Rhodococcus opacus PD630
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ABSTRACT:
PROVIDER: PRJNA30413 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| AGVD01.dat.gz | Other | |||
| AGVD01.fasta.gz | Fasta.gz | |||
| AGVD01.master.dat | Other | |||
| AGVD01.dat.gz | Other |
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Similar Datasets
Project description:The noncellulolytic actinomycete Rhodococcus opacus strain PD630 is the model oleaginous prokaryote with regard to the accumulation and biosynthesis of lipids, which serve as carbon and energy storage compounds and can account for as much as 87% of the dry mass of the cell in this strain. In order to establish cellulose degradation in R. opacus PD630, we engineered strains that episomally expressed six different cellulase genes from Cellulomonas fimi ATCC 484 (cenABC, cex, cbhA) and Thermobifida fusca DSM43792 (cel6A), thereby enabling R. opacus PD630 to degrade cellulosic substrates to cellobiose. Of all the enzymes tested, five exhibited a cellulase activity toward carboxymethyl cellulose (CMC) and/or microcrystalline cellulose (MCC) as high as 0.313 ± 0.01 U · ml(-1), but recombinant strains also hydrolyzed cotton, birch cellulose, copy paper, and wheat straw. Cocultivations of recombinant strains expressing different cellulase genes with MCC as the substrate were carried out to identify an appropriate set of cellulases for efficient hydrolysis of cellulose by R. opacus. Based on these experiments, the multicellulase gene expression plasmid pCellulose was constructed, which enabled R. opacus PD630 to hydrolyze as much as 9.3% ± 0.6% (wt/vol) of the cellulose provided. For the direct production of lipids from birch cellulose, a two-step cocultivation experiment was carried out. In the first step, 20% (wt/vol) of the substrate was hydrolyzed by recombinant strains expressing the whole set of cellulase genes. The second step was performed by a recombinant cellobiose-utilizing strain of R. opacus PD630, which accumulated 15.1% (wt/wt) fatty acids from the cellobiose formed in the first step.
| S-EPMC3753941 | biostudies-literature
Project description:Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM.
2013-11-04 | GSE42381 | GEO
Project description:Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM. PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform.
2013-11-04 | E-GEOD-42381 | biostudies-arrayexpress
Project description:The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.
| S-EPMC3169528 | biostudies-literature
Project description:Rhodococcus opacus PD630 is a gram-positive bacterium with promising attributes for the conversion of lignin into valuable fuels and chemicals. To develop an organism as a cellular factory, it is necessary to have a deep understanding of its metabolism and any heterologous pathways being expressed. For the purpose of quantifying gene transcription, reverse transcription quantitative PCR (RT-qPCR) is the gold standard due to its sensitivity and reproducibility. However, RT-qPCR requires the use of reference genes whose expression is stable across distinct growth or treatment conditions to normalize the results. Unfortunately, no in-depth analysis of stable reference genes has been conducted in Rhodococcus, inhibiting the utilization of RT-qPCR in R. opacus. In this work, ten candidate reference genes, chosen based on previously collected RNA sequencing data or literature, were examined under four distinct growth conditions using three mathematical programs (BestKeeper, Normfinder, and geNorm). Based on this analysis, the minimum number of reference genes required was found to be two, and two separate pairs of references genes were identified as optimal normalization factors for when ribosomal RNA is either present or depleted. This work represents the first validation of reference genes for Rhodococcus, providing a valuable starting point for future research.
| S-EPMC5902447 | biostudies-literature
Project description:Rhodococcus opacus PD630 Genome sequencing
| PRJNA249823 | ENA
Project description:Rhodococcus opacus PD630 Genome sequencing
| PRJNA178618 | ENA
Project description:Rhodococcus opacus PD630 Raw sequence reads
| PRJNA321175 | ENA
Project description:Rhodococcus opacus PD630 Genome sequencing
| PRJNA752705 | ENA
Project description:Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ability of carbon source biosynthesis and catabolism. The comparative transcriptome analysis from three culture conditions revealed the landscape of gene-altered expressions responsible for lipid accumulation. The LD proteomes further identified the proteins that mediate lipid synthesis, storage and other biological functions. Integrating these three omics uncovered 177 proteins that may be involved in lipid metabolism and LD dynamics. A LD structure-like protein LPD06283 was further verified to affect the LD morphology. Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development.
| S-EPMC3902926 | biostudies-literature