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Bioinformatics and Genomics of Iron- and Sulfur-Oxidizing Acidophiles

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Geomicrobiology: Molecular and Environmental Perspective

Abstract

Important protagonists in geomicrobiology are the “biomining” microorganisms which are used to recover valuable metals from mineral ores and concentrates. These microorganisms either convert insoluble metal sulfides to soluble metal sulfates, a process referred to as bioleaching, or weaken the ore by removing iron and/or sulfur making the valuable metal accessible to subsequent chemical treatment, a process known as biooxidation (Rawlings 2005; Rawlings and Johnson 2007). The drawback of this industrial biotechnology is the formation of acid mine drainage (AMD) from uncontrolled abandoned mines, mine dumps or tailing dams, and acid rock drainage when sulfide-rich ores are exposed to air and weathering.

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References

  • Acosta M, Beard S, Ponce J, Vera M, Mobarec JC, Jerez CA (2005) Identification of putative sulfurtransferase genes in the extremophilic Acidithiobacillus ferrooxidans ATCC23270 genome: structural and functional characterization of the proteins. OMICS 9:13–29

    Article  PubMed  CAS  Google Scholar 

  • Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci USA 104:1883–1888

    Article  PubMed  CAS  Google Scholar 

  • Amaro AM, Chamorro D, Seeger M, Arredondo R, Peirano I, Jerez CA (1991) Effect of external pH perturbations on in vivo protein synthesis by the acidophilic bacterium Thiobacillus ferrooxidans. J Bacteriol 173:910–915

    PubMed  CAS  Google Scholar 

  • Amouric A, Appia-Ayme C, Yarzabal A, Bonnefoy V (2009) Regulation of the iron and sulfur oxidation pathways in the acidophilic Acidithiobacillus ferrooxidans. Adv Mat Res 71–73:163–166

    Article  Google Scholar 

  • Appia-Ayme C, Guiliani N, Ratouchniak J, Bonnefoy V (1999) Characterization of an operon encoding two c-type cytochromes, an aa(3)-type cytochrome oxidase, and rusticyanin in Thiobacillus ferrooxidans ATCC 33020. Appl Environ Microbiol 65:4781–4787

    PubMed  CAS  Google Scholar 

  • Appia-Ayme C, Quatrini R, Denis Y et al (2006) Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans. Hydrometallurgy 83:273–280

    Article  CAS  Google Scholar 

  • Auernik KS, Kelly RM (2008) Identification of components of electron transport chains in the extremely thermoacidophilic crenarchaeon Metallosphaera sedula through iron and sulfur compound oxidation transcriptomes. Appl Environ Microbiol 74:7723–7732

    Article  PubMed  CAS  Google Scholar 

  • Auernik KS, Maezato Y, Blum PH, Kelly RM (2008) The genome sequence of the metal-mobilizing, extremely thermoacidophilic archaeon Metallosphaera sedula provides insights into bioleaching-associated metabolism. Appl Environ Microbiol 74:682–692

    Article  PubMed  CAS  Google Scholar 

  • Baker-Austin C, Dopson M, Wexler M, Sawers RG, Bond PL (2005) Molecular insight into extreme copper resistance in the extremophilic archaeon ‘Ferroplasma acidarmanus’ Fer1. Microbiology 151:2637–2646

    Article  PubMed  CAS  Google Scholar 

  • Baker-Austin C, Dopson M, Wexler M, Sawers RG, Stemmler A, Rosen BP, Bond PL (2007) Extreme arsenic resistance by the acidophilic archaeon ‘Ferroplasma acidarmanus’ Fer1. Extremophiles 11:425–434

    Article  PubMed  CAS  Google Scholar 

  • Barreto M, Quatrini R, Bueno S, Arriagada C, Valdes J, Silver S, Jedlicki E, Holmes DS (2003) Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an ­analysis of its partial genome sequence. Hydrometallurgy 71:97–105

