Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

Overexpression of chalcone isomerase in apple reduces phloridzin accumulation and increases susceptibility to herbivory by two-spotted mites

Apples (Malus spp.) accumulate significant quantities of the dihydrochalcone glycoside, phloridzin, whilst pears (Pyrus spp.) do not. To explain this difference, we hypothesized that a metabolic bottleneck in the phenylpropanoid pathway might exist in apple. Expression analysis indicated that transcript levels of early phenylpropanoid pathway genes in apple and pear leaves were similar, except for chalcone isomerase (CHI), which was much lower in apple. Apples also showed very low CHI activity compared with pear. To relieve the bottleneck at CHI, transgenic apple plants overexpressing the Arabidopsis AtCHI gene were produced. Unlike other transgenic apples where phenylpropanoid flux was manipulated, AtCHI overexpression (CHIox) plants were phenotypically indistinguishable from wild-type, except for an increase in red pigmentation in expanding leaves. CHIox plants accumulated slightly increased levels of flavanols and flavan-3-ols in the leaves, but the major change was a 2.8- to 19-fold drop in phloridzin concentrations compared with wild-type. The impact of these phytochemical changes on insect preference was studied using a two-choice leaf assay with the polyphagous apple pest, the two-spotted spider mite (Tetranychus urticae Koch). Transgenic CHIox leaves were more susceptible to herbivory, an effect that could be reversed (complemented) by application of phloridzin to transgenic leaves. Taken together, these findings shed new light on phenylpropanoid biosynthesis in apple and suggest a new physiological role for phloridzin as an antifeedant in leaves.

Natural Products as Modulators of CES1 Activity

Carboxylesterase (CES) 1 is the predominant esterase expressed in the human liver and is capable of catalyzing the hydrolysis of a wide range of therapeutic agents, toxins, and endogenous compounds. Accumulating studies have demonstrated associations between the expression and activity of CES1 and the pharmacokinetics and/or pharmacodynamics of CES1 substrate medications (e.g., methylphenidate, clopidogrel, oseltamivir). Therefore, any perturbation of CES1 by coingested xenobiotics could potentially compromise treatment. Natural products are known to alter drug disposition by modulating cytochrome P450 and UDP-glucuronosyltransferase enzymes, but this issue is less thoroughly explored with CES1. We report the results of a systematic literature search and discuss natural products as potential modulators of CES1 activity. The majority of research reports reviewed were in vitro investigations that require further confirmation through clinical study. Cannabis products (Δ ⁹-tetrahydrocannabinol, cannabidiol, cannabinol); supplements from various plant sources containing naringenin, quercetin, luteolin, oleanolic acid, and asiatic acid; and certain traditional medicines (danshen and zhizhuwan) appear to pose the highest inhibition potential. In addition, ursolic acid, gambogic acid, and glycyrrhetic acid, if delivered intravenously, may attain high enough systemic concentrations to significantly inhibit CES1. The provision of a translational interpretation of in vitro assessments of natural product actions and interactions is limited by the dearth of basic pharmacokinetic data of the natural compounds exhibiting potent in vitro influences on CES1 activity. This is a major impediment to assigning even potential clinical significance. The modulatory effects on CES1 expression after chronic exposure to natural products warrants further investigation. SIGNIFICANCE STATEMENT: Modulation of CES1 activity by natural products may alter the course of treatment and clinical outcome. In this review, we have summarized the natural products that can potentially interact with CES1 substrate medications. We have also noted the limitations of existing reports and outlined challenges and future directions in this field.

Characterization of a sweet basil acyltransferase involved in eugenol biosynthesis

Sweet basil (Ocimum basilicum) plants produce its characteristic phenylpropene-rich essential oil in specialized structures known as peltate glandular trichomes (PGTs). Eugenol and chavicol are the major phenylpropenes produced by sweet basil varieties whose synthetic pathways are not fully elucidated. Eugenol is derived from coniferyl acetate by a reaction catalysed by eugenol synthase. An acyltransferase is proposed to convert coniferyl alcohol to coniferyl acetate which is the first committed step towards eugenol synthesis. Here, we perform a comparative next-generation transcriptome sequencing of different tissues of sweet basil, namely PGT, leaf, leaf stripped of PGTs (leaf-PGT), and roots, to identify differentially expressed transcripts specific to PGT. From these data, we identified a PGT-enriched BAHD acyltransferase gene ObCAAT1 and functionally characterized it. In vitro coupled reaction of ObCAAT1 with eugenol synthase in the presence of coniferyl alcohol resulted in eugenol production. Analysis of ObCAAT1-RNAi transgenic lines showed decreased levels of eugenol and accumulation of coniferyl alcohol and its derivatives. Coniferyl alcohol acts as a common substrate for phenylpropene and lignin biosynthesis. No differences were found in total lignin content of PGTs and leaves of transgenic lines, indicating that phenylpropene biosynthesis is not coupled to lignification in sweet basil.

Terpinen-4-ol Enhances Disease Resistance of Postharvest Strawberry Fruit More Effectively than Tea Tree Oil by Activating the Phenylpropanoid Metabolism Pathway

This study aimed to reveal the effects and possible mechanism of terpinen-4-ol, the main component of tea tree oil (TTO), on the disease resistance of strawberry fruit. When the effects of TTO and its components were compared on the decay development in fruit inoculated with Botrytis cinerea after treatment, strawberry treated with terpinen-4-ol showed the lowest disease incidence (44.4%) after 48 h and also the smallest lesion diameter during the whole storage. This indicates that terpinen-4-ol induces the highest disease resistance in strawberry compared with TTO and other components. Untargeted metabolomic analysis showed that terpinen-4-ol treatment strongly activated phenylpropanoid biosynthesis and flavonoid metabolism pathway by increasing the accumulation of cinnamaldehyde, coniferyl aldehyde, naringenin, taxifolin, quercetin, and quercitrin in fruit at 12 h after treatment. In addition, terpinen-4-ol treatment also caused the accumulation of total phenolics and lignin by enhancing activities and relative gene expression of key enzymes in the phenylpropanoid metabolism pathway. These results suggest that terpinen-4-ol, as the key component of TTO, is the most important contributor to the effectiveness of TTO in improving disease resistance of strawberry fruit through activating the phenylpropanoid metabolism pathway.

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.

Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress

BACKGROUND

Foxtail millet [Setaria italica (L.) P. Beauv.] is an excellent crop known for its superior level of drought tolerance across the world. Especially, less water is needed during its germination period than the other cereal crops. However, the knowledge of the mechanisms underlying the abiotic stress effects on seed germination of foxtail millet is largely unknown.

