Ontology highlight
ABSTRACT:
PROVIDER: PRJNA514342 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8455560.fastq.gz | Fastqsanger.gz | |||
| SRR8455570.fastq.gz | Fastqsanger.gz | |||
| SRR8455561.fastq.gz | Fastqsanger.gz | |||
| SRR8455562.fastq.gz | Fastqsanger.gz | |||
| SRR8455563.fastq.gz | Fastqsanger.gz |
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Project description:Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. In this study, we analyzed the transcriptional profile of MI under acidic and oxidative stress conditions using RNA-seq. At the transcriptome level, 80 genes were shown [FC] ≥2.0 and p <0.05 under oxidative stress with 10 mM hydrogen peroxide. In detail, 77 genes were upregulated, while 3 genes were downregulated. Also, 878 genes were shown [FC] ≥2.0 and p <0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis revealed the activation of several pathways, including nitrogen and sulfur metabolism, under acidic stress conditions. On the contrary, oxidative stress conditions activated DNA replication and repair pathways. Our data demonstrate the activation of nitrogen and sulfur metabolism in MAC infection, which could be crucial for persistence and survival under stress conditions encountered within the host during infection. In conclusion, this study suggests the importance of stress responses in MAC pathogenesis and identifies potential therapeutic target pathways.
2024-02-21 | GSE244264 | GEO
Project description:Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. Journal of Bacteriology 188:7005-7015. Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends. Keywords: bacterial metabolism
2006-10-06 | GSE5256 | GEO
Project description:Bradyrhizobia are common members of soil microbiomes and known as N2-fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2O. Inoculation with compatible rhizobia is often needed for optimal N2-fixation, but the choice of inoculant may have consequences for N2O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2O. The N2O-reducing isolates had strong preference for N2O- over NO3--reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3- reductase) and Nos (N2O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3- reductase (Nar), reduced N2O and NO3- simultaneously. We propose that the control at the metabolic level, favoring N2O reduction over NO3- reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
2021-09-27 | PXD023200 | Pride
Project description:Unlike most cell types, many cancer cells survive at low extracellular pH (pHe), a chemical signature of tumors. Genes that facilitate survival under acid stress are therefore potential targets for cancer therapies. We performed a genome-wide CRISPR/Cas9 cell viability screen at physiological and acidic conditions to systematically identify gene knockouts associated with pH-related fitness defects in colorectal cancer cells. Knockouts of genes involved in oxidative phosphorylation (NDUFS1) and iron-sulfur cluster biogenesis (IBA57, NFU1) grew well at physiological pHe, but underwent profound cell death under acidic conditions. We identified several small-molecule inhibitors of mitochondrial metabolism that can kill cancer cells at low pHe only. Xenografts established from NDUFS1-/- cells grew considerably slower than their wild-type controls, but growth could be stimulated with systemic bicarbonate therapy which lessens the tumoral acid stress. These findings raise the possibility of therapeutically targeting mitochondrial metabolism in combination with acid stress as a cancer treatment option.
2022-02-26 | GSE195484 | GEO
Project description:In order to cause disease, the food- and water-borne pathogen Campylobacter jejuni must face the extreme acidity of the host stomach as well as cope with pH fluctuations in the intestine. In the present study, C. jejuni NCTC 11168 was grown under mild acidic conditions mimicking those encountered in the intestine. The resulting transcriptional profiles revealed how this bacterium fine-tunes gene expression in response to acid stress. This adaptation involves differential expression of respiratory pathways, induction of genes for phosphate transport and repression of energy generation and intermediary metabolism genes. Keywords: acid shock; dose response; transcriptional response to 3 mild-acidic pH growth conditions (pH6.5, pH 6.0 and pH5.0)
2008-01-21 | GSE9920 | GEO