caffeoyl-CoA O-methyltransferase Research Articles

Exogenous Melatonin Application Accelerated the Healing Process of Oriental Melon Grafted onto Squash by Promoting Lignin Accumulation.

Melatonin (MT) is a vital hormone factor in plant growth and development, yet its potential to influence the graft union healing process has not been reported. In this study, we examined the effects of MT on the healing of oriental melon scion grafted onto squash rootstock. The studies indicate that the exogenous MT treatment promotes the lignin content of oriental melon and squash stems by increasing the enzyme activities of hydroxycinnamoyl CoA ligase (HCT), hydroxy cinnamaldehyde dehydrogenase (HCALDH), caffeic acid/5-hydroxy-conifer aldehyde O-methyltransferase (COMT), caffeoyl-CoA O-methyltransferase (CCoAOMT), phenylalanine ammonia-lyase (PAL), 4-hydroxycinnamate CoA ligase (4CL), and cinnamyl alcohol dehydrogenase (CAD). Using the oriental melon and squash treated with the exogenous MT to graft, the connection of oriental melon scion and squash rootstock was more efficient and faster due to higher expression of wound-induced dedifferentiation 1 (WIND1), cyclin-dependent kinase (CDKB1;2), target of monopteros 6 (TMO6), and vascular-related NAC-domain 7 (VND7). Further research found that the exogenous MT increased the lignin content of the oriental melon scion stem by regulating CmCAD1 expression, and then accelerated the graft healing process. In addition, the root growth of grafted seedlings treated with the exogenous MT was more vigorous.

Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages.

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides in Stevia rebaudiana.

Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in S. rebaudiana leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of S. rebaudiana were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases 76G1, 76H1, 85C1, and 91A1, and several genes associated with the phenylpropanoid pathway, including peroxidase, caffeoyl-CoA O-methyltransferase, and malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase, along with 21 transcription factors like SCL3, WRK11, and MYB111, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in S. rebaudiana leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in S. rebaudiana as well as in other species.

Multiomics analyses of the effects of LED white light on the ripening of apricot fruits

IntroductionApricot (Prunus armeniaca L.) fruits are highly perishable and prone to quality deterioration during storage and transportation. ObjectivesTo investigate the effects of LED white light treatment on postharvest ripening of fruits using metabolomics, transcriptomics, and ATAC-Seq analysis. MethodsFruits were exposed to 5 μmol m−2 s−1 LED white light for 12 h followed by 12 h of darkness at 20 °C daily for 12 days. The effects of the treatments on the physiological and nutritional quality of the fruits were evaluated. These data were combined with transcriptomic, metabolomic, and ATAC-Seq data from fruits taken on 8 d of treatment to provide insight into the potential mechanism by which LED treatment delays ripening. ResultsLED treatment activated pathways involved in ascorbate and aldarate metabolism and flavonoid and phenylpropanoid biosynthesis. Specifically, LED treatment increased the expression of UDP-sugar pyrophosphorylase (USP), L-ascorbate peroxidase (AO), dihydroflavonol 4-reductase (DFR), chalcone synthase (CHS), and caffeoyl-CoA O-methyltransferase (CCOAOMT1), leading to the accumulation of caffeoyl quinic acid, epigallocatechin, and dihydroquercetin and the activation of anthocyanin biosynthesis. LED treatment also affected the expression of genes associated with plant hormone signal transduction, fruit texture and color transformation, and antioxidant activity. The notable genes affected by LED treatment included 1-aminocyclopropane-1-carboxylate synthase (ACS), 1-aminocyclopropane-1-carboxylate oxidase (ACO), hexokinase (HK), lipoxygenase (LOX), malate dehydrogenase (MDH), endoglucanase (CEL), various transcription factors (TCP, MYB, EFR), and peroxidase (POD). ATAC-Seq analysis further revealed that LED treatment primarily regulated phenylpropanoid biosynthesis. ConclusionThe results obtained in this study provide insights into the effects of LED light exposure on apricot fruits ripening. LEDs offer a promising approach for extending the shelf life of other fruits and vegetables.

