Flavonoid-targeted metabolomic analysis.
Ontology highlight
ABSTRACT: Flavonoids, one of the major groups of root exudates, are active molecules mediating plant-PGPR interactions. Flavonoids can alleviate nutrient deficiencies and drought stress to maintain normal plant growth. Here, We used flavonoid targeted metabolomic analysis to profile flavonoid components and content in tomato rhizosphere soil and roots.
INSTRUMENT(S): Liquid Chromatography MS - positive - hilic, Liquid Chromatography MS - negative - hilic
PROVIDER: MTBLS13507 | MetaboLights | 2025-12-14
REPOSITORIES: MetaboLights
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Project description:Forming symbiotic associations with beneficial microbes are important strategies for sessile plants to acquire nitrogen and phosphorus nutrients from the soil. Root exudates play key roles on set-up of the rhizosphere microbiome. According to the needs for nitrogen or phosphorus, plants can adjust the root exudates composition to attract proper microbes. Flavonoids are a group of secondary metabolites that are well studied in shaping the root microbiome, especially the root nodule symbiosis in legumes. Here, we show the medicago truncatula phosphate sensors SPX1 and SPX3 regulate flavonoids biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes were less recruited in spx1spx3 double mutant root rhizosphere. This was caused by lower flavonoids biosynthesis related genes expression, which resulted in lower flavonoids levels in the root exudates compared to wild type plant R108. Further analysis indicates the regulation of flavonoids biosynthesis is through the SPX1 and SPX3 interaction transcription factor PHR2. We propose the SPX-PHR phosphate homeostasis regulation network also control microbe-dependent nitrogen acquisition according to phosphate levels. Thus, SPX1 and SPX3 play important roles to keep a microbe-dependent nitrogen and phosphorus absorption balance for optimal growth.
2025-02-28 | GSE289310 | GEO
Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant drought resistance.
2022-10-19 | GSE184872 | GEO
Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant Na_H1 resistance.
2022-10-19 | GSE184873 | GEO
Project description:Plants have evolved a sophisticated defense system to survive under natural drought conditions. MicroRNAs (miRNA) are small noncoding RNAs that act as a post-transcriptional regulator in the environmental stress response and developmental process. Although many studies have reported the involvement of the miRNAs in drought response, molecular mechanisms by which miRNAs confer drought tolerance remain elusive. Here, we show that MIR171f, a member of MIR171 gene family, is mainly expressed in response to drought stress and regulate transcript levels of SCARECROW-LIKE6-I (SCL6-I) and SCL6-II. The SCL6 genes are known to be involved in shoot branching and flag leaf morphology. The MIR171f-overexpressing (MIR171f-OE) transgenic plants showed reduced drought symptoms as compared with non-transgenic (NT) control plants under both field drought and PEG-mediated dehydration stress conditions. Transcriptome analysis using the MIR171f-OE and mir171f-K/O mutants revealed that MIR171f regulates the expression of flavonoid biosynthesis genes, consequently leading to drought tolerance. Flavonoid biosynthesis genes were up-regulated in MIR171f-OE plants as compared with NT control plants under both normal and drought conditions. Together, our findings demonstrated that MIR171f plays an important role in plant drought-tolerance mechanism by regulating transcript levels of SCL6-I and SCL6-II.
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Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
2011-07-01 | E-MEXP-2812 | biostudies-arrayexpress
Project description:Flavonoid is an important secondary metabolite, which makes an important contribution to plant resistance to abiotic stress and human health. Fagopyrum tataricum (Tartary buckwheat) itself contains more flavonoids, so exploring the regulation of Tartary buckwheat flavonoid synthesis can provide a solid theoretical basis for the cultivation of new Tartary buckwheat varieties with high nutrition. In this paper, we studied the role of FtMYBs in regulating the biosynthesis of flavonoids in Tartary buckwheat.
2024-09-01 | GSE270048 | GEO
Project description:Nitrogen is a crucial nutrient element for plant growth and productivity, with both excess and deficiency in nitrogen fertilizer application posing adverse effects on plants and the environment. The internal mechanisms by which the medicinal plant Epimedium pubescens (E. pubescens) adapts to varying nitrogen levels remain unclear. This study employed one-year-old E. pubescens as the experimental material to systematically analyze the changes in plant growth traits, carbon metabolites, and Icariin-Flavonoids content under different exogenous nitrogen levels. Furthermore, it examined the transcriptional changes in gene expression within E. pubescens in response to varying nitrogen levels. The results showed that under moderate nitrogen levels (7.5 mmol/L NO3-), E. pubescens exhibited increased biomass accumulation and flavonoid synthesis. However, deficient or excessive nitrogen levels (0, 22.5 mmol/L NO3-) significantly inhibited photosynthesis in E. pubescens, reducing the content of starch, soluble sugars, and Icariin-Flavonoids, leading to decreased biomass and accompanied by changes in leaf color (pale green or browning). Transcriptome analysis revealed the underlying molecular mechanisms of these changes in plants regulated by different nitrogen levels. Nitrogen deficiency and excess triggered distinct transcriptional response patterns, with the number of differentially expressed genes (DEGs) peaking at S2 (36 days) under nitrogen deficiency and significantly declining at S3 (48 days), while the number of DEGs under excess nitrogen continuously increased over time from S1 to S3 (12-48 days). Both conditions significantly affected the expression of genes related to carbon and nitrogen metabolism, flavonoid synthesis, and stress response. Based on the correlation analysis of expression levels of genes related to these pathways, growth traits, and metabolite content indicators, we constructed regulatory network diagrams for carbon-nitrogen metabolism and Icariin-flavonoid metabolism-related genes. Furthermore, we identified hub genes that may be involved in regulating Icariin-flavonoid metabolism in response to nitrogen levels, such as UGT (Ebr06G044290), EpF3H (Ebr04G062950), EpCHS5 (Ebr03G073940) (Fig. 9A), UGT (Ebr06G044660), and EpUGT13_A (Ebr06G044210). Additionally, among the DEGs obtained at the S3 stage, we discovered the transcription factors MYB1_CROXC (Ebr04G001770) and MYB12_ARATH (Ebr01G065030). We constructed their associated gene networks under different nitrogen levels, which may primarily regulate the expression of genes like UGT, CHS, and F3H involved in the flavonoid synthesis stage of E. pubescens under varying nitrogen conditions. In summary, this study has revealed the growth performance and the variation patterns of Icariin-Flavonoid metabolism in E. pubescens in response to different exogenous nitrogen levels, as well as their complex underlying mechanisms. Additionally, key genes involved in regulating the synthesis of flavonol glycosides in E. pubescens by nitrogen levels have been identified. This provides an important basis for a deeper understanding of the mechanisms of nitrogen regulation on the growth and secondary metabolism of medicinal plants. Furthermore, it offers theoretical support and potential genetic resources for the efficient utilization of nitrogen fertilizers in E. pubescens cultivation and the breeding of high-nitrogen-use-efficiency varieties.
2024-08-02 | GSE273547 | GEO
Project description:Scutellaria viscidula Bunge (Labiatae), a perennial herb, is an important medicinal plant that possesses broad pharmacological actions. S. viscidula contains flavonoids with good bioactivities (e.g. baicalin, wogonoside, baicalein and wogonin) mainly in its dry root, which is used as alternative to Scutellaria baicalensis in the north of China. Furthermore, S. viscidula also has flavones with interesting diverged structures such as panicolin, viscidulin I, viscidulin II and viscidulin III. Tracing the dynamic process of gene expression will help reveal the mechanism of flavonoid synthesis in S. viscidula, as well as the 4'-deoxyflavone biosynthesis in S. baicalensis. One way is to generate and analyze the expressed sequence tags (ESTs). However, little is known on the transcriptome information of S. viscidula, particularly the key genes involved in flavonoid biosynthesis. In this study, we conducted de novo transcriptome analysis of S. viscidula and obtained 42,310,834 reads and 40,052 unigenes, respectively. We revealed 177 genes relating to flavonoid biosynthesis, where 23 key enzyme encoding genes including CHS, CHI, F3H, PAL and 4CL were annotated. Furthermore, we investigated the dynamic expression of CHS, CHI, F3H, MYB2, and bHLH of stem, root and leaf of S. viscidula in May, July and September. Our results showed that these key genes had important regulatory function and exhibited positive correlation with total flavonoid content in different growth stages of S. viscidula. Collectively, this study provides high-quality transcriptome data of S. viscidula, and further gives significant information for understanding the molecular mechanism of gene expression and active ingredients in Scutellaria plants.
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