    Article  CAS  Google Scholar 

  • Barreto M, Gehrke T, Harneit K, Sand W, Jedlicki E, Holmes DS (2005a) Unexpected insights into biofilm formation by Acidithiobacillus ferrooxidans revealed by genome analysis and experimental approaches. In: Harrison STL, Rawlings DE, Petersen J (eds) Proceedings of the 16th international biohydrometallurgy symposium. Compress, Cape Town, South Africa, pp 817–825

    Google Scholar 

  • Barreto M, Jedlicki E, Holmes DS (2005b) Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans. Appl Environ Microbiol 71:2902–2909

    Article  PubMed  CAS  Google Scholar 

  • Bathe S, Norris PR (2007) Ferrous iron- and sulfur-induced genes in Sulfolobus metallicus. Appl Environ Microbiol 73:2491–2497

    Article  PubMed  CAS  Google Scholar 

  • Baumler DJ, Jeong KC, Fox BG, Banfield JF, Kaspar CW (2005) Sulfate requirement for heterotrophic growth of “Ferroplasma acidarmanus” strain fer1. Res Microbiol 156:492–498

    Article  PubMed  CAS  Google Scholar 

  • Blackstock WP, Weir MP (1999) Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 17:121–127

    Article  PubMed  CAS  Google Scholar 

  • Bouchal P, Zdrahal Z, Helanova S, Janiczek O, Hallberg KB, Mandl M (2006) Proteomic and bioinformatic analysis of iron- and sulfur-oxidizing Acidithiobacillus ferrooxidans using immobilized pH gradients and mass spectrometry. Proteomics 15:4278–4285

    Article  CAS  Google Scholar 

  • Brasseur G, Bruscella P, Bonnefoy V, Lemesle-Meunier D (2002) The bc(1) complex of the iron-grown acidophilic chemolithotrophic bacterium Acidithiobacillus ferrooxidans functions in the reverse but not in the forward direction. Is there a second bc(1) complex? Biochim Biophys Acta 1555:37–43

    Article  PubMed  CAS  Google Scholar 

  • Brasseur G, Levican G, Bonnefoy V, Holmes D, Jedlicki E, Lemesle-Meunier D (2004) Apparent redundancy of electron transfer pathways via bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans. Biochim Biophys Acta 1656:114–126

    Article  PubMed  CAS  Google Scholar 

  • Bruscella P, Cassagnaud L, Ratouchniak J, Brasseur G, Lojou E, Amils R, Bonnefoy V (2005) The HiPIP from the acidophilic Acidithiobacillus ferrooxidans is correctly processed and translocated in Escherichia coli, in spite of the periplasm pH difference between these two micro-organisms. Microbiology 151:1421–1431

    Article  PubMed  CAS  Google Scholar 

  • Bruscella P, Appia-Ayme C, Levican G, Ratouchniak J, Jedlicki E, Holmes DS, Bonnefoy V (2007) Differential expression of two bc 1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation. Microbiology 153:102–110

    Article  PubMed  CAS  Google Scholar 

  • Buonfiglio V, Polidoro M, Soyer F, Valenti P, Shively J (1999) A novel gene encoding a sulfur-regulated outer membrane protein in Thiobacillus ferrooxidans. J Biotechnol 72:85–93

    Article  PubMed  CAS  Google Scholar 

  • Cardenas JP, Martinez V, Covarrubias PC, Holmes DS, Quatrini R (2009) Predicted CO/CO2 fixation in Ferroplasma spp. via a novel chimaeric pathway. Adv Mat Res 71–73:219–222

    Article  Google Scholar 

  • Castro M, Ruiz LM, Díaz M, Mamani S, Jerez CA, Holmes DS, Guiliani N (2009) c-di-GMP pathway in biomining bacteria. Adv Mat Res 71–73:223–226

    Article  Google Scholar 

  • Chen L, Brugger K, Skovgaard M et al (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 187:4992–4999

    Article  PubMed  CAS  Google Scholar 

  • Chi A, Valenzuela L, Beard S, Mackey AJ, Shabanowitz J, Hunt DF, Jerez CA (2007) Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis. Mol Cell Proteomics 6:2239–2251

