Rhodococcus jostii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA243026 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1209552.fastq.gz | Fastqsanger.gz | |||
| SRR1209553.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and is also generated in the degradation of plastics such as PET. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1’s tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams.
2024-03-15 | GSE261336 | GEO
Project description:Genes encoding vanillin dehydrogenase (vdh) and vanillate O-demethylase (vanAB) were identified in Rhodococcus jostii RHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes.
| S-EPMC3255756 | biostudies-literature
Project description:Oxysterols from steroid autooxidation have numerous harmful effects, but their biodegradation is poorly understood. Microarrays were used to study mineralization of the most common oxysterol, 7-ketocholesterol (7KC), by Rhodococcus jostii RHA1. Growth on 7KC versus growth on cholesterol resulted in 363 differentially expressed genes, including upregulation of two large gene clusters putatively encoding steroid catabolism. Despite this difference, 7KC degradation required key genes involved in cholesterol degradation, indicating a common catabolic route.
| S-EPMC2798662 | biostudies-literature
Project description:Rhododoccus jostii RHA1 was grown in the sterilized soil with pyruvate
| PRJNA128861 | ENA
Project description:Rhododoccus jostii RHA1 was grown in the sterilized soil with biphenyl
| PRJNA128859 | ENA
Project description:Polychlorinated biphenyl degrading bacterium
| PRJNA35695 | ENA
Project description:Transcriptional profiling of triacylglycerol biosynthesis in rhodococci and identification of a key diacylglyceride O-acyltransferase
| PRJNA309609 | ENA
Project description:Here we report the first transcriptomic analysis of a Gram-positive bacterium to desiccation. Filtered RHA1 cells incubated at either low relative humidity (20%), as an air drying treatment, or high relative humidity (100%), as a control, were transcriptionally profiled over a comprehensive time series. Keywords: stress response time course
2008-05-01 | GSE10378 | GEO
Project description:Rhodococcus jostii RHA1, a catabolically diverse soil actinomycete, is highly resistant to long-term nutrient starvation. After 2 years of carbon starvation, 10% of the bacterial culture remained viable. To study the molecular basis of such resistance, we monitored the abundance of about 1,600 cytosolic proteins during a 2-week period of carbon source (benzoate) starvation. Hierarchical cluster analysis elucidated 17 major protein clusters and showed that most changes occurred during transition to stationary phase. We identified 196 proteins. A decrease in benzoate catabolic enzymes correlated with benzoate depletion, as did induction of catabolism of alternative substrates, both endogenous (lipids, carbohydrates, and proteins) and exogenous. Thus, we detected a transient 5-fold abundance increase for phthalate, phthalate ester, biphenyl, and ethyl benzene catabolic enzymes, which coincided with at least 4-fold increases in phthalate and biphenyl catabolic activities. Stationary-phase cells demonstrated an ∼250-fold increase in carbon monoxide dehydrogenase (CODH) concurrent with a 130-fold increase in CODH activity, suggesting a switch to CO or CO(2) utilization. We observed two phases of stress response: an initial response occurred during the transition to stationary phase, and a second response occurred after the cells had attained stationary phase. Although SigG synthesis was induced during starvation, a ΔsigG deletion mutant showed only minor changes in cell survival. Stationary-phase cells underwent reductive cell division. The extreme capacity of RHA1 to survive starvation does not appear to involve novel mechanisms; rather, it seems to be due to the coordinated combination of earlier-described mechanisms.
| S-EPMC3426721 | biostudies-literature
Project description:Rhodococcus jostii RHA1 was engineered to utilise the cellulose component of lignocellulose, as well as the lignin fraction, by introduction of cellulase genes. The genome of R. jostii RHA1 was found to contain two β-glucosidase genes, RHA1_ro01034 and RHA1_ro02947, which support growth on cellobiose as growth substrate. Five Gram-positive endocellulase genes and one exocellulase gene were cloned into expression vector pTipQC2, and expressed in R. jostii RHA1. Endoglucanase activity was detected, with highest activity using Cellulomonas fimi cenA, and this recombinant strain grew on minimal media containing 0.5% carboxymethylcellulose (CMC). The R. jostii RHA1 genome was also found to contain a 3-dehydroshikimate dehydratase gene RHA1_ro01367, which supports growth on quinic acid as growth substrate, and conversion to protocatechuic acid. Therefore, this bacterium shows promise for further engineering to utilise cellulose for conversion to protocatechuic acid-derived bioproducts.
| S-EPMC10558750 | biostudies-literature