Metal-responsive promoter DNA compaction by the ferric uptake regulator

• Published in: Nature communications 2016-08, Vol.7 (1), p.12593-12593, Article 12593
• Main Authors: Roncarati, Davide, Pelliciari, Simone, Doniselli, Nicola, Maggi, Stefano, Vannini, Andrea, Valzania, Luca, Mazzei, Luca, Zambelli, Barbara, Rivetti, Claudio, Danielli, Alberto
• Format: Article
• Language: English
• Subjects: 38; 631/1647/328/1262; 631/326/421; 631/337/572/2102; Acids; Bacterial Proteins - metabolism; Base Sequence; DNA, Bacterial - genetics; Gene Expression Regulation, Bacterial - drug effects; Helicobacter pylori - drug effects; Helicobacter pylori - genetics; Helicobacter pylori - metabolism; Homeostasis; Humanities and Social Sciences; Ions; Iron - metabolism; Kinases; Macromolecular Substances - metabolism; Microscopy; Microscopy, Atomic Force; Models, Biological; multidisciplinary; Nickel; Nucleoproteins - metabolism; Operator Regions, Genetic - genetics; Promoter Regions, Genetic; Protein Binding; Repressor Proteins - metabolism; Science; Science (multidisciplinary); Transcription, Genetic - drug effects
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms12593

Short-range DNA looping has been proposed to affect promoter activity in many bacterial species and operator configurations, but only few examples have been experimentally investigated in molecular detail. Here we present evidence for a metal-responsive DNA condensation mechanism controlled by the Helicobacter pylori ferric uptake regulator (Fur), an orthologue of the widespread Fur family of prokaryotic metal-dependent regulators. H. pylori Fur represses the transcription of the essential arsRS acid acclimation operon through iron-responsive oligomerization and DNA compaction, encasing the arsR transcriptional start site in a repressive macromolecular complex. A second metal-dependent regulator NikR functions as nickel-dependent anti-repressor at this promoter, antagonizing the binding of Fur to the operator elements responsible for the DNA condensation. The results allow unifying H. pylori metal ion homeostasis and acid acclimation in a mechanistically coherent model, and demonstrate, for the first time, the existence of a selective metal-responsive DNA compaction mechanism controlling bacterial transcriptional regulation. The Fur protein regulates transcription of bacterial genes in response to metal ions. Here, the authors show that the Fur protein from Helicobacter pylori represses transcription by iron-responsive oligomerization and DNA compaction, encasing the transcriptional start site in a macromolecular complex.