A flavonoid-attracted Aeromonas spp enhances plant drought resistance without cry-for-help [Plant_RNA-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE184872 | GEO | 2022/10/19
REPOSITORIES: GEO
Similar Datasets
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:<p>Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.</p>
2024-03-19 | MTBLS6537 | MetaboLights
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.
2020-12-27 | GSE108555 | GEO
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants
2016-07-31 | GSE63474 | GEO
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants Roots were cut at the root/hypocotyl junction and collected into RLT buffer in the RNeasy plant mini kit. Approximately 60 roots were collected per replicate, with two biological replicates. RNA was extracted using the RNeasy Micro Kit. Probes for array analysis were preparedfrom 1μg total RNA with the one-cycle amplification protocol by Affymetrix according to the manufacturer's instructions. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Arabidopsis Whole Genome ATH1 Affymetrix GeneChips.
2016-07-31 | E-GEOD-63474 | biostudies-arrayexpress
Project description:Ginkgo biloba leaves are always resources for flavonoids pharmaceutical industry. Thus, artificial planting and industrial harvesting become the vital aspect to get higher drug yields. In this research, we performed de novo transcriptome sequencing of Ginkgo leaves coupled with high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry analyses to obtain a comprehensive understanding of the influence of elevation and plant age on flavonoid synthesis. A total of 557,659,530 clean reads were assembled into 188,155 unigenes, of which 135,102 (71.80%) were successfully annotated in seven public databases. The differentially expressed genes analysis indicated DFR, LAR and ANR were significantly up-regulated with the increase of elevation in young Ginkgo trees leaves. With less strict saliency, the relative concentration of flavonoid derivatives with high parent ion signal intensity was likely to support this conclusion. Complex gene variations were observed with the plant age change. However, flavonoid derivatives analysis predicted the potential possibility that the rise of plant age is more likely to be detrimental to the biosynthesis of Ginkgo flavonoids in leaves. From the overall DEGs involved in flavonoid biosynthesis, DFRs seemed to show more considerable variability towards the variation of elevation and plant age. Furthermore, our research effectively expanded the functional genomic library of Ginkgo and provided a reference for artificial planting and industrial harvesting.
2019-05-05 | ST001194 | MetabolomicsWorkbench
Project description:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
Project description:Growth inhibition of the pathogen Staphylococcus aureus with currently available antibiotics is problematic in part due to bacterial biofilm protection. While Although the recently characterized natural products, including 3´,4´,5-trihydroxy-6,7-dimethoxy-flavone [1], 3´,4´,5,6,7-pentahydroxy-flavone [2] and 5-hydroxy-4´,7-dimethoxy-flavone [3] exhibit both antibiotic and biofilm inhibitory activities, the mode of action of such hydroxylated flavonoids with respect to S. aureus inhibition has is yet to be characterized. Enzymatic digestion and high- resolution MS mass spectral analysis of differentially expressed proteins from S. aureus, with and without exposure to antibiotic flavonoids (1-3) has allowed for the characterization of global -protein alterations induced by metabolite treatment. A total of 56, 92, and 110 proteins are were differentially expressed with bacterial exposure to 1, 2 or 3, respectively. Connectivity of identified proteins is characterized using a search tool for the retrieval of interacting genes/proteins (STRING) with multi-targeted S. aureus inhibition of energy metabolism and biosynthesis by the assayed flavonoids observed. Identifying the mode of action of natural products as antibacterial agents is expected to provide insight into the potential use of flavonoids alone or in combination with known therapeutic agents to effectively control S. aureus infection.
2017-05-30 | PXD006030 | Pride