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Differential analysis of host small RNAs identified conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris- Rhizobium etli symbiosis

ABSTRACT: Differential analysis of host small RNAs identified conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris- Rhizobium etli symbiosis

PROVIDER: PRJNA649692 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12351452.fastq.gz	Fastqsanger.gz
	SRR12351453.fastq.gz	Fastqsanger.gz
	SRR12351454.fastq.gz	Fastqsanger.gz
	SRR12351455.fastq.gz	Fastqsanger.gz
	SRR12351456.fastq.gz	Fastqsanger.gz

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Similar Datasets

Differential analysis of host small RNAs identified conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris- Rhizobium etli symbiosis

Project description:We report an small RNA sequencing (sRNA-seq) approach to identify host sRNAs involved in the nitrogen fixing symbiosis between Mesoamerican Phaseolus vulgaris and Rhizobium etli strains with different degrees in nodulation efficiency. This approach identified conserved and known microRNAs (miRNAs) differentially accumulated in Mesoamerican P. vulgaris roots in response to a highly efficient strain, to a less efficient one or to both strains.

2020-11-01 | GSE155414 | GEO

Characterization of the NifA-RpoN Regulon in Rhizobium etli CFN42 in symbiosis using whole genome transcript analysis

Project description:The NifA-RpoN complex is a master regulator of the nitrogen fixation genes in alpha-proteobacteria. Based on the complete Rhizobium etli genome sequence, we constructed the R. etli CFN42 oligonucleotide (70 mer) microarray, and utilized this tool to survey changes in gene expression in R. etli CFN42 wild type compared with NifA CFNX247 mutant strain in symbiosis with Phaseolus vulgaris. As expected, the genes associated with a NifA and RpoN binding sites were downregulated in the NifA mutant strain.

2010-05-15 | GSE20638 | GEO

Rhizobium etli CFN42 wild type transcriptional profiling was compared between free living and symbiosis conditions

Project description:Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule.

2014-02-03 | GSE21638 | GEO

Rhizobium etli CFN42 wild type transcriptional profiling was compared between free living and symbiosis conditions

2014-02-03 | E-GEOD-21638 | biostudies-arrayexpress

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

Regulation of small RNAs and corresponding targets in Nod factors-induced Phaseolus vulgaris root hair cells

Project description:A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.

2017-05-01 | GSE81176 | GEO

Effective symbiosis between Rhizobium etli and Phaseolus vulgaris requires the alarmone ppGpp.

Project description:The symbiotic interaction between Rhizobium etli and Phaseolus vulgaris, the common bean plant, ultimately results in the formation of nitrogen-fixing nodules. Many aspects of the intermediate and late stages of this interaction are still poorly understood. The R. etli relA gene was identified through a genome-wide screening for R. etli symbiotic mutants. RelA has a pivotal role in cellular physiology, as it catalyzes the synthesis of (p)ppGpp, which mediates the stringent response in bacteria. The synthesis of ppGpp was abolished in an R. etli relA mutant strain under conditions of amino acid starvation. Plants nodulated by an R. etli relA mutant had a strongly reduced nitrogen fixation activity (75% reduction). Also, at the microscopic level, bacteroid morphology was altered, with the size of relA mutant bacteroids being increased compared to that of wild-type bacteroids. The expression of the sigma(N)-dependent nitrogen fixation genes rpoN2 and iscN was considerably reduced in the relA mutant. In addition, the expression of the relA gene was negatively regulated by RpoN2, the symbiosis-specific sigma(N) copy of R. etli. Therefore, an autoregulatory loop controlling the expression of relA and rpoN2 seems operative in bacteroids. The production of long- and short-chain acyl-homoserine-lactones by the cinIR and raiIR systems was decreased in an R. etli relA mutant. Our results suggest that relA may play an important role in the regulation of gene expression in R. etli bacteroids and in the adaptation of bacteroid physiology.

| S-EPMC1196010 | biostudies-literature

sRNAs in Rhizobium etli differentially expressed during free-living and host-associated growth

Project description:89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions. In order to study expression in the free-living state, wild-type R. etli CFN42 was grown at 30ËC in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, 0.7 and 6 hours after reaching the maximum OD, representing early/late exponential and stationary phase, respectively. In order to study gene expression during host-associated growth, common bean plants (Phaseolus vulgaris cv. Limburgse vroege) were cultivated and inoculated as described previously. Nodules were harvested 2 and 3 weeks after inoculation and the bacteroids were purified by differential centrifugation.

2010-06-19 | E-GEOD-18580 | biostudies-arrayexpress

R. etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network

Project description:Abstract A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30% and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of coexpression of transcriptional regulators (TF´s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF´s, TRN´s were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF´s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.

2022-09-27 | PXD035204 | Pride

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing [degradome-seq]

Project description:Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. Conclusions: We provide here a set of new small RNAs, which contribute to the broader scene of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Degradome sequencing from Phaseolus vulgaris seedling

2015-09-01 | E-GEOD-67432 | biostudies-arrayexpress

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