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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [Hybrid-Trap-seq]

ABSTRACT: The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [Hybrid-Trap-seq]

PROVIDER: PRJNA416319 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6234914.fastq.gz	Fastqsanger.gz
	SRR6234915.fastq.gz	Fastqsanger.gz
	SRR6234916.fastq.gz	Fastqsanger.gz
	SRR6234917.fastq.gz	Fastqsanger.gz

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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

Project description:The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

| PRJNA416918 | ENA

The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq]

Project description:The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq]

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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [Hybrid-Trap-seq]

Project description:Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. The key to target discovery lies in the differential analysis of RNA-seq data from captures with different sRNAs and from ΔrsaE and RsaE over-expressing strains. This strategy was applied to study RsaE, a regulatory RNA highly conserved amongst Firmicutes and revealed that RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. However, the relative activity of these motifs is substrate dependent. Metabolite quantifications in wild-type and ΔrsaE cultures indicate that the absence of RsaE affects amino acid metabolism. Collectively, the data support the model that RsaE acts as a global regulator downregulating functions associated to metabolic adaptation.

2018-06-16 | GSE106327 | GEO

The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq]

Project description:Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. In addition, the transcriptomic effects of sRNA deletion and sRNA accumulation were analyzed by differential expression analyzes of RNA-seq data. This strategy was applied to study RsaE, a regulatory RNA highly conserved amongst Firmicutes and revealed that RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. However, the relative activity of these motifs is substrate dependent. Metabolite quantifications in wild-type and ΔrsaE cultures indicate that the absence of RsaE affects amino acid metabolism. Collectively, the data support the model that RsaE acts as a global regulator downregulating functions associated to metabolic adaptation.

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Trap-80-dependence of TNF-alpha-induced genes

Project description:In fibroblasts, p65-dependent genes can be sub-divided, depending on whether they are Trap-80-dependent or -independent. To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation of NF-kappaB activity using TNF-alpha. RNA was extracted from three independent cultures of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation for 1 hour with 5ng/ml TNF-alpha. The unstimulated and stimulated wild-type samples, and the stimulated Trap-80 knock-down samples, were used for microarray analysis.

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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus.

Project description:RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ΔrsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.

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The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

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