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...

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Autores principales:	M. Volpicella, C. Leoni, C. Manzari, M. Chiara, E. Picardi, E. Piancone, F. Italiano, A. D’Erchia, M. Trotta, D. S. Horner, G. Pesole, L. R. Ceci
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e9cad0bc88a1424b9495f073d48e68a4
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spelling	oai:doaj.org-article:e9cad0bc88a1424b9495f073d48e68a42021-12-02T12:32:42ZTranscriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq10.1038/s41598-017-08934-72045-2322https://doaj.org/article/e9cad0bc88a1424b9495f073d48e68a42017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08934-7https://doaj.org/toc/2045-2322Abstract 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.M. VolpicellaC. LeoniC. ManzariM. ChiaraE. PicardiE. PianconeF. ItalianoA. D’ErchiaM. TrottaD. S. HornerG. PesoleL. R. CeciNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q M. Volpicella C. Leoni C. Manzari M. Chiara E. Picardi E. Piancone F. Italiano A. D’Erchia M. Trotta D. S. Horner G. Pesole L. R. Ceci Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
description	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.
format	article
author	M. Volpicella C. Leoni C. Manzari M. Chiara E. Picardi E. Piancone F. Italiano A. D’Erchia M. Trotta D. S. Horner G. Pesole L. R. Ceci
author_facet	M. Volpicella C. Leoni C. Manzari M. Chiara E. Picardi E. Piancone F. Italiano A. D’Erchia M. Trotta D. S. Horner G. Pesole L. R. Ceci
author_sort	M. Volpicella
title	Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
title_short	Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
title_full	Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
title_fullStr	Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
title_full_unstemmed	Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq
title_sort	transcriptomic analysis of nickel exposure in sphingobium sp. ba1 cells using rna-seq
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/e9cad0bc88a1424b9495f073d48e68a4
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Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq

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