Ontology highlight
ABSTRACT:
PROVIDER: PRJNA628805 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11621800.fastq.gz | Fastqsanger.gz | |||
| SRR11621801.fastq.gz | Fastqsanger.gz | |||
| SRR11621802.fastq.gz | Fastqsanger.gz | |||
| SRR11621762.fastq.gz | Fastqsanger.gz | |||
| SRR11621763.fastq.gz | Fastqsanger.gz |
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Project description:Sporadic Parkinson’s Disease (sPD) is a progressive neurodegenerative disorder caused by a combination of genetic and environmental factors, however, the etiology remains largely elusive. Here, we used human iPSCs from late onset sPD patients, which were cultivated in vitro for up to 60 passages and screened for known PD associated alterations. Following long-term in vitro cultivation, exclusively neural cells derived from sPD patients developed a reduced mitochondrial respiration and glucose consumption reflecting a sPD specific state of hypometabolism. Integrated analysis of transcriptome, proteome and non-targeted metabolome data identified the citric acid cycle as being the bottleneck in sPD metabolism. A 13C metabolic flux analysis further unraveled the α-ketoglutarate dehydrogenase complex as being central for a reduced flux through the citric acid cycle. This resulted in a substrate availability problem for the electron transport chain and thus a reduced mitochondrial ATP production. Notably, this alterations in basal cellular metabolism were introduced by altered SHH signal transduction due to dysfunctional primary cilia. Upon inhibiting the enhanced SHH signal transduction in sPD, glucose uptake and the activity of the α-ketoglutarate dehydrogenase complex could be restored. Thus, inhibiting overactive SHH signaling maybe a potential neuroprotective therapy for sPD.
2023-10-05 | PXD038399 | Pride
Project description:Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation. Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. Transcriptomic analysis showed that salt stress caused 333 genes to be upregulated and 1,765 to be downregulated. However, adding Spd during salt treatment significantly altered this pattern: 2,298 genes were upregulated and 844 were downregulated, which indicated Spd reverses some transcriptional changes caused by salt stress. KEGG pathway analysis suggested that Spd influenced key signaling pathways, including MAPK signaling, plant hormone signal transduction, and phenylalanine metabolism. Additionally, the bZIP transcription factor OsbZIP73 was upregulated after Spd treatment, which is confirmed by Western blot. Further insights into the interaction between OsbZIP73 and Spd were gained through fluorescence polarization experiments, showing that Spd enhances protein OsbZIP73's affinity for RNA. Functional enrichment analyses revealed that OsPYL1, OsSPARK1, and various SAUR family genes involved in Spd-affected pathways. The presence of G/A/C-box elements in these genes suggests they are potential targets for OsbZIP73. Conclusions: Our findings suggest a strategy of using spermidine as a chemical alleviator for salt stress and provide insights into the regulatory function of OsbZIP73 in mitigating salt stress in rice roots.
2024-08-01 | GSE189665 | GEO
Project description:Fruits of transgenic tomato (Solanum lycopersicum) plants engineered with ripening-induced, yeast S-adenosylmethionine decarboxylase (ySAMdc) gene, accumulate the higher polyamines spermidine (Spd) and spermine (Spm) and demonstrate ameliorated phytonutrient content, juice quality, and prolonged vine life. Enhanced nitrogen-carbon interactions were revealed by comprehensive Nuclear Magnetic Resonance (NMR) spectroscopy-based metabolite profiling of the transgenics, suggesting that Spd and Spm are perceived as nitrogenous metabolites by the fruit cells (Mattoo et al., 2006). The recent work by our colleagues identified the effects of Spd/Spm accumulation on various functional classes of tomato genes affected during ripening by probing 1522 ESTs on a custom-made array (Srivastava et al., 2007). In this study we monitored alterations of genome-wide transcriptional patterns in pericarp of Spd/Spm-accumulating tomatoes by means of direct comparison with azygous controls using DNA-microarray technology. Consistent with the ySAMdc expression pattern, very minor transcriptional alterations were detected in mature green developmental stage. For both breaker and red stages, large mutual and unique gene sets displayed altered levels of transcript. Ontological term analysis of up- and down-regulated transcript groups revealed processes in cell metabolism that are regulated by increased levels of Spd/Spm in ripening tomato fruits. These processes mainly involve carbohydrate and amino acids metabolism and protein synthesis. Additionally, transcript levels of representative genes encoding structural enzymes for related biosynthetic pathways show strong relationship to specific metabolites that were identified as regulated in Spd/Spm-accumulating transgenics.