Postharvest caffeic acid dipping enhances disease resistance and storage capacity of ‘Zaosu’ pear fruit via regulating phenylpropane metabolism

Caffeic acid, a naturally occurring and safe phenolic compound, acts as a precursor in lignin synthesis within the phenylpropane metabolism pathway. The aims of this study was to evaluate the impacts of postharvest caffeic acid immersion on Alternaria rot and postharvest quality of ‘Zaosu’ pear fruit, as well as elucidate the underlying mechanisms involved. Results showed that postharvest caffeic acid dipping effectively inhibited spore germination and colony diameter of Alternaria alternata, as well as lesion diameter in A. alternata-inoculated pears. Caffeic acid treatment also delayed the increase of weight loss and decline in flesh firmness, increased total soluble solids content, and reduced surface yellowing of pears. Additionally, caffeic acid treatment enhanced the enzymatic activities and gene transcription levels of phenylalanine ammonialyase, 4-coumarate/coenzyme A ligase, cinnamate 4-hydroxylase, peroxidase, cinnamyl alcohol dehydrogenase, and polyphenol oxidase in pears. Meanwhile, the transcription levels of p-coumarate-3-hydroxylase, caffeic acid O-methyltransferase, cinnamoyl CoA reductase, caffeoyl shikimate esterase, hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase, caffeoyl CoA O-methyltransferase, ferulic acid 5-hydroxylase, and laccase genes were also up-regulated by caffeic acid treatment in pears. Furthermore, caffeic acid dipping enhanced phenylalanine, flavonoids, caffeic acid, total phenolic compounds, and lignin levels in the fruit. Therefore, caffeic acid exhibits promising potential for enhancing resistance against A. alternata and maintaining the storage capacity of pears via inducing phenylpropane metabolism.

Phenolic Acids and Flavonoids Play Important Roles in Flower Bud Differentiation in Mikania micrantha: Transcriptomics and Metabolomics

Mikania micrantha is a highly invasive vine, and its ability to sexually reproduce is a major obstacle to its eradication. The long-distance dissemination of M. micrantha depends on the distribution of seeds; therefore, inhibiting M. micrantha flowering and seed production is an effective control strategy. The number of blooms of M. micrantha differs at different altitudes (200, 900, and 1300 m). In this study, we used a combination of metabolomics and transcriptomics methods to study the patterns of metabolite accumulation in the flower buds of M. micrantha. Using LC-MS/MS, 658 metabolites were found in the flower buds of M. micrantha at three different altitudes (200, 900, and 1300 m). Flavonoids and phenolic acids were found to be the main differential metabolites, and their concentrations were lower at 900 m than at 200 m and 1300 m, with the concentrations of benzoic acid, ferulic acid, and caffeic acid being the lowest. The biosynthesis pathways for flavonoids and phenolic compounds were significantly enriched for differentially expressed genes (DEGs), according to the results of transcriptome analysis. The production of flavonoid and phenolic acids was strongly linked with the expressions of phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and 4-coumarate-CoA ligase (4CL), according to the results of the combined transcriptome and metabolome analysis. These genes’ roles in the regulation of distinct phenolic acids and flavonoids during M. micrantha bud differentiation are still unknown. This study adds to our understanding of how phenolic acids and flavonoids are regulated in M. micrantha flower buds at various altitudes and identifies regulatory networks that may be involved in this phenomenon, offering a new approach for the prevention and management of M. micrantha.

Molecular Mechanisms Regulating Phenylpropanoid Metabolism in Exogenously-Sprayed Ethylene Forage Ramie Based on Transcriptomic and Metabolomic Analyses.

