Ontology highlight
ABSTRACT:
PROVIDER: PRJEB95891 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Multi-omics analyses of plant-microbe interaction in maize
| PRJNA626602 | ENA
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates.
2014-11-01 | GSE54987 | GEO
Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)
2014-11-01 | E-GEOD-54987 | biostudies-arrayexpress
Project description:We have performed genome-wide expression analyses as part of a multi-omics study on 34 colorectal cancer cell lines. The data were used for gene expression subtyping of cell lines, gene set analyses and integration with DNA and protein level data.
2017-07-07 | GSE97023 | GEO
Project description:Although some mechanisms are known how plant growth beneficial bacteria help plants to grow under stressful conditions, we still know little how the metabolism of host plants and bacteria is coordinated during the establishment of functional interaction. In the present work, using single and dual transcriptomics, we studied the reprograming of metabolic and signaling pathways of Enterobacter sp. SA187 with Arabidopsis thaliana during the change from free-living to endophytic host-microbe interaction. We could identify major changes in primary and secondary metabolic pathways in both the host and bacteria upon interaction, with an important role of the sulfur metabolism and retrograde signaling in mediating plant resistance to salt stress. Also, we studied the effect of SA187 endogenous compounds and its role on sulfur metabolism and consequently salt tolerance. These data should help future research in the field of beneficial plant-microbe interactions for developing sophisticated strategies to improve agriculture of crops under adverse environmental conditions. transcriptome of Arabidopsis thaliana organs with beneficial microbe, beneficial microbe endogenous compound, and ethylene precursor
2021-02-25 | GSE145884 | GEO
Project description:Plant proteases are key regulators of plant cell processes such as seed development, immune responses, senescence and programmed cell death (PCD). Apoplastic papain-like cysteine proteases (PLCPs) are hubs in plant-microbe interactions and play an important role during abiotic stresses. The apoplast is a crucial interface for the interaction between plant and microbes. So far, apoplastic maize PLCPs and their function have been mostly described for aerial parts. In this study, we focused on apoplastic PLCPs in the roots of maize plants. We have analyzed the phylogeny of maize PLCPs and investigated their protein abundance after salicylic acid treatment. Using activity-based protein profiling (ABPP) we have identified a novel root-specific PLCP belonging to the RD21-like subfamily, as well as three salicylic acid activated PLCPs. The root specific PLCP CP1C shares sequence and structural similarities to known CP1-like proteases. Biochemical analysis of recombinant CP1C revealed different substrate specificities and inhibitor affinities compared to the related proteases. This study characterized a root-specific PLCP and identifies differences between the SA-dependent activation of PLCPs in roots and leaves.
2019-05-27 | PXD013124 | Pride
Project description:Lipids play crucial roles in plant-microbe interactions, functioning as structural components, signaling molecules, and microbe-associated molecular patterns (MAMPs). However, the mechanisms underlying lipid perception and signaling in plants remain largely unknown. Here, we investigate the immune responses activated in barley (Hordeum vulgare L.) by lipid extracts from the beneficial root endophytic fungus Serendipita indica and compare them to responses elicited by chitohexaose and the fungal sterol ergosterol. We demonstrate that S. indica lipid extract induces hallmarks of pattern-triggered immunity (PTI) in barley. Ergosterol emerged as the primary immunogenic component and was detected in the apoplastic fluid of S. indica-colonized barley roots. Notably, S. indica colonization suppresses the ergosterol-induced burst of reactive oxygen species (ROS) in barley. By employing a multi-omics approach, which integrates transcriptomics, phosphoproteomics, and metabolomics, we provide evidence for the phosphorylation of phosphatidylinositol phosphate (PIP) metabolic enzymes and activation of diterpene biosynthesis upon exposure to fungal lipids. Furthermore, we show that phosphatidic acid (PA) enhances lipid-mediated apoplastic ROS production in barley. These findings indicate that plant lipids facilitate immune responses to fungal lipids in barley, providing new insights into lipid-based signaling mechanisms in plant-microbe interactions.
