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The small RNA RyhB is a regulator of cytochrome expression in Shewanella oneidensis

ABSTRACT: The small RNA RyhB is a regulator of cytochrome expression in Shewanella oneidensis

PROVIDER: PRJNA414224 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6170080.fastq.gz	Fastqsanger.gz
	SRR6170090.fastq.gz	Fastqsanger.gz
	SRR6170081.fastq.gz	Fastqsanger.gz
	SRR6170091.fastq.gz	Fastqsanger.gz
	SRR6170082.fastq.gz	Fastqsanger.gz

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The small RNA RyhB is a regulator of cytochrome expression in Shewanella oneidensis

Project description:Study of the roles played by Fur and RyhB in Shewanella oneidensis

2018-01-01 | GSE104952 | GEO

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Transcriptional targets of Shewanella oneidensis HnoC (SO_2540)

Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain. Transcript levels of a WT and hnoC deletion strain were measured after 15 hrs growth, 4 independent replicates were performed for each strain

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Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes

Project description:Transcriptomic analysis used to understand the influence of elevated intracellular cyclic-di-GMP in Shewanella oneidensis on expression of c-type cytochrome at transcript level.

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Quantitative proteome of Shewanella oneidensis MR-1

Project description:We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive ammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture.

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Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1

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The Small RNA RyhB Is a Regulator of Cytochrome Expression in <i>Shewanella oneidensis</i>.

Project description:Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.

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Shewanella oneidensis MR-1 etrA deletion mutant strain expression profiling determines fine-tuning regulatory role in anaerobic metabolism

Project description:Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Whole-genome expression profiling using a etrA gene deletion mutant as the experimental sample and the wild type strain as the reference, determine that EtrA fine-tunes the expression of genes involved in various anaerobic metabolic pathways, including nitrate, fumarate and dimethyl sulfoxide reduction. Moreover, genes involved in prophage activation and and genes implicated in aerobic metabolism were also differentially expressed. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and cofers physiological advantages to the strain under certain growth conditions.

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