Methylorubrum sp. GM97
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ABSTRACT:
PROVIDER: PRJDB13504 | ENA |
REPOSITORIES: ENA
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Project description:Methylorubrum extorquens AM1 is engineered to produce itaconic acid by heterologous expression of cis-aconitic acid decarboxylase. Mutation was also performed on phaR in Methylorubrum extorquens AM1, which regulate poly-beta-hydroxybutyrate accumulation, in attempt to increase carbon flux toward itaconic acid production. However, in our case, itaconic acid production by phaR mutant strain was not higher than that of the wildtype. Transcriptomic analysis was utilized in order to examine the cause for this phenomenon. RNA-seq analysis revealed that phaR mutation in the itaconic acid-producing strain might result in a complex regulatory rewiring at the gene expression level, which could cause a reduced resource flux toward ITA production. Also, RNA profiling gave a hint at the broad regulatory role of PhaR.
2018-07-27 | GSE117714 | GEO
Project description:Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation offers a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as sole source of carbon and energy for growth, Methylorubrum extorquens DM4 (formerly named Methyobacterium extorquens) is a longstanding reference Alphaproteobacteria strain. Here, its primary transcriptome was obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM.
2022-06-27 | E-MTAB-11726 | biostudies-arrayexpress
Project description:We report a genetic variant of Methylorubrum extorquens AM1 that hyperaccumulates the heavy lanthanide gadolinium. Using RNA-seq transcriptomics we identified wide-spread metabolic and physiological changes in this strain and experimentally validate several of them, including increased gadolinium transport and storage in an intracellular compartment we name the lanthasome.
2022-01-17 | GSE193171 | GEO
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
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Project description:The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5.
2015-07-22 | GSE71132 | 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