    Article  PubMed  CAS  Google Scholar 

  • Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC (2007a) Proteome analysis of Sulfolobus solfataricus P2 propanol metabolism. J Proteome Res 6:1430–1439

    Article  PubMed  CAS  Google Scholar 

  • Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC (2007b) Proteome and transcriptional analysis of ethanol-grown Sulfolobus solfataricus P2 reveals ADH2, a potential alcohol dehydrogenase. J Proteome Res 6:3985–3994

    Article  PubMed  CAS  Google Scholar 

  • Dharmadi Y, Gonzalez R (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog 20:1309–1324

    Article  PubMed  CAS  Google Scholar 

  • Dopson M, Baker-Austin C, Bond PL (2005) Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation. Microbiology 151:4127–4137

    Article  PubMed  CAS  Google Scholar 

  • Dopson M, Baker-Austin C, Bond P (2007) Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon ‘Ferroplasma acidarmanus’ Fer1. Extremophiles 11:159–168

    Article  PubMed  CAS  Google Scholar 

  • Esparza M, Bowien B, Holmes DS, Jedlicki E (2009) Gene organization and CO2-responsive expression of four cbb operons in the biomining bacterium Acidithiobacillus ferrooxidans. Adv Mat Res 71–73:207–210

    Article  Google Scholar 

  • Farah C, Vera M, Morin D, Haras D, Jerez CA, Guiliani N (2005) Evidence for a functional quorum-sensing type AI-1 system in the extremophilic bacterium Acidithiobacillus ferrooxidans. Appl Environ Microbiol 71:7033–7040

    Article  PubMed  CAS  Google Scholar 

  • Felício AP, Garcia Junior O, Bertolini MC, Ottoboni LMM, Novo MTM (2003) The effects of copper ions on the synthesis of periplasmic and membrane proteins in Acidithiobacillus ferrooxidans as analyzed by SDS-PAGE and 2D-PAGE. Hydrometallurgy 71:165–171

    Article  CAS  Google Scholar 

  • Ferrer M, Golyshina OV, Beloqui A, Golyshin PN, Timmis KN (2007) The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 445:91–94

    Article  PubMed  CAS  Google Scholar 

  • Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J (2005) Prokaryotic sulfur oxidation. Curr Opin Microbiol 8:253–259

    Article  PubMed  CAS  Google Scholar 

  • Gihring TM, Bond PL, Peters SC, Banfield JF (2003) Arsenic resistance in the archaeon “Ferroplasma acidarmanus”: new insights into the structure and evolution of the ars genes. Extremophiles 7:123–130

    PubMed  CAS  Google Scholar 

  • Goltsman DS, Denef VJ, Singer SW et al (2009) Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 75:4599–4615

    Article  PubMed  CAS  Google Scholar 

  • Götz D, Paytubi S, Munro S, Lundgren M, Bernander R, White MF (2007) Responses of hyperthermophilic crenarchaea to UV irradiation. Genome Biol 8:R220

    Article  PubMed  CAS  Google Scholar 

  • Hallberg KB, Johnson DB (2001) Biodiversity of acidophilic prokaryotes. Adv Appl Microbiol 49:37–84

    Article  PubMed  CAS  Google Scholar 

  • He Z, Zhong H, Hu Y, Xiao S, Liu J, Xu J, Li G (2005a) Analysis of differential-expressed proteins of Acidithiobacillus ferrooxidans grown under phosphate starvation. J Biochem Mol Biol 38:545–549

    Article  PubMed  CAS  Google Scholar 

  • He ZG, Hu YH, Zhong H, Hu WX, Xu J (2005b) Preliminary proteomic analysis of Thiobacillus ­ferrooxidans growing on elemental sulphur and Fe2+ separately. J Biochem Mol Biol 38:307–313

    Article  PubMed  CAS  Google Scholar 

  • Holmes DS, Bonnefoy V (2007) Genetic and bioinformatic insights into iron and sulfur oxidation mechanisms of bioleaching organisms. In: Rawlings DE, Johnson DB (eds) Biomining. Springer, Berlin/Heidelberg, pp 281–307

