RNA-Sequencing of spinach tissues with contrasting oxalate contents
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA611735 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11280525_1.fastq.gz | Fastqsanger.gz | |||
| SRR11280525_2.fastq.gz | Fastqsanger.gz | |||
| SRR11280526_1.fastq.gz | Fastqsanger.gz | |||
| SRR11280526_2.fastq.gz | Fastqsanger.gz | |||
| SRR11280527_1.fastq.gz | Fastqsanger.gz |
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2020-06-24 | GSE153070 | GEO
Project description:Elevated temperature limits plant growth and reproduction and poses a growing threat to agriculture. Plant heat stress response is highly conserved and fine-tuned in multiple pathways. Spinach (Spinacia oleracea L.) is a cold tolerant but heat sensitive green leafy vegetable. In this study, heat adaptation mechanisms in spinach sibling inbred heat-tolerant line Sp75 were investigated using physiology, proteomics, and phosphoproteomics approaches. The abundance patterns of 911 heat stress-responsive proteins, and phosphorylation level changes of 48 phosphopeptides representing 45 phosphoproteins indicated that heat induced calcium-mediated signaling, ROS homeostasis, endomembrane trafficking, and cross-membrane transport pathways, as well as > 15 transcription regulation factors. Although photosynthesis was inhibited, diverse primary and secondary metabolisms were employed for enhancing thermotolerance, such as glycolysis, pentose phosphate pathway, amino acid metabolism, fatty acid metabolism, nucleotide metabolism, vitamin metabolism, and isoprenoid biosynthesis. These data constitutes a heat stress-responsive metabolic atlas in spinach, which will springboard further investigation into the sophisticated molecular mechanism of plant heat adaptation and inform spinach molecular breeding initiatives.
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Project description:Metabolic dysfunction-associated steatohepatitis (MASH) is on the rise, and with limited pharmacological therapy available, identification of new metabolic targets is urgently needed. Oxalate is a terminal metabolite produced from glyoxylate by lactate dehydrogenase (LDHA). The liver-specific alanine-glyoxylate aminotransferase (AGXT) detoxifies glyoxylate, preventing oxalate accumulation. We report that AGXT is suppressed and LDHA is activated in livers from patients and mice with MASH, leading to oxalate overproduction. In turn, oxalate promotes steatosis in hepatocytes by inhibiting peroxisome proliferator activated receptor-alpha (PPARα) transcription and fatty acid β-oxidation (FAO), and induces monocyte chemotaxis via C-C motif chemokine ligand 2. In male mice with diet-induced MASH, blocking oxalate overproduction through hepatocyte-specific AGXT overexpression or pharmacological inhibition of LDHA potently lower steatosis, inflammation, and fibrosis by inducing PPARα-driven FAO, and suppressing monocyte chemotaxis, nuclear factor-kappaB and transforming growth factor-beta targets. These findings highlight hepatic oxalate overproduction as a new target for the treatment of MASH.
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Project description:Purpose: To examine the gene expression within the spinach root tissues as a response to exposure to nanoparticles. Methods: Sequenced reads were processed using CLC Genomics Workbench 7.0. The reads were trimmed based on quality, length and ambiguity. Resulting reads were assembled into transcript assemblies. Sequence reads were mapped back to the constructed transcriptome. TAs were BLAST searched against a local blast database of coding sequences of Arabidopsis thaliana. Statistical analysis was performed using Baggerley’s test. Transcript assemblies were tested for gene enrichment using GO annotations and the functional categories were determined. MapMan was used to visualize gene expression data of TAs and study the biological pathways. Results: De novo assembly of the trimmed reads yielded 147,733 Transcript Assemblies (TA) with an average length of 645 bp. Largest TA was 16,379 bp. Approximately 89% of the quality trimmed reads from the different samples mapped successfully to the assembly reference. Gene expression data for spinach TAs homologous to Arabidopsis genes show upregulation of protein degradation pathways in the nano-ZnO treatment compared to the non-nanoZnO, this upregulation is coupled with a down regulation of the genes in the protein synthesis pathways crucial role in the spinach plant responses to ZnO nanoparticle exposure. Genes associated (REDOX, signaling and transcription factors) with responses to stresses (both abiotic and biotic) were upregulated upon exposure to ZnO nanoparticles. Additionally genes in biosynthesis pathways of jasmonate and gibberellins genes were up-regulated upon exposure to ZnO nanoparticles in spinach. Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense.
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