Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide [P. aeruginosa]
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ABSTRACT:
PROVIDER: PRJNA791212 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17286800_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286800_2.fastq.gz | Fastqsanger.gz | |||
| SRR17286801_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286801_2.fastq.gz | Fastqsanger.gz | |||
| SRR17286802_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: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:Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics [E. coli]
| PRJNA791221 | ENA
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: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.
| S-EPMC9039886 | biostudies-literature
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:Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with a novel mode of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here we describe an alternative mode of action to affect the same process; allowing translation to proceed but causing co-translational aggregation of the nascent chain. We found a peptide that acts via this mechanism and is bactericidal against a wide range of pathogenic bacteria, including strains for which novel treatments are most urgently needed such as the ESKAPE pathogens, both in planktonic growth and in biofilms. Proteomics, transcriptomics and biochemical analyses of the inclusion bodies that form in bacteria upon peptide treatment reveal ribosomal proteins, mRNAs and their cognate nascent chains in amyloid-like structures assembled in polar inclusion bodies. The bacterial ssrA ribosome rescue pathway is activated but fails to prevent incorporation of hundreds of proteins into the inclusion bodies. Mechanistically, our results show that disrupting ribosomal quality control via co-translational aggregation constitutes a potent target mechanism for the development of broad-spectrum antibacterials.
2024-12-18 | GSE278706 | GEO
Project description:Infections associated with antimicrobial-resistant bacteria now represent a significant threat to human health using conventional therapy, necessitating the development of alternate and more effective antibacterial compounds. Silver nanoparticles (Ag NPs) have been proposed as potential antimicrobial agents to combat infections. A complete understanding of their antimicrobial activity is required before these molecules can be used in therapy. Lysozyme coated Ag NPs were synthesized and characterized by TEMEDS, XRD, UV-vis, FTIR spectroscopy, zeta potential, and oxidative potential assay. Biochemical assays and deep level transcriptional analysis using RNA sequencing were used to decipher how Ag NPs exert their antibacterial action against multi-drug resistant Klebsiella pneumoniae MGH78578. RNAseq data revealed that Ag NPs induced a triclosan-like bactericidal mechanism responsible for the inhibition of the type II fatty acid biosynthesis. Additionally, released AgC generated oxidative stress both extra and intracellularly in K. pneumoniae. The data showed that triclosan-like activity and oxidative stress cumulatively underpinned the antibacterial activity of Ag NPs. This result was confirmed by the analysis of the bactericidal effect of Ag NPs against the isogenic K. pneumoniae MGH78578 1soxS mutant, which exhibits a compromised oxidative stress response compared to the wild type. Silver nanoparticles induce a triclosan like antibacterial action mechanism in multi-drug resistant K. pneumoniae. This study extends our understanding of anti-Klebsiella mechanisms associated with exposure to Ag NPs. This allowed us to model how bacteria might develop resistance against silver nanoparticles, should the latter be used in therapy.
2021-01-31 | GSE151953 | GEO
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