title: Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans.
abstract: The gamma-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif), transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx, trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles.
authors.affiliation: Center for Bioinformatics and Genome Biology, MIFAB, Life Science Foundation and Andrés Bello University, Santiago, Chile. rquatrini@yahoo.com.ar
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
authors.forename: Claudia
authors.initials: C
authors.lastname: Lefimil
authors.forename: Felipe A
authors.initials: FA
authors.lastname: Veloso
authors.forename: Inti
authors.initials: I
authors.lastname: Pedroso
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.forename: Eugenia
authors.initials: E
authors.lastname: Jedlicki
mesh_terms: D042763:Acidithiobacillus / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D016384:Consensus Sequence; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics / Q000379:methods; D007501:Iron / Q000378:metabolism; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D018085:Regulon; D012097:Repressor Proteins / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; D007501:Iron