title: Comprehensive mapping of the Helicobacter pylori NikR regulon provides new insights in bacterial nickel responses.
abstract: Nickel homeostasis is important for pathogenic and ureolytic bacteria, which use this metal ion as enzymatic cofactor. For example, in the human pathogen Helicobacter pylori an optimal balance between nickel uptake and incorporation in metallo-enzymes is fundamental for colonization of the host. Nickel is also used as cofactor to modulate DNA binding of the NikR regulator, which controls transcription of genes involved in nickel trafficking or infection in many bacteria. Accordingly, there is much interest in a systematic characterization of NikR regulation. Herein we use H. pylori as a model to integrate RNA-seq and ChIP-seq data demonstrating that NikR not only regulates metal-ion transporters but also virulence factors, non-coding RNAs, as well as toxin-antitoxin systems in response to nickel stimulation. Altogether, results provide new insights into the pathobiology of H. pylori and contribute to understand the responses to nickel in other bacteria.
authors.affiliation: FaBiT - Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.|DIMES Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Vannini
authors.affiliation: Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy.
authors.forename: Eva
authors.initials: E
authors.lastname: Pinatel
authors.affiliation: FaBiT - Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
authors.forename: Paolo Emidio
authors.initials: PE
authors.lastname: Costantini
authors.affiliation: FaBiT - Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Pelliciari
authors.affiliation: FaBiT - Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Roncarati
authors.affiliation: Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy.|Doctoral School of Molecular and Translational Medicine, University of Milan, 20090 Segrate, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Puccio
authors.affiliation: Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.affiliation: DIMES Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy.
authors.forename: Clelia
authors.initials: C
authors.lastname: Peano
authors.affiliation: FaBiT - Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Danielli
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics / Q000378:metabolism*; D009532:Nickel / Q000378:metabolism* / Q000494:pharmacology; D012329:RNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D018085:Regulon / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000187:drug effects
chemical_list: D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; C523724:NikR protein, Helicobacter pylori; D012329:RNA, Bacterial; D012097:Repressor Proteins; D009532:Nickel