Phenylpropanoid Biosynthetic Pathway Research Articles

Stimulation of secondary metabolism in grape berry exocarps by a nature-based strategy of foliar application of polyols

In grapes under drought stress, polyols accumulate through tight coordination at the molecular level between increased membrane transport of polyols and inhibition of polyol oxidation. Here, the effects on grape metabolism of an exogenous foliar application of polyols as a potential sustainable viticultural practice to increase grapevine performance and berry quality were thoroughly assessed. Grapevines were pulverised with a polyol solution containing 2 mM mannitol and 2 mM sorbitol, and the metabolome of grape berry exocarps and important metabolic pathways associated with berry quality and polyol metabolism were analysed at véraison and mature stages. By combining metabolomics analysis using UPLC-MS, enzyme activity assays and targeted transcriptional analyses, it was demonstrated that foliar application of polyols stimulated by 3.5-fold and 6-fold abscisic acid (ABA) biosynthesis at véraison and mature grape berries, respectively. It also stimulated the concentration of anthocyanins, stilbenes and total phenolics in exocarps through the upregulation of phenylpropanoid, stilbenoid and anthocyanin biosynthetic pathways shown by increases in phenylalanine-ammonia lyase (PAL) activity (3-fold) and VviPAL1 expression, stilbene synthase 1 (VviSTS1) transcripts (ca. 5-fold), UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) activity and VviUFGT1 expression, among other results, at the mature stage, when these changes were most noticeable. Many secondary metabolites synthesised in these pathways identified by UPLC-MS analysis were present at higher quantities in exocarps from polyol-treated plants such as fertaric acid, E-resveratrol, E-piceatannol, piceid, pallidol, E-ε-viniferin, myricetin-hexoside 1, cyanidin-3-O-glucoside and malvidin-3-O-(6-p-coumaroyl)-glucoside. Foliar application of low-concentration polyols is, therefore, a promising biostimulant-based strategy to improve grape berry quality and nutritional value in the current context of climate change.

Revealing the specific regulations of nitric oxide on the postharvest ripening and senescence of bitter melon fruit

Bitter melon fruit is susceptible to yellowing, softening, and rotting under room-temperature storage conditions, resulting in reduced commercial value. Nitric oxide (NO) is an important signaling molecule and plays a crucial role in regulating the fruit postharvest quality. In this study, we investigated the effects of NO treatment on changes in sensory and firmness of bitter melon fruit during postharvest storage. Moreover, transcriptomic, metabolomic, and proteomic analyses were performed to elucidate the regulatory mechanisms through which NO treatment delays the ripening and senescence of bitter melon fruit. Our results show that differentially expressed genes (DEGs) were involved in fruit texture (CSLE, β-Gal, and PME), plant hormone signal transduction (ACS, JAR4, and AUX28), and fruit flavor and aroma (SUS2, LOX, and GDH2). In addition, proteins differentially abundant were associated with fruit texture (PLY, PME, and PGA) and plant hormone signal transduction (PBL15, JAR1, and PYL9). Moreover, NO significantly increased the abundance of key enzymes involved in the phenylpropanoid biosynthetic pathway, thus enhancing the disease resistance and alleviating softening of bitter melon fruit. Finally, differential metabolites mainly included phenolic acids, terpenoids, and flavonoids. These results provide a theoretical basis for further studies on the physiological changes associated with postharvest ripening and senescence of bitter melon fruit.

Expression Analysis of Phenylpropanoid Pathway Genes and Phenylpropanoid Accumulation in Different Organs of Chelidonium majus L.

