Rhodococcus jostii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA309609 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3114720.fastq.gz | Fastqsanger.gz | |||
| SRR3114721.fastq.gz | Fastqsanger.gz | |||
| SRR3114722.fastq.gz | Fastqsanger.gz | |||
| SRR3114723.fastq.gz | Fastqsanger.gz | |||
| SRR3114724.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome studies confirm the nitrogen limited physiological state of both the wild-type and mutant cells. In addition, multiple differentially expressed genes involved in the synthesis and consumption of pools of acetyl-CoA, acetoacetyl-CoA and 3-hydroxybutyryl-CoA, key metabolites for PHA and TAG synthesis, were identified. An enrichment analysis of differentially expressed genes in the nitrogen starved wild-type versus the isogenic RHA1_ro02104 mutant strain identified genes in the mutant involved in fatty acid and lipid as well as genes involved in acyl-CoA hydrolysis and triacylglycerol degradation.
2016-07-01 | GSE78828 | GEO
Project description:Transcriptome studies confirm the nitrogen limited physiological state of both the wild-type and mutant cells. In addition, multiple differentially expressed genes involved in the synthesis and consumption of pools of acetyl-CoA, acetoacetyl-CoA and 3-hydroxybutyryl-CoA, key metabolites for PHA and TAG synthesis, were identified. An enrichment analysis of differentially expressed genes in the nitrogen starved wild-type versus the isogenic RHA1_ro02104 mutant strain identified genes in the mutant involved in fatty acid and lipid as well as genes involved in acyl-CoA hydrolysis and triacylglycerol degradation. An 8 x 15K array study using total RNA recovered from triplicate cultures of Rhodococcus jostii RHA1 under nitrogen rich and nitrogen starved conditions and triplicate cultures of Rhodococcus jostii RHA1 TadA-homolog deletion mutants (2104) under nitrogen rich and nitrogen starved conditions.
2016-07-01 | E-GEOD-78828 | biostudies-arrayexpress
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:Polychlorinated biphenyl degrading bacterium
| PRJNA35695 | ENA
Project description:Characterisation of p-hydroxycinnamate catabolism in a soil Actinobacterum
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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:The Rhodococcus jostii RHA1 gene cluster required for ?-resorcylate (GRA) catabolism was characterized. The cluster includes tsdA, tsdB, tsdC, tsdD, tsdR, tsdT, and tsdX, which encode GRA decarboxylase, resorcinol 4-hydroxylase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, an IclR-type regulator, a major facilitator superfamily transporter, and a putative hydrolase, respectively. The tsdA gene conferred GRA decarboxylase activity on Escherichia coli. Purified TsdB oxidized NADH in the presence of resorcinol, suggesting that tsdB encodes a unique NADH-specific single-component resorcinol 4-hydroxylase. Mutations in either tsdA or tsdB resulted in growth deficiency on GRA. The tsdC and tsdD genes conferred hydroxyquinol 1,2-dioxygenase and maleylacetate reductase activities, respectively, on E. coli. Inactivation of tsdT significantly retarded the growth of RHA1 on GRA. The growth retardation was partially suppressed under acidic conditions, suggesting the involvement of tsdT in GRA uptake. Reverse transcription-PCR analysis revealed that the tsd genes constitute three transcriptional units, the tsdBADC and tsdTX operons and tsdR. Transcription of the tsdBADC and tsdTX operons was induced during growth on GRA. Inactivation of tsdR derepressed transcription of the tsdBADC and tsdTX operons in the absence of GRA, suggesting that tsd gene transcription is negatively regulated by the tsdR-encoded regulator. Binding of TsdR to the tsdR-tsdB and tsdT-tsdR intergenic regions was inhibited by the addition of GRA, indicating that GRA interacts with TsdR as an effector molecule.
| S-EPMC4592853 | biostudies-literature
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:Transcriptome analysis of Rhodococcus jostii RHA1 during growth in sterilized soil was performed. A total of 165 soil-specific genes were identified by subtracting genes upregulated in late growth phases and on solid medium from 264 genes commonly upregulated during growth on biphenyl or pyruvate in sterilized soil. Classification of the 165 genes into functional categories indicated that this soil-specific group is rich in genes for the metabolism of fatty acids, amino acids, carbohydrates, and nitrogen and relatively poor in those for cellular processes and signaling. The ro06365-ro06369 gene cluster, in which ro06365 to ro06368 were highly upregulated in transcriptome analysis, was characterized further. ro06365 and ro06366 show similarity to a nitrite/nitrate transporter and a nitrite reductase, respectively, suggesting their involvement in nitrogen metabolism. A strain with an ro06366 deletion, D6366, showed growth retardation when we used nitrate as the sole nitrogen source and no growth when we used nitrite. A strain with a deletion of ro06365 to ro06368, DNop, utilized neither nitrite nor nitrate and recovered growth using nitrite and nitrate by introduction of the deleted genes. Both of the mutants showed growth retardation in sterilized soil, and the growth retardation of DNop was more significant than that of D6366. When these mutants were cultivated in medium containing the same proportions of ammonium, nitrate, and nitrite ions as those in the sterilized soil, they showed growth retardation similar to that in the soil. These results suggest that the ro06365-ro06369 gene cluster has a significant role in nitrogen utilization in sterilized soil.
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