Rice Secondary Metabolites: Structures, Roles, Biosynthesis, and Metabolic Regulation

A plant growth-promoting bacterium supports cadmium detoxification of rice by inducing phenylpropanoid and flavonoid biosynthesis

Cadmium (Cd) is easily absorbed by rice and enters the food chain, posing a health risk to humans. Plant growth promoting bacteria (PGPB) can help the plant respond to Cd stress, but the mechanism of PGPB for Cd reduction is unclear. Therefore, this study was conducted and found inoculation with a newly isolated Pseudomonas koreensis promoted the growth of rice and reduced its Cd content. Fluorescent staining using PI and H2O2 probe indicated that PGPB attenuated oxidative damage in rice. Metabolomics revealed that 59 metabolites were upregulated after inoculation, with phenylpropanoids and flavonoids being significantly activated. Spectrophotometry analysis comfirmed the content of flavonoid, lignin, phenol, glutathione, proline and the activities of antioxidant enzymes were higher in the inoculated rice than in the control. Quantitative PCR showed the expression of genes related to phenylpropanoids (OsPAL, OsC4H, Os4CL) and flavonoids (OsCHS, OsCHI) was significantly increased by PGPB, while the genes of heavy metal transporters (OsNRAMP5, OsHMA2, OsIRT1) were significantly decreased. Overall, this study provides an insight into the PGPB-mediated detoxification mechanism in rice under Cd stress and emphasizes the role of phenylpropanoids and flavonoids in the production of low-Cd rice to ensure human health.

Elucidating the Underlying Allelopathy Effects of Euphorbia jolkinii on Arundinella hookeri Using Metabolomics Profiling

Euphorbia jolkinii dominates the subalpine meadows in Shangri-La (Southwest China) owing to its potent allelopathic effects. However, the effects underlying its allelopathy require further characterization at the physiological and molecular levels. In this study, the physiological, biochemical, and metabolic mechanisms underlying E. jolkinii allelopathy were investigated using Arundinella hookeri as a receptor plant. The treatment of A. hookeri seedlings with E. jolkinii aqueous extract (EJAE) disrupted their growth by inhibiting photosynthesis, disrupting oxidation systems, and increasing soluble sugar accumulation and chlorophyll synthesis. Collectively, this causes severe impairment accompanied by abnormal photosynthesis and reduced biomass accumulation. Moreover, EJAE treatment suppressed gibberellin, indoleacetic acid, zeatin, salicylic acid, and jasmonic acid levels while promoting abscisic acid accumulation. Further metabolomic analyses identified numerous differentially abundant metabolites primarily enriched in the α-linolenic, phenylpropanoid, and flavonoid biosynthesis pathways in EJAE-treated A. hookeri seedlings. This study demonstrated that E. jolkinii exhibits potent and comprehensive allelopathic effects on receptor plants, including a significant disruption of endogenous hormone synthesis, the inhibition of photosynthesis, an impairment of membrane and oxidation systems, and changes in crucial metabolic processes associated with α-linolenic, phenylpropanoid, and flavonoid biosynthesis. Thus, our study provides a solid theoretical foundation for understanding the regulatory mechanisms underlying E. jolkinii allelopathy.

Species- and organ-specific contribution of peroxisomal cinnamate:CoA ligases to benzoic and salicylic acid biosynthesis

Salicylic acid (SA) is a prominent defense hormone whose basal level, organ-specific accumulation, and physiological role vary widely among plant species. Of the 2 known pathways of plant SA biosynthesis, the phenylalanine ammonia lyase (PAL) pathway is more ancient and universal but its biosynthetic and physiological roles in diverse plant species remain unclear. Studies in which the PAL pathway is specifically or completely inhibited, as well as a direct comparison of diverse species and different organs within the same species, are needed. To this end, we analyzed the PAL pathway in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), 2 distantly related model plants whose basal SA levels and distributions differ tremendously at the organism and tissue levels. Based on our recent identification of the rice peroxisomal cinnamate:CoA ligases (CNLs), we identified 2 peroxisomal CNLs from Arabidopsis and showed CNL as the most functionally specific enzyme among the known enzymes of the PAL pathway. We then revealed the species- and organ-specific contribution of the PAL pathway to benzoic and salicylic acid biosynthesis and clarified its physiological importance in rice and Arabidopsis. Our findings highlight the necessity to consider species and organ types in future SA-related studies and may help to breed new disease-resistant crops.

Metabolomics analysis of rice fermented by medicinal fungi providing insights into the preparation of functional food

Rice, a primary staple food, may be improved in value via fermentation. Here, ten medicinal basidiomycetous fungi were separately applied for rice fermentation. After preliminary screening, Ganoderma boninense, Phylloporia pulla, Sanghuangporus sanghuang and Sanghuangporus weigelae were selected for further LC-MS based determination of the changes in metabolic profile after their fermentation with rice, and a total of 261, 296, 312, and 355 differential compounds were identified, respectively. Most of these compounds were up-regulated and involved in the metabolic pathways of amino acid metabolism, lipid metabolism, carbohydrate metabolism and the biosynthesis of other secondary metabolites. Sanghuangporus weigelae endowed the rice with the highest nutritional and bioactive values. The metabolic network of the identified differential compounds in rice fermented by S. weigelae illustrated their close relationships. In summary, this study provides insights into the preparation and application of potential functional food via the fermentation of rice with medicinal fungi.

Comprehensive multi-layered analyses of genotype-dependent proteo-metabolic networks reveal organellar crosstalk and biochemical pathways regulating aroma formation in rice

Molecular basis of rice aroma formation is sparsely known and developmental programs driving biochemical pathways towards aroma is in infancy. Here, discovery and targeted proteo-metabolome of non-aromatic and aromatic rice seeds across developmental stages identified a total of 442 aroma-responsive proteins (ARPs) and 824 aroma-responsive metabolites (ARMs) involved in metabolism, calcium and G-protein signaling. Biochemical examination revealed ARM/Ps were linked to 2-acetylpyrrolidine, γ-aminobutyrate, anthocyanin, tannins, flavonoids and related enzymes. Pairwise correlation and clustering showed positive correlation among ARM/Ps. Consistent with aroma-related QTLs, ARPs were mapped on chromosomes 3,4,5,8 and were mainly compartmentalized in cytoplasm and mitochondria. ARM/P-correlation network identified associations related to metabolism and signaling. Multiple reaction monitoring (MRM) confirmed role of catechins, quinic acid and quercetin in aroma formation. Pathway enrichment, multivariate analysis and qRT-PCR validated that calcium and G-protein signaling, aromatic/branched-chain aminoacid, 2-acetylpyrrolidine, oxylipin, melvonate and prenylpyrophosphate pathways, indole, phenylacetate, flavonoid, cinnamoic ester govern aroma formation in rice.

Akt-FoxO signaling drives co-adaptation to insecticide and host plant stresses in an herbivorous insect

INTRODUCTION

Ongoing interactions between host and herbivorous insect trigger a co-evolutionary arms race. Genetic diversity within insects facilitates their adaptation to phytochemicals and their derivatives, including plant-derived insecticides. Cytochrome P450s play important roles in metabolizing phytochemicals and insecticides, due to their diversity and almost perfect evolution.

OBJECTIVES

This study aims to uncover a common molecular mechanism in herbivorous insects by investigating the role of kinase-transcription factor regulation of P450s in conferring tolerance to both insecticides and phytochemicals.

