This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
... Vol. 22 (1998), p. 341 [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Bla... more ... Vol. 22 (1998), p. 341 [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Blake II, J. Eisen and DS Holmes: BMC genomics Vol. 9 (2008), p. 597 ... [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Blake II, J. Eisen and DS Holmes: BMC genomics Vol. ...
... 71-73 149 Page 8. [3] University of Copenhagen, Unpublished [4] DOE Joint Genome Institute, U... more ... 71-73 149 Page 8. [3] University of Copenhagen, Unpublished [4] DOE Joint Genome Institute, Unpublished [5] Center of Bioinformatics and Genome Biology Fundación Ciencia para la Vida, Unpublished [6] J. Valdés, I. Pedroso, R. Quatrini, RJ Dodson, H. Tettelin, R.2nd. ...
Background: Iron is an essential nutrient but can be toxic at high intracellular concentrations a... more Background: Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 10 18 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer) A. thiooxidans and A. caldus (sulfur oxidizers) that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below.
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
... Vol. 22 (1998), p. 341 [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Bla... more ... Vol. 22 (1998), p. 341 [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Blake II, J. Eisen and DS Holmes: BMC genomics Vol. 9 (2008), p. 597 ... [6] J. Valdés, I. Pedroso, R. Quatrini, R. Dodson, H. Tettelin, R. Blake II, J. Eisen and DS Holmes: BMC genomics Vol. ...
... 71-73 149 Page 8. [3] University of Copenhagen, Unpublished [4] DOE Joint Genome Institute, U... more ... 71-73 149 Page 8. [3] University of Copenhagen, Unpublished [4] DOE Joint Genome Institute, Unpublished [5] Center of Bioinformatics and Genome Biology Fundación Ciencia para la Vida, Unpublished [6] J. Valdés, I. Pedroso, R. Quatrini, RJ Dodson, H. Tettelin, R.2nd. ...
Background: Iron is an essential nutrient but can be toxic at high intracellular concentrations a... more Background: Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 10 18 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer) A. thiooxidans and A. caldus (sulfur oxidizers) that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below.
An understanding of the physiology and metabolic complexity of microbial consortia involved in me... more An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced Acidithiobacilli and other biomining genomes available in public databases. Species specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown roles that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.
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