Ramie (Boehmeria nivea [L.] Gaud.), a nutritious animal feed, is rich in protein and produces a variety of secondary metabolites that increase its palatability and functional composition. Ethylene (ETH) is an important plant hormone that regulates the growth and development of various crops. In this study, we investigated the impact of ETH sprays on the growth and metabolism of forage ramie. We explored the mechanism of ETH regulation on the growth and secondary metabolites of forage ramie using transcriptomic and metabolomic analyses. Spraying ramie with ETH elevated the contents of flavonoids and chlorogenic acid and decreased the lignin content in the leaves and stems. A total of 1076 differentially expressed genes (DEGs) and 51 differentially expressed metabolites (DEMs) were identified in the leaves, and 344 DEGs and 55 DEMs were identified in the stems. The DEGs that affect phenylpropanoid metabolism, including BGLU41, LCT, PER63, PER42, PER12, PER10, POD, BAHD1, SHT, and At4g26220 were significantly upregulated in the leaves. Ethylene sprays downregulated tyrosine and chlorogenic acid (3-O-caffeoylquinic acid) in the leaves, but lignin biosynthesis HCT genes, including ACT, BAHD1, and SHT, were up- and downregulated. These changes in expression may ultimately reduce lignin biosynthesis. In addition, the upregulation of caffeoyl CoA-O-methyltransferase (CCoAOMT) may have increased the abundance of its flavonoids. Ethylene significantly downregulated metabolites, affecting phenylpropanoid metabolism in the stems. The differential 4CL and HCT metabolites were downregulated, namely, phenylalanine and tyrosine. Additionally, ETH upregulated 2-hydroxycinnamic acid and the cinnamyl hydroxyl derivatives (caffeic acid and p-coumaric acid). Cinnamic acid is a crucial intermediate in the shikimic acid pathway, which serves as a precursor for the biosynthesis of flavonoids and lignin. The ETH-decreased gene expression and metabolite alteration reduced the lignin levels in the stem. Moreover, the HCT downregulation may explain the inhibited lignin biosynthesis to promote flavonoid biosynthesis. In conclusion, external ETH application can effectively reduce lignin contents and increase the secondary metabolites of ramie without affecting its growth and development. These results provide candidate genes for improving ramie and offer theoretical and practical guidance for cultivating ramie for forage.

Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo.

Lignin contributes to plant mechanical properties during bending loads. Meanwhile, phytohormone auxin controls various plant biological processes. However, the mechanism of auxin's role in bending-induced lignin biosynthesis was unclear, especially in bamboo, celebrated for its excellent deformation stability. Here, we reported that auxin response factors (ARF) 3 and ARF6 from Moso bamboo (Phyllostachys edulis (Carrière) J. Houz) directly regulate lignin biosynthesis pathway genes, and affect lignin biosynthesis in bamboo. Auxin and lignin exhibited asymmetric distribution patterns, and auxin promoted lignin biosynthesis in response to bending loads in bamboo. Employing transcriptomic and weighted gene co-expression network analysis approach, we discovered that expression patterns of ARF3 and ARF6 strongly correlated with lignin biosynthesis genes. ARF3 and ARF6 directly bind to the promoter regions of 4-coumarate: coenzyme A ligase (4CL3, 4CL7, and 4CL9) or caffeoyl-CoA O-methyltransferase (CCoAOMT2) genes, pivotal to lignin biosynthesis, and activate their expressions. Notably, the efficacy of this binding hinges on auxin levels. Alternation of the expressions of ARF3 and ARF6 substantially altered lignin accumulation in transgenic bamboo. Collectively, our study shed light on bamboo lignification genetics. Auxin signaling could directly modulate lignin biosynthesis genes to impact plant lignin content.

Mutant Bisexual and Wild Male Flowers Were Compared by Integrated Proteome and Transcriptome Analyses to Provide Insight into the Sex Conversion of Idesia polycarpa Maxim