Objective This study set out to examine the phenylpropanoid pathway gene expression and phenolic compound accumulation in different organs of Chelidonium majus (C. majus). Methods Total RNA was extracted and expression of phenylpropanoid biosynthesis genes was assessed using quantitative real-time polymerase chain reaction in different organs of C. majus. In addition, the phenylpropanoid compounds were analyzed from different organs of C. majus by using high-performance liquid chromatography. Results The results demonstrate the variance in the expression levels of phenylpropanoid pathway genes in the flowers, leaves, stems, and roots of C. majus. CmPAL and CmC4H were expressed at their greatest levels in the stem, while CmCHS and CmCHI were strongly expressed in the leaf, and CmF3H, CmFLS, Cm4CL, and CmDFR were more abundant in the flower. The total phenolic contents in the different organs also varied significantly. The highest value was recorded in the flowers (2152.89 ± 78.71 μg/g dry wt.), which was 54.26 times higher than the lowest values obtained from roots (39.68 ± 0.05 μg/g dry wt.). Except for roots, rutin showed the highest level in all other organs. According to a heat map, the majority of the phenolic compounds were highest in the flower. By using variable importance in projection analysis, the most significant metabolite was found to be chlorogenic acid, which had a positive association with all phenolic chemicals, but it showed a negative correlation with trans-cinnamic acid. Except for trans-cinnamic acid, all other phenolic compounds likewise showed positive correlation with other phenolic compounds. Conclusions This work offers pertinent data on the expression analysis of genes involved in the phenylpropanoid biosynthetic pathway and the presence of phenolic compounds in C. majus. These findings will be helpful for the researcher to understand the relationship between the expression level of phenylpropanoid pathway genes and phenylpropanoid compound accumulation in C. majus.

Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux

Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2–19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.

Exogenous Abscisic Acid Regulates Anthocyanin Biosynthesis and Gene Expression in Blueberry Leaves

Blueberry (Vaccinium corymbosum) leaves have a positive influence on health because of their phenolic contents, including anthocyanins. Phytohormone abscisic acid (ABA) promotes anthocyanin accumulation, but the underlying mechanisms are unclear in blueberry leaves. In this study, we found that exogenous ABA promotes anthocyanin accumulation in blueberry leaves and we explored the global molecular events involved in these physiological changes by treating in vitro-grown blueberry seedlings with ABA and performing transcriptome deep sequencing (RNA-seq). We identified 6390 differentially expressed genes (DEGs), with 2893 DEGs at 6 h and 4789 at 12 h of ABA treatment compared to the control. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to plant hormone signal transduction and phenylpropanoid and flavonoid biosynthesis were significantly enriched at both stages of the ABA treatment. Analysis of DEGs in plant hormone signal transduction pathways revealed that exogenous ABA affected the expression of genes from other plant hormone signaling pathways, especially brassinosteroid, auxin, and gibberellin signaling. To elucidate the mechanism driving anthocyanin biosynthesis in blueberry in response to ABA treatment, we screened anthocyanin biosynthesis structural genes (ASG) from the phenylpropanoid and flavonoid biosynthetic pathways, MYB transcription factor genes from R2R3-MYB subgroups 5, 6, and 7 and ABRE-binding factor (ABF) genes from the ABA signal transduction pathway. Pearson’s correlation coefficient (r) analysis indicated that the ABFs, MYBs, and structural genes form a network to regulate ABA-induced anthocyanin biosynthesis and MYBA1 is likely to play an important role in this regulatory network. These findings lay the foundation for improving anthocyanin biosynthesis in blueberry leaves.

An Insight into the Role of Phenolics in Abiotic Stress Tolerance in Plants: Current Perspective for Sustainable Environment

Phenolic compounds (PCs) are a prominent class of secondary metabolites produced by plants and are essential for the natural role of the entire plant life cycle. PCs are formed in plants under both favorable and unfavorable conditions and have essential functions in signaling pathways, such as cell division, nutrient mineralization, hormone control, and reproduction. Under abiotic stress conditions, plants produce more polyphenols, which aid them in adapting to their environment. The phenylpropanoid biosynthetic pathway is activated under various environmental stress conditions, such as drought, heavy metal toxicity, salinity, and high/low temperatures, resulting in the deposition of compounds. These compounds can neutralize reactive oxygen species (ROS) produced in excessive amounts in crops under stressful conditions and adversely affect plants. It is imperative to investigate the functions of PCs in response to several abiotic stresses, as the phenylpropanoid pathway plays a crucial role in the metabolic pathway in crop plants, leading to the biosynthesis of a wide range of PCs. These compounds play various roles in plant growth, development, and response to environmental stress. Therefore, this review provides a comprehensive understanding of PCs and their exchanges with other cellular components, which is crucial for harnessing their potential to improve crop resilience to environmental stresses.

