(Re)-definition of the holo- and apo-Fur direct regulons of Helicobacter pylori

• Published in: Journal of molecular biology 2024-05, Vol.436 (10), p.168573-168573, Article 168573
• Main Authors: Vannini, Andrea, Pinatel, Eva, Costantini, Paolo Emidio, Pelliciari, Simone, Roncarati, Davide, Puccio, Simone, De Bellis, Gianluca, Scarlato, Vincenzo, Peano, Clelia, Danielli, Alberto
• Format: Article
• Language: English
• Subjects: environmental response; Fur; Helicobacter pylori; HpFur; regulation of transcription
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2024.168573

[Display omitted] •H. pylori apo-/holo-Fur balance iron homeostasis by regulating partly known targets.•RNAseq and ChIPseq data integration comprehensively dissects direct holo-Fur regulons.•RNAseq-driven analysis unravels a large new portion of the direct apo-Fur regulon.•New targets of Fur are virulence factors, ncRNAs, unannotated ORFs, toxin-antitoxins.•(Re)defined Fur regulons link iron levels to adaptive reprogramming of the pathobiont. Iron homeostasis is a critical process for living organisms because this metal is an essential co-factor for fundamental biochemical activities, like energy production and detoxification, albeit its excess quickly leads to cell intoxication. The protein Fur (ferric uptake regulator) controls iron homeostasis in bacteria by switching from its apo- to holo-form as a function of the cytoplasmic level of ferrous ions, thereby modulating gene expression. The Helicobacter pylori HpFur protein has the rare ability to operate as a transcriptional commutator; apo- and holo-HpFur function as two different repressors with distinct DNA binding recognition properties for specific sets of target genes. Although the regulation of apo- and holo-HpFur in this bacterium has been extensively investigated, we propose a genome-wide redefinition of holo-HpFur direct regulon in H. pylori by integration of RNA-seq and ChIP-seq data, and a large extension of the apo-HpFur direct regulon. We show that in response to iron availability, new coding sequences, non-coding RNAs, toxin-antitoxin systems, and transcripts within open reading frames are directly regulated by apo- or holo-HpFur. These new targets and the more thorough validation and deeper characterization of those already known provide a complete and updated picture of the direct regulons of this two-faced transcriptional regulator.