Abstract
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.
Highlights
The genus Sphingobium is notable for the capacity of many of its members to degrade poly-aromatic hydrocarbons[1], including the insecticide hexachlorocyclohexane[2]
Uptake, accumulation and efflux systems have been identified in bacteria including Escherichia coli, Cupriavidus metallidurans, Helicobacter pylori and Achromobacter xylosoxidans
The up-regulation of several genes annotated as involved in copper ion homeostasis as well as genes encoding proteins belonging to active import systems, might indicate the presence of novel bioaccumulation mechanisms for the homeostasis of nickel ions in Sphingobium
Summary
The genus Sphingobium is notable for the capacity of many of its members to degrade poly-aromatic hydrocarbons[1], including the insecticide hexachlorocyclohexane[2] This genus and three closely related genera: Novosphingobium, Sphingomonas and Sphingopyxis were, until a few years ago, classified in the single α-Proteobacteria genus Sphingomonas, which included bacteria characterized by the presence of glycosphingolipids in their outer membranes[3]. Phylogenetic analyses of 16S rRNA gene, together with detailed characterization of fatty acid, glycosphingolipid and polyamine profiles led to their separation into the aforementioned sub-genera[4] These bacteria are often detected in clinical equipment and specimens, urban water plumbing systems, contaminated soils and waste-water, and in plants[5, 6]. The identification of adaptive mechanisms in the S. sp ba[1] strain, besides providing insights into the general responses to nickel ions in prokaryotes, may assist in the development of Sphingobium bacteria for biodegradation of xenobiotic compounds in metal-rich environments
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