Idesia polycarpa is a dioecious tree; in field surveys, there are rare sex conversions in I. polycarpa individuals with bisexual flowers. To identify the molecular mechanisms underlying sex conversion in this species, an integrative analysis of the proteome and transcriptome profiles of I. polycarpa male and bisexual flowers at key developmental stages was conducted in this study using isobaric tags for relative and absolute quantification and RNA-seq technology. A total of 15,003 proteins were identified; the differentially expressed proteins (DEPs) were enriched in metabolic pathways, biosynthesis of secondary metabolites, and flavonoid metabolism pathways in all comparison groups. A total of 290,442 unigenes were obtained; these were compared with seven databases, revealing 196,366 annotated unigenes. In general, the expression of proteins and genes tended to be positively correlated, with Spearman correlation coefficients in the ranges of 0.152–0.262 (all genes and all proteins) and 0.497–0.778 (DEPs and DEGs). The integrative analysis of DEPs and DEGs between male and bisexual flowers revealed that the most significantly enriched pathways were flavonoid pathways, metabolic pathways, and the biosynthesis of secondary metabolites. Finally, four co-expressed proteins and transcripts and one gene associated with the flavonoid biosynthesis pathway were screened out. The proteins identified were p-coumaroyl shikimate 3′-hydroxylase, and shikimate/quinate hydroxycinnamoyl transferase, and the gene was caffeoyl-CoA O-methyltransferase. The analysis has revealed key potential proteins and genes involved in sex conversion at the molecular level and has provided a basis for future investigations of artificial regulation of sex differentiation in I. polycarpa.

Wound-Induced Temporal Reprogramming of Gene Expression during Agarwood Formation in Aquilaria sinensis.

Agarwood is a resinous heartwood of Aquilaria sinensis that is formed in response to mechanical wounding. However, the transcriptional response of A. sinensis to mechanical wounding during the agarwood formation process is still unclear. Here, three five-year-old A. sinensis trees were mechanically damaged by a chisel, and time-series transcriptomic analysis of xylem tissues in the treated area (TA) was performed at 15 (TA1), 70 (TA2) and 180 days after treatment (TA3). Samples from untreated areas at the corresponding time points (UA1, UA2, UA3, respectively) were collected as controls. A total of 1862 (TA1 vs. UA1), 961 (TA2 vs. UA2), 1370 (TA3 vs. UA3), 3305 (TA2 vs. TA1), 2625 (TA3 vs. TA1), 2899 (TA3 vs. TA2), 782 (UA2 vs. UA1), 4443 (UA3 vs. UA1) and 4031 (UA3 vs. UA2) genes were differentially expressed (DEGs). Functional enrichment analysis showed that DEGs were significantly enriched for secondary metabolic processes, signal transduction and transcriptional regulation processes. Most of the genes involved in lignin biosynthesis were more abundant in the TA groups, which included phenylalanine ammonia-lyase, 4-coumarate CoA ligase, cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase and cinnamoyl-CoA reductase. DEGs involved in sesquiterpene biosynthesis were also identified. Hydroxymethylglutaryl-CoA synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase, phosphomevalonate kinase and terpene synthase genes were significantly increased in the TA groups, promoting sesquiterpene biosynthesis in the wounded xylem tissues. The TF-gene transcriptomic networks suggested that MYB DNA-binding, NAM, WRKY, HLH and AP2 TFs co-expressed with genes related to lignin and sesquiterpene synthesis, indicating their critical regulatory roles in the biosynthesis of these compounds. Overall, our study reveals a dynamic transcriptional response of A. sinensis to mechanical wounding, provides a resource for identifying candidate genes for molecular breeding of agarwood quality, and sheds light on the molecular mechanisms of agarwood formation in A. sinensis.

PoWRKY17 promotes drought tolerance in Paeonia ostii by modulating lignin accumulation

Drought is a detrimental environmental factor limiting sustainable agricultural development worldwide. Paeonia ostii, an oil-producing woody crop, while its endogenous mystery underlying this tolerance remains largely elusive to scholars. Herein, we reported that PoWRKY17, a WRKY transcription factor from IId subgroup, positively functioned in face of drought stress in P. ostii. PoWRKY17 expressed in significantly higher abundance when drought was applied. Silencing of PoWRKY17 substantially reduced drought resistance, with decreased leaf water content and protective enzyme activities, increased relative electric conductivity (REC), malondialdehyde (MDA) content, and reactive oxygen species (ROS) accumulation. On the contrary, overexpression of PoWRKY17 endowed plants with higher drought tolerance with opposite drought-relevant physiological indices. Notably, both PoWRKY17-silenced P. ostii and PoWRKY17-overexpressing plants showed changes in lignin content under drought stress. Based on this clue, we quantified the expression of lignin biosynthetic caffeoyl-CoA O-methyltransferase (CCoAOMT) gene in PoWRKY17-silenced P. ostii and found that PoCCoAOMT expression was significantly repressed. Next, protein-gene interaction assays showed that PoWRKY17 interacted with PoCCoAOMT promoter by targeting the W-box element and activated PoCCoAOMT expression under drought stress, which has been early verified to act as a positive participant in P. ostii drought tolerance. This study broadens our understanding of WRKY-mediated lignin biosynthesis regulation in response to drought stress in plants.

