Acidithiobacillus ferrooxidans metabolism

From genome sequence to industrial applications

Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J. Dodson, Herve Tettelin, Robert Blake, Jonathan A Eisen, David S. Holmes

Research output: Contribution to journalArticle

273 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number597
JournalBMC Genomics
Volume9
DOIs
StatePublished - Dec 11 2008

Fingerprint

Acidithiobacillus
Sulfur
Metals
Genome
Copper
Carbon
Iron
Anaerobiosis
Proteobacteria
Quorum Sensing
Nitrogen Fixation
Poisons
Genetic Association Studies
Biofilms
Computational Biology
Atmosphere
DNA Repair
Computer Simulation
Minerals
Hydrogen

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Valdés, J., Pedroso, I., Quatrini, R., Dodson, R. J., Tettelin, H., Blake, R., ... Holmes, D. S. (2008). Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications. BMC Genomics, 9, [597]. https://doi.org/10.1186/1471-2164-9-597

Acidithiobacillus ferrooxidans metabolism : From genome sequence to industrial applications. / Valdés, Jorge; Pedroso, Inti; Quatrini, Raquel; Dodson, Robert J.; Tettelin, Herve; Blake, Robert; Eisen, Jonathan A; Holmes, David S.

In: BMC Genomics, Vol. 9, 597, 11.12.2008.

Research output: Contribution to journalArticle

Valdés, J, Pedroso, I, Quatrini, R, Dodson, RJ, Tettelin, H, Blake, R, Eisen, JA & Holmes, DS 2008, 'Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications', BMC Genomics, vol. 9, 597. https://doi.org/10.1186/1471-2164-9-597
Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R et al. Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications. BMC Genomics. 2008 Dec 11;9. 597. https://doi.org/10.1186/1471-2164-9-597
Valdés, Jorge ; Pedroso, Inti ; Quatrini, Raquel ; Dodson, Robert J. ; Tettelin, Herve ; Blake, Robert ; Eisen, Jonathan A ; Holmes, David S. / Acidithiobacillus ferrooxidans metabolism : From genome sequence to industrial applications. In: BMC Genomics. 2008 ; Vol. 9.
@article{978ac34feb8842eca7e8c61e721634b3,
title = "Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications",
abstract = "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.",
author = "Jorge Vald{\'e}s and Inti Pedroso and Raquel Quatrini and Dodson, {Robert J.} and Herve Tettelin and Robert Blake and Eisen, {Jonathan A} and Holmes, {David S.}",
year = "2008",
month = "12",
day = "11",
doi = "10.1186/1471-2164-9-597",
language = "English (US)",
volume = "9",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",

}

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.

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

UR - http://www.scopus.com/inward/citedby.url?scp=58249113952&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-9-597

DO - 10.1186/1471-2164-9-597

M3 - Article

VL - 9

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 597

ER -