery and elucidation of further derivatives, genome mining led to the discovery of new putative biosynthetic genes. The genes involved in the biosynthesis of later austinoid products were characterized, and among them was a second polyketide synthase gene in the A. calidoustus cluster that was unusual because it was a noninterative polyketide synthase producing a diketide. This diketide product was then loaded onto the austinoid backbone, resulting in a new insecticidal derivative, calidodehydroaustin.

Lasso peptides are ribosomally synthesized and posttranslationally modified peptides with diverse biological functions. Recent genome mining has revealed that many species of actinomycetes possibly contain biosynthetic gene clusters of lasso peptides. With genome mining for lasso peptide biosynthesis, we screened several actinomycetes for lasso peptide production using high-performance liquid chromatography and electrospray ionization–mass spectrometry. Consequently, Streptomyces cattleya was identified as a producer of a new lasso peptide named cattlecin. Analysis of amino acid content on cattlecin indicated the presence of four moles each of Asp and His, three moles each of Gly and Tyr, and one mole of Ser. Tandem mass spectrometry (MS/MS) analysis of cattlecin revealed C-terminal sequence of WHHGWYGWWDD. The peptide sequence (SYHWGDYHDWHHGWYGWWDD) was the expected amino acid sequence of cattlecin based on genome mining. As a result of MS/MS analysis, the amine residue of the first Ser was proposed to form a macrolactam ring with the β-carboxyl residue of the ninth Asp. The biosynthetic gene cluster of cattlecin comprised four genes: catA, catC, catB1, and catB2, which is typical of a lasso peptide biosynthetic gene cluster in actinomycetes.

Endophytic actinomycetes associated with plant roots are a relatively untapped source of potential new bioactive compounds. This is becoming increasingly important, as the returns from discovery research on soil-dwelling microbes, have been continuously diminishing. We have isolated more than 1000 strains of actinomycetes from plant roots in our search for novel bioactive compounds, identified and assayed their bioactive metabolites, as well as investigated their biosynthetic genes for generating secondary metabolites. This has resulted in the discovery of several interesting compounds. Creation of plant root clone libraries enabled us to confirm that we had, indeed, isolated endophytes. In this paper, we introduce our approach to this promising line of research, incorporating data from other publications, and illustrate the potential that endophytic actinomycetes offer as a new source of novel lead compounds.

N-(2-Chloro-4-pyridyl)-N′-phenylurea (CPPU) is a cytokinin-like plant growth regulator, which application in melon fruit set often produced bitter fruit caused by cucurbitacin B (Cu B) accumulation. However, more evidence is required to uncover the role of CPPU in regulating Cu B synthesis. In this study, two oriental melon cultivars ‘YMR’ (easy to present bitter fruit in maturation) and ‘HDB’ (hardly produce bitter fruit at maturity) were used. Four concentrations of CPPU (2.5, 5, 10 and 20 mg L−1) were set and hand pollination was used as control. Cu B accumulated in roots and fruit of 7 days after flower (7 DAF), which in ‘YMR’ was higher than those in ‘HDB’, and consistent with Cu B biosynthetic genes expression patterns. Furthermore, Cu B content in fruit significantly increased with CPPU concentrations and reached the highest level at 7 DAF, then decreased after 14 DAF, and which treated by 20 mg L−1 CPPU was always higher than that of controls and other low CPPU concentrations. Meanwhile, fruit bitterness evaluation suggested 20 mg L−1 CPPU increased the occurrence of bitterness during melon maturation. Transcription analysis suggested that the expression of Cu B biosynthetic genes (CmBi, Cm710, CmACT) and CmBt, the fruit-specific transcription factor, were significantly induced by 20 mg L−1 CPPU. Transient over-expression of CmBt in young fruit of ‘YMR’ increased Cu B biosynthetic genes (CmBi, CmACT, Cm710 and Cm890) expression and promoted Cu B accumulation. Taken together, this study demonstrates that 20 mg L−1 CPPU promotes Cu B accumulation in melon fruit by inducing CmBt and its biosynthetic genes.

