Homeostatic regulation of flavonoid and lignin biosynthesis in phenylpropanoid pathway of transgenic tobacco

Metabolic and Transcriptional Analysis Reveals Flavonoid Involvement in the Drought Stress Response of Mulberry Leaves

Abiotic stress, especially drought stress, poses a significant threat to terrestrial plant growth, development, and productivity. Although mulberry has great genetic diversity and extensive stress-tolerant traits in agroforestry systems, only a few reports offer preliminary insight into the biochemical responses of mulberry leaves under drought conditions. In this study, we performed a comparative metabolomic and transcriptomic analysis on the "drooping mulberry" (Morus alba var. pendula Dippel) under PEG-6000-simulated drought stress. Our research revealed that drought stress significantly enhanced flavonoid accumulation and upregulated the expression of phenylpropanoid biosynthetic genes. Furthermore, the activities of superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) content were elevated. In vitro enzyme assays and fermentation tests indicated the involvement of flavonol synthase/flavanone 3-hydroxylase (XM_010098126.2) and anthocyanidin 3-O-glucosyltransferase 5 (XM_010101521.2) in the biosynthesis of flavonol aglycones and glycosides, respectively. The recombinant MaF3GT5 protein was found to recognize kaempferol, quercetin, and UDP-glucose as substrates but not 3-/7-O-glucosylated flavonols and UDP-rhamnose. MaF3GT5 is capable of forming 3-O- and 7-O-monoglucoside, but not di-O-glucosides, from kaempferol. This implies its role as a flavonol 3, 7-O-glucosyltransferase. The findings from this study provided insights into the biosynthesis of flavonoids and could have substantial implications for the future diversified utilization of mulberry.

Rhizophagus Irregularis regulates flavonoids metabolism in paper mulberry roots under cadmium stress

Broussonetia papyrifera is widely found in cadmium (Cd) contaminated areas, with an inherent enhanced flavonoids metabolism and inhibited lignin biosynthesis, colonized by lots of symbiotic fungi, such as arbuscular mycorrhizal fungi (AMF). However, the physiological and molecular mechanisms by which Rhizophagus irregularis, an AM fungus, regulates flavonoids and lignin in B. papyrifera under Cd stress remain unclear. Here, a pot experiment of B. papyrifera inoculated and non-inoculated with R. irregularis under Cd stress was carried out. We determined flavonoids and lignin concentrations in B. papyrifera roots by LC-MS and GC-MS, respectively, and measured the transcriptional levels of flavonoids- or lignin-related genes in B. papyrifera roots, aiming to ascertain the key components of flavonoids or lignin, and key genes regulated by R. irregularis in response to Cd stress. Without R. irregularis, the concentrations of eriodictyol, quercetin and myricetin were significantly increased under Cd stress. The concentrations of eriodictyol and genistein were significantly increased by R. irregularis, while the concentration of rutin was significantly decreased. Total lignin and lignin monomer had no alteration under Cd stress or with R. irregularis inoculation. As for flavonoids- or lignin-related genes, 26 genes were co-regulated by Cd stress and R. irregularis. Among these genes, BpC4H2, BpCHS8 and BpCHI5 were strongly positively associated with eriodictyol, indicating that these three genes participate in eriodictyol biosynthesis and were involved in R. irregularis assisting B. papyrifera to cope with Cd stress. This lays a foundation for further research revealing molecular mechanisms by which R. irregularis regulates flavonoids synthesis to enhance tolerance of B. papyrifera to Cd stress.

The Key Role of Plant Hormone Signaling Transduction and Flavonoid Biosynthesis Pathways in the Response of Chinese Pine (Pinus tabuliformis) to Feeding Stimulation by Pine Caterpillar (Dendrolimus tabulaeformis)