Metabolomic and Growth Responses of Houttyunia cordata to Varying Light Intensities and Subsequent Effects on Fermented Products

Suitable light intensities were studied to enable sustainable and efficient cultivation of Houttuynia cordata with a high yield of bioactive compounds which later can be a good quality material for fermentation. To achieve this goal, the evaluation of physiological adaptation and elucidation of the metabolic alterations of Houttuynia cordata in response to different light intensities were conducted. Four-month-old H. cordata was exposed to 3 different light intensities: high light, control, and low light (100, 50 and 20 % natural irradiances, respectively). Physiological responses were measured using leaf gas exchange. The same leaf samples were either methanolic extracted for LC-QTOF-MS analysis to generate metabolite fingerprints or fermented for 3 months prior to quercetin quantification. High light treatment had the greatest effects on both the physiology and metabolisms of H. cordata compared to control and low light treatments. Compared to the control, the key results observed in high-light-grown H. cordata were a significant increase in photosynthesis, a decrease in relative chlorophyll contents, the enrichment of the top 3 metabolic pathways (phenylpropanoid biosynthesis, pyruvate metabolism and fatty acid degradation) and increasing quercetin concentrations in both fresh and fermented leaves. Metabolite fingerprints of high light-grown H. cordata were distinctively different from those of the other 2 treatments according to PCA and hierarchical clustering analysis. In conclusion, H. cordata responded to high light intensity by enriching the phenylpropanoid biosynthetic pathway to elevate sunscreen pigments. Additional acetyl-CoA generated from pyruvate metabolism and fatty acid degradation was a key supporting factor in the above response. As high quercetin concentration was observed in both fresh and fermented leaves, this will lead to quality improvement of the fermented products. HIGHLIGHTS The remarkable effects of light intensities on Houttuynia cordata growth and abundance of bioactive compounds are substantial, but the underlying mechanism has never been investigated. Metabolomics technology was applied to gain insight into light-induced metabolic reconfiguration. GRAPHICAL ABSTRACT

Detection of a bibenzyl core scaffold in 28 common mangrove and associate species of the Indian Sundarbans: potential signature molecule for mangrove salinity stress acclimation.

Bibenzyl derivatives comprising two benzene rings are secondary plant metabolites with significant therapeutic value. To date, bibenzyl derivatives in the Plant kingdom have been primarily identified in bryophytes, orchids, and Cannabis sativa. The metabolic cost investment by plant species for the synthesis of these bioactive secondary metabolites is rationalized as a mechanism of plant defense in response to oxidative stress induced by biotic/abiotic factors. Bibenzyl derivatives are synthesized from core phenylpropanoid biosynthetic pathway offshoots in plant species. Mangrove and mangrove associate species thrive under extreme ecological niches such as a hypersaline intertidal environment through unique adaptive and acclimative characteristics, primarily involving osmotic adjustments followed by oxidative stress abatement. Several primary/secondary bioactive metabolites in mangrove species have been identified as components of salinity stress adaptation/acclimation/mitigation; however, the existence of a bibenzyl scaffold in mangrove species functioning in this context remains unknown. We here report the confirmed detection of a core bibenzyl scaffold from extensive gas chromatography-mass spectrometry and gas chromatography-flame ionization detection analyses of 28 mangrove and mangrove associate species from the Indian Sundarbans. We speculate that the common presence of this bibenzyl core molecule in 28 mangrove and associate species may be related to its synthesis via branches of the phenylpropanoid biosynthetic pathway induced under high salinity, which functions to detoxify reactive oxygen species as a protection for the maintenance of plant metabolic processes. This finding reveals a new eco-physiological functional role of bibenzyls in unique mangrove ecosystem.

Targeted mutagenesis of BnTTG1 homologues generated yellow-seeded rapeseed with increased oil content and seed germination under abiotic stress

Yellow seed is one desirable trait with great potential to improve seed oil quality and yield. The present study surveys the redundant role of BnTTG1 genes in the proanthocyanidins (PA) biosynthesis, oil content and abiotic stress resistance. Stable yellow seed mutants were generated after mutating BnTTG1 by CRISPR/Cas9 genome editing system. Yellow seed phenotype could be obtained only when both functional homologues of BnTTG1 were simultaneously knocked out. Homozygous mutants of BnTTG1 homologues showed decreased thickness and PA accumulation in seed coat. Transcriptome and qRT-PCR analysis indicated that BnTTG1 mutation inhibited the expression of genes involved in phenylpropanoid and flavonoid biosynthetic pathways. Increased seed oil content and alteration of fatty acid (FA) composition were observed in homozygous mutants of BnTTG1 with enriched expression of genes involved in FA biosynthesis pathway. In addition, target mutation of BnTTG1 accelerated seed germination rate under salt and cold stresses. Enhanced seed germination capacity in BnTTG1 mutants was correlated with the change of expression level of ABA responsive genes. Overall, this study elucidated the redundant role of BnTTG1 in regulating seed coat color and established an efficient approach for generating yellow-seeded oilseed rape genetic resources with increase oil content, modified FA composition and resistance to multiple abiotic stresses.

