GNPS Metabolomics Workbench ST001634 - GNPS A combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Glycine Max
SUBMITTER: 
Justin Renaud
PROVIDER: MSV000086897 | GNPS | Wed Feb 17 20:10:00 GMT 2021
REPOSITORIES: GNPS
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Project description:This study identified how the GmMYB176 protein complex affects the metabolome of soybean hairy roots using non-targeted high resolution mass spectrometry.
2020-12-17 | ST001634 | MetabolomicsWorkbench
Project description:GmMYB176, an R1 MYB transcription factor regulates isoflavonoid biosynthesis in soybean. In the current experiment, GmMYB176 was silenced (GmMYB176-Si) or overexpressed (GmMYB176-OE) in soybean hairy roots and their effect on transcriptome was studied. RNA-Seq analyses of GmMYB176-Si and GmMYB176-OE along with control non-transformed soybean hairy roots revealed that alteration of gene expression of GmMYB176 affects gene regulation of hundreds of genes in soybean.
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Project description:Increased root H+ secretion is known as a strategy of plant adaption to low phosphorus (P) stress by enhancing mobilization of sparingly soluble P-sources. However, it remains fragmentarywhether enhanced H+ exudation could reconstruct the plant rhizosphere microbial community under low P stress. The present study found that P deficiency led to enhanced H+ exudation from soybean (Glycine max) roots. Three out of all eleven soybean H+-pyrophosphatases (GmVP) geneswere up-regulated by Pi starvation in soybean roots. Among them, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-green fluorescent protein chimera in tobacco (Nicotiana tabacum) leaves, and functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that GmVP2 encoded a plasma membrane transporter that mediated H+ exudation. Meanwhile, GmVP2-overexpression in Arabidopsis thaliana resulted in enhanced root H+ exudation, promoted plant growth, and improved sparingly soluble Ca-P utilization. Overexpression of GmVP2 also changed the rhizospheric microbial community structures, as reflected by a preferential accumulation of acidobacteria in the rhizosphere soils. These results suggested that GmVP2 mediated Pi-starvation responsive H+ exudation,which is not only involved in plant growth and mobilization of sparingly soluble P-sources, but also affects microbial community structures in soils.
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Project description:Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.
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Project description:The regulatory effects of uneven phosphorus supplies on phosphorus transport in soybean roots is still unclear. To further analyze the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots and the effects of uneven phosphorus application on the physiological mechanism of phosphorus transport in soybean roots, dual-root soybean plants were prepared via grafting, and a sand culture experiment was performed.
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Project description:Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
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Project description:Soybean is an important economic crop for human diet, animal feeds and biodiesel due to high protein and oil content. Its productivity is significantly hampered by salt stress, which impairs plant growth and development by affecting gene expression, in part, through epigenetic modification of chromatin status. However, little is known about epigenetic regulation of stress response in soybean roots. Here, we used RNA-seq and ChIP-seq technologies to study the dynamics of genome-wide transcription and histone methylation patterns in soybean roots under salt stress. 8798 soybean genes changed their expression under salt stress treatment. Whole-genome ChIP-seq study of an epigenetic repressive mark, histone H3 lysine 27 trimethylation (H3K27me3), revealed the changes in H3K27me3 deposition during the response to salt stress. Unexpectedly, we found that most of the inactivation of genes under salt stress is strongly correlated with the de novo establishment of H3K27me3 in various parts of the promoter or coding regions where there is no H3K27me3 in control plants. In addition, the soybean histone modifiers were identified which may contribute to de novo histone methylation and gene silencing under salt stress. Thus, dynamic chromatin regulation, switch between active and inactive modes, occur at target loci in order to respond to salt stress in soybean. Our analysis demonstrates histone methylation modifications are correlated with the activation or inactivation of salt-inducible genes in soybean roots.
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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.
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