In nature, plants have developed a series of resistance mechanisms to face various external stresses. As understanding of the molecular mechanisms underlying plant resistance continues to deepen, exploring endogenous resistance in plants has become a hot topic in this field. Despite the multitude of studies on plant-induced resistance, how plants respond to stress under natural conditions remains relatively unclear. To address this gap, we investigated Chinese pine (Pinus tabuliformis) using pine caterpillar (Dendrolimus tabulaeformis) under natural conditions. Healthy Chinese pine trees, approximately 10 years old, were selected for studying induced resistance in Huangtuliangzi Forestry, Pingquan City, Chengde City, Hebei Province, China. Pine needles were collected at 2 h and 8 h after feeding stimulation (FS) via 10 pine caterpillars and leaf clipping control (LCC), to simulate mechanical damage caused by insect chewing for the quantification of plant hormones and transcriptome and metabolome assays. The results show that the different modes of treatments significantly influence the contents of JA and SA in time following treatment. Three types of differentially accumulated metabolites (DAMs) were found to be involved in the initial response, namely phenolic acids, lipids, and flavonoids. Weighted gene co-expression network analysis indicated that 722 differentially expressed genes (DEGs) are positively related to feeding stimulation and the specific enriched pathways are plant hormone signal transduction and flavonoid biosynthesis, among others. Two TIFY transcription factors (PtTIFY54 and PtTIFY22) and a MYB transcription factor (PtMYB26) were found to be involved in the interaction between plant hormones, mainly in the context of JA signal transduction and flavonoid biosynthesis. The results of this study provide an insight into how JA activates, serving as a reference for understanding the molecular mechanisms of resistance formation in conifers responding to mandibulate insects.

Analysis of ginseng rusty root symptoms transcriptome and its pathogenesis directed by reactive oxygen species theory

Ginseng rusty root symptoms (GRS) is a primary disease of ginseng, which seriously decreases the yield and quality of ginseng and causes enormous losses to ginseng production. GRS prevention and control is still challenging due to its unclear etiology. In this study, the phloem tissue of healthy Panax ginseng (AG), the nonred tissue of the phloem epidermis around the lesion (BG), and the red lesion site tissue of GRS (CG) were extracted for mRNA transcriptomic analysis; 35,958 differentially expressed genes (DEGs) were identified and were associated with multiple stress resistance pathways, reactive oxygen species (ROS), and iron ion binding. Further study showed that the contents of O2 •-, H2O2, and malondialdehyde (MDA) were significantly increased in BG and CG tissues. Under anaerobic conditions caused by excessive soil moisture, the overproduction of ROS destroys cell membranes, simultaneously converting Fe2+ to Fe3+ and depositing it in the cell wall, which results in GRS, as evidenced by the success of the GRS induction test.

Genome-Wide Association Study to Identify Marker-Trait Associations for Seed Color in Colored Wheat (Triticum aestivum L.)

This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among various traits. Genotyping using 81,587 SNP markers resulted in 3969 high-quality markers, revealing a genome-wide distribution with varying densities across chromosomes. A genome-wide association study using fixed and random model circulating probability unification (FarmCPU) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified 11 significant marker-trait associations (MTAs) associated with L*, a*, and b*, and chromosomal distribution patterns revealed predominant locations on chromosomes 2A, 2B, and 4B. A comprehensive annotation uncovered 69 genes within the genomic vicinity of each MTA, providing potential functional insights. Gene expression analysis during seed development identified greater than 2-fold increases or decreases in expression in colored wheat for 16 of 69 genes. Among these, eight genes, including transcription factors and genes related to flavonoid and ubiquitination pathways, exhibited distinct expression patterns during seed development, providing further approaches for exploring seed coloration. This comprehensive exploration expands our understanding of the genetic basis of seed color and paves the way for informed discussions on the molecular intricacies contributing to this phenotypic trait.

Comparative Analysis of Transcriptomics and Metabolomics Reveals Defense Mechanisms in Melon Cultivars against Pseudoperonospora cubensis Infection

Melon (Cucumis melo L.) represents an agriculturally significant horticultural crop that is widely grown for its flavorful fruits. Downy mildew (DM), a pervasive foliar disease, poses a significant threat to global melon production. Although several quantitative trait loci related to DM resistance have been identified, the comprehensive genetic underpinnings of this resistance remain largely uncharted. In this study, we utilized integrative transcriptomics and metabolomics approaches to identify potential resistance-associated genes and delineate the strategies involved in the defense against DM in two melon cultivars: the resistant 'PI442177' ('K10-1') and the susceptible 'Huangdanzi' ('K10-9'), post-P. cubensis infection. Even in the absence of the pathogen, there were distinctive differentially expressed genes (DEGs) between 'K10-1' and 'K10-9'. When P. cubensis was infected, certain genes, including flavin-containing monooxygenase (FMO), receptor-like protein kinase FERONIA (FER), and the HD-ZIP transcription factor member, AtHB7, displayed pronounced expression differences between the cultivars. Notably, our data suggest that following P. cubensis infection, both cultivars suppressed flavonoid biosynthesis via the down-regulation of associated genes whilst concurrently promoting lignin production. The complex interplay of transcriptomic and metabolic responses elucidated by this study provides foundational insights into melon's defense mechanisms against DM. The robust resilience of 'K10-1' to DM is attributed to the synergistic interaction of its inherent transcriptomic and metabolic reactions.

