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ABSTRACT:
PROVIDER: PRJNA96385 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE5268: Effects of biphenyl on Rhodococcus sp. RHA1 GSE5269: Effects of ethylbenzene on Rhodococcus sp. RHA1 GSE5270: Effects of benzoate on Rhodococcus sp. RHA1 Refer to individual Series
2010-07-01 | E-GEOD-5280 | biostudies-arrayexpress
Project description:three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures Keywords: growth substrate
2007-11-01 | GSE8480 | GEO
Project description:three late exponential phase Rhodococcus sp. RHA1 propane-grown cultures compared to pyruvate-grown cultures three two-colour microarrays
2010-06-25 | E-GEOD-8480 | biostudies-arrayexpress
Project description:Effects of ethylbenzene on Rhodococcus sp. RHA1
| PRJNA104297 | ENA
Project description:Effects of benzoate on Rhodococcus sp. RHA1
| PRJNA104299 | ENA
Project description:Effects of biphenyl on Rhodococcus sp. RHA1
| PRJNA104295 | ENA
Project description:Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.
2016-05-06 | GSE77158 | GEO
Project description:To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in a transconjugant Rhodococcus jostii RHA1 strain, transcriptome studies were performed. Transcriptome experiments comparing RHA1 wild-type and RHA1 transconjugant strains grown in rich media confirmed the presence of the pGKT2 plasmid.
2019-07-31 | GSE125548 | GEO
Project description:p-Hydroxycinnamates, such as p-coumarate and ferulate, are components of plant cell walls and have a number of commercial applications. Previously, we had shown that the soil Actinobacterium Rhodococcus jostii RHA1 (RHA1) grows on ferulate, catabolizing it via vanillate and the M-NM-2-ketoadipate pathway. We used transcriptomics to identify genes in RHA1 that were specifically up-regulated during growth on ferulate. These include three operons predicted to encode the uptake and M-NM-2-oxidative deacetylation of ferulate and p-coumarate: couHLT, couMNO and couR. A couL mutant did not grow on p-coumarate, ferulate or their dihydro derivatives, but grew on vanillate. Purified CouL catalyzed the thioesterification of several p-hydroxycinnamates. Among the tested substrates, the best were p-coumarate and caffeate (kcat/KM ~400 mM-1s-1), and sinapate was not transformed. Of these, p-coumarate was also RHA1M-bM-^@M-^Ys preferred growth substrate. Although the data indicate that p-hydroxycinnamates are catabolized via M-NM-2-oxidation, the pathway lacks a typical M-NM-2-ketothiolase. The data further suggest the involvement of two formaldehyde detoxification pathways in vanillate catabolism. This study augments our understanding of the bacterial catabolism of biomass and facilitates the production of aromatics from renewable feedstocks. Transcriptomes of R. jostii RHA1 from ferulate and benzoate cultures were analysed using Ion PGMTM system.
2014-09-28 | E-GEOD-56355 | biostudies-arrayexpress
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