scholarly journals Identification of miRNAs and their corresponding mRNA targets from chickpea nodules and functional characterization of candidate miRNAs by overexpression in chickpea roots

2020 ◽  
Author(s):  
Manish Tiwari ◽  
Baljinder Singh ◽  
Manisha Yadav ◽  
Vimal Pandey ◽  
Sabhyata Bhatia
Keyword(s):  
Nitrogen Fixation ◽  
Expression Profiling ◽  
Mirna Target ◽  
Bacterial Colonization ◽  
Root Nodules ◽  
Functional Characterization ◽  
List Type ◽  
Symbiotic Associations ◽  
Mrna Targets ◽  
Bacterial Small Rna

SummaryLegumes developed symbiotic associations with rhizobia to meet its nitrogen requirement. The nitrogen fixation takes place in root nodules which involves bacterial colonization, organogenesis and nitrogen fixation.One microRNA and four parallel analysis of RNA ends (PARE) libraries were sequenced to unravel the miRNA mediated regulation of symbiosis in chickpea.Sequencing of microRNA library identified a set of 91 miRNAs comprising of 84 conserved and 7 novel miRNAs. Additionally, PARE library analysis revealed 564 genes being targeted by 85 miRNAs.Phylogenetic analysis of the precursor sequences of the 91 miRNAs clearly indicated a clustering of two distinct miRNAs in the same clade representing a close ancestral precursor.Further, biogenesis of miRNAs was predicted using the miRNAs identified from different legume genomes.The miRNA reads from the nodule library were also mapped onto bacterial genomes from which bacterial small RNA were predicted.The antagonistic expression of some of the miRNA-target pairs was investigated and the negative co-related expression profiling proved the validity of the libraries and the miRNA-target pairs. Four miRNAs were selected based on the antagonistic expression profiling and were ectopically expressed in chickpea roots by hairy root transformation.The overexpression lines showed significant change in nodule numbers. The target of miR171f (NRK), miR394 (HP) and miR1509 (AK) are novel ones being reported for the first time. This analysis opens a wide arena for investigation of the novel miRNAs and target pairs, polycistronic miRNAs and the bacterial derived smRNAs predicted in this study.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

scholarly journals Mutation in the ntrR Gene, a Member of the vap Gene Family, Increases the Symbiotic Efficiency of Sinorhizobium meliloti

2001 ◽  
Vol 14 (7) ◽  
pp. 887-894 ◽  
Author(s):  
Boglárka Oláh ◽  
Erno Kiss ◽  
Zoltán Györgypál ◽  
Judit Borzi ◽  
Gyöngyi Cinege ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Pathogenic Bacteria ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Nifh Gene ◽  
Dry Weight ◽  
Nodule Occupancy ◽  
Gene Encoding ◽  
Symbiotic Efficiency ◽  
Host Interactions

In specific plant organs, namely the root nodules of alfalfa, fixed nitrogen (ammonia) produced by the symbiotic partner Sinorhizobium meliloti supports the growth of the host plant in nitrogen-depleted environment. Here, we report that a derivative of S. meliloti carrying a mutation in the chromosomal ntrR gene induced nodules with enhanced nitrogen fixation capacity, resulting in an increased dry weight and nitrogen content of alfalfa. The efficient nitrogen fixation is a result of the higher expression level of the nifH gene, encoding one of the subunits of the nitrogenase enzyme, and nifA, the transcriptional regulator of the nif operon. The ntrR gene, controlled negatively by its own product and positively by the symbiotic regulator syrM, is expressed in the same zone of nodules as the nif genes. As a result of the nitrogen-tolerant phenotype of the strain, the beneficial effect of the mutation on efficiency is not abolished in the presence of the exogenous nitrogen source. The ntrR mutant is highly competitive in nodule occupancy compared with the wild-type strain. Sequence analysis of the mutant region revealed a new cluster of genes, termed the “ntrPR operon,” which is highly homologous to a group of vap-related genes of various pathogenic bacteria that are presumably implicated in bacterium-host interactions. On the basis of its favorable properties, the strain is a good candidate for future agricultural utilization.