Alterations in plant anatomy and higher lignin synthesis provides drought tolerance in cluster bean [Cyamopsis tetragonoloba (L.) Taub.

Four contrasting varieties of guar, RGC-1002 and RGC-1038, drought tolerant, while, Sarada and RGC-936, drought sensitive, were monitored in watered and drought. The water status, phenolics, plant anatomy and transcript level of genes related to anatomical traits were assessed. The study aimed to decipher the anatomical adaptations of guar plants in response to water stress. The physiological determinants, relative water content (RWC), water potential (ψ), and leaf membrane damage, declined under drought in all four varieties although, the decrement was lesser in the tolerant varieties. Furthermore, the tolerant cultivars subjected to water stress recorded higher accumulation of total phenolic content, anthocyanin and lignin, which efficiently scavenge the reactive oxygen species. The results suggest that the cultivars RGC-1002 and RGC-1038 are better able to resist drought-induced oxidative stress than Sarada and RGC-936. Moreover, leaf, petiole, stem and root anatomical traits viz. size of epidermal cell, parenchyma, width of cortex layer, and diameter of xylem vessels were narrowed in all the varieties although, the decrement was lesser in the tolerant varieties under drought. The expression analysis of genes revealed that drought-tolerant varieties showed enhanced mechanical support for water conduction by up-regulation of genes, Phenylalanine ammonia-lyase1 (PAL1), cinnamate-4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), caffeoyl-CoA O-methyltransferase (CCOMT), and cinnamyl-alcohol dehydrogenase (CAD6) in water stress conditions. The alterations in physio-anatomical, biochemical and gene expression traits in tolerant guar varieties enabled them to maintain steady nutrient transport while reducing the risk of embolisms and increasing water-flow resistance for better survival in water stressed conditions.

Uncovering mechanisms governing stem growth in peanut (Arachis hypogaea L.) with varying plant heights through integrated transcriptome and metabolomics analyses

The mechanisms responsible for stem growth in peanut (Arachis hypogaea L.) cultivars with varying plant heights remain unclear, despite the significant impact of plant height on peanut yield. Therefore, this study aimed to investigate the underlying mechanisms of peanut stem growth using phenotypic, physiological, transcriptomic, and metabolomic analyses. The findings revealed that the tallest cultivar, HY33, exhibited the highest rate of stem growth and accumulated the most stem dry matter, followed by the intermediate cultivar, SH108, while the dwarf cultivar, Df216, displayed the lowest values. Furthermore, SH108 exhibited a higher harvest index, as well as superior pod and kernel yields compared to both HY33 and Df216. Transcriptome and metabolome analyses identified differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) associated with phenylpropanoid and flavonoid biosynthesis. Notably, downregulated DEGs in Df216/HY33 and Df216/SH108 included phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and ferulate-5-hydroxylase (F5H), while downregulated DEMs included p-coumaryl alcohol, chlorogenic acid, and L-epicatechin. Compared to HY33, the reduced activities of PAL, COMT, and F5H resulted in a decreased stem lignin content in Df216. Additionally, downregulated DEGs involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis were identified in Df216/HY33, which contributed to the lowest levels of GA1, GA3, and BR contents in Df216. The results suggest that the dwarf phenotype arises from impaired GA and BR biosynthesis and signaling, resulting in a slower stem growth rate and reduced lignin accumulation.

