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Comparative transcriptomic analysis of Rhodococcus erythropolis PR4 under hydrocarbon degrading conditions

ABSTRACT: The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil.

ORGANISM(S): Rhodococcus erythropolis PR4

PROVIDER: GSE56474 | GEO | 2014/04/21

SECONDARY ACCESSION(S): PRJNA243385

REPOSITORIES: GEO

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Comparative transcriptomic analysis of Rhodococcus erythropolis PR4 under hydrocarbon degrading conditions

Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil. Comparative transcriptomics of Rhodococcus erythropolis PR4 grown on n-hexadecane, diesel oil, and sodium acetate.

2014-04-21 | E-GEOD-56474 | biostudies-arrayexpress

A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source. Two-condition experiment, cells grown on pyruvate vs. cells grown on hexadecane, canola or diesel. For each condition 4 replicates were used, as for the control condition also 4 replicates were used for analysis.

2014-07-01 | E-GEOD-50528 | biostudies-arrayexpress

A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source.

2014-07-01 | GSE50528 | GEO

Rhodococcus sp. RHA1 grown on propane versus pyruvate

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

Comparative proteomics of Marinobacter sp. TT1 reveals Corexit impacts on hydrocarbon metabolism, chemotactic motility and biofilm formation

Project description:The application of chemical dispersants during marine oil spills can affect the community composition and activity of native marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced hydrocarbon-biodegradation rates. In this respect, a major knowledge gap exists in understanding the mechanisms underlying these observed physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions that varied regarding the supplied carbon sources (pyruvate vs. n-hexadecane) and whether or not dispersant (Corexit EC9500A) was added, or that contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF). We characterized the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a proposed metabolism of Corexit components as carbon substrates for the strain. Our findings implicate Corexit in affecting hydrocarbon metabolism, chemotactic motility, biofilm formation, and inducing solvent tolerance mechanisms like efflux pumps in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.

2020-12-22 | PXD021108 | Pride

Rhodococcus sp. RHA1 grown on propane versus pyruvate

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

Rhodococcus EP4 Aromatic Transcriptomics

Project description:Transcriptomics of Rhodococcus EP4 on ethylphenol, propylguiacol and succiate

2018-06-01 | GSE112193 | GEO

Effect of biphenyl, ethylbenzene, and benzoate on Rhodococcus sp. RHA1

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

Next Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia

2013-10-29 | GSE49830 | GEO

Next Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia

Project description:Purpose: Identification of transcriptionally active genes in the unculturable community constituent, Smithella, during hexadecane degradation; Differential gene expression analysis of hexadecane-relevant genes acoss three different conditions; Extension of metatranscriptomic datasets to other community constituents to identify interspecies relationships. mRNA profiles were generated for this community across three different conditions (hexadecane-, butyric acid-, caprylic acid-degrading conditions) using a modified version of Nextera and sequenced using Illumina's Miseq platform.

2013-10-29 | E-GEOD-49830 | biostudies-arrayexpress

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