Exogenous methylglyoxal alleviates drought-induced 'plant diabetes' and leaf senescence in maize.

Drought-induced leaf senescence is associated with high sugar levels, which bears some resemblance to the syndrome of diabetes in humans; however, the underlying mechanisms of such 'plant diabetes' on carbon imbalance and the corresponding detoxification strategy are not well understood. Here, we investigated the regulatory mechanism of exogenous methylglyoxal (MG) on 'plant diabetes' in maize plants under drought stress applied via foliar spraying during the grain-filling stage. Exogenous MG delayed leaf senescence and promoted photoassimilation, thereby reducing the yield loss induced by drought by 14%. Transcriptome and metabolite analyses revealed that drought increased sugar accumulation in leaves through inhibition of sugar transporters that facilitate phloem loading. This led to disequilibrium of glycolysis and overaccumulation of endogenous MG. Application of exogenous MG up-regulated glycolytic flux and the glyoxalase system that catabolyses endogenous MG and glycation end-products, ultimately alleviating 'plant diabetes'. In addition, the expression of genes facilitating anabolism and catabolism of trehalose-6-phosphate was promoted and suppressed by drought, respectively, and exogenous MG reversed this effect, implying that trehalose-6-phosphate signaling in the mediation of 'plant diabetes'. Furthermore, exogenous MG activated the phenylpropanoid biosynthetic pathway, promoting the production of lignin and phenolic compounds, which are associated with drought tolerance. Overall, our findings indicate that exogenous MG activates defense-related pathways to alleviate the toxicity derived from 'plant diabetes', thereby helping to maintain leaf function and yield production under drought.

Light spectra manipulation stimulates growth, specialized metabolites and nutritional quality in Anethum graveolens.

Light-Emitting Diodes (LED) play a major role in manipulating light spectra that helps in regulating the growth and specialized metabolite synthesis relevant to the plant defence system. In this study, we assessed photosynthetic performance, phytonutrients, and anatomical variations of an aromatic herb Anethum graveolens (also known as dill), grown under various combinations of LED lights viz. red (100R:0B), red:blue (50R:50B); blue (0R:100B) and warm white (WW, served as control). Exposure to 0R:100B LED lights led to the tallest stem height, whereas, the number of leaves were highest under 50R:50B LED lights. The photosynthetic performance was observed to be highest under 50R:50B LED lights. HPLC analysis revealed chlorogenic acid and rosmarinic acid as the major phenolic compounds accumulated under different spectral irradiations. The highest chlorogenic acid content was observed in 50R:50B LED treated dill plants, while 100R:0B light showed the highest accumulation of rosmarinic acid. Dill plants grown under 50R:50B light displayed a relatively higher content of volatile compounds including, myristicin (phenylpropene), psi-limonene, and α-phellandrene (monoterpenoids). Expression analyses of candidate genes of phenylpropanoid and monoterpenoid biosynthetic pathways showed good correlations with the enhanced phenolic compounds and monoterpenes detected under appropriate light treatments. Further, the stem anatomy revealed higher vascularization under the influence of 0R:100B LED lights, whereas, intense histochemical localization of specialized metabolites could be correlated with enhanced accumulation of phenolic compounds and terpenoids observed in this study. Taken together, these studies suggest that proper combinations of blue and red spectra of light could play important role to augment the growth and phytochemical characteristics of dill, thus improving its value addition in the food industry.

Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance

BackgroundLodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties.ResultsThe stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage.ConclusionOur findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.