Transcriptomic and metabolomic perspectives for the growth of alfalfa (Medicago sativa L.) seedlings with the effect of vanadium exposure

Hitherto, the effect of vanadium on higher plant growth remains an open topic. Therefore, nontargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to 0.1 mg L−1 (B group) and 0.5 mg L−1 (C group) pentavalent vanadium [(V(V)] versus control (A group) in this study. Results revealed that vanadium exposure significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up- and down-regulated was 21 and 23 in B_vs_A, 27 and 33 in C_vs_A, and 24 and 43 in C_vs_B, respectively. The number for significantly up- and down-regulated differential metabolites was 17 and 15 in B_vs_A, 43 and 20 in C_vs_A, and 24 and 16 in C_vs_B, respectively. Metabolomics and transcriptomics co-analysis characterized three significantly enriched metabolic pathways in C_vs_A comparing group, viz., α-linolenic acid metabolism, flavonoid biosynthesis, and phenylpropanoid biosynthesis, from which some differentially expressed genes and differential metabolites participated. The metabolite of traumatic acid in α-linolenic acid metabolism and apigenin in flavonoid biosynthesis were markedly upregulated, while phenylalanine in phenylpropanoid biosynthesis was remarkably downregulated. The genes of allene oxide cyclase (AOC) and acetyl-CoA acyltransferase (fadA) in α-linolenic acid metabolism, and chalcone synthase (CHS), flavonoid 3′-monooxygenase (CYP75B1), and flavonol synthase (FLS) in flavonoid biosynthesis, and caffeoyl-CoA O-methyltransferase (CCoAOMT) in phenylpropanoid biosynthesis were significantly downregulated. While shikimate O-hydroxycinnamoyltransferase (HCT) in flavanoid and phenylpropanoid biosynthesis were conspicuously upregulated. Briefly, vanadium exposure induces a readjustment yielding in metabolite and the correlative synthetic precursors (transcripts/unigenes) in some branched metabolic pathways. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by vanadium on plant growth and development.

Systematic approaches to C-lignin engineering in Medicago truncatula

BackgroundC-lignin is a homopolymer of caffeyl alcohol present in the seed coats of a variety of plant species including vanilla orchid, various cacti, and the ornamental plant Cleome hassleriana. Because of its unique chemical and physical properties, there is considerable interest in engineering C-lignin into the cell walls of bioenergy crops as a high-value co-product of bioprocessing. We have used information from a transcriptomic analysis of developing C. hassleriana seed coats to suggest strategies for engineering C-lignin in a heterologous system, using hairy roots of the model legume Medicago truncatula.ResultsWe systematically tested strategies for C-lignin engineering using a combination of gene overexpression and RNAi-mediated knockdown in the caffeic acid/5-hydroxy coniferaldehyde 3/5-O-methyltransferase (comt) mutant background, monitoring the outcomes by analysis of lignin composition and profiling of monolignol pathway metabolites. In all cases, C-lignin accumulation required strong down-regulation of caffeoyl CoA 3-O-methyltransferase (CCoAOMT) paired with loss of function of COMT. Overexpression of the Selaginella moellendorffii ferulate 5-hydroxylase (SmF5H) gene in comt mutant hairy roots resulted in lines that unexpectedly accumulated high levels of S-lignin.ConclusionC-Lignin accumulation of up to 15% of total lignin in lines with the greatest reduction in CCoAOMT expression required the strong down-regulation of both COMT and CCoAOMT, but did not require expression of a heterologous laccase, cinnamyl alcohol dehydrogenase (CAD) or cinnamoyl CoA reductase (CCR) with preference for 3,4-dihydroxy-substituted substrates in M. truncatula hairy roots. Cell wall fractionation studies suggested that the engineered C-units are not present in a heteropolymer with the bulk of the G-lignin.

A multifunctional true caffeoyl coenzyme A O-methyltransferase enzyme participates in the biosynthesis of polymethoxylated flavones in citrus.