METHODS

RNA interference, transcriptome sequencing, insecticide, and phytochemical bioassays were conducted to validate the functions of Akt, FoxO, and candidate P450s. Dual-luciferase activity assays were employed to identify the regulation of P450s by the Akt-FoxO signaling pathway. Recombinant P450 enzymes were utilized to investigate the metabolism of insecticides and phytochemicals.

RESULTS

We identified an Akt-FoxO signaling cascade, a representative of kinase-transcription factor pathways. This cascade mediates the expression of eight P450 enzymes involved in the metabolism of insecticides and phytochemicals in Nilaparvata lugens. These P450s are from different families and with different substrate selectivity, enabling them to respectively metabolize insecticides and phytochemicals with structure diversity. Nevertheless, the eight P450 genes were up-regulated by FoxO, which was inhibited in a higher cascade by Akt through phosphorylation. The discovery of the Akt-FoxO signaling pathway regulating a series of P450 genes elucidates the finely tuned regulatory mechanism in insects for adapting to phytochemicals and insecticides.

CONCLUSION

These finding sheds light on the physiological balance maintained by these regulatory processes. The work provides the experimental evidence of co-adaptation to the stresses imposed by host plant and insecticide within the model of the kinase-TF involving various P450s. This model provides a comprehensive view of how pests adapt to multiple environmental stresses.

Insights into the effects of anilofos on direct-seeded rice production system through untargeted metabolomics

Weed infestation is the major biological threat in direct-seeded rice production and can cause significant yield losses. The effective use of herbicides is particularly important in direct-seeded rice production. Anilofos, a pre-emergence herbicide, has been shown to be effective against the weed barnyardgrass. However, its impacts on crop yield and the direct-seeded rice production ecosystem remain underexplored. In this study, we conducted field trials and used untargeted metabolomics to investigate systemic effects of two different treatments (40 g/acre and 60 g/acre) on rice shoot and root as well as the rhizosphere soil during the critical tillering stage. Here, a total of 400 metabolites were determined in the crop and soil, with differential metabolites primarily comprising lipids and lipid-like molecules as well as phenylpropanoids and polyketides. Spearman correlation network analysis and a Zi-Pi plot revealed 7 key differential metabolites with significant topological roles, including succinic acid semialdehyde and riboflavin. KEGG pathway analysis showed that anilofos downregulated the amino acid metabolism while mainly promoted carbohydrate metabolism and secondary metabolites biosynthesis of the crop, which made minimal disruption on soil metabolism. Notably, we found 40 g/acre anilofos application could significantly improve the rice yield, potentially linked to the improved activity of flavonoid biosynthesis and starch and sucrose metabolism. This research provides a comprehensive evaluation of anilofos effects in the direct-seeded rice production system, offering new insights into optimizing herbicide use to improve agricultural sustainability and productivity.

Transcriptomic and metabolomic reveal OsCOI2 as the jasmonate-receptor master switch in rice root

Jasmonate is an essential phytohormone involved in plant development and stress responses. Its perception occurs through the CORONATINE INSENSITIVE (COI) nuclear receptor allowing to target the Jasmonate-ZIM domain (JAZ) repressors for degradation by the 26S proteasome. Consequently, repressed transcription factors are released and expression of jasmonate responsive genes is induced. In rice, three OsCOI genes have been identified, OsCOI1a and the closely related OsCOI1b homolog, and OsCOI2. While the roles of OsCOI1a and OsCOI1b in plant defense and leaf senescence are well-established, the significance of OsCOI2 in plant development and jasmonate signaling has only emerged recently. To unravel the role of OsCOI2 in regulating jasmonate signaling, we examined the transcriptomic and metabolomic responses of jasmonate-treated rice lines mutated in both the OsCOI1a and OsCOI1b genes or OsCOI2. RNA-seq data highlight OsCOI2 as the primary driver of the extensive transcriptional reprogramming observed after a jasmonate challenge in rice roots. A series of transcription factors exhibiting an OsCOI2-dependent expression were identified, including those involved in root development or stress responses. OsCOI2-dependent expression was also observed for genes involved in specific processes or pathways such as cell-growth and secondary metabolite biosynthesis (phenylpropanoids and diterpene phytoalexins). Although functional redundancy exists between OsCOI1a/b and OsCOI2 in regulating some genes, oscoi2 plants generally exhibit a weaker response compared to oscoi1ab plants. Metabolic data revealed a shift from the primary metabolism to the secondary metabolism primarily governed by OsCOI2. Additionally, differential accumulation of oryzalexins was also observed in oscoi1ab and oscoi2 lines. These findings underscore the pivotal role of OsCOI2 in jasmonate signaling and suggest its involvement in the control of the growth-defense trade-off in rice.

Metabolomics Uncovers the Mechanisms of Nitrogen Response to Anthocyanins Synthesis and Grain Quality of Colored Grain Wheat (Triticum aestivum L.)

Nitrogen (N) is a key factor for plant growth and affects anthocyanin synthesis. This study aimed to clarify the potential mechanisms of N levels (LN, 0 kg·ha-1; MN, 150 kg·ha-1; HN, 225 kg·ha-1) in anthocyanin synthesis and grain quality of colored grain wheat. HN increased the yield component traits and grain morphology traits in colored grain wheat while decreasing the processing and nutrient quality traits. Most quality traits were significantly negatively correlated with the yield composition and morphological traits. Anthocyanin was more accumulated under LN conditions, but other related yield and morphological traits of colored grain wheat declined. The anthocyanin content was the highest in blue wheat, followed by that in purple wheat. Cyanidin-3-O-(6-O-malonyl-β-d-glucoside) and cyanidin-3-O-rutinoside were the predominant anthocyanins in blue and purple wheat. The identified anthocyanin-related metabolites were associated with flavonoid biosynthesis, anthocyanin biosynthesis, and secondary metabolite biosynthesis. Therefore, the study provided information for optimizing nitrogen fertilizer management in producing high quality colored wheat and verified the close relationship between anthocyanin and low N condition.

SOS! Hydrogen Sulfide Enhances the Flavonoid Early Warning System in Rice Plants to Cope with Thiocyanate Pollution

The presence of thiocyanate (SCN-) in irrigation water has adverse effects on both plant growth and crop output. Hydrogen sulfide (H2S) is an important gaseous signaling molecule that can alleviate SCN- stress. Flavonoids are secondary compounds produced by plants and are ubiquitous in the plant kingdom. They play important roles in several physiological and biochemical processes. To investigate the effect of exogenous H2S on the growth of early rice plants under SCN- stress, we carried out a hydroponic experiment focusing on the interaction of exogenous H2S with flavonoids. In this study, a hydroponic experiment was performed to investigate the behavior of SCN- when subjected to varying effective doses (EC20: 24.0 mg/L; EC50: 96.0 mg/L; and EC75: 300.0 mg/L). The findings indicated that the relative growth rate (RGR) of the plants treated with H2S + SCN- was greater than that of the plants treated with SCN- alone. Higher amounts of flavonoids were detected in the shoots than in the roots, with more variability in the shoots. The early warning level results showed that most of the flavonoids were present at levels I and II, while quercetin was present at level IV. Genetic expression variation factor (GEVF) analyses revealed an increase in the quantity of "promoter genes" with increasing SCN- concentration in both rice tissues. Furthermore, administering external H2S while exposing rice tissues to SCN- resulted in a considerable decrease in the levels of reactive oxygen species. This study provides novel insights into the regulation of flavonoid levels in rice plants by exogenous H2S, facilitating enhanced resistance to SCN- stress and promoting sustainable agriculture.