2025-01-31 | GSE280369 | GEO
Project description:Lipids play crucial roles in plant-microbe interactions, functioning as structural components, signaling molecules, and microbe-associated molecular patterns (MAMPs); however, the mechanisms underlying lipid perception and signaling pathways in plants remain largely unknown. This study investigates the immune responses triggered in Hordeum vulgare (barley) by lipid extracts from the root endophytic fungus Serendipita indica. We compare these responses to those elicited by the carbohydrate MAMP chitohexaose and the fungal sterol lipid ergosterol, a 5,7-diene oxysterol recognized as a MAMP in plants. Our results demonstrate that S. indica lipid extract induces hallmarks of pattern-triggered immunity (PTI) in barley. Ergosterol was identified as the main immunogenic component and was detected in the apoplastic fluid of S. indica-colonized barley roots. Using a multi-omics approach combining transcriptomics, phosphoproteomics, and metabolomics, our data provide evidence for the activation of phosphatidylinositol phosphate (PIP) signaling and diterpene biosynthesis upon exposure to fungal lipids. Furthermore, we show that phosphatidic acid (PA) enhances lipid-mediated apoplastic reactive oxygen species (ROS) production in barley. These findings indicate that plant lipids mediate immune responses to fungal lipids in barley, advancing our understanding of lipid perception and signaling in plant-microbe interactions.
2025-01-31 | PXD056788 | Pride
Project description:Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that have a critical impact on plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present an atlas of gene regulatory logic involving transcription factors, potential cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integration of our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic. Overall, this study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.
2023-04-24 | GSE226826 | GEO
Project description:<p><strong>BACKGROUND:</strong> The coevolution and interaction between plants and microorganisms have long been a subject of significant research interest. Dark septate endophytes (DSE) have garnered great attention in contemporary research due to their functional diversity, in vitro cultivation ability, and ability to establish symbiotic associations with host plants. In the present study, three DSE strains, namely <em>Acrocalymma vagum</em>, <em>Zopfiella marina</em>, and <em>Phoma herbarum</em>, which were obtained from the roots of <em>Astragalus membranaceus</em>, were introduced into maize plants through inoculation. We evaluated the effects of DSE inoculation on maize growth and root secretion activity through a multi omics methods, and proposed mechanisms for 'internal pathways' and 'external pathways'.</p><p><strong>RESULTS:</strong> The findings indicated that A. vagum exhibited superior growth-promoting ability on maize compared to <em>Z. marina</em> and <em>P. herbarum</em>.GO and KEGG enrichment analysis found that <em>A. vagum</em> inoculation resulted in significant enrichment of differentially expressed genes in annotation functions related to hormone regulation and lipid metabolism. A. vagum inoculation revealed that the gene pathways involved in plant hormone signaling and plant pathogen interactions play a crucial role in promoting host growth, and <em>A. vagum</em> inoculation group exhibited the highest number of differentially expressed genes, the most intricate protein-protein interaction (PPI) model, and the most pronounced relationship between differentially expressed genes. After the inoculation of <em>A.vagum</em>, the levels of salicylic acid, zeatin, and IAA in maize plants significantly increased. Additionally, the diversity and abundance of endophytic fungi, as well as the proportion of harmful bacteria and beneficial fungi, had significantly increased. Compared with <em>Z. marina</em> and <em>P. herbarum</em>, the net photosynthetic rate (Pn) and stomatal conductance (Gs) of <em>A.vagum</em> inoculated plants significantly increased. Inoculation with <em>A.vagum</em> could enhance the ability of corn roots to secrete lipids, sugars, and amino acids, resulted in a notable augmentation of beneficial bacteria and fungi, accompanied by a significant reduction in the proportion of harmful bacteria in the rhizosphere soil, such as <em>Fusarium solani</em> and <em>Fusarium lacertarum</em>, exhibited significant inhibition, whereas <em>Bacillus niabensis</em> and <em>Bacillus nealsonii</em> demonstrated enrichment trends. Soil pH, organic matter, available potassium content, acid phosphatase, alkaline phosphatase and urease activity exhibited significant increases following the inoculation of <em>A. vagum</em>. Variance decomposition and structural equation modeling (SEM) analysis indicated that the 'internal pathway', maize growth is mainly influenced by the interaction of endogenous hormones, endophytic microorganisms, and photosynthetic parameters, whereas within the 'external pathway', the interaction between soil microorganisms and soil physicochemical properties exerted a dominant influence. Compared with the <em>Z. marina</em> and <em>P. herbarum</em> inoculation, <em>A. vagum</em> inoculation showed a more significant impact on maize growth, both in terms of 'internal pathway' and 'external pathway', in terms of pathway level and quantity.</p><p><strong>CONCLUSIONS:</strong> These findings provide a new perspective for understanding the potential mechanisms of 'microbe-plant' interactions and also contribute to the exploration of targeted functional microorganisms that promote growth and stress resistance.</p>
2023-12-15 | MTBLS8903 | MetaboLights