EBESD8
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REPOSITORIES: ENA
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Project description:Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a persistent nitramine explosive with long-lasting properties. Rhodococcus sp. strain DN22 has been discovered as one of the microorganisms capable of RDX degradation. Despite respectable studies on Rhodococcus sp. strain DN22, the proteins participating in RDX degradation (Oxidoreductase and Cytochrome P450) in the strain remain to be fragments. In this study, complete genome of Rhodococcus sp. strain DN22 was sequenced and analyzed, and the entire sequences of the two genes encoding Oxidoreductase and Cytochrome P450 in Rhodococcus sp. strain DN22 were predicted, which were validated through proteomic data. Besides, despite the identification of certain chemical substances as proposed characterized degradation intermediates of RDX, few studies have investigated the physiological changes and metabolic pathways occurring within Rhodococcus sp. cells when treated with RDX, particularly through the use of mass spectrometry-based omics. Hence, proteomics and metabolomics of Rhodococcus sp. strain DN22 were performed and analyzed with the presence or absence of RDX in the medium. A total of 3186 protein groups were identified and quantified between the two groups, with 117 proteins being significantly differentially expressed proteins. A total of 1056 metabolites were identified after merging positive and negative ion modes, among which 131 metabolites were significantly differential. Through the combined analysis of differential proteomics and metabolomics, several KEGG pathways, including two-component system, ABC transporters, alanine, aspartate and glutamate metabolism, arginine biosynthesis, purine metabolism, nitrogen metabolism, and phosphotransferase system (PTS) were found to be significantly enriched. We expect that our investigation will expand the acquaintance of Rhodococcus sp. strain DN22, and the knowledge of microbial degradation.
2024-05-22 | PXD044565 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE5268: Effects of biphenyl on Rhodococcus sp. RHA1 GSE5269: Effects of ethylbenzene on Rhodococcus sp. RHA1 GSE5270: Effects of benzoate on Rhodococcus sp. RHA1 Refer to individual Series
2010-07-01 | E-GEOD-5280 | biostudies-arrayexpress
Project description:Purpose: find testosterone/17 beta-estradiol degrading genes in strain Comamonas testosteroni JLU460ET
2021-09-17 | GSE184154 | GEO
Project description:ChIP followed by deep sequencing was performed with antibodies to ERalpha in U2OS-ERalpha cells treated with 17beta-estradiol.
2011-05-03 | GSE28918 | GEO
Project description:three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures Keywords: growth substrate
2007-11-01 | GSE8480 | GEO
Project description:The genus Rhodococcus comprises numerous strains recognized for pollutant degradation, secondary metabolite production including biosurfactant, lignin breakdown, or utilization of volatile organic compounds. Often gene redundancies and evolution of alternative pathways are attributed to such characteristics. Rhodococcus opacus 1CP initially isolated as a chlorophenol degrading strain was found to be a model organism comprising several such features. In this study, we analyzed the genome and transcriptome and demonstrated that the strain 1CP undergo three different routes of ortho, meta, and side chain attack in degrading aromatic compounds. The wild type strain, single or double knock-out mutant of phenol hydroxylases, well compensated the loss and chooses the classical ortho-route to attack substituted phenols, while the triple knock-out mutant takes the meta-pathway to act on p-cresol indicating that this pathway serves as a reserve in strain 1CP. Growth of 1CP in phenol, p-cresol and styrene induces several gene clusters that are associated in lignin metabolization. Catechol, protocatechuate, and phenylacetic acid are major key intermediates that are funneled into central pathways which enable the strain 1CP to degrade acetophenone, benzoate, phenol, 2-phenylethanol, and styrene. Strain 1CP has an alternative option with the modified ortho-cleavage pathway which enables it to degrade 2-chlorophenol. Interestingly, in almost all cases, redundant genes were identified, but only in minor cases as phenol hydroxylases, they were found to be active and simultaneously involved in metabolic activities. The transcriptome and kinetic data showed that the redundant styrene-oxide isomerase is upregulated and involved in styrene degradation.
2026-03-27 | GSE294731 | GEO
Project description:We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
2023-09-12 | GSE242785 | GEO
Project description:We isolated an efficient tetracycline degrading strain Sphingobacterium sp. WM1. To investigate gene expression patterns during tetracycline degradation by strain WM1, we conducted a comparative transcriptomic analysis using cultures of strain WM1 with and without tetracycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Sphingobacterium sp. WM1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.
2023-09-21 | GSE234909 | GEO
Project description:PURPOSE: The hypothesis tested in the study was that the effect of estrogen and progesterone on the lacrimal gland is mediated through specific receptors and that hormonal effects involve the regulation of gene expression and protein synthesis. METHODS: Lacrimal glands were collected from young adult, ovariectomized mice, that were treated with 17beta-estradiol, progesterone, 17beta-estradiol plus progesterone or vehicle for 2 weeks. Glands were pooled according to treatment, processed for the isolation of RNA, and evaluated for differentially expressed mRNAs by using gene microarrays. Bioarray data were analyzed with sophisticated bioinformatics and statistical programs. The expression of selected genes was verified by using gene chips and quantitative real-time PCR methods. RESULTS: The results demonstrate that 17beta-estradiol, progesterone, or both hormones together significantly influences the expression of hundreds of genes in the mouse lacrimal gland. Sex steroid treatment led to numerous alterations in gene activities related to transcriptional control, cell growth and/or maintenance, cell communication, signal transduction, enzyme catalysis, immune expression, and the binding and metabolism of nucleic acids and proteins. A number of the 17beta-estradiol, progesterone or 17beta-estradiol plus progesterone effects on gene expression were similar, but most were unique to each treatment. Of particular interest was the finding that these hormones seem to contribute little to the known sex-related differences in gene expression of the lacrimal gland. CONCLUSIONS: These results support the hypothesis that estrogen's and progesterone's action on the lacrimal gland involves the regulation of numerous genes. However, these hormone effects do not appear to represent a major factor underlying the sexual dimorphism of gene expression in lacrimal tissue. Keywords: Placeco vs Hormone Treatment
2008-01-01 | GSE5783 | GEO
Project description:The goal of this study is to determine the oviduct responds to 17beta-estradiol (E2) in an in vivo environment using mouse models
2021-01-06 | GSE164291 | GEO