Chitin-induced disease resistance in plants: A review

Chitin is composed of N-acetylglucosamine units. Chitin a polysaccharide found in the cell walls of fungi and exoskeletons of insects and crustaceans, can elicit a potent defense response in plants. Through the activation of defense genes, stimulation of defensive compound production, and reinforcement of physical barriers, chitin enhances the plant's ability to defend against pathogens. Chitin-based treatments have shown efficacy against various plant diseases caused by fungal, bacterial, viral, and nematode pathogens, and have been integrated into sustainable agricultural practices. Furthermore, chitin treatments have demonstrated additional benefits, such as promoting plant growth and improving tolerance to abiotic stresses. Further research is necessary to optimize treatment parameters, explore chitin derivatives, and conduct long-term field studies. Continued efforts in these areas will contribute to the development of innovative and sustainable strategies for disease management in agriculture, ultimately leading to improved crop productivity and reduced reliance on chemical pesticides.

An investigation into the effects of various processing methods on the characteristic compounds of highland barley using a widely targeted metabolomics approach

This study explored the influence of diverse processing methods (cooking (CO), extrusion puffing (EX), and steam explosion puffing (SE), stir-frying (SF) and fermentation (FE)) on highland barley (Qingke) chemical composition using UHPLC-MS/MS based widely targeted metabolomics. Overall, 827 metabolites were identified and categorized into 16 classes, encompassing secondary metabolites, amino acids, nucleotides, lipids, etc. There 43, 85, 131, 51 and 98 differential metabolites were respectively selected from five comparative groups (raw materials (RM) vs CO/EX/SE/SF/FE), mainly involved in amino acids, nucleotides, flavonoids, and alkaloids. Compared to other treated groups, FE group possessed the higher content of crude protein (15.12 g/100 g DW), and the relative levels of free amino acids (1.32 %), key polyphenols and arachidonic acid (0.01 %). EX group had the higher content of anthocyanins (4.22 mg/100 g DW), and the relative levels of free amino acids (2.02 %) and key polyphenols. SE group showed the higher relative levels of phenolic acids (0.14 %), flavonoids (0.20 %) and alkaloids (1.17 %), but the lowest free amino acids (0.75 %). Different processing methods all decreased Qingke's antioxidant capacity, with the iron reduction capacity (988.93 μmol/100 g DW) in SE group was the lowest. On the whole, FE and EX were alleged in improving Qingke's nutritional value. CO and SF were also suitable for Qingke processing since fewer differential metabolites were identified in CO vs RM and SF vs RM groups. Differential metabolites were connected to 14 metabolic pathways, with alanine, aspartate, and glutamate metabolism being central. This study contributed theoretical groundwork for the scientific processing and quality control of Qingke products.

Chemical Structure Diversity and Extensive Biological Functions of Specialized Metabolites in Rice

Rice (Oryza sativa L.) is thought to have been domesticated many times independently in China and India, and many modern cultivars are available. All rice tissues are rich in specialized metabolites (SPMs). To date, a total of 181 terpenoids, 199 phenolics, 41 alkaloids, and 26 other types of compounds have been detected in rice. Some volatile sesquiterpenoids released by rice are known to attract the natural enemies of rice herbivores, and play an indirect role in defense. Momilactone, phytocassane, and oryzalic acid are the most common diterpenoids found in rice, and are found at all growth stages. Indolamides, including serotonin, tryptamine, and N-benzoylserotonin, are the main rice alkaloids. The SPMs mainly exhibit defense functions with direct roles in resisting herbivory and pathogenic infections. In addition, phenolics are also important in indirect defense, and enhance wax deposition in leaves and promote the lignification of stems. Meanwhile, rice SPMs also have allelopathic effects and are crucial in the regulation of the relationships between different plants or between plants and microorganisms. In this study, we reviewed the various structures and functions of rice SPMs. This paper will provide useful information and methodological resources to inform the improvement of rice resistance and the promotion of the rice industry.

Geographic differences and variation of functional components of brown rice in 690 mini-core collections from global germplasms

Objective

To understand the geographic differences and variations in the functional components of brown rice cores collected from global rice germplasms.

Methods

Four functional components, γ-aminobutyric acid (GABA), resistant starch (RS), total flavonoids, and alkaloids, in brown rice from 690 mini-core collections from 31 countries from five continents and the International Rice Research Institute, were analyzed using a spectrophotometry colorimetric method, and the results were statistically validated.

Conclusion

The highest average amounts of functional components were obtained in Asian germplasms, except for GABA, and total flavonoids were highest in brown rice from Europe and Oceania, followed by Asia. The highest coefficient of variation for GABA was observed in Asia; that for RS and total flavonoids was observed in Africa, followed by Asia; and that for alkaloids was observed in America, followed by Asia. Overall, Asian countries were the most prominent and representative zones with the highest genotypic potential for functional components of brown rice. Forty-one rice accessions with enriched functional components originated mostly from biodiversity-rich areas in China, followed by those in the Philippines. Late sowing favored the enrichment of these components in brown rice. The current study provides a reference for rice breeding with enriched functional constituents, and guidelines for screening functional rice that could be used for human chronic disease research.

The role of signaling compounds in enhancing rice allelochemicals for sustainable agriculture: an overview

MAIN CONCLUSION

Plant phytotoxin synthesis is influenced by intricate signaling networks like jasmonic acid (JA) and salicylic acid (SA). These compounds not only induce allelochemical production but also aid weed suppression and plant immunity. (-)-Loliolide, JA, SA, and their derivatives trigger rice allelochemical synthesis and gene expression. Enhancing allelochemical synthesis in crops offers an alternative, reducing reliance on traditional herbicides for effective weed management. Rice (Oryza sativa L.) serves as a crucial staple food crop, nourishing over half of the global population, particularly in South Asia. Within rice plants, various secondary metabolites are produced, contributing to its nutritional value and providing energy to consumers. Over the last 5 decades, researchers have investigated 276 distinct types of secondary metabolites found in rice plants. These metabolites predominantly include phenolic acids, flavonoids, steroids, alkaloids, terpenoids, and their derivatives. The role of these secondary metabolites is to regulate the growth and development of the rice plant. In this research paper, we have focused on the allelopathic potential of rice, which involves its active defense strategy to suppress other species in its vicinity. This defense mechanism is regulated by plant signaling compounds. These signaling compounds enable rice plants to recognize and detect competitors, pathogens, and herbivores in their environment. As a response, the rice plants elevate the production of defensive secondary metabolites. One crucial aspect of rice allelopathy is the phenomenon of neighbor detection. Rice plants can sense the presence of neighboring plants and respond accordingly to establish their competitive advantage and ensure their survival. This paper specifically highlights the impact of exogenously applied signaling compounds, namely Methyl salicylate (MeSA) and Methyl Jasmonate (MeJA), on paddy rice. The aim is to provide deeper insights into the signaling mechanisms involved in rice allelopathy and how the exogenous application of signaling compounds influence the induction and regulation of defensive secondary metabolites in rice plants. Comprehensive analysis of various researchers' studies clearly reveals that the application of these elicitor compounds noticeably augments the allelopathic potential of rice, resulting in heightened accumulation of phenolic acid compounds. Expansion in more enlistment of phenolics may be because of expansion in the activities of enzymes, such as cinnamate 4-hydroxylase (C4H) and phenylalanine ammonia-lyase (PAL), the two main enzymes of the phenylpropanoid pathway, which are associated with allelopathic crop plants, and along this, they recognize the presence of weeds and react by expanding allelochemical focuses. Consequently, substantial endeavors have been dedicated in recent times to discover and characterize plant-derived signaling molecules. In bioassays conducted by Patni et al. in 2019, both competitive and non-competitive rice genotypes exhibited elevated phytotoxicity against Echino colona following treatment with MeSA. MeSA-treated rice plants displayed accelerated growth, increased yield, and concurrently demonstrated weed-suppressing properties. Published studies from 1976 to 2021 are reviewed in this paper. The study indicates that signaling compounds induce allelochemical concentrations, enhancing allelopathic activity. This insight may lead to development of novel herbicides for effective sustainable weed management.