scholarly journals NITROGEN FIXATION BY EXCISED SOY BEAN ROOT NODULES

1954 ◽  
Vol 208 (1) ◽  
pp. 29-39
Author(s):  
M.H. Aprison ◽  
Wayne E. Magee ◽  
R.H. Burris
Keyword(s):  
Nitrogen Fixation ◽  
Root Nodules ◽  
Bean Root

scholarly journals Mammary Fat of Breast Cancer: Gene Expression Profiling and Functional Characterization

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e109742 ◽  
Author(s):  
Fengliang Wang ◽  
Sheng Gao ◽  
Fei Chen ◽  
Ziyi Fu ◽  
Hong Yin ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Functional Characterization ◽  
Cancer Gene ◽  
Breast Cancer Gene

scholarly journals Multimodal Spectroscopic Imaging of Pea Root Nodules to Assess the Nitrogen Fixation in the Presence of Biofertilizer Based on Nod-Factors

2021 ◽  
Vol 22 (23) ◽  
pp. 12991
Author(s):  
Katarzyna Susniak ◽  
Mikolaj Krysa ◽  
Dominika Kidaj ◽  
Monika Szymanska-Chargot ◽  
Iwona Komaniecka ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Mass Spectrometry Imaging ◽  
Root Nodules ◽  
Spectroscopic Imaging ◽  
Ionization Mass ◽  
Nod Factors ◽  
Pea Root ◽  
Ft Ir ◽  
Ir And Raman ◽  
Apparent Distribution

Multimodal spectroscopic imaging methods such as Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI), Fourier Transform Infrared spectroscopy (FT-IR) and Raman spectroscopy were used to monitor the changes in distribution and to determine semi quantitatively selected metabolites involved in nitrogen fixation in pea root nodules. These approaches were used to evaluate the effectiveness of nitrogen fixation by pea plants treated with biofertilizer preparations containing Nod factors. To assess the effectiveness of biofertilizer, the fresh and dry masses of plants were determined. The biofertilizer was shown to be effective in enhancing the growth of the pea plants. In case of metabolic changes, the biofertilizer caused a change in the apparent distribution of the leghaemoglobin from the edges of the nodule to its centre (the active zone of nodule). Moreover, the enhanced nitrogen fixation and presumably the accelerated maturation form of the nodules were observed with the use of a biofertilizer.

Morphological and biochemical changes in peanut nodules during photosynthate stress

1992 ◽  
Vol 38 (6) ◽  
pp. 526-533 ◽  
Author(s):  
A. B. M. Siddique ◽  
A. K. Bal
Keyword(s):  
Nitrogen Fixation ◽  
Root Nodules ◽  
Ultrastructural Level ◽  
Malate Synthase ◽  
Morphological Evidence ◽  
Lipid Bodies ◽  
Biochemical Status ◽  
Short Period ◽  
Infected Cells ◽  
Ultrastructural Damage

Nitrogen fixation in legume root nodules is believed to be supported by the supply of photosynthate of the current photoperiod. However, in peanut nodules, prolonged periods of darkness or detopping do not disrupt nitrogen fixation for at least 48 h. During this period, nodule oleosomes (lipid bodies) have been shown to decrease in number within the infected cells, and it has been suggested that lipids from oleosomes are mobilized to maintain the energy and carbon requirements of the nitrogen-fixing nodules. We present morphological evidence, at the ultrastructural level, for the utilization of oleosomes during photosynthate stress. The biochemical status of the nodule has also been assessed and correlated with ultrastructure. For comparison cowpea nodules were used that totally lacked oleosomes. In peanut nodules leghemoglobin and total protein remained unchanged along with integrated ultrastructure on nodule cells for 48 h, whereas in cowpea a decline in proteins with ultrastructural damage became apparent within a very short period of photosynthate stress. In peanut nodules empty or partially empty oleosomes were taken as evidence for their utilization during the stress period. Key words: N2 fixation, photosynthate stress, lipid bodies, catalase, malate synthase, peanut nodule, β-oxidation.

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