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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq.

M Volpicella¹, C Leoni¹, C Manzari²

¹Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.

Scientific Reports

|August 17, 2017

Summary

This study reveals novel nickel (Ni2+) tolerance mechanisms in Sphingobium sp. ba1. The bacteria adapt to high nickel concentrations using specific efflux systems, suggesting potential for bioremediation in metal-rich environments.

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Area of Science:

Microbiology
Environmental Science
Biochemistry

Background:

Nickel is an essential cofactor for bacterial enzymes, requiring precise homeostasis.
Efficient nickel ion (Ni2+) efflux or accumulation systems are crucial for bacterial survival in high-concentration environments.
Nickel tolerance mechanisms in the Sphingobium genus remain largely uncharacterized.

Purpose of the Study:

To investigate the adaptive mechanisms of the novel Sphingobium sp. ba1 strain to high nickel concentrations.
To identify genes and pathways involved in nickel tolerance in Sphingobium.
To explore the potential of Sphingobium sp. ba1 for bioremediation in metal-contaminated areas.

Main Methods:

Differential gene expression analysis using RNA-sequencing (RNA-seq) on Sphingobium sp. ba1 cultured in 10 mM Ni2+.
Comparative genomic analysis of nickel-related gene clusters across thirty Sphingobium species.
Identification and characterization of differentially expressed genes related to metal ion transport and homeostasis.

Main Results:

RNA-seq identified 118 differentially expressed genes, with 90 up-regulated in response to Ni2+.
A conserved gene cluster for nickel and metal ion efflux systems (similar to cnrCBA, nccCBA, cznABC) and a NreB-like permease was identified.
Comparative genomics revealed the variable conservation of this cluster across Sphingobium species.
Differential expression of potential Ni2+-accumulator proteins (HupE/UreJ-like, NreA) and copper-homeostasis systems was also observed.

Conclusions:

Sphingobium sp. ba1 possesses sophisticated adaptive mechanisms for nickel ion tolerance, involving efflux and potentially accumulation systems.
The identified nickel resistance gene cluster shows variable conservation within the Sphingobium genus.
Understanding these mechanisms can facilitate the application of Sphingobium sp. ba1 in bioremediating poly-aromatic compounds in nickel-rich environments.