Metabolomic analysis for disclosing nutritional and therapeutic prospective of traditional rice cultivars of Cauvery deltaic region, India

Traditional rice is gaining popularity worldwide due to its high nutritional and pharmaceutical value, as well as its high resistance to abiotic and biotic stresses. This has attracted significant attention from breeders, nutritionists, and plant protection scientists in recent years. Hence, it is critical to investigate the grain metabolome to reveal germination and nutritional importance. This research aimed to explore non-targeted metabolites of five traditional rice varieties, viz., Chinnar, Chithiraikar, Karunguruvai, Kichili samba, and Thooyamalli, for their nutritional and therapeutic properties. Approximately 149 metabolites were identified using the National Institute of Standards and Technology (NIST) library and Human Metabolome Database (HMDB) and were grouped into 34 chemical classes. Major classes include fatty acids (31.1-56.3%), steroids and their derivatives (1.80-22.4%), dihydrofurans (8.98-11.6%), prenol lipids (0.66-4.44%), organooxygen compounds (0.12-6.45%), benzene and substituted derivatives (0.53-3.73%), glycerolipids (0.36-2.28%), and hydroxy acids and derivatives (0.03-2.70%). Significant variations in metabolite composition among the rice varieties were also observed through the combination of univariate and multivariate statistical analyses. Principal component analysis (PCA) reduced the dimensionality of 149 metabolites into five principle components (PCs), which explained 96% of the total variance. Two clusters were revealed by hierarchical cluster analysis, indicating the distinctiveness of the traditional varieties. Additionally, a partial least squares-discriminant analysis (PLS-DA) found 17 variables important in the projection (VIP) scores of metabolites. The findings of this study reveal the biochemical intricate and distinctive metabolomes of the traditional therapeutic rice varieties. This will serve as the foundation for future research on developing new rice varieties with traditional rice grain metabolisms to increase grain quality and production with various nutritional and therapeutic benefits.

Metabolomic and transcriptomic analyses of rice plant interaction with invasive weed Leptochloa chinensis

Introduction

Leptochloa chinensis is an annual weed in paddy fields, which can engage in competition with rice, leading to a severe yield reduction. However, theunderlying mechanism governing this interaction remain unknown.

Methods

In this study, we investigated the mutual inhibition between rice and the weed undermono-culture and co-culture conditions. We found that the root exudates of both species played essential roles in mediating the mutual inhibition. Further metabolomic analysis identified a significant number of differential metabolites. These metabolites were predominantly enriched in the phenylpropanoid and flavonoid biosynthesis pathways in weed and rice. Transcriptomic analysis revealed that the differentially expressed genes responding to the interaction were also enriched in these pathways.

Results

Phenylpropanoid and flavonoid biosynthesis pathways are associated with allelopathy, indicating their pivotal role in the response of rice-weed mutual inhibition.

Discussion

Our findings shed light on the conserved molecular responses of rice and L. chinensis during theirinteraction, provide evidence to dissect the mechanisms underlying the allelopathic interaction and offer potential strategies for weed management in rice paddies.

Salinity Treatments Promote the Accumulations of Momilactones and Phenolic Compounds in Germinated Brown Rice

This is the first investigation, conducted in a completely randomized design (CRD), to determine the effects of different salinity levels (75 and 150 mM) and germination periods (3, 4, and 5 days) on momilactone and phenolic accumulations in germinated brown rice (GBR) var. Koshihikari. Particularly, the identification of bioactive compounds was confirmed using electrospray ionization-mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) spectroscopy (¹H and ¹³C). Momilactone A (MA) and momilactone B (MB) amounts were determined by ultra-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS), whereas other compounds were quantified by spectrophotometry and high-performance liquid chromatography (HPLC). Accordingly, GBR under B2 treatment (75 mM salinity for 4 days) showed the greatest total phenolic and flavonoid contents (14.50 mg gallic acid and 11.06 mg rutin equivalents, respectively, per g dry weight). GBR treated with B2 also accumulated the highest quantities of MA, MB, ρ-coumaric, ferulic, cinnamic, salicylic acids, and tricin (18.94, 41.00, 93.77, 139.03, 46.05, 596.26, and 107.63 µg/g DW, respectively), which were consistent with the strongest antiradical activities in DPPH and ABTS assays (IC₅₀ = 1.58 and 1.78 mg/mL, respectively). These findings have implications for promoting the value of GBR consumption and rice-based products that benefit human health.

Rice-Magnaporthe transcriptomics reveals host defense activation induced by red seaweed-biostimulant in rice plants

Red seaweed extracts have been shown to trigger the biotic stress tolerance in several crops. However, reports on transcriptional modifications in plants treated with seaweed biostimulant are limited. To understand the specific response of rice to blast disease in seaweed-biostimulant-primed and non-primed plants, transcriptomics of a susceptible rice cultivar IR-64 was carried out at zero and 48 h post inoculation with Magnaporthe oryzae (strain MG-01). A total of 3498 differentially expressed genes (DEGs) were identified; 1116 DEGs were explicitly regulated in pathogen-inoculated treatments. Functional analysis showed that most DEGs were involved in metabolism, transport, signaling, and defense. In a glass house, artificial inoculation of MG-01 on seaweed-primed plants resulted in the restricted spread of the pathogen leading to the confined blast disease lesions, primarily attributed to reactive oxygen species (ROS) accumulation. The DEGs in the primed plants were defense-related transcription factors, kinases, pathogenesis-related genes, peroxidases, and growth-related genes. The beta-D-xylosidase, a putative gene that helps in secondary cell wall reinforcement, was downregulated in non-primed plants, whereas it upregulated in the primed plants indicating its role in the host defense. Additionally, Phenylalanine ammonia-lyase, pathogenesis-related Bet-v-I family protein, chalcone synthase, chitinases, WRKY, AP2/ERF, and MYB families were upregulated in seaweed and challenge inoculated rice plants. Thus, our study shows that priming rice plants with seaweed bio-stimulants resulted in the induction of the defense in rice against blast disease. This phenomenon is contributed to early protection through ROS, protein kinase, accumulation of secondary metabolites, and cell wall strengthening.

Metabolic engineering of plant secondary metabolites: prospects and its technological challenges

Plants produce a wide range of secondary metabolites that play vital roles for their primary functions such as growth, defence, adaptations or reproduction. Some of the plant secondary metabolites are beneficial to mankind as nutraceuticals and pharmaceuticals. Metabolic pathways and their regulatory mechanism are crucial for targeting metabolite engineering. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated system has been widely applied in genome editing with high accuracy, efficiency, and multiplex targeting ability. Besides its vast application in genetic improvement, the technique also facilitates a comprehensive profiling approach to functional genomics related to gene discovery involved in various plant secondary metabolic pathways. Despite these wide applications, several challenges limit CRISPR/Cas system applicability in genome editing in plants. This review highlights updated applications of CRISPR/Cas system-mediated metabolic engineering of plants and its challenges.

