TY - JOUR
T1 - Acidithiobacillus ferrooxidans metabolism
T2 - From genome sequence to industrial applications
AU - Valdés, Jorge
AU - Pedroso, Inti
AU - Quatrini, Raquel
AU - Dodson, Robert J.
AU - Tettelin, Herve
AU - Blake, Robert
AU - Eisen, Jonathan A.
AU - Holmes, David S.
N1 - Funding Information:
We thank Joel Malek, the laboratory, IT and Bioinformatics staff at The Institute for Genomic Research (now incorporated within the JC Venter Institute) for assistance with sequencing and analysis. Work supported by Fondecyt 1050063, Fondecyt 11060164, DI-UNAB 34-06, DI-UNAB 15-06/ I, and a Microsoft Sponsored Research Award. The sequencing and annotation was supported by the U.S. Department of Energy, Office of Biological Energy Research, Cooperative Agreement DE-FC02-95ER61962 to TIGR.
PY - 2008/12/11
Y1 - 2008/12/11
N2 - Background: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
AB - Background: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. Results: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. Conclusion: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
UR - http://www.scopus.com/inward/record.url?scp=58249113952&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-9-597
DO - 10.1186/1471-2164-9-597
M3 - Article
C2 - 19077236
AN - SCOPUS:58249113952
VL - 9
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 597
ER -