Gene editing of authentic Brassica rapa flavonol synthase 1 generates dihydroflavonol-accumulating Chinese cabbage

Abstract Flavonols are the major class of flavonoids of green Chinese cabbage (Brassica rapa subsp. pekinensis). The B. rapa genome harbors seven flavonol synthase genes (BrFLSs), but they have not been functionally characterized. Here, transcriptome analysis showed four BrFLSs mainly expressed in Chinese cabbage. Among them, only BrFLS1 showed major FLS activity and additional flavanone 3β-hydroxylase (F3H) activity, while BrFLS2 and BrFLS3.1 exhibited only marginal F3H activities. We generated BrFLS1-knockout (BrFLS1-KO) Chinese cabbages using CRISPR/Cas9-mediated genome editing and obtained transgene-free homozygous plants without off-target mutation in the T1 generation, which were further advanced to the T2 generation showing normal phenotype. UPLC-ESI-QTOF-MS analysis revealed that flavonol glycosides were dramatically decreased in the T2 plants, while dihydroflavonol glycosides accumulated concomitantly to levels corresponding to the reduced levels of flavonols. Quantitative PCR analysis revealed that the early steps of phenylpropanoid and flavonoid biosynthetic pathway were upregulated in the BrFLS1-KO plants. In accordance, total phenolic contents were slightly enhanced in the BrFLS1-KO plants, which suggests a negative role of flavonols in phenylpropanoid and flavonoid biosynthesis in Chinese cabbage. Phenotypic surveys revealed that the BrFLS1-KO Chinese cabbages showed normal head formation and reproductive phenotypes, but subtle morphological changes in their heads were observed. In addition, their seedlings were susceptible to osmotic stress compared to the controls, suggesting that flavonols play a positive role for osmotic stress tolerance in B.rapa seedling. In this study, we showed that CRISPR/Cas9-mediated BrFLS1-KO successfully generated a valuable breeding resource of Chinese cabbage with distinctive metabolic traits and that CRISPR/Cas9 can be efficiently applied in functional Chinese cabbage breeding.

Metabolomics analysis reveals the effect of removing cotyledons on salt tolerance in castor plant roots during early seedling establishment

Castor is an important oil crop with moderate salt tolerance that is grown worldwide. The early seedling stage is the most vulnerable phase during a plant’s lifecycle in a saline environment. Cotyledons play an important role in seedling establishment as the storage and first photosynthetic organ, and in the resistance of the seedling to salt stress. However, how cotyledons affect the metabolic response of castor roots in saline environments is unclear. Here, liquid chromatography-mass spectrometry analytical methods were used to examine the effects of removing cotyledons (no cotyledons removed, NR; one cotyledon removed, OR; both cotyledons removed, TR) on the metabolite changes in the roots under salt stress. The results showed that removing cotyledons inhibited the growth of TR roots much greater than NR or OR roots. Metabolomics analysis showed that the roots of TR seedlings had fewer metabolites involved in the salt stress response than NR seedlings. Moreover, the KEGG pathway enrichment analysis demonstrated that salt-induced metabolites were associated with major biological pathways related to tropane, piperidine, and pyridine alkaloid biosynthesis; amino acid biosynthesis; phenylpropanoid biosynthesis; amino sugar and nucleotide sugar metabolism, as well as arginine and proline metabolism. However, the contents of these metabolites decreased or did not change significantly in the TR roots compared to the NR roots under salt stress. Additionally, the contents of caffeyl alcohol, scopoletin, and syringin in the phenylpropanoid biosynthetic pathway increased significantly in the roots of TR seedlings under salt stress compared to the control treatment. Therefore, we concluded that castor plants with cotyledons enhanced particular metabolic pathways in the roots that protected cell membrane structure, maintained cell osmotic potential, resisted reactive oxygen species and provided energy under salt stress. In addition, the roots of castor plants without cotyledons may be resistant to salt stress by enhancing phenylpropanoid biosynthesis to maintain cell differentiation and enhance root lignification. Taken together, these findings provide new insight into the physiological functions of cotyledons in the aboveground-belowground interactions of castor plants under salt stress.

Functions of arbuscular mycorrhizal fungi in regulating endangered species Heptacodium miconioides growth and drought stress tolerance.