2008-09-21 | GSE12338 | GEO
Project description:Fruits of transgenic tomato (Solanum lycopersicum) plants engineered with ripening-induced, yeast S-adenosylmethionine decarboxylase (ySAMdc) gene, accumulate the higher polyamines spermidine (Spd) and spermine (Spm) and demonstrate ameliorated phytonutrient content, juice quality, and prolonged vine life. Enhanced nitrogen-carbon interactions were revealed by comprehensive Nuclear Magnetic Resonance (NMR) spectroscopy-based metabolite profiling of the transgenics, suggesting that Spd and Spm are perceived as nitrogenous metabolites by the fruit cells (Mattoo et al., 2006). The recent work by our colleagues identified the effects of Spd/Spm accumulation on various functional classes of tomato genes affected during ripening by probing 1522 ESTs on a custom-made array (Srivastava et al., 2007). In this study we monitored alterations of genome-wide transcriptional patterns in pericarp of Spd/Spm-accumulating tomatoes by means of direct comparison with azygous controls using DNA-microarray technology. Consistent with the ySAMdc expression pattern, very minor transcriptional alterations were detected in mature green developmental stage. For both breaker and red stages, large mutual and unique gene sets displayed altered levels of transcript. Ontological term analysis of up- and down-regulated transcript groups revealed processes in cell metabolism that are regulated by increased levels of Spd/Spm in ripening tomato fruits. These processes mainly involve carbohydrate and amino acids metabolism and protein synthesis. Additionally, transcript levels of representative genes encoding structural enzymes for related biosynthetic pathways show strong relationship to specific metabolites that were identified as regulated in Spd/Spm-accumulating transgenics. Plants of both genotypes were grown in randomized blocks (3 blockes 8-10 plants each). At each of 3 developmental stages (mature green, breaker and pink-red) a single fruit was harvested from a randomly chosen plant of each genotype within each block. In each harvest different plants in each block were taken to represent each genotype. Following harvest, equal pericarp samples were cut from the equator region of each fruit. These samples were pooled according to genotype prior to RNA extraction, allowing equal representation of each block in the final sample. A total of 3 harvests taken from each genotype were eventually analyzed– each harvest representing a biological repeat.
2008-09-21 | E-GEOD-12338 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae (S.pneumoniae) is a Gram-positive bacterial pathogen that colonizes on the mucosal surfaces of the host's nasopharynx and upper respiratory tract and results in pneumonia. In order to survive and infect the host, S.pneumoniae must have obtain essential nutrients, such as transition metal ions . Our previous study had shown that the mRNA and protein levels of SPD-0090 are significantly upregulated in the ΔpiuA/ΔpiaA/ΔpitA triple mutant (three major iron transports), but its detailed biological function is unknown. In this study, we found that the knockout spd-0090 gene induced a delayed growth in the medium with different sugar sources. F urther iTRAQ quantitative proteomics studies revealed that SPD-0090 affects galactose metabolism and iron ion transport system. Then RT-qPCR and intracellular galactose content assays showed that SPD-0090 affects galactose uptake, leads to reduced galactose utilization. In addition, in vitro biochemical assays showed that SPD-0090 is a hemin transporter and affects iron uptake. Notably the knockout of spd-0090 resulted in an enhanced infection ability of S.pneumonaie to Our study reveals that the dual function of SPD-0090 plays an important role in the virulence of S.pneumoniae.
2022-06-01 | PXD030183 | Pride
Project description:Spermidine (SPD), a polyamine naturally present in living organisms, is known to prolong lifespan in animals. In this study, the role of SPD in melanogenesis were investigated and showed the possibility as a pigmenting agent. SPD treatment increased melanin production in melanocytes in a dose dependent manner. Computational analysis with RNA-sequencing data revealed the alteration of protein degradation by SPD treatment without changing the expressions of melanogenesis-related genes. Indeed, SPD treatment significantly increased the stabilities of tyrosinase-related protein (TRP)-1 and -2 while inhibiting ubiquitination, which was confirmed by treatment of proteasome inhibitor MG132. Inhibition of protein synthesis by cycloheximide (CHX) showed that SPD treatment increased the resistance of TRP-1 and TRP-2 to protein degradation. To identify the proteins involved in SPD transportation in melanocytes, the expression of several solute carrier (SLC) membrane transporters was assessed and, among 27 transporter genes, SLC3A2, SLC7A1, SLC18B1, and SLC22A18 were highly expressed, implying they are putative SPD transporters in melanocytes. Furthermore, SLC7A1 and SLC22A18 were downregulated by SPD treatment, indicating their active involvement in polyamine homeostasis. Finally, we applied SPD to a human skin equivalent and observed elevated melanin production. Our results identify SPD as a potential natural product to alleviate hypopigmentation.
2022-07-25 | GSE209538 | GEO
Project description:In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to methionine. Transcriptome comparison of the S. pneumoniae D39 wild-type grown in chemically defined medium (CDM) with 0mM to 10mM methionine revealed the elevated expression of various genes/operons involved in methionine synthesis and transport (fhs, folD, gshT, metA, metB, metEF, metQ, tcyB, spd-0150, spd-0431, and spd-0618). We further demonstrated by β-galactosidase assays and quantitative RT-PCR studies that the transcriptional regulator, CmhR (SPD-0588) acts as a transcriptional activator of the fhs, folD, metB, metEF, metQ, and spd-0431 genes. We identified a putative regulatory site of CmhR in the promoter region of CmhR regulated genes and this CmhR site was further confirmed by promoter mutational experiments.
2016-10-15 | GSE88766 | GEO
Project description:To uncover the mechanism of SPD-induced autophagy in FGSCs, we used RNA sequencing technology to compare the mRNA expression differences between the control groups and the SPD treated groups. FGSCs mRNA profiles of the control groups and the SPD treated groups were generated by deep sequencing, in two replicates. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina HiSeq 2500 platform was used for RNA sequencing. The quality of RNA-seq reads was examined using FastQC.
2024-01-05 | GSE164387 | GEO