title: Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis.
abstract: BACKGROUND
  Acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at pH2 and obtains energy by the oxidation of sulfur and iron. It is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. Effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. Nearly complete genome sequences of A. ferrooxidans are available from two public sources and we have exploited this information to reconstruct aspects of its sulfur metabolism.
  
  
  RESULTS
  Two candidate mechanisms for sulfate uptake from the environment were detected but both belong to large paralogous families of membrane transporters and their identification remains tentative. Prospective genes, pathways and regulatory mechanisms were identified that are likely to be involved in the assimilation of sulfate into cysteine and in the formation of Fe-S centers. Genes and regulatory networks were also uncovered that may link sulfur assimilation with nitrogen fixation, hydrogen utilization and sulfur reduction. Potential pathways were identified for sulfation of extracellular metabolites that may possibly be involved in cellular attachment to pyrite, sulfur and other solid substrates.
  
  
  CONCLUSIONS
  A bioinformatic analysis of the genome sequence of A. ferrooxidans has revealed candidate genes, metabolic process and control mechanisms potentially involved in aspects of sulfur metabolism. Metabolic modeling provides an important preliminary step in understanding the unusual physiology of this extremophile especially given the severe difficulties involved in its genetic manipulation and biochemical analysis.
authors.affiliation: Laboratory of Bioinformatics and Genome Biology, University of Santiago (USACH), Santiago, Chile. joorge77@yahoo.com.mx
authors.forename: Jorge
authors.initials: J
authors.lastname: Valdés
authors.forename: Felipe
authors.initials: F
authors.lastname: Veloso
authors.forename: Eugenia
authors.initials: E
authors.lastname: Jedlicki
authors.forename: David
authors.initials: D
authors.lastname: Holmes
mesh_terms: D000250:Adenosine Phosphosulfate / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D020563:Gammaproteobacteria / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D007506:Iron-Sulfur Proteins / Q000235:genetics / Q000378:metabolism; D026901:Membrane Transport Proteins; D008954:Models, Biological; D008969:Molecular Sequence Data; D010724:Phosphoadenosine Phosphosulfate / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013430:Sulfate Adenylyltransferase / Q000235:genetics / Q000378:metabolism; D000076988:Sulfate Transporters; D013431:Sulfates / Q000378:metabolism; D013440:Sulfides / Q000378:metabolism; D013447:Sulfites / Q000378:metabolism; D013455:Sulfur / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D007506:Iron-Sulfur Proteins; D026901:Membrane Transport Proteins; C085609:SLC26A4 protein, human; D000076988:Sulfate Transporters; D013431:Sulfates; D013440:Sulfides; D013447:Sulfites; D010724:Phosphoadenosine Phosphosulfate; D000250:Adenosine Phosphosulfate; D013455:Sulfur; D013430:Sulfate Adenylyltransferase