Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules
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ABSTRACT:
PROVIDER: PRJNA479468 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7468250_1.fastq.gz | Fastqsanger.gz | |||
| SRR7468250_2.fastq.gz | Fastqsanger.gz | |||
| SRR7468251_1.fastq.gz | Fastqsanger.gz | |||
| SRR7468251_2.fastq.gz | Fastqsanger.gz | |||
| SRR7468252_1.fastq.gz | Fastqsanger.gz |
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Project description:Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, fragmentary information is available in regards to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2,055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including 8 Pi transporters (PTs), 8 proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway specifically involved in maintaining Pi homeostasis in nodules.
2018-11-20 | GSE116593 | GEO
Project description:Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, only fragmentary information is available in regard to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis in soybean nodules grown under P-sufficient (500 μM KH₂PO₄) and P-deficient (25 μM KH₂PO₄) conditions to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of (differentially expressed genes) DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including eight Pi transporters (PTs), eight genes coding proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway, are involved in maintaining Pi homeostasis in nodules.
| S-EPMC6213598 | biostudies-literature
Project description:Expression data from B. japonicum soybean root nodules including a nodulation time-course experiment with soybean nodules harvested at 10, 13, 21 and 31 dpi and transcriptome of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma 54. Two reference data sets were established using B. japonicum cells grown in PSY medium under either aerobic or micro-aerobic conditions. Keywords: genetic modification, time course, growth conditions
2007-07-14 | GSE8478 | GEO
Project description:Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt phosphate limitation condition. To know the underlying molecular mechanisms responsible for LP stress response. A label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate condition was performed.
2021-09-09 | PXD023343 | Pride
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:Metabolomics and transcriptomics of Bradyrhizobium diazoefficiens-induced root nodules Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection -time of flight mass spectrometry analysis the metabolome of i) nodules and roots from four different B. diazoefficiens host plants, ii) soybean nodules harvested at different time points during nodule development, and iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by transcriptomics data that was generated for the two mutant strains and were helpful to separate for some examples the respective bacterial and plant contributions to the metabolic profile. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.
2016-11-28 | GSE79811 | GEO
Project description:To dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodules from three plants were pooled with three biological replications, and total RNA was extracted.
2018-10-01 | GSE104582 | GEO
Project description:Global bottom-up proteomics analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Nine glycoproteins containing Lewis-a N-glycans, with 3 distinct Lewis-a epitopes (Hex:5 HexNAc:4 dHex:3 Pent:1, Hex:4 HexNAc:4 dHex:2 Pent:1, and Hex:4 HexNAc:3 dHex:2 Pent:1) were observed. Proteins purified from WT and nifH- infected soybean root nodules (five biological replicates each) were reduced using dithiothreitol, alkylated with iodoacetamide and trypsin digested followed by C18 SPE clean-up and LC-MS/MS analysis. Raw data files were processed using FragPipe v17.1, then output files 'combined_modified_peptide.tsv' and 'combined_protein.tsv' were used to identify glycopeptides and for global protein quantitation. These files, along with Excel files containing global quantitation analysis files for soybean nodule (Glycine max) and bacterial (Bradyrhizobium), are available in directory 'Quantification/MSFragger_results'. Glycopeptide data were also processed with PMI Byonic, and Excel file results are available in directory 'Quantification/PMI_Byonic_results'.
2022-01-31 | MSV000088754 | MassIVE
Project description:Proteins of B. japonicum expressed in soybean nodules
2010-04-29 | PRD000813 | Pride
Project description:Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate(Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated.Taken together, identification of differential phosphoproteins not only reveled complex regulatory pathways in soybean adaptation to Pi starvation through reversible protein phosphorylation.
2021-06-13 | PXD025771 | Pride