OsWRKY10 extensively activates multiple rice diterpenoid phytoalexin biosynthesis to enhance rice blast resistance

Phytoalexin is the main chemical weapon against disease pathogens in plants. Rice produces a number of phytoalexins to defend pathogens, most of which belong to diterpenoid phytoalexins. Three biosynthetic gene clusters (BGCs) and a few non-cluster genes are responsible for rice diterpenoid phytoalexin biosynthesis. The corresponding regulatory mechanism of these phytoalexins in response to pathogen challenges still remains unclear. Here we identified a transcription factor, OsWRKY10, positively regulating rice diterpenoid phytoalexin biosynthesis. Knockout mutants of OsWRKY10 obtained by the CRISPR/Cas9 technology are more susceptible to Magnaporthe oryzae infection, while overexpression of OsWRKY10 enhances resistance to rice blast. Further analysis reveals that overexpression of OsWRKY10 increases accumulation of multiple rice diterpenoid phytoalexins and expression of genes in three BGCs and non-clustered genes in response to M. oryzae infection. Knockout of OsWRKY10 impairs upregulation of rice diterpenoid phytoalexin biosynthesis gene expression by blast pathogen and CuCl₂ treatment. OsWRKY10 directly binds to the W-boxes or W-box-like elements (WLEs) of rice diterpenoid phytoalexin biosynthesis gene promoters to regulate the corresponding gene expression. This study identified an extensive regulator (OsWRKY10) with the broad transcriptional regulation on rice diterpenoid phytoalexin biosynthesis, providing the insight to characterize regulation of rice chemical defense for improving disease resistance.

Composition, Microbiota, Mechanisms, and Anti-Obesity Properties of Rice Bran

Rice is a major cereal crop and a staple food for nearly 50% of people worldwide. Rice bran (RB) is a nutrient-rich by-product of rice processing. RB is rich in carbohydrates, fibers, proteins, lipids, minerals, and several trace elements (phosphorus, calcium, magnesium, potassium, and manganese). The extraction process and storage have influenced RB extracts and RB oil's quality. The RB composition has also varied on the rice cultivars. The color of RB indicates the richness of the bioactive compounds, especially anthocyanins. γ-oryzanol, tocopherols, tocotrienols, and unsaturated fatty acids are major components of RB oil. It has been established that RB supplementation could improve the host's health status. Several preclinical and clinical studies have reported that RB has antioxidant, anticancer, anti-inflammatory, anticolitis, and antidiabetic properties. The beneficial biological properties of RB are partially attributed to its ability to alter the host microbiome and help to maintain and restore eubiosis. Non-communicable diseases (NCDs), including heart disease, diabetes, cancer, and lung disease, account for 74% of deaths worldwide. Obesity is a global health problem and is a major reason for the development of NCDs. The medical procedures for managing obesity are expensive and long-term health supplements are required to maintain a healthy weight. Thus, cost-effective natural adjuvant therapeutic strategy is crucial to treat and manage obesity. Several studies have revealed that RB could be a complementary pharmacological candidate to treat obesity. A comprehensive document with basic information and recent scientific results on the anti-obesity activity of RB and RB compounds is obligatory. Thus, the current manuscript was prepared to summarize the composition of RB and the influence of RB on the host microbiome, possible mechanisms, and preclinical and clinical studies on the anti-obesity properties of RB. This study suggested that the consumption of RB oil and dietary RB extracts might assist in managing obesity-associated health consequences. Further, extended clinical studies in several ethnic groups are required to develop dietary RB-based functional and nutritional supplements, which could serve as an adjuvant therapeutic strategy to treat obesity.

OsGLP3-7 positively regulates rice immune response by activating hydrogen peroxide, jasmonic acid, and phytoalexin metabolic pathways

Although germin-like proteins (GLPs) have been demonstrated to participate in plant biotic stress responses, their specific functions in rice disease resistance are still largely unknown. Here, we report the identification and characterization of OsGLP3-7, a member of the GLP family in rice. Expression of OsGLP3-7 was significantly induced by pathogen infection, jasmonic acid (JA) treatment, and hydrogen peroxide (H₂ O₂ ) treatment. OsGLP3-7 was highly expressed in leaves and sublocalized in the cytoplasm. Overexpression of OsGLP3-7 increased plant resistance to leaf blast, panicle blast, and bacterial blight, whereas disease resistance in OsGLP3-7 RNAi silenced plants was remarkably compromised, suggesting this gene is a positive regulator of disease resistance in rice. Further analysis showed that OsGLP3-7 has superoxide dismutase (SOD) activity and can influence the accumulation of H₂ O₂ in transgenic plants. Many genes involved in JA and phytoalexin biosynthesis were strongly induced, accompanied with elevated levels of JA and phytoalexins in OsGLP3-7-overexpressing plants, while expression of these genes was significantly suppressed and the levels of JA and phytoalexins were reduced in OsGLP3-7 RNAi plants compared with control plants, both before and after pathogen inoculation. Moreover, we showed that OsGLP3-7-dependent phytoalexin accumulation may, at least partially, be attributed to the elevated JA levels observed after pathogen infection. Taken together, our results indicate that OsGLP3-7 positively regulates rice disease resistance by activating JA and phytoalexin metabolic pathways, thus providing novel insights into the disease resistance mechanisms conferred by GLPs in rice.

Co-Application of Silver Nanoparticles and Symbiotic Fungus Piriformospora indica Improves Secondary Metabolite Production in Black Rice

In the current research, unique Nano-Embedded Fungus (NEF), made by the synergic association of silver nanoparticles (AgNPs) and endophytic fungus (Piriformospora indica), is studied, and the impact of NEF on black rice secondary metabolites is reported. AgNPs were synthesized by chemical reduction process using the temperature-dependent method and characterized for morphological and structural features through UV visible absorption spectroscopy, zeta potential, XRD, SEM-EDX, and FTIR spectroscopy. The NEF, prepared by optimizing the AgNPs concentration (300 ppm) in agar and broth media, showed better fungal biomass, colony diameter, spore count, and spore size than the control P. indica. Treatment with AgNPs, P. indica, and NEF resulted in growth enhancement in black rice. NEF and AgNPs stimulated the production of secondary metabolites in its leaves. The concentrations of chlorophyll, carotenoids, flavonoids, and terpenoids were increased in plants inoculated with P. indica and AgNPs. The findings of the study highlight the synergistic effect of AgNPs and the fungal symbionts in augmenting the secondary metabolites in leaves of black rice.

Rice Phytoalexins: Half a Century of Amazing Discoveries; Part I: Distribution, Biosynthesis, Chemical Synthesis, and Biological Activities

Cultivated rice is a staple food for more than half of the world's population, providing approximately 20% of the world's food energy needs. A broad spectrum of pathogenic microorganisms causes rice diseases leading to huge yield losses worldwide. Wild and cultivated rice species are known to possess a wide variety of antimicrobial secondary metabolites, known as phytoalexins, which are part of their active defense mechanisms. These compounds are biosynthesized transiently by rice in response to pathogens and certain abiotic stresses. Rice phytoalexins have been intensively studied for over half a century, both for their biological role and their potential application in agronomic and pharmaceutical fields. In recent decades, the growing interest of the research community, combined with advances in chemical, biological, and biomolecular investigation methods, has led to a notable acceleration in the growth of knowledge on rice phytoalexins. This review provides an overview of the knowledge gained in recent decades on the diversity, distribution, biosynthesis, chemical synthesis, and bioactivity of rice phytoalexins, with particular attention to the most recent advances in this research field.