The important values of AMF in regulating endangered species Heptacodium miconioides growth and drought stress tolerance. The wild endangered tree Heptacodium miconioides is distributed sporadically in mountainous areas and often subjected to various abiotic stresses, such as drought. The mutualistic association between plants and arbuscular mycorrhizal fungi (AMF) is known to have a significant impact on plant growth and their ability to withstand drought conditions. However, the role of AMF in H. miconioides seedlings in regulating drought tolerance remains unknown. This study investigated the ability of AMF symbionts to mitigate drought and their underlying mechanism on H. miconioides leaves. The results showed that drought stress dramatically decreased the leaf biomass and damaged the chloroplast structure in seedlings. Conversely, inoculation with AMF noticeably alleviated the deleterious effects of drought stress by restoring leaf morphology and improving the photosynthetic capacity. Moreover, plants inoculated with AMF enhanced the proportion of palisade tissue to spongy tissue in the leaves and the size of starch grains and number of plastoglobules in the chloroplast ultrastructure. A transcriptomic analysis showed that 2157 genes (691 upregulated and 1466 downregulated) were differentially expressed between drought stress with AMF inoculation and drought treatment. Further examination demonstrated that the genes exhibiting differential expression were predominantly associated with the advancement of photosynthesis, sucrose and starch metabolism, nitrogen metabolism, chloroplast development, and phenylpropanoid biosynthetic pathways, and the key potential genes were screened. These findings conclusively provided the physiological and molecular mechanisms that underlie improved drought resistance in H. miconioides in the presence of AMF, which could contribute to improving the survival and species conservation of H. miconioides.

Characterization of color variation in bamboo sheath of Chimonobambusa hejiangensis by UPLC-ESI-MS/MS and RNA sequencing

BackgroundChimonobambusa hejiangensis (C.hejiangensis) is a high-quality bamboo species native to China, known for its shoots that are a popular nutritional food. Three C.hejiangensis cultivars exhibit unique color variation in their shoot sheaths, however, the molecular mechanism behind this color change remains unclear.MethodsWe investigated flavonoid accumulation in the three bamboo cultivar sheaths using metabolomics and transcriptomics.ResultsUPLC-MS/MS identified 969 metabolites, with 187, 103, and 132 having differential accumulation in the yellow-sheath (YShe) vs. spot-sheath (SShe)/black-sheath (BShe) and SShe vs. BShe comparison groups. Flavonoids were the major metabolites that determined bamboo sheath color through differential accumulation of metabolites (DAMs) analysis. Additionally, there were 33 significantly differentially expressed flavonoid structural genes involved in the anthocyanin synthesis pathway based on transcriptome data. We conducted a KEGG analysis on DEGs and DAMs, revealing significant enrichment of phenylpropanoid and flavonoid biosynthetic pathways. Using gene co-expression network analysis, we identified nine structural genes and 29 transcription factors strongly linked to anthocyanin biosynthesis.ConclusionWe identified a comprehensive regulatory network for flavonoid biosynthesis which should improve our comprehension of the molecular mechanisms responsible for color variation and flavonoid biosynthesis in bamboo sheaths.

Transcriptomics and metabolomics profiling reveals involvement of flavonoids in early nodulation of Caucasian clover (Trifolium ambiguum)

Caucasian clover (Trifolium ambiguum) is a perennial rooted and tillering leguminous forage with strong adaptability, outstanding stress tolerance and other preferable traits. However, the specificity with rhizobia limits the extended application of Caucasian clover. Therefore, it is important to study the changes of genes and metabolites in the early process of nodulation in Caucasian clover to improve its nodulation and nitrogen fixation ability. In this study, we used Caucasian clover as the experimental material to investigate its nodulation mechanism using transcriptomic and metabolomic approaches, such that to break the nitrogen fixation barrier for the promotion of Caucasian clover. Metabolomic and transcriptomic profiling revealed that both DAMs and DEGs were significantly enriched in the phenylpropanoid and flavonoid biosynthetic pathways, with DEGs showing up-regulation at 3 days and 6 days post inoculation (dpi) with rhizobia, and some DEGs showing down-regulation at 9 dpi. Accumulation of flavonoids was significantly increased at both 3 dpi and 6 dpi, and some compounds were significantly decreased at 9 dpi. A total of 35 DEGs were involved in flavonoid synthesis by WGCNA analysis, among which HCT, CCR, COMT and F3H played an important role. This study provides insights in understanding the molecular mechanism of nodulation and nitrogen fixation in Caucasian clover.

