Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21583700_1.fastq.gz | Fastqsanger.gz | |||
| SRR21583700_2.fastq.gz | Fastqsanger.gz | |||
| SRR21583701_1.fastq.gz | Fastqsanger.gz | |||
| SRR21583701_2.fastq.gz | Fastqsanger.gz | |||
| SRR21583702_1.fastq.gz | Fastqsanger.gz |
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Project description:Antibiotic resistance (AMR) in aquatic bacteria affecting aquaculture has been a growing concern given the potential for mixing of bacterial populations in the aquatic environment and exposure to different pharmaceuticals from drugs used in aquaculture, as well as wastewater effluent and agricultural run-off. To better understand the mechanism for AMR in a common aquatic fish pathogen exposed to low dose antibiotics we monitored the genetic changes, as well as gene expression, in Aeromonas hydrophila as the bacteria was exposed to incremental doses of oxytetracycline (OTC), a commonly used drug in aquaculture. We were able to render all three isolates of our original A. hydrophila resistant to therapeutic levels of OTC (i.e. ≥100ppm). The relatively quick phenotypic adaptation (often less than 3 days) to different OTC concentrations was very similar across our replicates. Our whole genome sequencing data and transcriptome results suggested several genes underwent point mutations across all replicates. Further differential gene expression was observed and likely impacted several pathways which may explain the progressive resistance to OTC associated with incremental exposure to the drug. The specific mutations consistently identified in isolates exposed to OTC were on AHA_ 2785 (associated with an outer membrane protein), AHA_2910 (involved in the efflux pump mechanism), and AHA_0308 (associated with the small ribosomal subunit protein S10). The pathways involved in the differential gene expression included efflux- pump mechanisms, outer membrane proteins, and ribosomal protein OTC target. Our findings support the notion that AMR can occur via genetic regulation of several intrinsic mechanisms within a bacterial population. This finding could have implications in aquaculture where bacteria such as A. hydrophila can be exposed to varying levels of antibiotics during in-feed treatments.
2025-10-01 | GSE290492 | GEO
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2023-05-16 | GSE232318 | GEO
Project description:Ammonia production via glutamate dehydrogenase is inhibited by SIRT4, a sirtuin that displays both amidase and non-amidase activities. The processes underlying the regulation of ammonia removal by amino acids remain unclear. Here, we report that SIRT4 acts as a decarbamylase that responds to amino acid sufficiency and regulates ammonia removal. Amino acids promote lysine 307 carbamylation (OTCCP-K307) of ornithine transcarbamylase (OTC), which activates OTC and the urea cycle. Proteomic and interactome screening identified OTC as a substrate of SIRT4. SIRT4 decarbamylates OTCCP-K307 and inactivates OTC in a NAD+-dependent manner. SIRT4 expression was transcriptionally upregulated by the amino acid insufficiency-activated GCN2–eIF2a–ATF4 axis. SIRT4 knockout in cultured cells caused higher OTCCP-K307 levels, activated OTC, elevated urea cycle intermediates, and urea production via amino acid catabolism. Sirt4 ablation decreased mouse blood ammonia levels and ameliorated CCl4-induced hepatic encephalopathy phenotypes. We reveal that SIRT4 safeguards cellular ammonia toxicity during amino acid catabolism.
2023-03-29 | PXD037101 | Pride
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2024-01-26 | PXD042182 | Pride
Project description:Global warming is strongly affecting the Maritime Antarctica climate and the consequent melting of perennial snow and ice covers resulted in increased colonization by plants. Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Antarctic Peninsula and understanding how the plant is responding to global warming is a new challenging target for modern cell physiology. To this aim, we performed differential proteomic analysis on C. quitensis plants grown in natural conditions compared to plants grown for one year inside Open Top Chambers (OTCs) which determine an increase of about 4 °C at midday, mimicking the effect of global warming. A thorough analysis of the up- and down-regulated proteins highlighted an extensive metabolism reprogramming leading to the hypothesis that (i) photorespiration could play an important role in reducing ROS-mediated photodamage improving OTC plants protection against photoinhibition; (ii) OTC plants activate stronger antioxidant defenses as confirmed by enzymatic activity and TBARS content measurement; (iii) the deposition of cell wall components is impaired in OTC plants due to the down-regulation of many enzymes involved in their biosyn-thesis; (iv) OTC plants could suffer of a reduced freezing tolerance due to lower concentration of soluble sugars acting as osmoprotectants.
2021-07-26 | PXD027038 | Pride