    Chapter  Google Scholar 

  • Janosch C, Thyssen C, Vera M, Bonnefoy V, Rohwerder T, Sand W (2009) Sulfur oxygenase reductase in different Acidithiobacillus caldus-like strains. Adv Mat Res 71–73:239–242

    Article  Google Scholar 

  • Jeans C, Singer SW, Chan CS, Verberkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP (2008) Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J 2:542–550

    Article  PubMed  CAS  Google Scholar 

  • Jerez CA (2007) Proteomics and metaproteomics applied to biomining microorganisms. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Dordrecht, The Netherlands, pp 241–251

    Chapter  Google Scholar 

  • Jerez CA, Varela P, Osorio G, Seeger M, Amaro AM, Toledo H (1995) Differential gene expression of Thiobacillus ferrooxidans under different environmental conditions. In: Holmes DS, Smith RW (eds) Mineral bioprocessing (vol 2). The Minerals, Metals and Materials Society, Warrendale, PA, pp 111–121

    Google Scholar 

  • Kanao T, Kamimura K, Sugio T (2007) Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans. J Biotechnol 132:16–22

    Article  PubMed  CAS  Google Scholar 

  • Kawarabayasi Y, Hino Y, Horikawa H et al (2001) Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 8:123–140

    Article  PubMed  CAS  Google Scholar 

  • Levicán G, Bruscella P, Guacunano M, Inostroza C, Bonnefoy V, Holmes DS, Jedlicki E (2002) Characterization of the petI and res operons of Acidithiobacillus ferrooxidans. J Bacteriol 184:1498–1501

    Article  PubMed  CAS  Google Scholar 

  • Levicán G, Ugalde JA, Ehrenfeld N, Maass A, Parada P (2008) Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9:581

    Article  PubMed  CAS  Google Scholar 

  • Lo I, Denef VJ, Verberkmoes NC et al (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537–541

    Article  PubMed  CAS  Google Scholar 

  • Lundgren M, Bernander R (2007) Genome-wide transcription map of an archaeal cell cycle. Proc Natl Acad Sci USA 104:2939–2944

    Article  PubMed  CAS  Google Scholar 

  • Moreno-Paz M, Parro V (2006) Amplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions. Environ Microbiol 8:1064–1073

    Article  PubMed  CAS  Google Scholar 

  • Muller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A (2004) Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol 53:1147–1160

    Article  PubMed  CAS  Google Scholar 

  • Norris PR (2007) Acidophile diversity in mineral sulfide oxidation. In: Rawlings DE, Johnson DB (eds) Biomining. Springer, Berlin/Heidelberg, pp 199–216

    Chapter  Google Scholar 

  • Novo MT, da Silva AC, Moreto R, Cabral PC, Costacurta A, Garcia O Jr, Ottoboni LM (2000) Thiobacillus ferrooxidans response to copper and other heavy metals: growth, protein synthesis and protein phosphorylation. Antonie Leeuwenhoek 77:187–195

    Article  PubMed  CAS  Google Scholar 

  • Novo MT, Garcia Junior O, Ottoboni LM (2003) Protein profile of Acidithiobacillus ferrooxidans strains exhibiting different levels of tolerance to metal sulfates. Curr Microbiol 47:492–496

    Article  PubMed  CAS  Google Scholar 

  • Osorio G, Varela P, Arredondo R, Seeger M, Amaro AM, Jerez CA (1993) Changes in global gene expression of Thiobacillus ferrooxidans when grown on elemental sulfur. In: Torma AE, Apel ML, Brierley CL (eds) Biohydrometallurgical technologies (vol 2). The Minerals, Metals and Material Society, Warrendale, PA, pp 565–575

    Google Scholar 

  • Osorio H, Martinez V, Nieto PA, Holmes DS, Quatrini R (2008a) Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiol 8:203

    Article  PubMed  CAS  Google Scholar 

  • Osorio H, Martinez V, Veloso FA, Pedroso I, Valdes J, Jedlicki E, Holmes DS, Quatrini R (2008b) Iron homeostasis strategies in acidophilic iron oxidizers: studies in Acidithiobacillus and Leptospirillum. Hydrometallurgy 94:175–179