An LcMYB111-LcHY5 Module Differentially Activates an LcFLS Promoter in Different Litchi Cultivars

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS,LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time.

Mutation of MYB36 affects isoflavonoid metabolism, growth, and stress responses in Lotus japonicus

Isoflavonoids are mostly produced by legumes although little is known about why and how legumes are able to regulate the biosynthesis of these particular compounds. Understanding the role of potential regulatory genes of the isoflavonoid biosynthetic pathway constitutes an important topic of research. The LORE1 mutation of the gene encoding the transcription factor MYB36 allowed the identification of this gene as a regulator of isoflavonoid biosynthesis in Lotus japonicus plants. The levels of several isoflavonoid compounds were considerably lower in two lines of Ljmyb36 mutant plants compared to the WT. In addition, we found that Ljmyb36 mutant plants were significantly smaller and showed a substantial decrease in the chlorophyll levels under normal growth conditions. The analysis of plants subjected to different types of abiotic stress conditions further revealed that mutant plants presented a higher sensitivity than WT plants, indicating that the MYB36 transcription factor is also involved in the stress response in L. japonicus plants.

Genome-Wide Identification of WRKY Gene Family and Functional Characterization of CcWRKY25 in Capsicum chinense

Pepper is renowned worldwide for its distinctive spicy flavor. While the gene expression characteristics of the capsaicinoid biosynthesis pathway have been extensively studied, there are already a few reports regarding transcriptional regulation in capsaicin biosynthesis. In this study, 73 WRKYs were identified in the genome of Capsicum chinense, and their physicochemical traits, DNA, and protein sequence characteristics were found to be complex. Combining RNA-seq and qRT-PCR data, the WRKY transcription factor CA06g13580, which was associated with the accumulation tendency of capsaicinoid, was screened and named CcWRKY25. CcWRKY25 was highly expressed in the placenta of spicy peppers. The heterologous expression of CcWRKY25 in Arabidopsis promoted the expression of genes PAL, 4CL1, 4CL2, 4CL3, CCR, and CCoAOMT and led to the accumulation of lignin and flavonoids. Furthermore, the expression of the capsaicinoid biosynthesis pathway genes (CBGs) pAMT, AT3, and KAS was significantly reduced in CcWRKY25-silenced pepper plants, resulting in a decrease in the amount of capsaicin. However, there was no noticeable difference in lignin accumulation. The findings suggested that CcWRKY25 could be involved in regulating capsaicinoid synthesis by promoting the expression of genes upstream of the phenylpropanoid pathway and inhibiting CBGs' expression. Moreover, the results highlighted the role of CcWRKY25 in controlling the pungency of pepper and suggested that the competitive relationship between lignin and capsaicin could also regulate the spiciness of the pepper.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

Metabolites and Plant Hormones Related to the Resistance Response to Feeding Stimulation and Leaf Clipping Control in Chinese Pine (Pinus tabuliformis Carr.)

