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Sphingobium Nickel resistance analysis by RNA-seq approach

ABSTRACT: Sphingobium Nickel resistance analysis by RNA-seq approach

PROVIDER: PRJEB21342 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2010650_1.fastq.gz	Fastqsanger.gz
	ERR2010650_2.fastq.gz	Fastqsanger.gz
	ERR2010645_1.fastq.gz	Fastqsanger.gz
	ERR2010645_2.fastq.gz	Fastqsanger.gz
	ERR2010646_1.fastq.gz	Fastqsanger.gz

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Sphingobium Nickel resistance analysis by RNA-seq approach

Project description:Nickel is an essential component of many eukaryotic and prokaryotic metallo-enzymes. Due to its employment in many industrial applications, wastewaters from industrial plants often contain millimolar concentrations of Ni2+ that are toxic and life-threatening for many organism. Several lines of preliminary evidence suggest that members of the genus Sphingobium are able to grow in the presence of high concentrations of metal ions. We have isolated a novel Sphingobium strain (sp. ba1) able to grow in the presence of high concentrations (up to 20 mM) of NiCl2. Sequencing of its genome allowed the identification of several genes coding for proteins potentially involved in efflux-mediated resistance mechanisms. Here we use the RNA-seq approach to analyze the response of the Sphingobium sp. ba1 strain to high concentrations (10 mM) of Ni ions. Transcriptomic data show the differential expression of about one-hundred and twenty genes, most of which are up-regulated and encode proteins such as membrane proteins and components of metal efflux systems, enzymes involved in oxidative stress responses (catalases, peroxidases) and signal transduction systems.

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Project description:Nickel-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. The reference strain which was used to select this nickel-resistant mutant could not grow even at 0.5 mM NiCl2 whereas this mutant was shown to be resistant upto 5.3 mM NiCl2 concentration. Whole-genome microarray analysis might be promising to identify the nickel resistance mechanisms in the yeast cells. The reference Saccharomyces cerevisiae strain and the nickel-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which correspond to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

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Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq.

Project description:Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni2+ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni2+ concentrations. Differential gene expression in cells cultured in 10 mM Ni2+, investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni2+-accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.

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