Rhodococcus sp. NJ-530
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA506529 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR10019385_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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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.
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Project description:three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures Keywords: growth substrate
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Project description:Biofilms represent a protective survival mode in which bacteria adapt themselves to the natural environment for survival purposes. Biofilm formation is regulated by 3,5-cyclic diguanylic acid (c-di-GMP), which is a universal second messenger molecule in bacteria. Diguanylate cyclase (DGC) catalyses c-di-GMP intracellular synthesis, which plays important roles in bacterial adaptation to the natural environment. In this study, the DGC gene was first cloned from Antarctic Rhodococcus sp. NJ-530. DGC contained 948 nucleotides and encoded 315 amino acids with a molecular weight of 34.6 KDa and an isoelectric point of 5.58. qRT-PCR demonstrated that the DGC expression level was significantly affected by lower salinity and temperature. Consistently, more biofilm formation occurred under the same stress. It has been shown that Rhodococcus sp. NJ-530 can adapt to the extreme environment in Antarctica, which is closely related to biofilm formation. These results provide an important reference for studying the adaptive mechanism of Antarctic microorganisms to this extreme environment.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-021-03093-z.
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Project description:Marine bacterium Rhodococcus sp. NJ-530 has developed several ultraviolet (UV) adaptive characteristics for survival and growth in extreme Antarctic environment. Rhodococcus sp. NJ-530 DNA photolyase encoded by a 1146 bp photolyase-homologous region (phr) was identified in genome. Quantitative real-time PCR demonstrated that transcriptional levels of phr were highly up-regulated by ultraviolet-B (UV-B) radiation (90 μW·cm-2) and increased to a maximum of 149.17-fold after exposure for 20 min. According to the results of SDS-PAGE and western blot, PHR was effectively induced by isopropyl-β-d-1-thiogalactopyranoside (IPTG) at the genetically engineered BL21(DE3)-pET-32a( +)-phr construct under the condition of 15 °C for 16 h and 37 °C for 4 h. In terms of in vivo activity, compared with a phr-defective E. coli strain, phr-transformed E. coli exhibited higher survival rate under high UV-B intensity of 90 μW·cm-2. Meanwhile, the purified PHR, with blue light, presented obvious photorepair activity toward UV-induced DNA damage in vitro assays. To sum up, studying the mechanisms of Rhodococcus sp. NJ-530 photolyase is of great interest to understand the adaptation of polar bacteria to high UV radiation, and such data present important therapeutic value for further UV-induced human skin and genetic damage diseases.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-021-02660-8.
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