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

Effect of ginsenosides on microbial community and enzyme activity in continuous cropping soil of ginseng

Root exudates contain plant metabolites secreted by the roots into the soil, such as ginsenosides secreted by the ginseng root. However, little is known about ginseng root exudate and its impact on the chemical and microbial properties of soil. In this study, the effect of increasing concentrations of ginsenosides on the chemical and microbial properties of soil was tested. Chemical analysis and high-throughput sequencing techniques were used to evaluate the soil chemical properties and microbial characteristics following exogenous application of 0.1 mg·L^-1, 1 mg·L^-1, and 10 mg·L^-1 ginsenosides. Ginsenosides application significantly altered soil enzyme activities; SOM-dominated physicochemical properties were significantly reduced which altered the composition and structure of the soil microbial community. In particular, treatment with 10 mg∙L^-1 ginsenosides significantly increased the relative abundance of pathogenic fungi such as Fusarium, Gibberella and Neocosmospora. These findings indicate that ginsenosides in root exudates are important factors that may lead to increased deterioration of soil during ginseng cultivation and provided new research direction for the subsequent study on the mechanism of interaction between ginsenosides and soil microbial communities.

The effects of allelochemicals from root exudates of Flaveria bidentis on two Bacillus species

To determine the allelopathic effects of root exudates from Flaveria bidentis on function of Bacillus, pot experiment was used to collect root exudates from living plants and test its allelopathic effects on function of Bacillus frigoritolerans and Bacillus megaterium, which were two dominant bacteria in the rhizosphere soil of F. bidentis. To obtain the allelopathic substances, the root exudates were successively extracted by N-hexane, dichloromethane, ethyl acetate, and N-butanol, and their allelopathic effects were tested. The results showed that B. frigoritolerans and B. megaterium considerably increased the concentration of available phosphorus and nitrogen, respectively, when the soil was treated with different concentrations of root exudates. Among the four organic solvent extracts, dichloromethane extracts significantly increased the abundances of B. frigoritolerans and B. megaterium and promoted their nitrogen-fixing and phosphate-solubilizing abilities. Phenol was detected in dichloromethane extracts by gas chromatograph-mass spectrometer (GC-MS). Meanwhile, phenol promoted the ability to fix nitrogen of B. megaterium and its growth by increasing the soil available nitrogen concentration, but phenol promoted the ability to solubilize phosphate of B. frigoritolerans only in 0.1mg/mL concentration. Therefore, phenol was an allelochemicals in the root exudates of F. bidentis that affects the growth and activities of B. megaterium.

Plagiodera versicolora feeding induces systemic and sexually differential defense responses in poplars

Dioecious plants have evolved effective defense strategies to deal with various biotic and abiotic stresses. However, little is known regarding sexual differences in their defense against herbivores. In this study, we investigated the mechanism of systemic defense responses in male and female Populus cathayana attacked by Plagiodera versicolora Laicharting. The results revealed that P. cathayana exhibits sexually differential responses to a defoliator. The percentage of damaged leaf area was greater in males than in females. Furthermore, the observed saccharide changes imply that males and females exhibit different response times to defoliators. The contents of flavonoids and anthocyanins were significantly increased in both sexes but were higher in females. Specifically, the jasmonic acid (JA) pathway plays an important role. Expression of pest-related genes further revealed that hormones induce changes in downstream genes and metabolites, and upregulation of JA ZIM-domain (JAZ) and CORONATINE INSENSITIVE 1 (COI1) was more significant in females. In the undamaged adjacent leaves, metabolite and gene changes displayed similar patterns to the damaged local leaves, but levels of JA, JAZ1, and COI1 were higher in females. Therefore, our data confirmed that plants initiate the JA pathway to defend against herbivores, that there is systematic signal transduction, and that this ability is stronger in females than in males. This study provides new insights into the resistance of dioecious plants to herbivory and adds a new theoretical basis for the systemic signal transduction of plants in response to biotic stress.

Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense

Plant cell wall is a complex and changeable structure, which is very important for plant growth and development. It is clear that cell wall polysaccharide synthases have critical functions in rice growth and abiotic stress, yet their role in plant response to pathogen invasion is poorly understood. Here, we describe a dwarf and narrowed leaf in Hejiang 19 (dnl19) mutant in rice, which shows multiple growth defects such as reduced plant height, enlarged lamina joint angle, curled leaf morphology, and a decrease in panicle length and seed setting. MutMap analysis, genetic complementation and gene knockout mutant show that cellulose synthase-like D4 (OsCSLD4) is the causal gene for DNL19. Loss function of OsCSLD4 leads to a constitutive activation of defense response in rice. After inoculation with rice blast and bacterial blight, dnl19 displays an enhanced disease resistance. Widely targeted metabolomics analysis reveals that disruption of OsCSLD4 in dnl19 resulted in significant increase of L-valine, L-asparagine, L-histidine, L-alanine, gentisic acid, but significant decrease of L-aspartic acid, malic acid, 6-phosphogluconic acid, glucose 6-phosphate, galactose 1-phosphate, gluconic acid, D-aspartic acid. Collectively, our data reveals the importance of OsCSLD4 in balancing the trade-off between rice growth and defense.

Onion anthocyanins: Extraction, stability, bioavailability, dietary effect, and health implications

Anthocyanins are high-value compounds, and their use as functional foods and their natural colorant have potential health benefits. Anthocyanins seem to possess antioxidant properties, which help prevent neuronal diseases and thereby exhibit anti-inflammatory, chemotherapeutic, cardioprotective, hepatoprotective, and neuroprotective activities. They also show different therapeutic effects against various chronic diseases. Anthocyanins are present in high concentrations in onion. In recent years, although both conventional and improved methods have been used for extraction of anthocyanins, nowadays, improved methods are of great importance because of their higher yield and stability of anthocyanins. In this review, we compile anthocyanins and their derivatives found in onion and the factors affecting their stability. We also analyze different extraction techniques of anthocyanins. From this point of view, it is very important to be precisely aware of the impact that each parameter has on the stability and subsequently potentiate its bioavailability or beneficial health effects. We present up-to-date information on bioavailability, dietary effects, and health implications of anthocyanins such as antioxidant, antidiabetic, anticancerous, antiobesity, cardioprotective, and hepatoprotective activities.

Identification of the rice genes and metabolites involved in dual resistance against brown planthopper and rice blast fungus

Brown planthopper (BPH) and blast disease jointly or individually cause big yield losses every year. To identify genes and metabolites with potential contributions to the dual resistance against both biotic-stress factors, we carried out a transcriptome and metabolome analysis for susceptible and resistant rice varieties after BPH and rice blast infestations. Coexpression network analysis identified a modular pattern that had the highest correlation coefficients (0.81) after the BPH and rice blast (-0.81) treatments. In total, 134 phenylpropanoid biosynthesis pathway-related genes were detected in this group. We found that the flavanone 3-hydroxylase gene (OsF3H) had opposite expression trends in response to BPH and rice blast infestations whereas the OsF3'H had similar expression patterns. Genetics analysis confirmed that the OsF3H gene knockdown lines demonstrated the opposite resistance phenotypes against BPH and rice blast, whereas the OsF3'H knockout lines enhanced rice resistance against both pests. Consistently, our metabolomics analysis identified the metabolite eriodictyol, one putative essential product of these two genes, that was more highly accumulated in the resistant rice variety of RHT than in the susceptible variety MDJ. This study highlights a useful strategy for identifying more genes and metabolites that have potential synergistic effects on rice against to multiple biotic stresses.