Background: Anoectochilus roxburghii is a medicinal plant and contains a variety of bioactive components, including triterpene, which exhibits important pharmacological properties with low toxicity. However, little is known about the biosynthetic pathway of triterpene or about the genome and transcriptome in A. roxburghii. Results: In order to analyze transcriptional determinants related to the biosynthesis of the bioactive components, we performed transcriptome sequencing in A. roxburghii (SRX1818644, SRX1818642 and SRX1818641) and annotated the sequences from three samples. In total, 137,679,059 clean reads were obtained, corresponding to 12.20 Gb of total nucleotides. They were then assembled into 86,382 contigs and 68,938 unigenes, which were further annotated according to sequence similarity with known genes in COG, EST, Nr, Pfam and Uniprot databases, leading to 10,040，29,442，39,551，34,991 and 28,082 unigenes, respectively. GO analysis classified all unigenes into three functional categories, i.e. biological processes (43,206 unigenes in 22 categories), molecular functions (46,978 unigenes in 15 categories) and cellular components (20,951 unigenes in 18 categories). Candidate triterpenes biosynthetic genes ArHMGR1 in MEV pathway, ArDXS1, ArDXS4 ArDXS5, ArDXS8-10, ArDXR1-2 and ArHDR1-2 in MEP pathway and ArFDS1, ArSM and ArOCS were selected based on RNA-seq and gene-to-metabolites correlation analysis. Conclusion: The transcriptomes of A. roxburghii plant include 86,382 contigs and 68,938 unigenes. The assembled dataset allowed identification of genes encoding enzymes in the biosynthesis of bioactive components in A. roxburghii plant. Candidate genes that encode enzymes being important in triterpenes biosynthetic pathway were selected. This will facilitate the study of expression and regulation in the biosynthesis of bioactive component in A.roxburghii.

One strain many compounds (OSMAC) strategy was an effective method to activate the silent biosynthetic genes of microorganisms. Comparison with our previous investigations on the secondary metabolites of the marine-derived fungus Aspergillus sp. SCSIO 41501, in this study, three new cyclopentenone derivatives, aspergispones A-C (1–3), and five new cyclohexenone derivatives, aspergispones D-H (4–8), together with two known analogues, were further isolated from the fungal strain by altering culture medium compositions. The structures of new compounds were elucidated by extensive spectroscopic analysis. And the absolute configurations of 4 and 7 were further confirmed by single-crystal X-ray diffraction experiments.

Historically, discovering natural products with novel structures and biological activities has increased motivation for drug development. Fungi have been recognized as a promising source of pharmaceutically beneficial natural products. Next-generation sequencing analysis of several Aspergillus fungi has revealed that one fungal strain has far more biosynthetic gene clusters that are estimated from the number of previously isolated natural products, and bioinformatics analysis has indicated that most biosynthetic gene clusters are not linked to their associated metabolites. Hence, there are many cryptic natural products hidden in the fungal genome. Such “cryptic” biosynthetic genes may be the next frontier in the exploration of novel natural products. Recently it has seen the rapid emergence of a new style of natural product discovery research for obtaining new natural products from cryptic biosynthetic genes. In this article, we would like to introduce the methods for activating secondary metabolite production in fungi by using low molecular chemicals.

Metabolomics has become an integral part of a broad understanding of the plant phenome. It involves large-scale quantitative and qualitative analyses of metabolites present in plant tissues. Metabolomics can generally be divided into targeted and non-targeted analyses. Every year, new tools are developed and used to better understand unknown metabolomes. These tools help to identify new metabolites but also increase our understanding of biosynthetic pathways that were inexplicable using only genomics data. This article reviews existing and new metabolomics tools and their integrated utility in the discovery of plant biosynthetic genes. It covers literature and data from approximately 2010–19. This article provides a basis for an average reader to understand how plant metabolites are identified, validated, and used to understand their biosynthetic origin using integrated genomics, transcriptomics, and metabolomics.

Microbial natural products represent a rich resource of evolved chemistry that forms the basis for the majority of pharmacotherapeutics. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a particularly interesting class of natural products noted for their unique mode of biosynthesis and biological activities. Analyses of sequenced microbial genomes have revealed an enormous number of biosynthetic loci encoding RiPPs but whose products remain cryptic. In parallel, analyses of bacterial metabolomes typically assign chemical structures to only a minority of detected metabolites. Aligning these 2 disparate sources of data could provide a comprehensive strategy for natural product discovery. Here we present DeepRiPP, an integrated genomic and metabolomic platform that employs machine learning to automate the selective discovery and isolation of novel RiPPs. DeepRiPP includes 3 modules. The first, NLPPrecursor, identifies RiPPs independent of genomic context and neighboring biosynthetic genes. The second module, BARLEY, prioritizes loci that encode novel compounds, while the third, CLAMS, automates the isolation of their corresponding products from complex bacterial extracts. DeepRiPP pinpoints target metabolites using large-scale comparative metabolomics analysis across a database of 10,498 extracts generated from 463 strains. We apply the DeepRiPP platform to expand the landscape of novel RiPPs encoded within sequenced genomes and to discover 3 novel RiPPs, whose structures are exactly as predicted by our platform. By building on advances in machine learning technologies, DeepRiPP integrates genomic and metabolomic data to guide the isolation of novel RiPPs in an automated manner.