Polymethoxylated flavones (PMFs) have received extensive attention due to their abundant bioactivities. Citrus peels specifically accumulate abundant PMFs, and methylation modification is a key step in PMF biosynthesis; however, the function of reported O-methyltransferase (OMT) in citrus is insufficient to elucidate the complete methylation process of PMFs. In this study, we analyzed the accumulation pattern of PMFs in the flavedo of the sweet orange (Citrus sinensis) cultivar "Bingtangcheng" at different developmental stages. We found that accumulation of PMFs was completed at the early stage of fruit development (60-d after flowering). Furthermore, we characterized a true caffeoyl-CoA O-methyltransferase (named CsCCoAOMT1) from C. sinensis. Functional analysis in vitro showed that CsCCoAOMT1 preferred flavonoids to caffeoyl-CoA and esculetin. This enzyme efficiently methylated the 6-, 7- 8-, and 3'-OH of a wide array of flavonoids with vicinal hydroxyl groups with a strong preference for quercetin (flavonol) and flavones. The transient overexpression and virus-induced gene silencing experiments verified that CsCCoAOMT1 could promote the accumulation of PMFs in citrus. These results reveal the function of true CCoAOMTs and indicate that CsCCoAOMT1 is a highly efficient multifunctional O-methyltransferase involved in the biosynthesis of PMFs in citrus.

Transcriptomic and metabolomic profiling reveal the role of BoMYB2 in flavor regulation mechanism and coloration in the postharvest purple cauliflower

Purple (Pr) mutant cauliflower has a bright color and high nutritional value. During postharvest storage, purple cauliflower fades in color and gradually develops a pungent flavor, which directly affects its commercial value. In this study, six anthocyanin-related metabolites were identified in postharvest Pr mutants via metabolomic analyses. Gene–metabolite association analysis revealed that 6-gingerol was the main component responsible for the pungent flavor of the Pr mutant, and that this compound was a component of the stilbenoid, diarylheptanoid, and gingerol biosynthesis pathways. The pungent flavor was correlated with the expression level of caffeoyl coenzyme A O-methyltransferase (CCoAOMT). In vitro experiments confirmed that the transcription factor (TF) BoMYB2 specifically binds to the BoCCoAOMT promoter through the MBS site. Additionally, transient expression analysis confirmed that BoMYB2 negatively regulates BoCCoAOMT transcription and promotes 6-gingerol accumulation, thereby influencing flavor formation in the Pr mutant. Our findings reveal the key genes and TF for the flavor-related transcriptional regulatory mechanism of postharvest Pr mutant cauliflower, and provide a valuable basis for developing postharvest preservation technology for commercial crops.

Comparative Transcriptome Analysis of MeJA Responsive Enzymes Involved in Phillyrin Biosynthesis of Forsythia suspensa.

Forsythia suspensa (Thunb.) has been widely used in traditional medicines in Asia. According to the 2020 edition of Chinese Pharmacopoeia, phillyrin is the main active ingredient in F. suspensa, which is effective in clearing heat, reducing swelling, and dispersing nodules. F. suspensa leaf is a non-toxic substance and it can be used to make a health tea. Here, we combine elicitors and transcriptomics to investigate the inducible biosynthesis of the phillyrin from the F. suspensa. After the fruits and leaves of F. suspensa were treated with different concentrations of methyl jasmonate (MeJA), the content of phillyrin in the fruits reached a peak at 200 µM MeJA for 12 h, but which was decreased in leaves. To analyze the differences in key enzyme genes involved in the phillyrin biosynthesis, we sequenced the transcriptome of F. suspensa leaves and fruits treated with 200 µM MeJA for 12 h. We hypothesized that nine genes related to coniferin synthesis including: F. suspensa UDP-glycosyltransferase (FsUGT); F. suspensa 4-coumarate coenzyme CoA ligase (Fs4CL); and F. suspensa Caffeoyl-CoA O-methyltransferase (FsCCoAOMT) etc. The qRT-PCR analysis of genes related to phillyrin biosynthesis was consistent with RNA-seq analysis. We also investigated the dynamic changes of genes in F. suspensa leaves and fruits at different time points after 200 µM MeJA treatment, which laid the foundation for further study of the molecular mechanisms regulating the biosynthesis of phillyrin.