    Article  CAS  Google Scholar 

  • Osorio H, Cárdenas JP, Valdés J, Holmes DS (2009) Prediction of Fnr regulated genes and metabolic pathways potentially involved in anaerobic growth of Acidithiobacillus ferrooxidans. Adv Mat Res 71–73:195–198

    Article  Google Scholar 

  • Parro V, Moreno-Paz M (2003) Gene function analysis in environmental isolates: the nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc Natl Acad Sci USA 100:7883–7888

    Article  PubMed  CAS  Google Scholar 

  • Parro V, Moreno-Paz M (2004) Nitrogen fixation in acidophile iron-oxidizing bacteria: the nif regulon of Leptospirillum ferrooxidans. Res Microbiol 155:703–709

    Article  PubMed  CAS  Google Scholar 

  • Paulino LC, de Mello MP, Ottoboni LM (2002) Differential gene expression in response to copper in Acidithiobacillus ferrooxidans analyzed by RNA arbitrarily primed polymerase chain reaction. Electrophoresis 23:520–527

    Article  PubMed  CAS  Google Scholar 

  • Quatrini R, Jedlicki E, Holmes DS (2005) Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans. J Ind Microbiol Biotechnol 32:606–614

    Article  PubMed  CAS  Google Scholar 

  • Quatrini R, Appia-Ayme C, Denis Y et al (2006) Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling. Hydrometallurgy 83:263–272

    Article  CAS  Google Scholar 

  • Quatrini R, Lefimil C, Veloso FA, Pedroso I, Holmes DS, Jedlicki E (2007a) Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res 35:2153–2166

    Article  PubMed  CAS  Google Scholar 

  • Quatrini R, Martinez V, Osorio H, Veloso FA, Pedroso I, Valdés J, Jedlicki E, Holmes DS (2007b) Iron homeostasis strategies in acidophilic iron oxidizers: comparative genomic analyses. Adv Mat Res 20–21:531–534

    Article  Google Scholar 

  • Quatrini R, Valdés J, Jedlicki E, Holmes DS (2007c) The use of bioinformatics and genomic ­biology to advance our understanding of bioleaching microorganisms. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Dordrecht, The Netherlands, pp 221–239

    Chapter  Google Scholar 

  • Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes DS, Bonnefoy V (2009) Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10:394

    Article  PubMed  CAS  Google Scholar 

  • Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915–1920

    Article  PubMed  CAS  Google Scholar 

  • Ramirez P, Toledo H, Guiliani N, Jerez CA (2002) An exported rhodanese-like protein is induced during growth of Acidithiobacillus ferrooxidans in metal sulfides and different sulfur compounds. Appl Environ Microbiol 68:1837–1845

    Article  PubMed  CAS  Google Scholar 

  • Ramirez P, Guiliani N, Valenzuela L, Beard S, Jerez CA (2004) Differential protein expression during growth of Acidithiobacillus ferrooxidans on ferrous iron, sulfur compounds, or metal sulfides. Appl Environ Microbiol 70:4491–4498

    Article  PubMed  CAS  Google Scholar 

  • Rawlings DE (2002) Heavy metal mining using microbes. Annu Rev Microbiol 56:65–91

    Article  PubMed  CAS  Google Scholar 

  • Rawlings DE (2005) Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microb Cell Fact 4:13

    Article  PubMed  CAS  Google Scholar 

  • Rawlings DE, Johnson DB (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153:315–324

    Article  PubMed  CAS  Google Scholar 

  • Rivas M, Seeger M, Jedlicki E, Holmes DS (2007) Second acyl homoserine lactone production system in the extreme acidophile Acidithiobacillus ferrooxidans. Appl Environ Microbiol 73:3225–3231

    Article  PubMed  CAS  Google Scholar 

  • Rohwerder T, Sand W (2007) Mechanisms and biochemical fundamentals of bacterial metal sulfide oxidation. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Dordrecht, The Netherlands, pp 35–58

