Expression data of Nodule Cysteine-Rich (NCR) Defensin-Like (DEFL) genes in different stages of nodule development in Medicago truncatula
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ABSTRACT:
ORGANISM(S): Medicago truncatula
PROVIDER: GSE34803 | GEO | 2013/03/05
SECONDARY ACCESSION(S): PRJNA151133
REPOSITORIES: GEO
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Project description:We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule. We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression patterns of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) at marked developmental stages and nodules inoculated with various mutants derived from Sm1021 totalling 14 different treatments. Each treatment was supported by three biological replicates giving a grand total of 42 samples.
2013-03-05 | E-GEOD-34803 | biostudies-arrayexpress
Project description:We have undertaken a detailed study to identify expression polymorphism of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in four different accessions of Medicago truncatula. Each accession was inoculated with two different rhizobial strains to assess the NCR expression differences caused by host-symbiont specificity. The NCRs displayed significant expression differences among the ecotypes but had subtle differences in gene expression because of strain difference. We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression polymorphism of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) and Sinorhizobium medicae (SmA321) totalling 8 different treatments. Each treatment was supported by three biological replicates giving a grand total of 24 samples.
2014-06-20 | E-GEOD-34804 | biostudies-arrayexpress
Project description:We have undertaken a detailed study to identify expression polymorphism of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in four different accessions of Medicago truncatula. Each accession was inoculated with two different rhizobial strains to assess the NCR expression differences caused by host-symbiont specificity. The NCRs displayed significant expression differences among the ecotypes but had subtle differences in gene expression because of strain difference.
2014-06-20 | GSE34804 | GEO
Project description:Medicago truncatula engages in root nodule symbiosis by developing a de novo plant organ (known as nodule) in its roots in response to the infection by rhizobia. These nodules are de novo plant organs that provide an optimal environment for the rhizobia to fix nitrogen in exchange for photosynthates. The establishment of root nodule symbioses (RNS) requires the coordination of two distinct processes: bacterial infection and nodule organogenesis. In this study we used single-cell RNA-seq to investigate the first hours of the establishment of the root nodule symbiosis aiming to identify the transcriptional mechanisms governing this process.
2024-01-17 | GSE224539 | GEO
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.
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Project description:Legumes establish symbiosis with soil rhizobia forming root nodules that fix atmospheric nitrogen. The central role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in nodule biology has been clearly established. Recently, hydrogen sulfide (H2S) and other reactive sulfur species (RSS) have emerged as novel signaling molecules in animals and plants. A major mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification of proteins. To identify possible functions of H2S in nodule development and senescence, we used the tag-switch method to analyze quantitative changes in the persulfidation profile of common bean (Phaseolus vulgaris) nodules at different developmental stages. The proteomic analysis suggests that persulfidation plays a major regulatory role in plant and bacteroid metabolism and senescence. In addition, the effect of a H2S donor on several proteins involved in ROS and RNS homeostasis was investigated. The results obtained using nodule extracts and recombinant proteins suggest a crosstalk between H2S, ROS, and RNS, and a protective function of persulfidation on redox-sensitive enzymes from oxidative modifications that may cause enzyme inactivation. It is concluded that the general decrease of persulfidation levels observed in plant proteins of aging nodules is one of the mechanisms that cause the disruption of redox homeostasis leading to senescence.
2024-06-16 | PXD039852 | Pride
Project description:Rhizobia are soil bacteria that can enter into complex symbiotic relationships with legumes, where rhizobia induce the formation of nodules on the plant root. Inside nodules, rhizobia differentiate into nitrogen-fixing bacteroids that reduce atmospheric nitrogen into ammonia, secreting it to the plant host in exchange for carbon. During the transition from free-living bacteria to bacteroids, rhizobial metabolism undergoes major changes. To investigate the metabolism of bacteroids and contrast it with the free-living state, we quantified the proteome of unlabelled bacteroids relative to 15N-labelled free-living rhizobia. The data were used to build a core metabolic model of pea bacteroids for the strain Rhizobium leguminosarum bv. viciae 3841.
2021-09-09 | PXD019467 | Pride
Project description:During the legume-rhizobium symbiosis, free-living soil bacteria known as rhizobia trigger the formation of root nodules. The rhizobia infect these organs and adopt an intracellular lifestyle within the symbiotic nodule cells where they become nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this differentiation process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, Bradyrhizobium sp. ORS285 proceeds until the intracellular infection of nodule cells but the bacteria cannot differentiate into enlarged polyploid bacteroids and fix nitrogen. The nodule bacteria of the bclA mutant constitute thus an intermediate stage between the free-living soil bacteria and the intracellular nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the ORS285 wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules discriminated nodule-induced genes that are specific to differentiated and nitrogen-fixing bacteroids and others that are activated in the host microenvironment irrespective of bacterial differentiation and nitrogen fixation. These analyses demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but that are expressed to extremely elevated levels. The transcriptomes further highlighted the dynamics of oxygen and redox regulation of gene expression during nodule formation and we discovered that bclA represses the expression of non-ribosomal peptide synthetase gene clusters suggesting a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.
2019-06-01 | GSE126971 | GEO
Project description:Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy‐intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data‐independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain‐associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.
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Project description:Brassinosteroid (BR) is an essential hormone in plant growth and development. BR signaling pathway has been extensively studied, in which Brassinazole resistant 1 (BZR1) functions as a key regulator. Here, we carried out a functional study of the homolog of BZR1 in Medicago truncatula, whose expression was induced in nodules upon rhizobial inoculation. We identified a loss-of-function mutant mtbzr1-1 and generated 35S:MtBZR1 transgenic lines for further analysis at the genetic level. Both the mutant and the overexpressor lines of MtBZR1 showed no obvious phenotypic changes under normal growth condition. After rhizobial inoculation, however, the shoot and root dry mass was reduced in mtbzr1-1 compared with the wild-type, caused by partially impaired nodule development. The transcriptomic analysis identified 1,319 differentially expressed genes in mtbzr1-1 compared with wild-type, many of which are involved in nodule development and secondary metabolite biosynthesis. Our results demonstrate an essential role of MtBZR1 in nodule development in M. truncatula, shedding light on the potential role of BR in legume-rhizobium symbiosis.
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