RNA Sequencing of Mycobacterium dioxanotrophicus PH-06
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacterium dioxanotrophicus
PROVIDER: GSE103019 | GEO | 2018/08/01
REPOSITORIES: GEO
Similar Datasets
Project description:Whole Genome sequencing and assembly of Mycobacterium sp. PH-06
| PRJNA357161 | ENA
Project description:We evaluated liver tissues of B6D2F1/Crl mice exposed to 0, 40, 200, 600, 2000, or 6000 ppm 1,4-dioxane in drinking water for 7, 28, or 90 days in support of an investigation of the mode of action for 1,4-dioxane-induced murine liver tumors. TempO-Seq technology was used to measure global hepatic gene expression. Exposure-induced transcriptional responses increased by dose and exposure duration, with few differentially expressed genes at 40 and 200 ppm regardless of exposure duration. Pathway enrichment analysis identified significant perturbations in pathways associated with xenobiotic metabolism, complement and coagulation cascades and fatty acid metabolism in 600, 2000, and 6000 ppm groups at all timepoints compared to time-matched control groups. A significant transcriptomic proliferative response was only observed in 6000 ppm exposed mice at 90 days. Differential gene expression and pathway enrichment analysis results suggest 600 ppm as a potential threshold concentration for hepatic transcriptomic response to 1,4-dioxane in female mice.
2021-01-21 | GSE154899 | GEO
Project description:1,4-Dioxane (1,4-DX) is an environmental contaminant found in drinking water throughout the United States (US). While it is a suspected liver carcinogen, there is no federal or state maximum contaminant level for 1,4-DX in drinking water. Very little is known about the mechanisms by which this chemical elicits liver carcinogenicity. In the present study, we performed chronic and short-term dosing studies in female BDF-1 mice to explore the toxic effects of 1,4-DX. Histopathology studies and a multi-omics approach (transcriptomics and metabolomics) were performed to investigate potential mechanisms of toxicity. Mice were exposed to various concentrations of 1,4-DX (0, 50, 500 and 5,000 mg/L) in their drinking water for one or four weeks. Immunohistochemical analysis of the liver revealed an increase in the number of H2AXγ-positive hepatocytes (a marker of DNA double strand breaks) in mice exposed to 5,000 mg/L 1,4-DX for one and four weeks. In addition, an expansion of precholangiocytes was observed after four weeks of 5,000 mg/L 1,4-DX exposure, as reflected by CK-7 immunostaining. An increase in these markers reflect both DNA damage and repair mechanisms. Liver transcriptomics profiling showed that exposure to 5,000 mg/L 1,4-DX for four weeks resulted in the differential expression of 65 genes compared to controls. Pathway analysis of the transcriptomic data revealed 1,4-DX-induced perturbations in multiple signaling pathways in the liver, including those involved in xenobiotic metabolism, nicotine degradation and glutathione-mediated detoxification. Changes to these pathways as a result of 1,4-DX exposure reflect would be predicted to impact the oxidative stress response, detoxification, and DNA damage. Liver, kidney, stool and urine metabolomics profiling revealed no effect of 5,000 mg/L 1,4-DX exposure for one or four weeks on metabolites. We speculate that this may be reflective of DNA damage being counterbalanced by the repair response, with the net result being a null overall effect on the systemic biochemistry of the exposed mice. Our results show a novel approach for the investigation of environmental chemicals that do not elicit cell death, but have activated the repair systems in response to 1,4-DX exposure
2021-01-25 | GSE158087 | GEO
Project description:Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR. Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites. DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified. 20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.
2018-05-01 | GSE97757 | GEO
Project description:Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR. Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites. DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified. 20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.
2018-05-01 | GSE97756 | GEO
Project description:Human MondoA requires glucose as well as other modulatory signals to function in transcription. One such signal is acidosis, which increases MondoA activity and also drives a protective gene signature breast cancer. How low pH controls MondoA transcriptional activity is unknown. We found that low pH medium increases mitochondrial ATP (mtATP), which is subsequently exported from the mitochondrial matrix. Mitochondria-bound hexokinase transfers a phosphate from mtATP to cytoplasmic glucose to generate glucose-6-phosphate (G6P), which is an established MondoA activator. The outer mitochondrial membrane localization of MondoA suggests that it is positioned to coordinate the adaptive transcriptional response to a cell’s most abundant energy sources, cytoplasmic glucose and mtATP. In response to acidosis, MondoA shows preferential binding to just two targets, TXNIP and its paralog ARRDC4. Because these transcriptional targets are suppressors of glucose uptake we propose that MondoA is critical for restoring metabolic homeostasis in response to high energy charge.
2019-01-23 | GSE125089 | GEO