Transcriptome and metabolome reveal the effects of three canopy types on the flavonoids and phenolic acids in ‘Merlot’ (Vitis vinifera L.) berry pericarp

The flavonoids and phenolic acids in grape berries greatly influence the quality of wine. Various methods are used to shape and prune grapevines, but their effects on the flavonoids and phenolic acids remain unclear. The flavonoids and phenolic acids in the berry pericarps from grapevines pruned using three types of leaf canopy, namely, V-shaped, T-shaped, and vertical shoot-positioned (VSP) canopies, were compared in this study. Results showed that the V-shaped canopy was more favorable for the accumulation of flavonoids and phenolic acids. Transcriptome and metabolome analyses revealed that the differentially expressed genes (DEGs) and differentially regulated metabolites (DRMs) were significantly enriched in the flavonoid and phenylpropanoid biosynthesis pathways. A total of 96 flavonoids and 32 phenolic acids were detected among the DRMs. Their contents were higher in the V-shaped canopy than in the T-shaped and VSP canopies. Conjoint analysis of transcriptome and metabolome showed that nine DEGs (e.g., cytochrome P450 98A9 and 98A2) were significantly correlated to nine phenolic acids (e.g., gentisic acid and neochlorogenic acid) and three genes (i.e., chalcone isomerase, UDP-glycosyltransferase 88A1, and caffeoyl-CoA O-methyltransferase) significantly correlated to 15 flavonoids (e.g., baimaside and tricin-7-O-rutinoside). These genes may be involved in the regulation of various flavonoids and phenolic acids in grape berries, but their functions need validation. This study provides novel insights into the effects of leaf canopy on flavonoids and phenolic acids in the skin of grape berries and reveals the potential regulatory networks involved in this phenomenon.

Essential oils nano-emulsion confers resistance against Penicillium digitatum in 'Newhall' navel orange by promoting phenylpropanoid metabolism

Inducing natural resistance against pathogen infection in postharvest citrus by exogenous elicitor is a promising alternative to reduce postharvest losses. Here, the potential induced resistance mechanism of blended cinnamaldehyde, carvacrol and eugenol nano-emulsion against P. digitatum in ‘Newhall’ navel orange (Citrus sinensis (L.) Osbeck) was evaluated through combined transcriptomic and metabolomics analysis. Application of nano-emulsion maintained fruit firmness after P. digitatum inoculation, nano-emulsion reduced H2O2 and MDA accumulation of citrus fruit, increased PAL, C4H, 4CL and CAD activity, and higher contents of flavonoids, lignin and total phenolic compounds. Furthermore, higher activities of SOD, CAT, POD and APX in nano-emulsion treated fruit possibly benefited reducing ROS accumulation and lipid peroxidation. The activities of the defense enzymes CHI, GLU were higher in the nano-emulsion treated fruits. RNA-seq identified 653 differentially expressed genes (DEGs) between the control and the nano-emulsion-treated fruit at 48 hpi, including 444 up-regulated and 209 downregulated genes. Genes encoding shikimate O-hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT), caffeic acid 3-O-methyltransferase / acetylserotonin O-methyltransferase (COMT), cinnamyl-alcohol dehydrogenase (CAD) and peroxidase (POD) were differentially expressed by nano-emulsion treatment. In addition, 175 differential accumulated metabolites between the control and the nano-emulsion-treated fruit at 48 hpi also were identified, the different accumulated metabolites from phenylpropanoid biosynthesis pathway related with disease resistance including L-phenylalanine, caffeic acid, caffeoyl quinic acid, coniferyl alcohol, coniferaldehyde. The integrated transcriptomic and metabolomic profiling indicated that the differentially expressed genes (DEGs) and the differentially accumulated metabolites (DAMs) were mainly involved in phenylpropanoid biosynthesis pathway. Besides, the nano-emulsion significantly induced accumulation of primary metabolites including amino acids, soluble sugars, organic acids, lipids, sugar and alcohols. All these results indicated that blended essential oil nano-emulsion as an antifungal delivery system to induce resistance against P. digitatum infection of ‘Newhall’ navel orange by promoting phenylpropanoid metabolism.