RESULTS

The water uptake pattern of foxtail millet seeds was ploted during germination period, according to which the germination time course of millet was separated into three phases. We sequenced the transcriptome of foxtail millet seeds, which were treated by PEG during different germination phases after sowing. The transcriptional studies revealed that more DEGs were identified during the further increase in water uptake period (phase III) than during the rapid initial uptake period (phase I) and the plateau period (phase II) under PEG stress. The pathway analysis of DEGs showed that the highly enriched categories were related to phenylpropanoid biosynthesis, plant hormone signal transduction and phenylalanine metabolism during phase III. The 20 phenylpropanoids-related genes of germinating foxtail millet were found to be down-regulated during the further increase in water uptake period under PEG stress. Further expression analysis identified 4 genes of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase 3, cinnamoyl-CoA reductase 1, cationic peroxidase SPC4 in phenylpropanoids-related pathway, which played important roles in foxtail millet in response to PEG stress during different germination periods. The studies of metabolites in phenylpropanoid biosynthesis pathway revealed that higher amount of cinnamic acid was accumulated in germinating seeds under PEG stress, while the contents of p-coumaric acid, caffeic acid, ferulic acid and sinapic acid were decreased. And the effects of five phenolic compounds on germination and growth of foxtail millet showed that 1 mM concentration of cinnamic acid inhibited shoot and root growth, especially root development. Ferulic acid, caffeic acid, sinapic acid and p-coumaric acid could increase the root length and root/sprout in lower concentration.

CONCLUSIONS

These findings suggest that key genes and metabolites of foxtail millet related with phenylpropanoids pathway may play prominent roles in the regulation of resistance to drought during germination. Foxtail millet can probably avoid drought by regulating the levels of endogenous allelochemicals.

Nanocrystal technology for improving therapeutic efficacy of flavonoids

BACKGROUND

Bioflavonoids, secondary metabolites of plants, are beneficial in regulating human physiological mechanisms. Bioflavonoids majorly exist in the dietary intake of fruits, vegetables, legumes, pulses, etc. In addition to their cardio-protective and neuroprotective activities, they also possess prominent pharmacological effects including anti-oxidant, anti-inflammatory, anti-proliferative and anti-thrombogenic actions. However, therapeutic efficacy of the bioflavonoids is hampered by their lipophilic nature, low solubility and variable bioavailability which catch the eyes of formulation scientists.

PURPOSE

Nanocrystal formulations were studied for many bioflavonoids, although enough attention has not been given to their commercial exploitation, unlike drug nanocrystals. Nanocrystals of bioflavonoid can be prepared by top-down technique, bottom-up technique or combination of both. This review primarily focuses on nanocrystal technology for bioflavonoids, methods of production, critical process parameters, in vitro and in vivo studies conducted to evaluate the efficiency.

METHOD

The detailed literature survey was systematically carried out using different electronic databases. It includes Scopus, Web of Science, Medline via PubMed, EMBASE, and Google Scholar. Also up-to-date patent search was conducted to understand the prior art and available intellectual properties.

RESULT AND CONCLUSION

It was observed that several formulation and process parameters have an impact on flavonoids nanocrystals and their therapeutic efficacy. Also, clinical studies of flavonoid nanocrystals are barely done so far and thus, substantial safety and efficacy data is necessary for its commercial applications. Nevertheless, nanocrystals can be explored as a promising technology platform for improving overall therapeutic performance of flavonoids in future.

The style and substance of plant flavonoid decoration; towards defining both structure and function

Over 8000 different flavonoids have been described and a considerable number of new flavonoid structures are being elucidated every year. The advent of metabolomics alongside the development of phytochemical genetics - wherein the genetic basis underlying the regulation of the levels of plant metabolites is determined - has provided a massive boost to such efforts. That said our understanding of the individual function(s) of the vast majority of the metabolites that constitute this important class of phytochemicals remains unknown. Here we review what is known concerning the major decorative modifications of flavonoids in plants, namely hydroxylation, glycosylation, methylation and acylation. Our major focus is with regard to the in planta function of these modified compounds, however, we also highlight the demonstrated bioactive roles which they possess. We additionally performed a comprehensive survey of the flavonoids listed in the KNApSAcK database in order to assess the frequency of occurrence of each type of flavonoid modification. We conclude that whilst considerable research has been carried out regarding the biological roles of flavonoids most studies to date have merely provided information on the compound class or sub-classes thereof as a whole with too little currently known on the specific role of individual metabolites. We, therefore, finally suggest a framework based on currently available tools by which the relative importance of the individual compounds can be assessed under various biological conditions in order to fill this knowledge-gap.

Biosynthetic pathways and metabolic engineering of spice flavors

Historically, spices have played an important economic role, due to their large applications and unique flavor. The supply and cost of spice materials and their corresponding natural products are often affected by environmental, geopolitical and climatic conditions. Secondary metabolite composition, including certain flavor compounds in spice plants, is recognized and considered closely related to plant classification. Both genes and enzymes involved in the biosynthesis of spice flavors are constantly identified, which provides insight into metabolic engineering of flavor compounds (i.e. aroma and pungent compounds) from spice plants. In this review, a systematic meta-analysis was carried out based on a comprehensive literature survey of the flavor profiles of 36 spice plants from nine families. We also reviewed typical biosynthetic pathways and metabolic engineering of most representative aroma and pungent compounds that may assist in the future study of spice plants as biosynthetic factories facing a new challenge in creating spice products.

Phyto-derived Products as Matrix Metalloproteinases Inhibitors in Cardiovascular Diseases

Matrix metalloproteinases (MMPs) are enzymes that present a metallic element in their structure. These enzymes are ubiquitously distributed and function as extracellular matrix (ECM) remodelers. MMPs play a broad role in cardiovascular biology regulating processes such as cell adhesion and function, cellular communication and differentiation, integration of mechanical force and force transmission, tissue remodeling, modulation of damaged-tissue structural integrity, cellular survival or apoptosis and regulation of inflammation-related cytokines and growth factors. MMPs inhibition and downregulation are correlated with minimization of cardiac damage, i.e., Chinese herbal medicine has shown to stabilize abdominal aorta aneurysm due to its antiinflammatory, antioxidant and MMP-2 and 9 inhibitory properties. Thus phyto-derived products rise as promising sources for novel therapies focusing on MMPs inhibition and downregulation to treat or prevent cardiovascular disorders.

Identification of key taste components in loquat using widely targeted metabolomics

Loquats can be divided into white- and yellow-fleshed cultivars. Generally, white-fleshed cultivars taste better than yellow-fleshed cultivars. Currently, metabolic causes of differences in taste are unknown, due to the lack of a large-scale and comprehensive investigation of metabolites in loquat fruit. Here, we performed a LC-MS/MS-based widely targeted metabolome analysis on two cultivars, 'Baiyu' (white-fleshed) and 'ZaozhongNo. 6' (yellow-fleshed). A total of 536 metabolites were identified, 193 of which (including 7 carbohydrates, 12 organic acids and 8 amino acids) were different between the cultivars. Pathway enrichment analysis also identified significant differences in phenolic pathways between the cultivars. Our results suggest that taste differences between the cultivars can be explained by variations in composition and abundance of carbohydrates, organic acids, amino acids, and phenolics. This study provides new insights into the underlying metabolic causes of taste variation in loquat.

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host-pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited. In this work, we have obtained an RNA-seq-based differential expression profile of Mexican lime plants challenged against CLas infection, at both asymptomatic and symptomatic stages. Typical HLB-responsive differentially expressed genes (DEGs) are involved in photosynthesis, secondary metabolism, and phytohormone homeostasis. Enrichment of DEGs associated with biotic response showed that genes related to cell wall, secondary metabolism, transcription factors, signaling, and redox reactions could play a role in the tolerance of Mexican lime against CLas infection. Interestingly, despite some concordance observed between transcriptional responses of different tolerant citrus species, a subset of DEGs appeared to be species-specific. Our data highlights the importance of studying the host response during HLB disease using as model tolerant citrus species, in order to design new and opportune diagnostic and management methods.