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

An Adenylate Kinase OsAK3 Involves Brassinosteroid Signaling and Grain Length in Rice (Oryza sativa L.)

BACKGROUND

Grain size is one of the major determinants of cereal crop yield. As a class of plant polyhydroxysteroids, brassinosteroids (BRs) play essential roles in the regulation of grain size and plant architecture in rice. In a previous research, we cloned qGL3/OsPPKL1 encoding a protein phosphatase with Kelch-like repeat domains, which negatively regulates BR signaling and grain length in rice.

RESULTS

Here, we screened qGL3-interacting proteins (GIPs) via yeast two-hybrid assay and analyzed the phenotypes of the T-DNA insertion mutants of GIPs. Among these mutants, mutant osak3 presents shorter grain length and dwarfing phenotype. OsAK3 encodes an adenylate kinase, which regulates grain size by controlling cell expansion of rice spikelet glume. Overexpression of OsAK3 resulted in longer grain length. OsAK3 interacts with qGL3 in vivo and in vitro. Lamina inclination, coleoptile elongation and root inhibition experiments showed that the osak3 mutant was less sensitive to exogenous brassinolide (BL) treatment. The transcriptional level of OsAK3 was up-regulated under BL induction. In addition, RNA-Seq data indicate that OsAK3 is involved in a variety of biological processes that regulate BR signaling and grain development in rice.

CONCLUSIONS

Our study reveals a novel BR signaling component OsAK3 in the regulation of grain length, and provides novel clues for uncovering the potential functions of OsAK3 in rice growth and development.

Identification of Key Genes in 'Luang Pratahn', Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of 'Luang Pratahn' rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis

Simple Summary

The freezing stress during overwintering brings great challenges to the normal growth of Camellia sinensis. The current research on C. sinensis mainly focuses on cold resistance, but less on freezing resistance. In the present study, the transcriptome and metabolome of C. sinensis under freezing stress were studied. Results showed that Pyr/PYL-PP2C-SnRK2 played a critical role in the signal transduction of freezing stress. Three metabolic pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis contributed to the freezing resistance of C. sinensis. This study provides substantial insights for the breeding of C. sinensis.

Abstract

Freezing stress in winter is the biggest obstacle to the survival of C. sinensis in mid-latitude and high-latitude areas, which has a great impact on the yield, quality, and even life of C. sinensis every year. In this study, transcriptome and metabolome were used to clarify the freezing resistance mechanism of 60-year-old natural overwintering C. sinensis under freezing stress. Next, 3880 DEGs and 353 DAMs were obtained. The enrichment analysis showed that pathways of MAPK and ABA played a key role in the signal transduction of freezing stress, and Pyr/PYL-PP2C-SnRK2 in the ABA pathway promoted stomatal closure. Then, the water holding capacity and the freezing resistance of C. sinensis were improved. The pathway analysis showed that DEGs and DAMs were significantly enriched and up-regulated in the three-related pathways of phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and flavonoid biosynthesis. In addition, the carbohydrate and fatty acid synthesis pathways also had a significant enrichment, and the synthesis of these substances facilitated the freezing resistance. These results are of great significance to elucidate the freezing resistance mechanism and the freezing resistance breeding of C. sinensis.

A review: biosynthesis of plant-derived labdane-related diterpenoids

Plant-derived labdane-related diterpenoids (LRDs) represent a large group of terpenoids. LRDs possess either a labdane-type bicyclic core structure or more complex ring systems derived from labdane-type skeletons, such as abietane, pimarane, kaurane, etc. Due to their various pharmaceutical activities and unique properties, many of LRDs have been widely used in pharmaceutical, food and perfume industries. Biosynthesis of various LRDs has been extensively studied, leading to characterization of a large number of new biosynthetic enzymes. The biosynthetic pathways of important LRDs and the relevant enzymes (especially diterpene synthases and cytochrome P450 enzymes) were summarized in this review.

Applications of Metabolomics to Precision Nutrition

BACKGROUND

For thousands of years, disabilities due to nutrient deficiencies have plagued humanity. Rickets, scurvy, anemia, stunted growth, blindness, and mental handicaps due to nutrient deficiencies affected up to 1/10 of the world's population prior to 1900. The discovery of essential amino acids, vitamins, and minerals, in the early 1900s, led to a fundamental change in our understanding of food and a revolution in human health. Widespread vitamin and mineral supplementation, the development of recommended dietary allowances, and the implementation of food labeling and testing along with significant improvements in food production and food quality have meant that nutrient-related disorders have almost vanished in the developed world. The success of nutritional science in preventing disease at a population-wide level is one of the great scientific triumphs of the 20th century. The challenge for nutritional science in the 21st century is to understand how to use nutrients and other food constituents to enhance human health or prevent disease at a more personal level. This is the primary goal of precision nutrition.

SUMMARY

Precision nutrition is an emerging branch of nutrition science that aims to use modern omics technologies (genomics, proteomics, and metabolomics) to assess an individual's response to specific foods or dietary patterns and thereby determine the most effective diet or lifestyle interventions to prevent or treat specific diseases in that individual. Metabolomics is vital to nearly every aspect of precision nutrition. It can be used to comprehensively characterize the thousands of chemicals in foods, to identify food byproducts in human biofluids or tissues, to characterize nutrient deficiencies or excesses, to monitor biochemical responses to dietary interventions, to track long-term or short-term dietary habits, and to guide the development of nutritional therapies. In this review, we will describe how metabolomics has been used to advance the field of precision nutrition by providing some notable examples or use cases. First, we will describe how metabolomics helped launch the field of precision nutrition through the diagnosis and dietary therapy of individuals with inborn errors of metabolism. Next, we will describe how metabolomics is being used to comprehensively characterize the full chemical complexity of many key foods, and how this is revealing much more about nutrients than ever imagined. Third, we will describe how metabolomics is being used to identify food consumption biomarkers and how this opens the door to a more objective and quantitative assessments of an individual's diet and their response to certain foods. Finally, we will describe how metabolomics is being coupled with other omics technologies to develop custom diets and lifestyle interventions that are leading to positive health benefits. Key Message: Metabolomics is vital to the advancement of nutritional science and in making the dream of precision nutrition a reality.

Ginseng Omics for Ginsenoside Biosynthesis

Ginseng, also known as the king of herbs, has been regarded as an important traditional medicine for several millennia. Ginsenosides, a group of triterpenoid saponins, have been characterized as bioactive compounds of ginseng. The complexity of ginsenosides hindered ginseng research and development both in cultivation and clinical research. Therefore, deciphering the ginsenoside biosynthesis pathway has been a focus of interest for researchers worldwide. The new emergence of biological research tools consisting of omics and bioinformatic tools or computational biology tools are the research trend in the new century. Ginseng is one of the main subjects analyzed using these new quantification tools, including tools of genomics, transcriptomics, and proteomics. Here, we review the current progress of ginseng omics research and provide results for the ginsenoside biosynthesis pathway. Organization and expression of the entire pathway, including the upstream MVA pathway, the cyclization of ginsenoside precursors, and the glycosylation process, are illustrated. Regulatory gene families such as transcriptional factors and transporters are also discussed in this review.

