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RNA-seq of Gordonia rubripertincta CWB2 to uncover the styrene specific degradation pathway

ABSTRACT: RNA-seq of Gordonia rubripertincta CWB2 to uncover the styrene specific degradation pathway

PROVIDER: PRJEB22260 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2106430_1.fastq.gz	Fastqsanger.gz
	ERR2106430_2.fastq.gz	Fastqsanger.gz
	ERR2106440_1.fastq.gz	Fastqsanger.gz
	ERR2106440_2.fastq.gz	Fastqsanger.gz
	ERR2106431_1.fastq.gz	Fastqsanger.gz

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RNA-seq of Gordonia rubripertincta CWB2 to uncover the styrene specific degradation pathway

Project description:Gordonia rubripertincta CWB2 was grown at 30 °C in minimal media with fructose (with and without Fe) and styrene as sole source of carbon, respectively. After 5 days of cultivation the culture was diluted 1/10 in fresh media and incubated for 24 h with the respective substrate in a set of four Erlenmeyer flasks. Prior harvesting the cells, 10 % of an ice-cold STOP-solution (10 % buffered phenol in ethanol) was added to the culture followed by centrifugation at 11,000 x g for 5 minutes at 4 °C. The supernatant was discarded and the pellet was stored until RNA isolation at -80 °C. To break up the cells, 150 µl of a 5 mg ml-1 lysozyme solution were added to the pellet, mixed and incubated at room temperature for 5 minutes. 450 µl of buffer RLT (Qiagen) and 50 mg of (0.1 mm) glass beads were added to resuspend and break the cells by repeated vortexing at 4 °C. The suspension was applied to QIAshredder column for homogenization and to remove particles from the sample. Extraction of total RNA Extraction was done by applying the RNeasy Mini Kit including on-column DNA digestion (Qiagen). Isolated RNA was stored at -80 °C and quality was controlled on the 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent). RNA quality and quantity was again checked by an Agilent 2100 Bioanalyzer run (Agilent Technologies, Böblingen, Germany) and Trinean Xpose sytem (Gentbrugge, Belgium) prior and after rRNA depletion by Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, San Diego, CA, USA). TruSeq Stranded mRNA Library Prep Kit from (Illumina, (San Diego, CA, USA) was used to prepare the cDNA libraries to analyze the whole transcriptome. The resulting cDNAs were then sequenced paired end on an Illumina MiSeq and HiSeq 1500 system (San Diego, CA, USA) using 2 x 75 nt read length.

2017-08-13 | E-MTAB-6012 | biostudies-arrayexpress

Gordonia rubripertincta

Project description:Gordonia rubripertincta overview

| PRJNA81065 | ENA

Gordonia rubripertincta strain:SD5

Project description:Gordonia rubripertincta strain:SD5 Genome sequencing

| PRJNA649373 | ENA

Gordonia rubripertincta strain:CWB2

Project description:Gordonia rubripertincta CWB2 Genome sequencing and assembly

| PRJNA394617 | ENA

Gordonia rubripertincta strain:112

Project description:Gordonia rubripertincta strain:112 Genome sequencing and assembly

| PRJNA953757 | ENA

Gordonia rubripertincta strain:W3S5

Project description:Gordonia rubripertincta strain:W3S5 Genome sequencing and assembly

| PRJNA555169 | ENA

Gordonia rubripertincta NBRC 101908

Project description:Gordonia rubripertincta NBRC 101908 Genome sequencing and assembly

| PRJDA71851 | ENA

Gordonia rubripertincta CWB2_negative

Project description:The siderophore production of Gordonia rubripertincta CWB2 was investigated with special regards to the effects of rare earth metals on siderophore production.

2019-07-30 | MSV000084155 | MassIVE

Gordonia rubripertincta CWB2_positive

Project description:The siderophore production of Gordonia rubripertincta CWB2 was investigated with special regards to the effects of rare earth metals on siderophore production.

2019-07-29 | MSV000084154 | MassIVE

On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2.

Project description:Among bacteria, only a single styrene-specific degradation pathway has been reported so far. It comprises the activity of styrene monooxygenase, styrene oxide isomerase, and phenylacetaldehyde dehydrogenase, yielding phenylacetic acid as the central metabolite. The alternative route comprises ring-hydroxylating enzymes and yields vinyl catechol as central metabolite, which undergoes meta-cleavage. This was reported to be unspecific and also allows the degradation of benzene derivatives. However, some bacteria had been described to degrade styrene but do not employ one of those routes or only parts of them. Here, we describe a novel "hybrid" degradation pathway for styrene located on a plasmid of foreign origin. As putatively also unspecific, it allows metabolizing chemically analogous compounds (e.g., halogenated and/or alkylated styrene derivatives). Gordonia rubripertincta CWB2 was isolated with styrene as the sole source of carbon and energy. It employs an assembled route of the styrene side-chain degradation and isoprene degradation pathways that also funnels into phenylacetic acid as the central metabolite. Metabolites, enzyme activity, genome, transcriptome, and proteome data reinforce this observation and allow us to understand this biotechnologically relevant pathway, which can be used for the production of ibuprofen.IMPORTANCE The degradation of xenobiotics by bacteria is not only important for bioremediation but also because the involved enzymes are potential catalysts in biotechnological applications. This study reveals a novel degradation pathway for the hazardous organic compound styrene in Gordonia rubripertincta CWB2. This study provides an impressive illustration of horizontal gene transfer, which enables novel metabolic capabilities. This study presents glutathione-dependent styrene metabolization in an (actino-)bacterium. Further, the genomic background of the ability of strain CWB2 to produce ibuprofen is demonstrated.

| S-EPMC5930330 | biostudies-literature

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