Structures related to resprouting potential of two Myrtaceae species from Cerrado: morpho-anatomical and chemical studies

Resprouting is a functional trait in species which occur in fire-prone ecosystems. These plants can resprout from aerial buds and by recruiting belowground bud bank using carbohydrates allocated in roots as resource. In this study, we present morpho-anatomical features and chemical composition related to the resprouting potential of two species of Eugenia L. in an area of the Cerrado (Brazilian savanna) under regeneration, after the clear-cutting of Pinus sp. with the later burning of pine needles layer. We used standard histological techniques for belowground organs analysis and aerial buds protection degree. Belowground buds in layer from soil surface down to 10 depth were counted and the chemical analyses were performed on roots. In all aerial buds, there were relevant protection traits. The belowground organ is a sobole and the number of buds in its upper portion varied from 24 to 517 between individuals of both species. Phenolic compounds, flavonoids, starch and other carbohydrates were detected in roots. The protection of aerial buds, the large number of belowground buds and the storing and protective compounds may have favored the resprouting of the species in the area.

Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon

As an important appearance trait, the rind color of watermelon fruit affects the commodity value and further determines consumption choices. In this study, a comparative transcriptome analysis was conducted to elucidate the genes and pathways involved in the formation of yellow rind fruit in watermelon using a yellow rind inbred line WT4 and a green rind inbred line WM102. A total of 2,362 differentially expressed genes (DEGs) between WT4 and WM102 at three different stages (0, 7, and 14 DAP) were identified and 9,770 DEGs were obtained by comparing the expression level at 7 DAP and 14 DAP with the former stages of WT4. The function enrichment of DEGs revealed a number of pathways and terms in biological processes, cellular components, and molecular functions that were related to plant pigment metabolism, suggesting that there may be a group of common core genes regulating rind color formation. In addition, next-generation sequencing aided bulked-segregant analysis (BSA-seq) of the yellow rind pool and green rind pool selected from an F₂ population revealed that the yellow rind gene (Clyr) was mapped on the top end of chromosome 4. Based on the BSA-seq analysis result, Clyr was further confined to a region of 91.42 kb by linkage analysis using 1,106 F₂ plants. These results will aid in identifying the key genes and pathways associated with yellow rind formation and elucidating the molecular mechanism of rind color formation in watermelon.

In Vitro and In Vivo Effects of Flavonoids on Peripheral Neuropathic Pain

Neuropathic pain is a common symptom and is associated with an impaired quality of life. It is caused by the lesion or disease of the somatosensory system. Neuropathic pain syndromes can be subdivided into two categories: central and peripheral neuropathic pain. The present review highlights the peripheral neuropathic models, including spared nerve injury, spinal nerve ligation, partial sciatic nerve injury, diabetes-induced neuropathy, chemotherapy-induced neuropathy, chronic constriction injury, and related conditions. The drugs which are currently used to attenuate peripheral neuropathy, such as antidepressants, anticonvulsants, baclofen, and clonidine, are associated with adverse side effects. These negative side effects necessitate the investigation of alternative therapeutics for treating neuropathic pain conditions. Flavonoids have been reported to alleviate neuropathic pain in murine models. The present review elucidates that several flavonoids attenuate different peripheral neuropathic pain conditions at behavioral, electrophysiological, biochemical and molecular biological levels in different murine models. Therefore, the flavonoids hold future promise and can be effectively used in treating or mitigating peripheral neuropathic conditions. Thus, future studies should focus on the structure-activity relationships among different categories of flavonoids and develop therapeutic products that enhance their antineuropathic effects.

Overexpression of stilbene synthase genes to modulate the properties of plants and plant cell cultures

Plant stilbenes have attracted special attention as they possess valuable health benefits and improve plant resistance to environmental stresses. Stilbenes are synthesized via the phenylpropanoid pathway, where stilbene synthase (STS, EC 2.3.1.95) directly catalyzes the formation of t-resveratrol (monomeric stilbene). This review discusses the features of using STS genes in genetic engineering and plant biotechnology with the purpose to increase plant resistance to environmental stresses and to modify secondary metabolite production.

Physiological and transcriptomic analysis provide novel insight into cobalt stress responses in willow

Cobalt (Co) is an essential component of several enzymes and coenzymes in living organisms. Excess Co is highly toxic to plants. The knowledge of molecular response mechanisms to cobalt stress in plants is still limited, especially in woody plants. The responses of weeping willow (Salix babylonica) seedlings to Co stress were studied using morphological and physiochemical measurements and RNA-seq analysis. The physiological and biochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in willow seedlings under Co stress. The metal ion concentrations in willow including Cu, Zn and Mg were disturbed due to excess Co. Of 2002 differentially expressed genes (DEGs), 1165 were root-specific DEGs and 837 were stem and leaf-specific DEGs. Further analysis of DEGs showed there were multiple complex cascades in the response network at the transcriptome level under Co stress. Detailed elucidation of responses to oxidative stress, phytohormone signaling-related genes and transcription factors (TFs), and detoxification of excess cellular Co ion indicated the various defense mechanisms in plants respond to cobalt stress. Our findings provide new and comprehensive insights into the plant tolerance to excess Co stress.

Comparative transcriptome provides molecular insight into defense-associated mechanisms against spider mite in resistant and susceptible common bean cultivars

Common bean (Phaseolus vulgaris L.) is a major source of proteins and one of the most important edible foods for more than three hundred million people in the world. The common bean plants are frequently attacked by spider mite (Tetranychus urticae Koch), leading to a significant decrease in plant growth and economic performance. The use of resistant cultivars and the identification of the genes involved in plant-mite resistance are practical solutions to this problem. Hence, a comprehensive study of the molecular interactions between resistant and susceptible common bean cultivars and spider mite can shed light into the understanding of mechanisms and biological pathways of resistance. In this study, one resistant (Naz) and one susceptible (Akhtar) cultivars were selected for a transcriptome comparison at different time points (0, 1 and 5 days) after spider mite feeding. The comparison of cultivars in different time points revealed several key genes, which showed a change increase in transcript abundance via spider mite infestation. These included genes involved in flavonoid biosynthesis process; a conserved MYB-bHLH-WD40 (MBW) regulatory complex; transcription factors (TFs) TT2, TT8, TCP, Cys2/His2-type and C2H2-type zinc finger proteins; the ethylene response factors (ERFs) ERF1 and ERF9; genes related to metabolism of auxin and jasmonic acid (JA); pathogenesis-related (PR) proteins and heat shock proteins.

