Shewanella halifaxensis HAW-EB4
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ABSTRACT:
PROVIDER: PRJNA20241 | ENA |
REPOSITORIES: ENA
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Project description:Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-degrading bacterium
| PRJNA18789 | ENA
Project description:Investigation of gene expression level changes in Gordonia sp. KTR9 upon exposure to RDX and Nitrogen Limitation, compared to controls with no RDX. The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72.
2013-02-06 | GSE42340 | GEO
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:Investigation of gene expression level changes in Gordonia sp. KTR9 upon exposure to RDX and Nitrogen Limitation, compared to controls with no RDX. The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72. A 12 x 135K array study using total RNA recovered from triplicate cultures of KTR9 exposed to RDX, triplicate cultures of KTR9 exposed to RDX and high nitrogen conditions, triplicate cultures of KTR9 exposed to low nitrogen, and triplicate cultures of controls exposed to high nitrogen.
2013-02-06 | E-GEOD-42340 | biostudies-arrayexpress
Project description:RDX (Hexahydro-1,3,5-trinitro-1,3,5-triazine) is a synthetic, high-impact, relatively stable explosive that has been in use since WWII. Exposure to RDX can occur either occupationally or through ordnance that lays unexploded on training ranges. The toxicology of RDX is dominated by acute tonic-clonic seizures at high doses, which remit when exposure is removed and internal RDX levels decrease. Sub-chronic studies have revealed few other toxic effects. The objective of this study was to examine the effect of a single oral dose of RDX on global gene expression in the mammalian brain and liver, using a rodent model. Keywords: time course, dose response
2009-03-13 | GSE12196 | GEO
Project description:Short title: Coral Meta-Transcriptomics Reveal Pollutant Stress Background: Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater). Results: RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5). Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral / zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (ie. cytochrome P450 and UDP glucuronosyltransferase 2) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal. Conclusions: Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts.
2014-03-26 | GSE27624 | GEO
Project description:RDX (Hexahydro-1,3,5-trinitro-1,3,5-triazine) is a synthetic, high-impact, relatively stable explosive that has been in use since WWII. Exposure to RDX can occur either occupationally or through ordnance that lays unexploded on training ranges. The toxicology of RDX is dominated by acute tonic-clonic seizures at high doses, which remit when exposure is removed and internal RDX levels decrease. Sub-chronic studies have revealed few other toxic effects. The objective of this study was to examine the effect of a single oral dose of RDX on global gene expression in the mammalian brain and liver, using a rodent model. Experiment Overall Design: Male Sprague-Dawley rats were given a single, oral, non-seizure inducing dose of either 3 or 18 mg/kg RDX in a gel capsule. Rats were euthanized at times 0, 4, 24, and 48 hours. RNA purified from brain cortex or liver was hybridized to Affymetrix rat 230.2 arrays.
2009-03-21 | E-GEOD-12196 | biostudies-arrayexpress
Project description:Shewanella canadensis strain:HAW-EB2 Genome sequencing and assembly
| PRJNA510207 | ENA
Project description:Shewanella atlantica strain:HAW-EB5 Genome sequencing and assembly
| PRJNA510208 | ENA
Project description:Bacterial anaerobic respiration using extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the bacterial adaptive mechanisms to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration is not clear, which limits us to optimize the strategies for the bioremediation of contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium Shewanella decolorationis S12 when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to higher filamentous cell rate and decolorization ability in subcultural cells compared with parental strains. Additionally, the expression of genes involved in cell division, chemotaxi system, energy conservation, damage repair, and material transport in filamentous cells were significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells were identified by site-directed mutagenesis, such as the outer membrane porin genes ompA and ompW, the cytochrome C genes arpC and arpD, the global regulatory factor gene rpoS and methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present, and the mechanisms in which these toxic organics were biodegraded as the extracellular electron acceptors.
2019-06-18 | GSE64532 | GEO