Lignin Biosynthesis Gene Expression Is Associated with Age-related Resistance of Winter Squash to Phytophthora capsici

The Oomycete plant pathogen, Phytophthora capsici, causes root, crown, and fruit rot of winter squash (Cucurbita moschata) and limits production. Some C. moschata cultivars develop age-related resistance (ARR), whereby fruit develop resistance to P. capsici 14 to 21 days postpollination (DPP) because of thickened exocarp; however, wounding negates ARR. We uncovered the genetic mechanisms of ARR of two C. moschata cultivars, Chieftain and Dickenson Field, that exhibit ARR at 14 and 21 DPP, respectively, using RNA sequencing. The sequencing was conducted using RNA samples from ‘Chieftain’ and ‘Dickenson Field’ fruit at 7, 10, 14, and 21 DPP. A differential expression and subsequent gene set enrichment analysis revealed an overrepresentation of upregulated genes in functional categories relevant to cell wall structure biosynthesis, cell wall modification/organization, transcription regulation, and metabolic processes. A pathway enrichment analysis detected upregulated genes in cutin, suberin monomer, and phenylpropanoid biosynthetic pathways. A further analysis of the expression profile of genes in those pathways revealed upregulation of genes in monolignol biosynthesis and lignin polymerization in the resistant fruit peel. Our findings suggest a shift in gene expression toward the physical strengthening of the cell wall associated with ARR to P. capsici. These findings provide candidate genes for developing Cucurbita cultivars with resistance to P. capsici and improve fruit rot management in Cucurbita species.

Histone Deacetylase Inhibitor, Sodium Butyrate-Induced Metabolic Modulation in Platycodon grandiflorus Roots Enhances Anti-Melanogenic Properties.

While the status of histone acetylation is a critical regulator of chromatin's structure with a significant impact on plant physiology, our understanding of epigenetic regulation in the biosynthesis of active compounds in plants is limited. In this study, Platycodon grandiflorus was treated with sodium butyrate (NaB), a histone deacetylase inhibitor, to investigate the influence of histone acetylation on secondary metabolism. Its treatment with NaB increased the acetylation of histone H3 at lysine 9, 14, and 27 and enhanced the anti-melanogenic properties of P. grandiflorus roots. Through transcriptome and differentially expressed gene analyses, we found that NaB influenced the expression of genes that were involved in both primary and secondary metabolic pathways. In addition, NaB treatment caused the accumulation of polyphenolic compounds, including dihydroquercetin, gallic acid, and 2,4-dihydroxybenzoic acid. The NaB-induced transcriptional activation of genes in the phenylpropanoid biosynthetic pathway influenced the anti-melanogenic properties of P. grandiflorus roots. Overall, these findings suggest the potential of an epigenomic approach to enhance the medicinal qualities of medicinal plants.

Combined transcriptomic and metabolomic analyses identifies CsERF003, a citrus ERF transcription factor, as flavonoid activator

Transcription factor (TF) modulation is a promising strategy for plant flavonoid improvement. Here, we observed evident decreases in some major flavones and flavonols and the expression of some key related genes in a ‘Newhall’ navel orange mutant (MT) relative to the wild type (WT). A consistently downregulated ERF TF CsERF003 in MT could increase the contents of major flavonoids and the precursor phenylalanine when transiently overexpressed in citrus fruit. Overexpression of CsERF003 in ‘Micro-Tom’ tomato (OE) resulted in a darker and redder fruit color than wild type ‘Micro-Tom’ (WTm). Two major flavonoids, naringeninchalcone and kaempferolrutinoside, were averagely induced by 7.99- and 36.83-fold in OEs, respectively, while little change was observed in other polyphenols, such as caffeic acid, ferulic acid, and gallic acid. Key genes involved in the initiation of phenylpropanoid (PAL, 4CH, and 4CL) and flavonoid (CHS and CHI) biosynthesis were up-regulated, while most genes participating in the biosynthesis of other polyphenols, such as HCT and CCR, were down-regulated in OEs. Therefore, it could be concluded that carbon flux floods into the phenylpropanoid biosynthetic pathway and is then specifically directed for flavonoid biosynthesis. CsERF003 may be a potentially promising gene for fruit quality improvement and engineering of natural flavonoid components.