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Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia

ABSTRACT: Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia

PROVIDER: PRJNA487592 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7747350.fastq.gz	Fastqsanger.gz
	SRR7747351.fastq.gz	Fastqsanger.gz
	SRR7747352.fastq.gz	Fastqsanger.gz
	SRR7747353.fastq.gz	Fastqsanger.gz
	SRR7747354.fastq.gz	Fastqsanger.gz

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Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia

Project description:We report how phosphate deficiency early rhizobia-induced genes in Phaseolus vulgaris (common bean)

2018-11-14 | GSE118968 | GEO

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia.

Project description:Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, which are genes controlling the nodulation process were significantly reduced in Pi-deficient common bean seedlings. In addition, whole-genome transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Moreover, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule numbers, was higher in Pi-deficient seedlings compared to control seedlings. The data presented in this study provides a mechanistic model to better understand how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia.

| S-EPMC6210973 | biostudies-literature

Medicago truncatula R108 in symbiosis with rhizobia wt or rhizobia mutant for BacA. Comparison of the transcriptomic response of Medicago truncatula plants.

Project description:12plex_medicago_2013-08 - r108 in symbiosis with rhizobia wt or rhizobia mutant for baca. - Two experiments to compare the transcriptomic response of medicago plants: Agar medium versus Phytagel medium (exp1) and rhizobium WT versus BacA (exp2). - Medicago truncatula ecotype R108 was inoculated with the symbiotic rhizobium Sinorhizobium meliloti strain Sm1021 and with its derivative mutant delta bacA. Nodules were collected 13 days after inoculation, and RNA were prepared for transcriptome analysis, there were three biological independant experiements.

2018-11-01 | GSE121775 | GEO

Transcriptional Impacts of prophage within the rhizobia-legume symbiosis

Project description:Transcriptional Impacts of prophage within the rhizobia-legume symbiosis

| PRJEB82617 | ENA

MACE-seq transcriptomic analysis of MtCLE35 overexpressing roots of M. truncatula without rhizobia inoculation and at 11 dpi after inoculation with S. meliloti.

Project description:CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides are systemic regulators of legume-rhizobium symbiosis that negatively control the number of nitrogen-fixing nodules. In Medicago truncatula, the expression of the MtCLE35 gene is activated in response to rhizobial inoculation and nitrate treatment, and its overexpression systemically inhibits nodulation. However, little is known about the molecular mechanisms underlying MtCLE35-mediated inhibition of nodulation. In order to elucidate target genes regulated by the MtCLE35-induced signaling cascade, we analyzed the transcriptome of MtCLE35 overexpressing roots inoculated by rhizobia using MACE (Massive Analysis of cDNA Ends) sequencing. Totally, 1390 genes were found to be differentially expressed between MtCLE35-overexpressing (35S::MtCLE35) and control (35S::GUS) roots after rhizobial inoculation, among them 268 genes were upregulated and 1122 genes were downregulated. Among downregulated genes, many known regulators of legume-rhizobia symbiosis were found, where upregulated genes included, among others, genes associated with defense response and cellular redox status. Furthermore, stable transgenic plants overexpressing the MtCLE35 gene were obtained in this study, and gene expression analysis of selected differentially expressed genes in rhizobia inoculated roots was performed in such plants. Collectively, our data suggest that overexpression of the MtCLE35 gene prevents the induction of nodulation program, which is accompanied by the expression of defense-related gene in MtCLE35-overexpressing rhizobia-inoculated M. truncatula roots.

2025-04-30 | GSE261468 | GEO

The MicroRNA319d/TCP10 Node Regulates the Common Bean - Rhizobia Nitrogen-Fixing Symbiosis.

Project description:Micro-RNAs from legume plants are emerging as relevant regulators of the rhizobia nitrogen-fixing symbiosis. In this work we functionally characterized the role of the node conformed by micro-RNA319 (miR319) - TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factor in the common bean (Phaseolus vulgaris) - Rhizobium tropici symbiosis. The miR319d, one of nine miR319 isoforms from common bean, was highly expressed in root and nodules from inoculated plants as compared to roots from fertilized plants. The miR319d targets TCP10 (Phvul.005G067950), identified by degradome analysis, whose expression showed a negative correlation with miR319d expression. The phenotypic analysis of R. tropici-inoculated composite plants with transgenic roots/nodules overexpressing or silencing the function of miR319d demonstrated the relevant role of the miR319d/TCP10 node in the common bean rhizobia symbiosis. Increased miR319d resulted in reduced root length/width ratio, increased rhizobial infection evidenced by more deformed root hairs and infection threads, and decreased nodule formation and nitrogenase activity per plant. In addition, these plants with lower TCP10 levels showed decreased expression level of the jasmonic acid (JA) biosynthetic gene: LOX2. The transcription of LOX2 by TCPs has been demonstrated for Arabidopsis and in several plants LOX2 level and JA content have been associate with TCP levels. On this basis, we propose that in roots/nodules of inoculated common bean plants TCP10 could be the transcriptional regulator of LOX2 and the miR319d/TCP10 node could affect nodulation through JA signaling. However, given the complexity of nodulation, the participation of other signaling pathways in the phenotypes observed cannot be ruled out.

| S-EPMC6095992 | biostudies-literature

The absence of quorum sensing signals triggers the expression of the symbiotic genes in broad host range rhizobia

Project description:Plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called Nod factors. They are responsible for the initial root hair curling during onset of root nodule development. This signal exchange is believed to be essential for initiating the plant symbiosis with rhizobia affiliated with the alphaproteobacteria. Here, we provide evidence that in broad host range rhizobia the complete lack of quorum sensing molecules results in an elevated copy number of its symbiotic plasmid (pNGR234a). This in turn triggers the expression of symbiotic genes and the production of Nod factors in the absence of plant signals. Therefore, increasing the copy number of specific plasmids could be a widespread mechanism of specialized bacterial populations bridging gaps in signalling cascades and providing a competitive advantage.

2017-02-10 | GSE78039 | GEO

Medicago truncatula R108 in symbiosis with rhizobia wt or rhizobia mutant for BacA. Comparison of the transcriptomic response of Medicago truncatula plants.

Project description:Medicago truncatula R108 in symbiosis with rhizobia wt or rhizobia mutant for BacA. Comparison of the transcriptomic response of Medicago truncatula plants.

| PRJNA498513 | ENA

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis.

Project description:The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.

| S-EPMC5748670 | biostudies-literature

Molecular bases of strain-specific responses of Phaseolus vulgaris roots to symbiotic bacteria with different efficiency in nitrogen-fixing symbiosis

Project description:Some legume plants can establish a nitrogen-fixing symbiosis with rhizobia. Compatibilty between rhizobia and legumes is determined at species-specific level, but there are variations on the efficiency of the process determined by the capacity of the plant to select specific strains that are better partners in terms of the biological outcome. In this work we used a model system based in the coevolution of two genetic pools of common bean (Phaseolus vulgaris) with strains of R. etli that establish a more efficient interaction to study the transcriptional changes occurring in roots at an early time of the interaction.

2020-12-10 | GSE155568 | GEO

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