Role of digestive protease enzymes and related genes in host plant adaptation of a polyphagous pest, Spodoptera frugiperda

The evolutionary success of phytophagous insects depends on their ability to efficiently exploit plants as a source of energy for survival. Herbivorous insects largely depend on the efficiency, flexibility, and diversity of their digestive physiology and sophistication of their detoxification system to use chemically diverse host plants as food sources. The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a polyphagous pest of many commercially important crops. To elucidate the ability of this insect pest to adapt to host plant mechanisms, we evaluated the impact of primary (corn) and alternate (rice) host plants after 11 generations on gut digestive enzymatic activity and expression profiles of related genes. Results indicated that the total protease and class-specific trypsin- and chymotrypsin-like protease activity of S. frugiperda significantly differed among host plant treatments. The class-specific protease profiles greatly differed in S. frugiperda midguts upon larval exposure to different treatments with inhibitors compared with treatments without inhibitors. Similarly, the single and cumulative effects of the enzyme-specific inhibitors TLCK, TPCK, and E-64 significantly increased larval mortality and reduced larval growth/mass across different plant treatments. Furthermore, the quantitative reverse transcription polymerase chain reaction results revealed increased transcription of two trypsin (SfTry-3, SfTry-7) and one chymotrypsin gene (Sfchym-9), which indicated that they have roles in host plant adaptation. Knockdown of these genes resulted in significantly reduced mRNA expression levels of the trypsin genes. This was related to the increased mortality observed in treatments compared with the dsRED control. This result indicates possible roles of S. frugiperda gut digestive enzymes and related genes in host plant adaptation.

Biochemistry of Terpenes and Recent Advances in Plant Protection

Biodiversity is adversely affected by the growing levels of synthetic chemicals released into the environment due to agricultural activities. This has been the driving force for embracing sustainable agriculture. Plant secondary metabolites offer promising alternatives for protecting plants against microbes, feeding herbivores, and weeds. Terpenes are the largest among PSMs and have been extensively studied for their potential as antimicrobial, insecticidal, and weed control agents. They also attract natural enemies of pests and beneficial insects, such as pollinators and dispersers. However, most of these research findings are shelved and fail to pass beyond the laboratory and greenhouse stages. This review provides an overview of terpenes, types, biosynthesis, and their roles in protecting plants against microbial pathogens, insect pests, and weeds to rekindle the debate on using terpenes for the development of environmentally friendly biopesticides and herbicides.

The Predicted Functional Compartmentation of Rice Terpenoid Metabolism by Trans-Prenyltransferase Structural Analysis, Expression and Localization

Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with allylic substrates. The in silico structural comparative analyses of rice trans-PTs with 136 plant trans-PT genes allowed twelve rice PTs to be identified as GGPS_LSU (OsGGPS1), homomeric G(G)PS (OsGPS) and GGPS_SSU-II (OsGRP) in Group I; two solanesyl-PP synthase (OsSPS2 and 3) and two polyprenyl-PP synthases (OsSPS1 and 4) in Group II; and five FPSs (OsFPS1, 2, 3, 4 and 5) in Group III. Additionally, several residues in "three floors" for the chain length and several essential domains for enzymatic activities specifically varied in rice, potentiating evolutionarily rice-specific biochemical functions of twelve trans-PTs. Moreover, expression profiling and localization patterns revealed their functional compartmentation in rice. Taken together, we propose the predicted topology-based working model of rice PTs with corresponding terpene metabolites: GPP/GGPPs mainly in plastoglobuli, SPPs in stroma, PPPs in cytosol, mitochondria and chloroplast and FPPs in cytosol. Our findings could be suitably applied to metabolic engineering for producing functional terpene metabolites in rice systems.

Engineered Rhodobacter capsulatus as a Phototrophic Platform Organism for the Synthesis of Plant Sesquiterpenoids

Sesquiterpenoids are a large class of natural compounds offering manifold properties valuable for food, cosmetics, agriculture, and pharma industry. Production in microorganisms is a sustainable approach to provide sesquiterpenoids for research and industrial use independent of their natural sources. This requires the functional transfer of the respective biocatalytic pathways in an adequate host microorganism offering a sufficient supply of precursors that is ideally adjusted to the individual demand of the recombinant biosynthesis route. The phototrophic purple bacterium Rhodobacter capsulatus offers unique physiological properties that are favorable for biosynthesis of hydrophobic terpenes. Under phototrophic conditions, it develops a large intracytoplasmic membrane suitable for hosting membrane-bound enzymes and metabolites of respective biosynthetic pathways. In addition, Rhodobacter harbors an intrinsic carotenoid biosynthesis that can be engineered toward the production of foreign terpenes. Here, we evaluate R. capsulatus as host for the production of plant sesquiterpenoids under phototrophic conditions using patchoulol and valencene as a proof of concept. The heterologous expression of patchoulol synthase PcPS from Pogostemon cablin as well as the valencene synthases CsVS from Citrus sinensis and CnVS from Callitropsis nootkatensis led to the production of the respective sesquiterpenoids in R. capsulatus. To analyze, if gradually adjustable formation of the key precursor farnesylpyrophosphate (FPP) is beneficial for sesquiterpene synthesis under phototrophic conditions, the intrinsic 1-deoxy-D-xylulose 5-phosphate (DXP) pathway genes as well as the heterologous mevalonate pathway genes were modularly expressed in various combinations. To this end, different plasmids and chromosomally integrated expression tools were developed harboring the strong and tightly controlled P_nif promoter for heterologous gene expression. Notably, comparative studies identified a distinct combination of precursor biosynthetic genes as best-performing setup for each of the tested sesquiterpene synthases. In summary, we could demonstrate that R. capsulatus is a promising alternative platform organism that is suited for sustainable sesquiterpenoid formation under phototrophic cultivation conditions. A modular engineering of R. capsulatus strains via tailored co-expression of FPP biosynthetic genes further allowed adaptation of sesquiterpene precursor formation to its catalytic conversion by different plant terpene synthases.

Antibacterial Properties of Nootkatone Against Gram-Positive Bacteria

Nootkatone is one of the sesquiterpenes contained in citrus peels, especially in grapefruits. It is known that nootkatone has various physiological activities such as antioxidative and antifibrotic actions. This study showed that nootkatone, a natural sesquiterpene, exhibited antibacterial activities against Gram-positive bacteria such as Staphylococcus aureus, Enterococcus faecalis, Listeria monocytogenes, Corynebacterium diphtheriae, and Bacillus cereus, with the antibacterial effect against C. diphtheriae being most pronounced. However, no growth-inhibitory effects or bactericidal activity was observed against Gram-negative bacteria. In addition, the bactericidal activity of nootkatone at a high concentration was observed against Gram-positive bacilli. These results suggested that nootkatone may exert an antibacterial effect by targeting cell wall structures or a particular metabolite. Moreover, even at a low concentration (0.25 mM), nootkatone was capable of inhibiting biofilm formation by Staphylococcus aureus. Thus, this study demonstrated antibacterial efficacy for nootkatone against Gram-positive bacteria, indicating that nootkatone could be a potential candidate for the development of new antibacterial agents.