title: Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida).
abstract: The Ferric uptake regulator (Fur) is a global transcription factor that affects expression of bacterial genes in an iron-dependent fashion. Although the Fur protein and its iron-responsive regulon are well studied, there are still important questions that remain to be answered. For example, the consensus Fur binding site also known as the "Fur box" is under debate, and it is still unclear which Fur residues directly interact with the DNA. Our long-term goal is to dissect the biological roles of Fur in the development of the disease cold-water vibriosis, which is caused by the psychrophilic bacteria Aliivibrio salmonicida (also known as Vibrio salmonicida). Here, we have used experimental and computational methods to characterise the Fur protein from A. salmonicida (AS-Fur). Electrophoretic mobility shift assays show that AS-Fur binds to the recently proposed vibrio Fur box consensus in addition to nine promoter regions that contain Fur boxes. Binding appears to be dependent on the number of Fur boxes, and the predicted "strength" of Fur boxes. Finally, structure modeling and molecular dynamics simulations provide new insights into potential AS-Fur-DNA interactions.
authors.affiliation: Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Tromsø, N-9037, Norway.
authors.forename: Hege Lynum
authors.initials: HL
authors.lastname: Pedersen
authors.forename: Rafi
authors.initials: R
authors.lastname: Ahmad
authors.forename: Ellen Kristin
authors.initials: EK
authors.lastname: Riise
authors.forename: Hanna-Kirsti Schrøder
authors.initials: HK
authors.lastname: Leiros
authors.forename: Stefan
authors.initials: S
authors.lastname: Hauglid
authors.forename: Sigrun
authors.initials: S
authors.lastname: Espelid
authors.forename: Bjøn Olav
authors.initials: BO
authors.lastname: Brandsdal
authors.forename: Ingar
authors.initials: I
authors.lastname: Leiros
authors.forename: Nils-Peder
authors.initials: NP
authors.lastname: Willassen
authors.forename: Peik
authors.initials: P
authors.lastname: Haugen
mesh_terms: D044165:Aliivibrio salmonicida / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D005290:Ferric Compounds / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005290:Ferric Compounds; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial