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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 394.
Published online Aug 24, 2009. doi:  10.1186/1471-2164-10-394
PMCID: PMC2754497
Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans
Raquel Quatrini,#1 Corinne Appia-Ayme,#2,5 Yann Denis,3 Eugenia Jedlicki,4 David S Holmes,1 and Violaine Bonnefoycorresponding author2
1Center for Bioinformatics and Genome Biology, MIFAB, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile
2Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Marseille, France
3Platforme Transcriptome, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Marseille, France
4Cellular and Molecular Biology, Faculty of Medicine, University of Chile, Santiago, Chile
5Institute for Food Research, Norwich Research Park, Colney Lane, Norwich, NR4 7AU, UK
corresponding authorCorresponding author.
#Contributed equally.
Raquel Quatrini: rquatrini/at/yahoo.com.ar; Corinne Appia-Ayme: appiaayme/at/gmail.com; Yann Denis: ydenis/at/ifr88.cnrs-mrs.fr; Eugenia Jedlicki: e.jedlicki/at/yahoo.com; David S Holmes: dsholmes2000/at/yahoo.com; Violaine Bonnefoy: bonnefoy/at/ifr88.cnrs-mrs.fr
Received May 17, 2009; Accepted August 24, 2009.
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.
Conclusion
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.
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