The exact mechanics of specialized metabolism and its importance throughout plant evolution remain mysterious. Specialized metabolites and their corresponding biosynthetic genes are crucial to understand the reason for the prevalence of certain metabolism. Even though mass spectrometry-based metabolomics has enabled us to acquire data about the structural properties of unknown specialized metabolites as well as known metabolites and their corresponding isomers/analogs, extensive analytical approaches are still required. Herein, we review the most advanced analytical approaches using stable isotope labeling that can be used to identify the unknown specialized metabolites.

The interspecies communication roles of γ-butyrolactones (GBLs) have been described for a long time but are still poorly understood. Herein, we analyzed more than 1000 Streptomyces strains and noticed a big quantitative gap between the strains with GBL biosynthetic genes and the strains with GBL receptor genes, which implies the wide-spread of GBLs as interspecies signals in Streptomyces and their great potential in the activation of silent natural product gene clusters. Streptomyces albidoflavus J1074, which has one GBL receptor gene but no GBL biosynthetic gene, was chosen as a target to study the possible interspecies communication roles of GBLs. At first, the GBL biosynthetic genes from Streptomyces coelicolor M145 were expressed in S. albidoflavus J1074, which enabled the S. albidoflavus strains to synthesize Streptomyces coelicolor butanolides (SCBs) and activated the production of paulomycins. Further studies showed that this activation process requires the participation of the GBL receptor gene XNR_4681. The results suggest that the expression of exogenous GBL biosynthetic genes can modulate the metabolisms of GBL non-producing strains, and this regulation role might be meaningful for silent gene cluster activation in Streptomyces. At final, we synthesized racemic-SCB2 and tried to simplify the activation process by adding SCB2 directly to S. albidoflavus J1074, which unfortunately failed to induce paulomycin production.

Current understanding of the role of plant hormones during cereal grain filling is confounded by contradictory reports on hormone production that is based on poor methodology. We report here on the accurate measurement of indole-3-acetic acid (IAA) and abscisic acid (ABA) by combined liquid chromatography-tandem mass spectrometry in multiple reaction-monitoring mode with heavy isotope labelled internal standards. ABA and IAA contents of superior versus inferior rice grains (ABA maxima 159 ng g–1 FW and 109 ng g–1 FW, IAA maxima 2 µg g–1 FW and 1.7 µg g–1 FW respectively) correlated with the expression of biosynthetic genes and with grain fill. Results confirm that grain ABA is produced primarily by OsNCED2(5), but suggest that ABA import and metabolism also play important roles in ABA regulation. The IAA content of grains is primarily influenced by OsYUC9 and OsYUC11. However, the distinct expression profile of OsYUC12 suggests a specific role for IAA produced by this enzyme. Co-expression of OsYUC12 with OsIAA29 indicates their involvement in a common signalling pathway. Co-expression and cis-element analysis identified several aleurone-specific transcriptional regulators as well as glutelin as strong candidates for detailed investigation for direct regulation by the auxin-signalling pathway.

In actinomycetes, many secondary metabolite biosynthetic genes are not expressed under typical laboratory culture conditions and various efforts have been made to activate these dormant genes. In this study, we focused on high-temperature culture. First, we examined the thermotolerance of 3160 actinomycete strains from our laboratory culture collection and selected 57 thermotolerant actinomycetes that grew well at 45 °C. These 57 thermotolerant actinomycetes were cultured for 5 days in liquid medium at both 30 °C and 45 °C. Culture broths were extracted with 1-butanol, and each extract was subjected to LC/MS analysis. The metabolic profiles of each strain were compared between the 30 °C and 45 °C cultures. We found that almost half of these thermotolerant actinomycetes produced secondary metabolites that were detected only in the 45 °C culture. This result suggests that high-temperature culture induces the production of dormant secondary metabolites. These compounds were named “heat shock metabolites (HSMs).” To examine HSM production in more detail, 18 strains were selected at random from the initial 57 strains and cultivated in six different media at 30 °C and 45 °C; as before, metabolic profiles of each strain in each medium were compared between the 30 °C and 45 °C cultures. From this analysis, we found a total of 131 HSMs. We identified several angucycline-related compounds as HSMs from two thermotolerant Streptomyces species. Furthermore, we discovered a new compound, murecholamide, as an HSM from thermotolerant Streptomyces sp. AY2. We propose that high-temperature culture of actinomycetes is a convenient method for activating dormant secondary metabolite biosynthetic genes.

Background: Pueraria candollei var. mirifica , a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown. Results: A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers.A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidatesinvolved in these biosyntheticpathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica . To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor ( At MYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins ledto the production of the isoflavone genistein. Conclusions: Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for unraveling biosynthetic pathways in plants.

Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.