Increased Flavonol Levels in Tobacco Expressing AcFLS Affect Flower Color and Root Growth

The onion (Allium cepa L.) flavonol synthase (AcFLS-HRB) gene, encoding an enzyme responsible for flavonol biosynthesis in yellow onion, was recently identified and enzymatically characterized. Here, we performed an in vivo feeding assay involving bacterial expression of AcFLS-HRB and observed that it exhibited both flavanone 3-hydroxylase (F3H) and FLS activity. Transgenic tobacco (Nicotiana tabacum) expressing AcFLS-HRB produced lighter-pink flowers compared to wild-type plants. In transgenic petals, AcFLS-HRB was highly expressed at the mRNA and protein levels, and most AcFLS-HRB protein accumulated in the insoluble microsomal fractions. High-performance liquid chromatography (HPLC) analysis showed that flavonol levels increased but anthocyanin levels decreased in transgenic petals, indicating that AcFLS-HRB is a functional gene in planta. Gene expression analysis showed the reduced transcript levels of general phenylpropanoid biosynthetic genes and flavonoid biosynthetic genes in AcFLS-HRB overexpressed tobacco petals. Additionally, transgenic tobacco plants at the seedling stages showed increased primary root and root hair length and enhanced quercetin signals in roots. Exogenous supplementation with quercetin 3-O-rutinoside (rutin) led to the same phenotypic changes in root growth, suggesting that rutin is the causal compound that promotes root growth in tobacco. Therefore, augmenting flavonol levels affects both flower color and root growth in tobacco.

Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis

Adenylate-forming enzymes represent one of the most important enzyme classes in biology, responsible for the activation of carboxylate substrates for biosynthetic modifications. The byproduct of the adenylate-forming enzyme acetyl-CoA synthetase, acetyl-CoA, is incorporated into virtually every primary and secondary metabolic pathway. Modification of acetyl-CoA by an array of other adenylate-forming enzymes produces complex classes of natural products including nonribosomal peptides, polyketides, phenylpropanoids, lipopeptides, and terpenes. Adenylation domains possess a variety of unique structural and functional features that provide for such diversification in their resulting metabolites. As the number of organisms with sequenced genomes increases, more adenylate-forming enzymes are being identified, each with roles in metabolite production that have yet to be characterized. In this Review, we explore the broad role of class I adenylate-forming enzymes in the context of natural product biosynthesis and how they contribute to primary and secondary metabolism by focusing on important work conducted in the field. We highlight features of subclasses from this family that facilitate the production of structurally diverse metabolites, including those from noncanonical adenylation domains, and additionally discuss when biological roles for these compounds are known.

Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

BACKGROUND

Anthocyanins are common substances with many agro-food industrial applications. However, anthocyanins are generally considered to be found only in natural plants. Our previous study isolated and purified the fungus Aspergillus sydowii H-1, which can produce purple pigments during fermentation. To understand the characteristics of this strain, a transcriptomic and metabolomic comparative analysis was performed with A. sydowii H-1 from the second and eighth days of fermentation, which confer different pigment production.

RESULTS

We found five anthocyanins with remarkably different production in A. sydowii H-1 on the eighth day of fermentation compared to the second day of fermentation. LC-MS/MS combined with other characteristics of anthocyanins suggested that the purple pigment contained anthocyanins. A total of 28 transcripts related to the anthocyanin biosynthesis pathway was identified in A. sydowii H-1, and almost all of the identified genes displayed high correlations with the metabolome. Among them, the chalcone synthase gene (CHS) and cinnamate-4-hydroxylase gene (C4H) were only found using the de novo assembly method. Interestingly, the best hits of these two genes belonged to plant species. Finally, we also identified 530 lncRNAs in our datasets, and among them, three lncRNAs targeted the genes related to anthocyanin biosynthesis via cis-regulation, which provided clues for understanding the underlying mechanism of anthocyanin production in fungi.

CONCLUSION

We first reported that anthocyanin can be produced in fungus, A. sydowii H-1. Totally, 31 candidate transcripts were identified involved in anthocyanin biosynthesis, in which CHS and C4H, known as the key genes in anthocyanin biosynthesis, were only found in strain H1, which indicated that these two genes may contribute to anthocyanins producing in H-1. This discovery expanded our knowledges of the biosynthesis of anthocyanins and provided a direction for the production of anthocyanin.

Expression response of chalcone synthase gene to inducing conditions and its effect on flavonoids accumulation in two medicinal species of Anoectochilus

Anoectochilus roxburghii and Anoectochilus formasanus are the major species of genus Anoectochilus used in traditional Chinese medicine for their abundant content of flavonoids and some other medicinal constituents. In recent years, their wild resources are gradually exhausted due to over-collection and ecological deterioration. Artificial cultivation and tissue culture are employed to increase production. In this study, the open reading frame, promoter and genomic sequences of the chalcone synthase (CHS) gene were cloned from these two species according to their transcriptome information, and used for expression analysis in response to the induction of phenylalanine, ultraviolet light and NaCl, and its effect investigation on accumulation of flavonoids. The results showed that the expression of the CHS genes was upregulated in response to these inductions and resulted in increasing accumulation of total flavonoids. However, the increased flavonoids induced by phenylalanine and ultraviolet light were mainly allocated into the anthocyanidin branch of flavonoids biosynthesis. Not only did it improved the medicinal value, but might have inhibitory effect on plant growth because of the increased malondialdehyde accumulation. Under the induction of appropriate concentration of NaCl, the medicinal constituents of flavonoids were increased without inhibition to plant growth.

MdMYB46 could enhance salt and osmotic stress tolerance in apple by directly activating stress-responsive signals

To expand the cultivation area of apple (Malus×domestica Borkh.) and select resistant varieties by genetic engineering, it is necessary to clarify the mechanism of salt and osmotic stress tolerance in apple. The MdMYB46 transcription factor was identified, and the stress treatment test of MdMYB46-overexpressing and MdMYB46-RNAi apple lines indicated that MdMYB46 could enhance the salt and osmotic stress tolerance in apple. In transgenic Arabidopsis and apple, MdMYB46 promoted the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of lignin biosynthesis-related genes. To explore whether MdMYB46 could coordinate stress signal transduction pathways to cooperate with the formation of secondary walls to enhance the stress tolerance of plants, MdABRE1A, MdDREB2A and dehydration-responsive genes MdRD22 and MdRD29A were screened out for their positive correlation with osmotic stress, salt stress and the transcriptional level of MdMYB46. The further verification test demonstrated that MdMYB46 could activate their transcription by directly binding to the promoters of these genes. The above results indicate that MdMYB46 could enhance the salt and osmotic stress tolerance in apple not only by activating secondary cell wall biosynthesis pathways, but also by directly activating stress-responsive signals.

Looking for New Antifungal Drugs from Flavonoids: Impact of the Genetic Diversity of Candida albicans on the in-vitro Response

BACKGROUND

In an era in which antimicrobial resistance is increasing at an alarming pace, it is very important to find new antimicrobial agents effective against pathogenic microrganisms resistant to traditional treatments. Among the notable breakthroughs in the past years of research in natural-drug discovery, there is the identification and testing of flavonoids, a group of plant-derived substances capable of promoting many beneficial effects on humans. These compounds show different biological activities such as inhibition of neuroinflammation and tumor growth as well as antimicrobial activity against many microbial pathogens.

METHODS

We undertook a review of protocols and standard strains used in studies reporting the inhibitory effects of flavonoids against Candida albicans by focusing our attention on genetic characterization of the strains examined. Moreover, using the C. albicans MLST-database, we performed a phylogenetic analysis showing the genetic variation occurring in this species.

RESULTS

Today, we have enough information to estimate genetic diversity within microbial species and recent data revealed that most of fungal pathogens show complex population structures in which not a single isolate can be designated as representative of the entire taxon. This is especially true for the highly divergent fungal pathogen C. albicans, in which the assumption that one or few "standard strains" can represent the whole species is overly unrealistic and should be laid to rest.

