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

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.

TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation

“…Transcriptome and proteome analysis was done for certain sphingomonads grown under certain unique physiological conditions. These omics studies showed substrate specific expression patterns of TBDTs [14,16,33,34,36,[38][39][40]. About 32 TBDTs showed differential expression in the presence of heavy metals, xenobiotics, temperature stress, and poor nutrient conditions ( Table 1).…”

“…Sphingomonads survive in various stressful environments. They survive in a nutrient-poor phyllosphere [14], extremely cold marine waters [15] and highly toxic and polluted environments with metals [16], phenanthrene [17][18][19][20], polyethylene glycol [21], alkylphenols [22], dioxins [23], naphthalene [20], diphenyl ethers [24], organophosphates [25,26] and organochlorides [27][28][29]. Their survival under these stressful conditions depends on their ability to use these unusual substrates, hitherto unknown to natural habitats, as a carbon source ( Table 2).…”

“…Sphingomonads like Sphongobium sp. BA1, Sphingobium cupriresistence, and Novosphingobium PPIY can also withstand the stress imposed by metal ions like Ni 2+ , Cu 2+ , and Pb 2+ , respectively, due to increased expression of TBDTs [16]. Differential expression of TBDTs was evident in Sphingomonas wittichii RW1 strains grown in the presence of dibenzofuran (DF) and dibenzo-p-dioxin (DD).…”

The response of Sphingopyxis granuli strain TFA to the hostile anoxic condition

“…A number of sphingomonads have been described as oligotrophic bacteria 6 , some of which play an important role in marine environments 7 , and a number of genes for marine adaptation and quorum sensing have been identified 8 . From an environmental point of view, sphingomonads show a high capacity of adaptation to stressing environments such as those rich in metals 9 , and a great metabolic versatility, being many strains of this group reported as able to metabolise many different compounds recalcitrant to microbial degradation such as polyaromatic hydrocarbons from crude oils 10 or different xenobiotic compounds.…”

Bacterial copper storage proteins

“…A transcriptomic study of the Gram negative bacterium Sphingobium sp. ba1 has shown upregulation of Csp1 and Csp3 in response to 10 mM Ni(II), but under these conditions known Cu efflux systems, including CopA, are also up-regulated (90).…”