title: Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans.
abstract: BACKGROUND
  Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus.
  
  
  RESULTS
  Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa3 oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool.
  
  
  CONCLUSIONS
  Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.
authors.affiliation: Center for Bioinformatics and Genome Biology, MIFAB, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile. rquatrini@yahoo.com.ar
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
authors.forename: Corinne
authors.initials: C
authors.lastname: Appia-Ayme
authors.forename: Yann
authors.initials: Y
authors.lastname: Denis
authors.forename: Eugenia
authors.initials: E
authors.lastname: Jedlicki
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
authors.forename: Violaine
authors.initials: V
authors.lastname: Bonnefoy
mesh_terms: D042763:Acidithiobacillus / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007501:Iron / Q000378:metabolism*; D055432:Metabolomics; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D012329:RNA, Bacterial / Q000235:genetics; D013457:Sulfur Compounds / Q000378:metabolism*
chemical_list: D012329:RNA, Bacterial; D013457:Sulfur Compounds; D007501:Iron
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