CONCLUSION

The goal of this article is to shed light on the extent of genetic variation in C. albicans and how this phenomenon can largely influence the activity of flavonoids against this species.

Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds

BACKGROUND

Ramet propagation in strawberry (Fragaria × ananassa) is the most effective way in production. However, the lack of systematically phenotypic observations and high-throughput methods limits our ability to analyze the key factors regulating the heterogeneity in strawberry stolon buds.

RESULTS

From observation, we found that the axillary bud located in the first node quickly stepped into dormancy (DSB), after several bract and leaf buds were differentiated. The stolon apical meristem (SAM) degenerated as the new ramet leaf buds (RLB), and the new active axillary stolon buds (ASB) differentiated continually after the differentiation of the first leaf. Using the tandem mass tags (TMT) labeling method, a total of 7271 strawberry proteins were identified. Between ASB and DSB, the spliceosome DEPs, such as Ser/Arg-rich (SR) and heterogeneous nuclear ribonucleoprotein particle (hnRNP), showed the highest enrichment and high PPI connectivity. This indicated that the differences in DEPs (e.g., SF-3A and PK) at the transcriptional level may be causing the differences between the physiological statuses of ASB and DSB. As expected, the photosynthetic pre-form RLB mainly differentiated from ASB and DSB judging by the DEP enrichment of photosynthesis. However, there are still other specialized features of DEPs between RLB and DSB and between ASB and DSB. The DEPs relative to DNA duplication [e.g., minichromosome maintenance protein (MCM 2, 3, 4, 7)], provide a strong hint of functional gene duplication leading the bud heterogeneity between RLB and DSB. In addition, the top fold change DEP of LSH 10-like might be involved in the degeneration of SAM into RLBs, based on its significant function in modulating the plant shoot initiation. As for RLB/ASB, the phenylpropanoid biosynthesis pathway probably regulates the ramet axillary bud specialization, and further promotes the differentiation of xylem when ASB develops into a new stolon [e.g., cinnamyl alcohol dehydrogenase 1 (CAD1) and phenylalanine ammonia-lyase 1 (PAL1)].

CONCLUSIONS

By using phenotypic observation combined with proteomic networks with different types of strawberry stolon buds, the definite dormancy phase of DSB was identified, and the biological pathways and gene networks that might be responsible for heterogeneity among different stolon buds in strawberry were also revealed.

Integrative analysis of metabolome and transcriptome reveals the mechanism of color formation in pepper fruit (Capsicum annuum L.)

To understand the mechanism of the color formation of pepper fruit, integrative analysis of the metabolome and transcriptome profiles was performed in pepper varieties with 4 different fruit colors. A total of 188 flavonoids were identified, and most of the anthocyanins, flavonols and flavones showed markedly higher abundances in purple variety than in other varieties, which was linked to the high expression of flavonoid synthesis and regulatory genes. Using weighted gene co-expression network analyses, modules related to flavonoid synthesis and candidate genes that regulate flavonoid synthesis and transport were identified. Furthermore, the analysis of 12 carotenoids showed that the content of xanthophylls at 50 days after anthesis was significantly different between the four pepper varieties, which was resulted from the differential expressions of genes downstream of the carotenoid pathway. Our results provide new insights into the understanding of the synthesis and accumulation of flavonoids and carotenoids in pepper fruit.

Flavonoid accumulation in spontaneous cotton mutant results in red coloration and enhanced disease resistance

Cotton, the leading natural fiber, is cultivated worldwide, but its production is seriously threatened by pathogens. Accordingly, the selection of resistant cultivars has become a key priority of cotton breeding programs. In this study, a spontaneous mutant with red coloration (S156) and a control cultivar (S78) were used as experimental materials for a comparative analysis. Metabolomic analysis revealed the enrichment of flavonoids in S156 leaves compared with S78 leaves, and transcriptomic analysis revealed the upregulated expression of flavonoid biosynthesis genes in S156 leaves relative to S78 leaves. In addition, the red mutant showed a significantly increase in resistance to Verticillium dahliae, a fungal pathogen that poses a major threat to cotton production. The pathogen invasion process was suppressed in the red cotton cultivar. This study reveals the mechanism underlying the red coloration of S156 cotton and indicates the great potential of red cotton in pathogen- and insect-resistant breeding of cotton.

Investigating the correlation of biomass recalcitrance with pyrolysis oil using poplar as the feedstock

Pyrolysis of five poplar samples with differing degrees of recalcitrance was performed; the correlations between the poplar enzymatic hydrolysis glucose yields and the physicochemical properties of pyrolysis product were investigated in this study. Sugar release of five poplar samples varied from 48.1 to 112.3 mg/g for glucose, and 12.0 to 32.4 mg/g for xylose. The yield of pyrolysis products was calculated and the molecular weight distribution of pyrolysis oils was measured by GPC, ranging from 268 to 289 g/mol for its weight-average molecular weight. GC-MS analysis of the bio-oil exhibited a strong correlation between biomass recalcitrance and guaiacyl-type structures in bio-oils. The correlation between biomass recalcitrance and the ratio of syringyl-to-guaiacyl-type-related structures was also assessed. The results from quantitative ³¹P NMR indicated some correlation between biomass recalcitrance and the guaiacyl hydroxyl groups in bio-oils. These results illustrate correlations and differences between converting biomass to biofuels via the biological and thermal platform.

The spatio-temporal expression of some genes involved in the biosynthetic pathways of terpenes/phenylpropanoids in yarrow (Achillea millefolium)

Yarrow (Achillea millefolium) is a medicinal plant from the Asteracea which biosynthesize different secondary metabolites especially terpenes and phenylpropanoids. To improve our understanding of the regulatory mechanisms behind the biosynthesis of these compounds we analyzed the expression of some genes associated with the biosynthesis of terpenes and phenylpropanoids in different tissues and in response to trans-cinnamic acid (tCA) as an inhibitor of PAL activity. Isolation and expression analysis of DXR, GPPS, PAL and CHS genes together with linalool synthase (LIS) as monoterpene synthase was conducted in different developmental stages of leaves, flowers and in response to trans-cinnamic acid (tCA). Differential expression of these genes observed in different tissues. tCA up-regulated the biosynthetic genes of monterpenes and down-regulated the biosynthetic genes of phenylpropanoids. Gene expression analysis in intact leaves and leaves without glandular trichomes showed that DXR, LIS, PAL and CHS are highly expressed in glandular trichomes while GPPS expressed ubiquitously. Analysis of essential oils composition showed that sesquiterpenes and monoterpenes are main compounds; in which from 57 identified compounds the highest were germacreneD (% 11.5), guaiol (%10.38), spatulenol (%8.73) and caryophyllene oxide (%7.48).

Exogenous application of rosmarinic acid improves saccharification without affecting growth and lignification of maize

Biomimetically incorporated into the lignin structure, rosmarinic acid improves in vitro maize cell wall saccharification; however, no in planta studies have been performed. We hypothesized that rosmarinic acid, itself, could inducer saccharification without disturbing plant growth. Its effects on growth, enzymes of the phenylpropanoid pathway, lignin, monomeric composition, and saccharification of maize were evaluated. In a short-term (24 h) exposure, rosmarinic acid caused deleterious effects on maize roots, inhibiting the first enzymes of the phenylpropanoid pathway, phenylalanine ammonia-lyase and tyrosine ammonia-lyase, altering lignin composition and slightly increasing saccharification. In a long-term (14 d) exposure, rosmarinic acid increased saccharification of maize stems by about 50% without any deleterious effects on plant growth, the phenylpropanoid pathway and lignin formation. This demonstrated that exogenous application of rosmarinic acid on maize plants improved saccharification, and represented an interesting approach in facilitating enzymatic hydrolysis of biomass polysaccharides and increasing bioethanol production.

Phenolic acids: Natural versatile molecules with promising therapeutic applications

Plant phenolics are considered to be a vital human dietary component and exhibit a tremendous antioxidant activity as well as other health benefits. Epidemiology evidence indicates that a diet rich in antioxidant fruits and vegetables significantly reduces the risk of many oxidative stress related diseases viz. cancers, diabetes and cardiovascular. The number and position of hydroxyl group in a particular phenolic compound leads to the variation in their antioxidant potential. Polyphenols are the main source of dietary antioxidants, and are effortlessly absorbed in the intestine. Phenolic acids, a sub class of plant phenolics, possess phenol moiety and resonance stabilized structure which causes the H-atom donation results in antioxidant property through radical scavenging mechanism. Other mode such as radical quenching via electron donation and singlet oxygen quenching are also known for the antioxidant activity of phenolic acids. Furthermore, phenolic acids are found ubiquitously and well documented for other health protective effects like antimicrobial, anticancer, anti-inflammatory, anti-mutagenic etc. The contribution emphasize on the phenolic acids potential in drug discovery. In addition their occurrence, biosynthesis, metabolism and health effects are discussed in detail.

Root verbascoside and oleuropein are potential indicators of drought resistance in olive trees (Olea europaea L.)

Polyphenols are constituents of all higher plants. However, their biosynthesis is often induced when plants are exposed to abiotic stresses, such as drought. The aim of the present work was to determine the phenolic status in the roots of olive trees grown under water deficit conditions. The results revealed that roots of water-stressed plants had a higher content of total phenols. The main compound detected in well-watered olive tree roots was verbascoside. Oleuropein was established as the predominant phenolic compound of water-stressed plants. The oleuropein/verbascoside ratio varied between 0.31 and 6.02 in well-watered and water-stressed plants respectively, which could be a useful indicator of drought tolerance in olive trees. Furthermore, this study is the first to provide experimental evidence showing that luteolin-7-rutinoside, luteolin-7-glucoside and apigenin-7-glucoside were the dominant flavonoid glucosides in olive tree roots and showed the most significant variations under water stress.

Resistance against Sclerotinia sclerotiorum in soybean involves a reprogramming of the phenylpropanoid pathway and up-regulation of antifungal activity targeting ergosterol biosynthesis

Sclerotinia sclerotiorum, a predominately necrotrophic fungal pathogen with a broad host range, causes a significant yield-limiting disease of soybean called Sclerotinia stem rot. Resistance mechanisms against this pathogen in soybean are poorly understood, thus hindering the commercial deployment of resistant varieties. We used a multiomic approach utilizing RNA-sequencing, gas chromatography-mass spectrometry-based metabolomics and chemical genomics in yeast to decipher the molecular mechanisms governing resistance to S. sclerotiorum in soybean. Transcripts and metabolites of two soybean recombinant inbred lines, one resistant and one susceptible to S. sclerotiorum were analysed in a time course experiment. The combined results show that resistance to S. sclerotiorum in soybean is associated in part with an early accumulation of JA-Ile ((+)-7-iso-jasmonoyl-L-isoleucine), a bioactive jasmonate, increased ability to scavenge reactive oxygen species, and importantly, a reprogramming of the phenylpropanoid pathway leading to increased antifungal activities. Indeed, we noted that phenylpropanoid pathway intermediates, such as 4-hydroxybenzoate, cinnamic acid, ferulic acid and caffeic acid, were highly accumulated in the resistant line. In vitro assays show that these metabolites and total stem extracts from the resistant line clearly affect S. sclerotiorum growth and development. Using chemical genomics in yeast, we further show that this antifungal activity targets ergosterol biosynthesis in the fungus, by disrupting enzymes involved in lipid and sterol biosynthesis. Overall, our results are consistent with a model where resistance to S. sclerotiorum in soybean coincides with an early recognition of the pathogen, leading to the modulation of the redox capacity of the host and the production of antifungal metabolites.

Trichoderma harzianum- and Methyl Jasmonate-Induced Resistance to Bipolaris sorokiniana Through Enhanced Phenylpropanoid Activities in Bread Wheat (Triticum aestivum L.)

The aim of the present study was to evaluate the impact of Trichoderma harzianum UBSTH-501- and methyl jasmonate-induced systemic resistance and their integration on the spot blotch pathogen, Bipolaris sorokiniana through enhanced phenylpropanoid activities in bread wheat (Triticum aestivum L.). It was found that the application of MeJA (>100 mg L^-1) inhibits the germination of B. sorokiniana spores under controlled laboratory conditions. To assess the effect of MeJA (150 mg L^-1) in combination with the biocontrol agent T. harzianum UBSTH-501 in vivo, a green house experiment was conducted. For this, biocontrol agent T. harzianum UBSTH-501 was applied as seed treatment, whereas MeJA (150 mg L^-1) was applied 5 days prior to pathogen inoculation. Results indicated that application of MeJA (150 mg L^-1) did not affect the root colonization of wheat by T. harzianum UBSTH-501 in the rhizosphere. The combined application of T. harzianum UBSTH-501 and MeJA also enhanced indole acetic acid production in the rhizosphere (4.92 μg g^-1 of soil) which in turn helps in plant growth and development. Further, the combined application found to enhance the activities of defense related enzymes viz. catalase (5.92 EU min^-1 g^-1 fresh wt.), ascorbate peroxidase [μmol ascorbate oxidized (mg prot)^-1 min^-1], phenylalanine ammonia lyase (102.25 μmol cinnamic acid h^-1 mg^-1 fresh wt.) and peroxidase (6.95 Unit mg^-1 min^-1 fresh wt.) significantly in the plants under treatment which was further confirmed by assessing the transcript level of PAL and peroxidase genes using semi-quantitative PCR approach. The results showed manifold increase in salicylic acid (SA) along with enhanced accumulation of total free phenolics, ferulic acid, caffeic acid, coumaric acid, and chlorogenic acid in the leaves of the plants treated with the biocontrol agent alone or in combination with MeJA. A significant decrease in the disease severity (17.46%) and area under disease progress curve (630.32) were also observed in the treatments with biocontrol agent and MeJA in combination as compared to B. sorokiniana alone treated plant (56.95% and 945.50, respectively). Up-regulation of phenylpropanoid cascades in response to exogenous application of MeJA and the biocontrol agent was observed. It was depicted from the results that PAL is the primary route for lignin production in wheat which reduces cell wall disruption and tissue disintegration and increases suberization and lignification of the plant cell as seen by Scanning Electron microphotographs. These results clearly indicated that exogenous application of MeJA with T. harzianum inducing JA- and/or SA-dependent defense signaling after pathogen challenge may increase the resistance to spot blotch by stimulating enzymatic activities and the accumulation of phenolic compounds in a cooperative manner. This study apparently provides the evidence of biochemical cross-talk and physiological responses in wheat following MeJA and biocontrol agent treatment during the bio-trophic infection.

Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae

Rice is staple food of nearly half the world’s population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed.

Proteome and metabolome analyses reveal differential responses in tomato -Verticillium dahliae-interactions

Verticillium dahliae colonizes vascular tissue and causes vascular discoloration in susceptible hosts. Two well-defined races exist in V. dahliae populations from tomato and lettuce. In this study, proteins and metabolites obtained from stems of race 1-incompatible (Beefsteak) and -compatible (Early Pak) tomato cultivars were characterized. A total of 814 and 584 proteins in Beefsteak; and 456 and 637 proteins in Early Pak were identified in stem extracts of plants inoculated with races 1 and 2, respectively. A significant number of defense-related proteins were expressed in each tomato-V. dahliae interaction, as anticipated. However, phenylalanine ammonia-lyase (PAL), an important defense-associated enzyme of the phenylpropanoid pathway, in addition to remorin 1, NAD-dependent epimerase/dehydratase, and polyphenol oxidase were uniquely expressed in the incompatible interaction. Compared with the uninoculated control, significant overexpression of gene ontology terms associated with lignin biosynthesis, phenylpropanoid pathway and carbohydrate methylation were identified exclusively in the incompatible interaction. Phenolic compounds known to be involved in plant defense mechanisms were at higher levels in the incompatible relative to the compatible interactions. Based on our findings, PAL and enzymes involved defense-related secondary metabolism and the strengthening of cell walls is likely critical to confer resistance to race 1 of V. dahliae in tomato. SIGNIFICANCE: Verticillium dahliae, a soilborne fungal pathogen and a widely distributed fungal pathogen, colonizes vascular tissue and causes vascular discoloration in roots and stems, leaf wilting, and death of susceptible plant hosts. It causes billions of dollars in annual crop losses all over the world. The study focused on the proteomic and metabalomic of V. dahliae interactions (incompatible with Beefsteak and compatible with Early Pak tomato cultivars). Based on our findings, PAL and enzymes involved defense-related secondary metabolism and the strengthening of cell walls is likely critical to confer resistance to race 1 of V. dahliae in tomato.

Biotechnological Advances in Resveratrol Production and its Chemical Diversity

The very well-known bioactive natural product, resveratrol (3,5,4'-trihydroxystilbene), is a highly studied secondary metabolite produced by several plants, particularly grapes, passion fruit, white tea, and berries. It is in high demand not only because of its wide range of biological activities against various kinds of cardiovascular and nerve-related diseases, but also as important ingredients in pharmaceuticals and nutritional supplements. Due to its very low content in plants, multi-step isolation and purification processes, and environmental and chemical hazards issues, resveratrol extraction from plants is difficult, time consuming, impracticable, and unsustainable. Therefore, microbial hosts, such as Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum, are commonly used as an alternative production source by improvising resveratrol biosynthetic genes in them. The biosynthesis genes are rewired applying combinatorial biosynthetic systems, including metabolic engineering and synthetic biology, while optimizing the various production processes. The native biosynthesis of resveratrol is not present in microbes, which are easy to manipulate genetically, so the use of microbial hosts is increasing these days. This review will mainly focus on the recent biotechnological advances for the production of resveratrol, including the various strategies used to produce its chemically diverse derivatives.

Comparing the chemical composition of dietary fibres prepared from sugarcane, psyllium husk and wheat dextrin

A dietary fibre prepared from sugarcane stalk was compared with psyllium husk and wheat dextrin. In contrast to the other dietary fibres, sugarcane fibre was found to contain significant amounts of insoluble dietary fibre (73-86%), lignin (18.66-20.23%), and rare minerals such as chromium (0.67-2.54 mg/100 g) and manganese (1.07-2.34 mg/100 g). Analysis of the ethanol extract also detected compounds with antioxidant activity. Characterisation of five sugarcane fibres prepared from selected strains, harvest periods (growth or storage phase), and processing conditions showed these factors influenced the final composition. Furthermore, using in vitro digestion, we found that potassium, magnesium, chromium, and zinc in were bioaccessible in sugarcane samples. Also, sodium was shown to bind to the sugarcane fibre potentially indicating bile salt binding activity. Results from this study support the use of sugarcane as a source of dietary fibre in functional foods.

Gene isolation, heterologous expression, purification and functional confirmation of sesamin synthase from Sesamum indicum L

Members of Cytochromes P450 super family of enzymes catalyse important biochemical reactions in plants. Some of these reactions are so important that they contribute to enormous chemical diversity seen in plants. Many unique secondary metabolites formed by mediation of these enzymes play key role in plant defence and often contribute to maintenance of human health. In oilseed crop Sesamum indicum, the reaction leading to the formation of clinically important sesamin is catalyzed by a unique methylene-di-oxy bridge forming Cytochrome P450 enzyme sesamin synthase. It is encoded by the gene CYP81Q1. In order to elucidate the structure - function relationship of this enzyme and to apply biotechnological tools for enhancing the production of sesamin in the crop, it was intended to clone and express the enzyme in a heterologous system. In this paper we present our results on synthesis of cDNA, cloning, expression and purification of CYP81Q1 from the developing seeds of sesame crop. Following the same procedure we have also cloned a CYP reductase1 (CPR1) gene (CPR1) to facilitate transfer of electron from NADPH to CYP81Q1 enzyme from the same crop. Functional characterization was performed by expressing the recombinant proteins in E. coli (pET28a/BL21-DE3 codon plus) and its activity was evaluated in vitro by HPLC. We demonstrate that purified CYP81Q1 enzyme, on its own, has limited level of activity in the conversion of pinoresinol to sesamin. Its activity gets considerably enhanced in the presence of CPR1.

Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases

Various computational methodologies can be applied to enzymological studies on enzymes in the fatty acid, polyketide, and non-ribosomal peptide biosynthetic pathways. These multi-domain complexes are called fatty acid synthases, polyketide synthases, and non-ribosomal peptide synthetases. These mega-synthases biosynthesize chemically diverse and complex bioactive molecules, with the intermediates being chauffeured between catalytic partners via a carrier protein. Recent efforts have been made to engineer these systems to expand their product diversity. A major stumbling block is our poor understanding of the transient protein-protein and protein-substrate interactions between the carrier protein and its many catalytic partner domains and product intermediates. The innate reactivity of pathway intermediates in two major classes of polyketide synthases has frustrated our mechanistic understanding of these interactions during the biosynthesis of these natural products, ultimately impeding the engineering of these systems for the generation of engineered natural products. Computational techniques described in this chapter can aid data interpretation or used to generate testable models of these experimentally intractable transient interactions, thereby providing insight into key interactions that are difficult to capture otherwise, with the potential to expand the diversity in these systems.

