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Pseudmonas aeruginosa PAO1 wild-type and delta prpC cultured on MOPS Succinate and MOPS Succinate + Propionate

ABSTRACT: Pseudmonas aeruginosa PAO1 wild-type and delta prpC cultured on MOPS Succinate and MOPS Succinate + Propionate

PROVIDER: PRJEB42871 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5236920.fastq.gz	Fastqsanger.gz
	ERR5236930.fastq.gz	Fastqsanger.gz
	ERR5236921.fastq.gz	Fastqsanger.gz
	ERR5236922.fastq.gz	Fastqsanger.gz
	ERR5236923.fastq.gz	Fastqsanger.gz

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Pseudmonas aeruginosa PAO1 wild-type and delta prpC cultured on MOPS Succinate and MOPS Succinate + Propionate

Project description:Pseudomonas aeruginosa strain PAO1 (wild-ype and prpC) was grown in 40 ml MOPS with succinate as the sole carbon source, 37 °C with shaking (250 rpm) in baffled flasks (500 ml). During exponential growth, 500 uM propionate was added to the cultures (H2O added to controls). Samples were harvested during mid-exponential growth. Four conditions, 12 samples total (triplicate). 5 ml of culture was harvested from each sample and added to an equal volume of RNAlater® RNA stabilization solution. Samples were then centrifuged at 4000 rpm for 15 min (4 °C) and the pellets were stored at – 80 °C. RNA was extracted using a RNAeasy Mini-Kit according to the manufacturers instructions. RNA was estimated with a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies Inc, USA) and using agarose gel electrophoresis. Ribosomal RNA (rRNA) was then depleted from each sample (5 µg each) using the bacterial Ribo-Zero rRNA Removal Kit (Illumina). The integrity of the RNA was evaluated using an RNA 6000 Nano LabChip and an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany). Eight indexed, strand-specific cDNA libraries were prepared, and samples were sequenced on an Illumina HiSeq 2000 with a 51-bp single-end read length (GATC Biotech, Germany).

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Project description:Pseudmonas aeruginosa PAO1 wild-type cultured in MOPS Glycerol compared to MOPS Glycerol Hypoxia (restricted oxygen). P. aeruginosa strain PAO1 was grown in 40 ml MOPS with glycerol as sole carbon source (triplicate), 37 °C with shaking (250 rpm) in baffled flasks (500 ml). For the restricted oxygen condition, P. aerugionosa was cultured in the same conditions, except non-baffled flasks were used, and the shaking speed was 80 rpm (gentle aggitation). A thin layer 10 ml of mineral oil was overlaid on top of these cultures to restrict oxygen transfer.

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Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol, MOPS Acetate

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Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol and MOPS Acetate

Project description:Drastic alterations in transcripts associated with central carbon metabolism and associatedprocesses have been repeatedly observed a common expression program as P. aeruginosa adapts to the cystic fibrosis lung when compared to standard laboratory conditions. However, we have limited knowledge of how well these transcriptomic changes correlate with actual alterations in metabolic flux; the rate of turnover of molecules through metabolic pathways. We have compared the proteome of Pseudomonas aeruginosa PAO1 during growth on the carbon sources acetate and glycerol.

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Pseudmonas aeruginosa PAO1 wild-type cultured in MOPS Glycerol compared to MOPS Glycerol Hypoxia (restricted oxygen).

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Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol, MOPS Acetate

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Project description:Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the gamma-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. The typical downregulation of the citric acid cycle under anoxic conditions is only partially responsible for the inability to use propionate under anoxic conditions since an arcA mutant shows very limited growth on propionate. RT-PCR and transcriptomic analysis revealed a post-transcriptional regulation of the prp-genecluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA was hydrolyzed in the 3`-5` direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R catalyzes the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli.

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