Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1328261 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Biological nitrogen fixation (BNF) is a primary input of nitrogen to natural and agricultural systems globally. BNF is a temperature-dependant enzymatic process and can be conducted by microbes (including Rhizobia) hosted symbiotically in root nodules of some plants. Heat shock proteins (Hsps) have been implicated in the process of acquiring thermotolerance or acclimating to elevated temperature, as they play a vital role in maintaining cell integrity and homeostasis during heat stress. Although the BNF response to temperature may crucially impact future ecosystem productivity in the face of global climate change, little is known about Hsp expression in nodules of N-fixing non-agricultural species, such as tropical N-fixing trees in the Fabaceae family. This project aimed to characterize small (15-20kDa) Hsp (sHsp) expression in nodule tissue to examine the biochemical mechanisms of heat response in these tissues. To first identify Hsps in nodule tissues, Vachellia farnesiana and Acacia confusa nodules were excised, heat shock was induced, and protein content was isolated via chemical treatment before separation of protein species and analysis with SDS-PAGE. Two polyacrylamide gels yielded bands in the 15-20 kDa region that displayed differential Coomassie staining, which were sent for further characterization by HPLC-MS analysis for protein sequencing. Ten rhizobial sHsps were detected in these samples in addition to seven Acacia sHsps when compared independently to reference rhizobial and plant proteome databases. In an attempt quantify relative expression of Hsps in nodule and root tissue, we performed western blot experiments using Anti-Hsp20 antibodies raised against human and mouse Hsp proteins, with anti-beta actin loading control. While nonuniform beta-actin expression across tissue types (A. confusa nodules versus root control) prevented quantitative analysis, the experiments validated that Hsp20s are expressed in Acacia nodules as well as in root tissue. These experiments could provide a foundation for future studies that aim to determine variation in responses to key stressors predicted to increase with global climate change and help determine the implications of warming across the tropics and beyond.
2024-10-09 | PXD055599 | Pride
Project description:In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilisation to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.
2022-08-11 | PXD033875 | Pride
Project description:We have used deep sequencing of small RNAs from nodules and root apexes of the model legume Medicago truncatula, to identify 113 novel candidate miRNAs. These miRNAs (legume or Mt-specific) are encoded by 278 putative hairpin precursors in the M. truncatula genome. Several miRNAs are differentially expressed in nodules and root tips and large variety of targets could be predicted for these genes. Specific miRNA isoforms showed contrasting expression patterns in these tissues Keywords: Transcriptome analysis
2009-07-07 | GSE15438 | GEO
Project description:We have used deep sequencing of small RNAs from nodules and root apexes of the model legume Medicago truncatula, to identify 113 novel candidate miRNAs. These miRNAs (legume or Mt-specific) are encoded by 278 putative hairpin precursors in the M. truncatula genome. Several miRNAs are differentially expressed in nodules and root tips and large variety of targets could be predicted for these genes. Specific miRNA isoforms showed contrasting expression patterns in these tissues Keywords: Transcriptome analysis 3 samples examined: nodules, root tips, and root tips + NaCl
2009-07-07 | E-GEOD-15438 | biostudies-arrayexpress
Project description:Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules (EN), mature nodules (MN), emerging lateral roots (ELR) and young lateral roots (YLR), and constructed strand-specific RNAseq libraries using polyA-enriched RNA preparations. Root sections above and below these organs devoid of any lateral organs were used to construct respective control tissue libraries (ABEN, ABMN, ABELR, ABYLR respectively). High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analysis of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets especially from leguminous plants these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.
2019-04-10 | GSE129509 | GEO
Project description:Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in <i>Ardisia crenata</i> (Primulaceae) and <i>Psychotria punctata</i> (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of <i>A. crenata</i>. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of <i>A. crenata.</i> In contrast, pavettamine was only detected in <i>P. punctata</i> and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in <i>A. crenata</i> leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.
2021-08-26 | MTBLS2870 | MetaboLights
Project description:Sequencing Endophytes bacteria strains from Black Acacia Nodules
| PRJEB65983 | ENA
Project description:We studied potentially amyloidogenic proteins (e.g. protein forming polymers and complexes that are resistant to treatment with ionic detergents) in root nodules formed by two lines of garden pea (P. sativum L.): Sprint-2 (Fix+ phenotype) and Sprint-2Fix- (sym31) (Fix- phenotype) inoculated with the Rhizobium leguminosarum bv. viciae RCAM1026 root nodule bacteria. The Fix+ phenotype is characterized by effective (ability to fix nitrogen) root nodules formation. The Fix- line is a descendant of the Fix+ line and forms ineffective root nodules (unable to fix nitrogen) with undifferentiated bacteroids. We demonstrated the presence of both plant and bacterial proteins in detergent resistant fractions, including previously identified amyloid proteins RopA and RopB of R. leguminosarum and vicilin of P. sativum L.
2022-10-25 | PXD035724 | Pride
Project description:Nitrogen assimilation in plants is a tightly regulated process that integrates developmental and environmental signals. The legume-rhizobial symbiosis results in the formation of a specialized organ called root nodule, where the rhizobia fixes atmospheric nitrogen into ammonia. Ammonia is assimilated by the plant enzyme glutamine synthetase, which is specifically inhibited by PPT. The expression of key genes related to the regulation of root nodule metabolism will likely be affected by glutamine synthetase inhibition. We used microarrays to detail the global programme of gene expression in response to Glutamine synthetase inhibition in root nodules and identified genes differentially expressed over a time course. Medicago truncatula nodulated plants (20 days post inoculation) were treated with 0.25 mM of PPT. Root nodules were harvested at 4, 8 and 24 hours after PPT application. As a control, root nodules collected just before PPT application were used (PPT 0h). Three biological replicates consisting of pools of root nodules harvested from five distinct plants were used for RNA extraction and hybridization on Affymetrix GeneChips.
2012-05-08 | E-GEOD-34155 | biostudies-arrayexpress
Project description:Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results prove a decrease in the efficiency of nitrogen fixation as well as extensive changes in plant and bacterial transcriptomes shortly after watering cessation. We show for the first time that not only symbiotic plant component, but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrate that both M. truncatula and L. japonicus root nodules are susceptible to water deprivation, they indicate significant differences in plant and bacterial response to drought between tested species, which may be related to various type of root nodules formed by these species.
2019-02-26 | GSE126986 | GEO