This experiment was conducted to define changes in metabolic pathways in response to mandibulate insect feeding and to provide a reference for further investigation of the molecular mechanisms underlying the development of conifer resistance. Chinese pine (Pinus tabuliformis Carr.) in good growth status in natural condition was chosen for stimulation by 10 pine caterpillars (Dendrolimus tabulaefomis Tsai et Liu) as feeding stimulation (FS), leaf clipping control (LCC) as mechanical damage, and CK group (with no treatment) (recorded as 0 h). The metabolome and total flavonoid content were measured in the needles at 0, 2, and 8 h after treatment. Plant hormones were measured with needles at 0, 0.5, 1, 1.5, 2, 4, 6, and 8 h after different treatments. The results show that a total of 30.8% flavonoids are identified by metabolomics analysis. Compared with leaf clipping control, feeding stimulation of Chinese pine caterpillars significantly induced the upregulation of metabolites in the flavonoid pathway in Chinese pine, and the plant hormones JA and IAA showed expression trends consistent with those of the metabolome. According to the biological processes of the four plant hormones involved, JA and SA are mostly involved in resistance formation, and in this study, both of them also have fluctuating expressions influenced by feeding stimulation, while the expressions of the growth-related hormones IAA and ABA have no significant changes at other time points except for 1 h after treatment. Thus, the flavonoid pathway is one of the main pathways involved in resistance formation in conifers, and JA and IAA are involved in the formation of resistance.

MePAL6 regulates lignin accumulation to shape cassava resistance against two-spotted spider mite

INTRODUCTION

The two-spotted spider mite (TSSM) is a devastating pest of cassava production in China. Lignin is considered as an important defensive barrier against pests and diseases, several genes participate in lignin biosynthesis, however, how these genes modulate lignin accumulation in cassava and shape TSSM-resistance is largely unknown.

METHODS

To fill this knowledge gap, while under TSSM infestation, the cassava lignin biosynthesis related genes were subjected to expression pattern analysis followed by family identification, and genes with significant induction were used for further function exploration.

RESULTS

Most genes involved in lignin biosynthesis were up-regulated when the mite-resistant cassava cultivars were infested by TSSM, noticeably, the MePAL gene presented the most vigorous induction among these genes. Therefore, we paid more attention to dissect the function of MePAL gene during cassava-TSSM interaction. Gene family identification showed that there are 6 MePAL members identified in cassava genome, further phylogenetic analysis, gene duplication, cis-elements and conserved motif prediction speculated that these genes may probably contribute to biotic stress responses in cassava. The transcription profile of the 6 MePAL genes in TSSM-resistant cassava cultivar SC9 indicated a universal up-regulation pattern. To further elucidate the potential correlation between MePAL expression and TSSM-resistance, the most strongly induced gene MePAL6 were silenced using virus-induced gene silencing (VIGS) assay, we found that silencing of MePAL6 in SC9 not only simultaneously suppressed the expression of other lignin biosynthesis genes such as 4-coumarate--CoA ligase (4CL), hydroxycinnamoyltransferase (HCT) and cinnamoyl-CoA reductase (CCR), but also resulted in decrease of lignin content. Ultimately, the suppression of MePAL6 in SC9 can lead to significant deterioration of TSSM-resistance.

DISCUSSION

This study accurately identified MePAL6 as critical genes in conferring cassava resistance to TSSM, which could be considered as promising marker gene for evaluating cassava resistance to insect pest.

Analysis of the different growth years accumulation of flavonoids in Dendrobium moniliforme (L.) Sw. by the integration of metabolomic and transcriptomic approaches

Dendrobium moniliforme (L.) Sw. is a valuable herbal crop, and flavonoids are primarily distributed as active ingredients in the stem, but the composition and synthesis mechanisms of flavonoids in different growth years are not clear. The accumulation of flavonoids in D. moniliforme from four different years was investigated, using a combined metabolomics and transcriptomics approach in this study. The phenylpropanoid and flavonoid biosynthetic pathways were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). The widely targeted metabolomics technique revealed a total of 173 kinds of flavonoid metabolites. The metabolomics data confirmed the trend of total flavonoids (TF) content in stems of D. moniliforme, with chalcone, naringenin, eriodictyol, dihydroquercetin, and other flavonoids considerably up-accumulating in the third year. Twenty DEGs were detected that regulate flavonoid synthesis and the expression of these genes in different growth years was verified using real-time quantitative PCR (qRT-PCR). Furthermore, a comprehensive regulatory network was built for flavonoid biosynthesis and it was discovered that there is one FLS gene, one CCR gene and two MYB transcription factors (TFs) with a high connection with flavonoid biosynthesis by weighted gene co-expression network analysis (WGCNA). In this study, the correlation between genes involved in flavonoid biosynthesis and metabolites was revealed, and a new regulatory mechanism related to flavonoid biosynthesis in D. moniliforme was proposed. These results provide an important reference for the farmers involved in the cultivation of D. moniliforme.