New technology for the derivatization of peptide natural products is required for drug development. Despite the recent advances in the genome sequencing technique enabling us to search for the biosynthetic genes for wide variety of natural products, the technical methods to get access to them are limited. A class of RiPPs, a recently emerged natural product family such as thioviridamide, is one of those possessing such unexplored chemical space. In this paper, we report a streamlined method to generate new thioviridamide derivatives and to assess their biological activities. Heterologous expression of 42 constructs in an engineered Streptomyces avermitilis host gave 35 designed thioviridamide derivatives, along with several unprecedented analogues. Moreover, cytotoxicity assay revealed that several derivatives showed more potent activities than those of prethioviridamide. These results indicate that this strategy can become one of the potential ways to produce supreme unnatural products.

Microalgae are a promising biofuel resource, but their high cost and low productivity hinder their commercial applications. In the present study, Monoraphidium sp. QLZ-3 was cultivated in walnut shell extracts (WSE) supplemented with carbon dioxide (CO2). Biomass was enhanced from 0.40 g L−1 to 1.18 g L−1, and lipid content reached 49.54% in WSE-12% CO2 media. Biomass and lipid productivity reached 196.88 and 97.52 mg L−1 d−1, which were 1.33- and 1.57-fold higher than those of the control, respectively. The amount of carbohydrates increased, but the protein contents decreased. Furthermore, the application of CO2 promoted nutrient and polyphenol absorption and upregulated the expression levels of lipid biosynthetic genes of this WSE-cultivated alga. These results indicated that coupling WSE and CO2 could be an efficient strategy to enhance biofuel production by microalgae.

Chlorophyll (Chl) biosynthesis requires highly efficient metabolic regulation during chloroplast biogenesis in angiosperms. The intermediates of Chl biosynthesis and Chls are easily activated by li...

Sacred lotus (Nelumbo nucifera) is an important aquatic ornamental plant which contains several diverse flower colors, but the underlying mechanisms of its flower coloration remain unclear. In this study, seven complementary DNA (cDNA) clones of genes involved in flavonoid biosynthesis, including chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS), were isolated and characterized. Moreover, expression patterns of these seven genes and pigment profiles were investigated across four N. nucifera cultivars with different flower colors: Zhongguohongbeijing [ZGH (red)], Xinghuafen [XHF (pink)], Molingqiuse [MLQS (yellow)], and Zhufengcuiying [ZFCY (white)]. Real-time quantitative polymerase chain reaction (qRT-PCR) analysis showed that during flower development, transcripts of early biosynthetic genes (NnCHS, NnCHI, and NnF3H) were abundant at the early stage; noticeably, highest expression of NnCHI in MLQS probably induced abundant anthoxanthin synthesis and displayed yellow. Expression of late biosynthetic genes, especially NnDFR and NnANS, was generally consistent with change patterns of anthocyanins in ZGH and XHF, but NnF3′H was barely detectable in the pink cultivars. Meanwhile, negligible expression of NnDFR and NnANS was detected in MLQS and ZFCY, respectively, which blocked their colored anthocyanin biosynthesis. Spatial expression analysis revealed that most flavonoid biosynthetic genes were highly expressed in floral tissues, rather than leaves. These results suggest that in N. nucifera cultivars with different flower colors, flavonoid biosynthesis is differentially regulated by the expression of these flavonoid biosynthetic genes, among which, NnCHI, NnF3′H, NnDFR, and NnANS are supposed to be critical for pigment accumulation, and therefore, affect different flower coloration.

Exocarp protects the fruit against external stresses by means of its special physical and biochemical properties. It is also a commercially important quality for fruits characterized with certain color and structure. The color of sand pear exocarp can be divided into three types of russet, semi-russet and green. The green of exocarp is formed by accumulation of chlorophyll in epidermal cells. Russeting is a disorder of the fruit skin that results from microscopic cracks caused by growth stresses and several additional factors and the subsequent formation of higher plasticity periderm membranes by the accumulation of suberin on the inner part of the cell wall of the outer epidermal cell layers. Genes and pathways that are specific to exocarp russet formation have been identified in sand pear and its genetically related apple. The cuticle biosynthetic genes were repressed while stress response genes and suberin deposition genes were enhanced underlying the exocarp russeting. One major ‘QTL’ associated with russet of exocarp was identified at the top of LG 8. However, despite these advances, important aspects of russet and semi-russet inheritance remain obscure. Central questions include whether russet and semi-russet are belong to one type of quantitative trait or not, and their genetic characters. These issues are reviewed. Greater emphasis on gene mapping and cloning, biochemical characterization of metabolic intermediates and putative enzymes identified to put together correct and detailed pathways will be required to solve these unknowns of the mechanisms underlying the exocarp russet and semi-russet formation.