Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics [E. coli]
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ABSTRACT:
PROVIDER: PRJNA791221 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17286830_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286830_2.fastq.gz | Fastqsanger.gz | |||
| SRR17286831_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286831_2.fastq.gz | Fastqsanger.gz | |||
| SRR17286832_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide
| PRJNA791217 | ENA
Project description:Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide [P. aeruginosa]
| PRJNA791212 | ENA
Project description:Previously, we found that ASP-ASP-ASP-TYR (DDDY) from Dendrobium aphyllum has a minimum inhibitory concentration of 36.15 mg/mL against Pseudomonas aeruginosa. Here, we explored the antibacterial mechanism of DDDY and its potential preservation applications. Metabolomic and transcriptomic analyses revealed that DDDY mainly affects genes involved in P. aeruginosa membrane transport and amino acid metabolism pathways. Molecular dynamics simulation revealed that DDDY had a stronger effect on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine phospholipid membranes than on 1-palmitoyl-2-oleoyl-lecithin or 1-palmitoyl-2-oleoyl phosphatidylglycerol membranes, with high DDDY concentrations displaying stronger efficacy on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine. Mechanistically, the N-terminal of DDDY first bound to the phospholipid head group, while its C-terminal amino acid residue bound the hydrophobic tail, thereby creating a gap in the membrane when the phospholipids were clustered by hydrogen bonding. Finally, DDDY inhibited the growth of food microorganisms inoculated onto chestnut kernels, suggesting that DDDY is a promising antibacterial agent against multidrug-resistant gram-negative bacteria. Inhibitory effect of ASP-ASP-ASP-TYR (DDDY) from Dendrobium on Pseudomonas aeruginosa
2021-12-24 | GSE192340 | GEO
Project description:In this study, the mechanism of action of the small molecular peptide (DYDD) exhibiting antibacterial properties the application of the peptide in the field of food preservation have been presented. Metabolomics and transcriptomic techniques were used to analyze the metabolic effects of DYDD on E. coli. The differential metabolite screening and cluster analysis techniques were used for analyzing the data. It was found that DYDD could up-regulate 44 metabolites, down-regulate 105 metabolites and DYDD primarily affected 35 metabolic pathways in E. coli. Combined with transcriptome analysis, DYDD primarily influenced the metabolic pathways of E. coli by regulating the genes participating in the amino acid metabolic pathways and sulfur metabolic pathways. Then, the effects of DYDD on POPC-, POPE-, and POPG-based membranes were analyzed using the molecular dynamics simulation. The results showed that DYDD had the strongest binding with Pope membrane, and the insertion of DYDD not only led to the disorder of phospholipid head groups, but also increased the surface area and permeability of the membrane. Finally, DYDD was applied to chestnut kernel infected by E. coli. The results showed that DYDD had good antibacterial effect, could delay the decay and browning of chestnut kernel, and had fresh-keeping effect.
2021-12-24 | GSE192346 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-12-24 | GSE192347 | GEO
Project description:Proteogenic dipeptides are not only intermediates of proteolysis but also an emerging class of small molecule regulators, with diverse and specific functions. We have recently reported a novel in vitro interaction between the dipeptide Tyr-Asp and the Arabidopsis glycolytic enzyme glyceraldehyde 3- phosphate dehydrogenase (GAPDH). To understand the functional significance of Tyr-Asp/GAPDH binding, we examined the effect produced on the enzymatic activity. Results demonstrate that low to mid micro-molar concentrations of Tyr-Asp, but none of the other tested dipeptides, inhibit GAPDH activity both in vitro and in planta. Inhibition of the GAPDH activity was associated with a shift of the flux from glycolysis towards the pentose phosphate pathway and an increase in the NADPH/NADP+ ratio, a known response to cope with oxidative stress. In addition to GAPDH, the Tyr-Asp protein interactome comprised further stress-related proteins, including multiple chaperones. In line with the molecular data, Tyr-Asp supplementation improved growth performance of both Arabidopsis and tobacco seedlings subjected to oxidative stress conditions. By contrast, no such improvement was measured, neither for the free amino acids nor the other tested dipeptides, demonstrating that the action of Tyr-Asp is specific and independent of the degradation of Tyr-Asp to the constituent amino acids. Finally, inhibition of Arabidopsis phosphoenolpyruvate carboxykinase activity reveals a multisite regulation of glycolytic/gluconeogenic flux by dipeptides. In summary, our data suggest proteogenic dipeptides as a novel class of small-molecule regulators operating at the nexus of stress, protein degradation and metabolism.
2021-05-10 | PXD019332 | Pride
Project description:ASP induces the expression of early auxin response genes by activates auxin response, and affects responses to other signals associated with the auxin signaling pathway. We used microarrays to detail the effect of ASP on Arabidopsis global gene expression, and identified distinct classes of up-regulated or down genes during this process
2019-07-24 | GSE134746 | GEO
Project description:We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions. Treatment with ASP or alpha-MSH was performed for 3 hr, 1 day, 2 days, 3 days and 4 days, in triplicate. Each biological replicate was submitted to a direct hybridization (treated/untreated samples) after coupling with Cy5 or Cy3 and to a reverse dye-swap, leading to 2 replicated hybridization for each biological sample. A total of 6 hybridized arrays was used for each of the 5 time points, for each drug.
2009-02-02 | E-GEOD-14089 | biostudies-arrayexpress
Project description:The human pathogenic fungus Aspergillus fumigatus is readily eradicated by the innate immunity of immunocompetent human hosts, but can cause severe infections, such as invasive aspergillosis (IA), in immunocompromised individuals. During infection, the fungal redox homeostasis can be challenged by reactive oxygen (ROS) species, either derived from the oxidative burst of innate immune cells or the action of antifungal drugs. The peroxiredoxin Asp f3 was found to be essential to cause IA in mice, but how Asp f3 integrates to fungal redox homeostasis remains unknown. Here, we show that in vivo, Asp f3 acts as a sensor for ROS. While global transcription in fungal hyphae under minimal growth conditions was fully independent of Asp f3, a robust induction of the oxidative stress response required the presence of the peroxiredoxin. Hyphae devoid of Aspf 3 failed to activate several redox active genes, like members of the gliotoxin biosynthesis gene cluster and integral members of the Afyap1 regulon, the central activator of the ROS defence machinery in fungi. Upon deletion of the asp f3 gene Afyap1 displayed significantly reduced nuclear localization during ROS exposure, indicating that Asp f3 can act as an intracellular redox sensor for several target proteins
2021-06-03 | GSE173349 | GEO
Project description:We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions.
2009-02-03 | GSE14089 | GEO