Deposition of lignin in four species of Saccharum

We used primers designed on conserved gene regions of several species to isolate the most expressed genes of the lignin pathway in four Saccharum species. S. officinarum and S. barberi have more sucrose in the culms than S. spontaneum and S. robustum, but less polysaccharides and lignin in the cell wall. S. spontaneum, and S. robustum had the lowest S/G ratio and a lower rate of saccharification in mature internodes. Surprisingly, except for CAD, 4CL, and CCoAOMT for which we found three, two, and two genes, respectively, only one gene was found for the other enzymes and their sequences were highly similar among the species. S. spontaneum had the highest expression for most genes. CCR and CCoAOMT B presented the highest expression; 4CL and F5H showed increased expression in mature tissues; C3H and CCR had higher expression in S. spontaneum, and one of the CADs isolated (CAD B) had higher expression in S. officinarum. The similarity among the most expressed genes isolated from these species was unexpected and indicated that lignin biosynthesis is conserved in Saccharum including commercial varieties Thus the lignin biosynthesis control in sugarcane may be only fully understood with the knowledge of the promotor region of each gene.

De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar 'Tieguanyin' compared with cultivar 'Benshan'

Background

The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma, taste, and genetic make-up, but it lacks the “Yin Rhyme” flavor. We aimed to identify differences in biochemical characteristics and gene expression among these tea plants.

Results

The results of spectrophotometric, high performance liquid chromatography (HPLC), and gas chromatography-mass spectrometry (GC-MS) analyses revealed that TGY (Wei) and TGY (Wang) had deeper purple-colored leaves and higher contents of anthocyanin, catechins, caffeine, and limonene compared with BS. Analyses of transcriptome data revealed 12,420 differentially expressed genes (DEGs) among the cultivars. According to a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the flavonoid, caffeine, and limonene metabolic pathways were highly enriched. The transcript levels of the genes involved in these three metabolic pathways were not significantly different between TGY (Wei) and TGY (Wang), except for two unigenes encoding IMPDH and SAMS, which are involved in caffeine metabolism. The comparison of TGY vs. BS revealed eight up-regulated genes (PAL, C4H, CHS, F3’H, F3H, DFR, ANS, and ANR) and two down-regulated genes (FLS and CCR) in flavonoid metabolism, four up-regulated genes (AMPD, IMPDH, SAMS, and 5′-Nase) and one down-regulated XDH gene in caffeine metabolism; and two down-regulated genes (ALDH and HIBADH) in limonene degradation. In addition, the expression levels of the transcription factor (TF) PAP1 were significantly higher in TGY than in BS. Therefore, high accumulation of flavonoids, caffeine, and limonene metabolites and the expression patterns of their related genes in TGY might be beneficial for the formation of the “Yin Rhyme” flavor.

Conclusions

Transcriptomic, HPLC, and GC-MS analyses of TGY (Wei), TGY (Wang), and BS indicated that the expression levels of genes related to secondary metabolism and high contents of catechins, anthocyanin, caffeine, and limonene may contribute to the formation of the “Yin Rhyme” flavor in TGY. These findings provide new insights into the relationship between the accumulation of secondary metabolites and sensory quality, and the molecular mechanisms underlying the formation of the unique flavor “Yin Rhyme” in TGY.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5643-z) contains supplementary material, which is available to authorized users.

Suppression of tryptophan synthase activates cotton immunity by triggering cell death via promoting SA synthesis

Primary metabolism plays an important role in plant growth and development, however the relationship between primary metabolism and the adaptive immune response is largely unknown. Here, we employed RNA interference (RNAi), virus-induced gene silencing (VIGS) technology, phytohormone profiling, genetic studies, and transcriptome and metabolome analysis to investigate the function of the tryptophan synthesis pathway in the resistance of cotton to V. dahliae. We found that knock-down of GbTSA1 (Tryptophan Synthase α) and GbTSB1 (tryptophan synthase β) induced a spontaneous cell death phenotype in a salicylic acid (SA)-dependent manner and enhanced resistance to V. dahliae in cotton plants. Metabolome analysis showed that indole and indolic metabolites were highly accumulated in GbTSA1- or GbTSB1-silenced plants. Transcriptomic analysis showed that exogenous indole promotes the expression levels of genes involved in SA synthesis and the defense response. Similarly, indole application strongly enhanced cotton resistance to V. dahliae. These results suggested that metabolic intermediates in the Trp synthesis pathway may be a signal to activate SA synthesis. These results also provided a strategy to elicit plant defense responses by the application of indole.

A Dihydroflavonol-4-Reductase-Like Protein Interacts with NFR5 and Regulates Rhizobial Infection in Lotus japonicus

In almost all symbiotic interactions between rhizobia and leguminous plants, host flavonoid-induced synthesis of Nod factors in rhizobia is required to initiate symbiotic response in plants. In this study, we found that Lotus japonicus Nod factor receptor 5 (LjNFR5) might directly regulate flavonoid biosynthesis during symbiotic interaction with rhizobia. A yeast two-hybrid analysis revealed that a dihydroflavonol-4-reductase-like protein (LjDFL1) interacts with LjNFR5. The interaction between MtDFL1 and MtNFP, two Medicago truncatula proteins with homology to LjDFL1 and LjNFR5, respectively, was also shown, suggesting that interaction between these two proteins might be conserved in different legumes. LjDFL1 was highly expressed in root hairs and epidermal cells of root tips. Lotus ljdfl1 mutants and Medicago mtdfl1 mutants produced significantly fewer infection threads (ITs) than the wild-type control plants following rhizobial treatment. Furthermore, the roots of stable transgenic L. japonicus plants overexpressing LjDFL1 formed more ITs than control roots after exposure to rhizobia. These data indicated that LjDFL1 is a positive regulator of symbiotic signaling. However, the expression of LjDFL1 was suppressed by rhizobial treatment, suggesting that a negative feedback loop might be involved in regulation of the symbiotic response in L. japonicus.

Lead optimization for promising monoamine oxidase inhibitor from eugenol for the treatment of neurological disorder: synthesis and in silico based study

Natural based inhibitors of monoamine oxidase are promising drug candidates for the treatment of several neurodegenerative and neuropsychological disorders including depression, anxiety, Parkinson’s disease and Alzheimer’s disease. In the present study we designed and synthesized the eugenol based derivatives and investigated them for human MAO inhibitory potential as promising candidates for therapeutics of neurological disorders. Moreover, radical scavenging activity of designed derivatives was tested by and H₂O₂ and DPPH scavenging methods. Eugenol based derivatives were designed and synthesized for human MAO inhibitory action. The in silico and in vitro models were utilized for the evaluation of hMAO inhibition. The insight into molecular interactions among the compounds and both hMAO-A and hMAO-B active site was achieved by molecular docking studies. The two spectrophotometric titrations techniques were used to evaluate antioxidant potential. Compounds 5b and 16 were found as most active hMAO-A inhibitors with IC₅₀ values of 5.989 ± 0.007 µM and 7.348 ± 0.027 µM respectively, through an appreciable selectivity index value of 0.19 and 0.14 respectively. In case of hMAO-B inhibition compounds 13a and 13b were found as most active hMAO-B inhibitors with IC₅₀ values of 7.494 ± 0.014 µM and 9.183 ± 0.034 µM receptively and outstanding value of selectivity index of 5.14 and 5.72 respectively. Radical scavenging assay showed that compounds 5b, 5a, 9b, 9a were active antioxidants. The findings of present study indicated excellent correlation among dry lab and wet lab hMAO inhibitory experiments. Interestingly, the compounds exhibiting better MAO inhibition activity was also appeared as good antioxidant agents.