    Chapter  Google Scholar 

  • Ruiz LM, Sand W, Jerez CA, Guiliani N (2007) c-di-GMP pathway in Acidithiobacillus ferrooxidans: analysis of putative diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) bifunctional proteins. Adv Mat Res 20–21:551–555

    Article  Google Scholar 

  • Rzhepishevska OI, Valdés J, Marcinkeviciene L, Gallardo CA, Meskys R, Bonnefoy V, Holmes DS, Dopson M (2007) Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds. Appl Environ Microbiol 73:7367–7372

    Article  PubMed  CAS  Google Scholar 

  • Salzano AM, Febbraio F, Farias T, Cetrangolo GP, Nucci R, Scaloni A, Manco G (2007) Redox stress proteins are involved in adaptation response of the hyperthermoacidophilic archaeon Sulfolobus solfataricus to nickel challenge. Microb Cell Fact 6:25

    Article  PubMed  CAS  Google Scholar 

  • Schippers A (2007) Microorganisms involved in bioleaching and nucleic acid-based molecular methods for their identification and quantification. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Dordrecht, The Netherlands, pp 3–33

    Chapter  Google Scholar 

  • Seeger M, Jerez CA (1993a) Phosphate-starvation induced changes in Thiobacillus ferrooxidans. FEMS Microbiol Lett 108:35–41

    Article  PubMed  CAS  Google Scholar 

  • Seeger M, Jerez CA (1993b) Response of Thiobacillus ferrooxidans to phosphate limitation. FEMS Microbiol Rev 11:37–42

    Article  CAS  Google Scholar 

  • Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M (2000) Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. Proc Natl Acad Sci USA 97:3509–3514

    Article  PubMed  CAS  Google Scholar 

  • She Q, Singh RK, Confalonieri F et al (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835–7840

    Article  PubMed  CAS  Google Scholar 

  • Shmaryahu A, Holmes DS (2007) Discovery of small regulatory RNAs in the extremophile Acidithiobacillus genus suggests novel genetic regulation. Adv Mat Res 20–21:535–538

    Article  Google Scholar 

  • Shmaryahu A, Lefimil C, Jedlicki E, Holmes DS (2009) Small regulatory RNA genes in Acidithiobacillus ferrooxidans: case studies of 6S RNA and Frr. Adv Mat Res 71–73:223–226

    Google Scholar 

  • Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF (2008) Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol 6:e177

    Article  PubMed  CAS  Google Scholar 

  • Singer SW, Chan CS, Zemla A, VerBerkmoes NC, Hwang M, Hettich RL, Banfield JF, Thelen MP (2008) Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community. Appl Environ Microbiol 74:4454–4462

    Article  PubMed  CAS  Google Scholar 

  • Snijders AP, Walther J, Peter S, Kinnman I, de Vos MG, van de Werken HJ, Brouns SJ, van der Oost J, Wright PC (2006) Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis. Proteomics 6:1518–1529

    Article  PubMed  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  PubMed  CAS  Google Scholar 

  • Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71:6319–6324

    Article  PubMed  CAS  Google Scholar 

  • Urich T, Bandeiras TM, Leal SS et al (2004) The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Biochem J 381:137–146

    Article  PubMed  CAS  Google Scholar 

  • Valdés JH, Holmes DS (2009) Genomic lessons from biomining organisms: case study of the Acidithiobacillus genus. Adv Mat Res 71–73:215–218

    Article  Google Scholar 

  • Valdés J, Veloso F, Jedlicki E, Holmes D (2003) Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis. BMC Genomics 4:51

    Article  PubMed  Google Scholar 

  • Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R 2nd, Eisen JA, Holmes DS (2008a) Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9:597

    Article  PubMed  CAS  Google Scholar 

  • Valdés J, Pedroso I, Quatrini R, Holmes DS (2008b) Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: insights into their metabolism and ecophysiology. Hydrometallurgy 94:180–184

    Article  CAS  Google Scholar 

  • Valdés J, Quatrini R, Hallberg K, Mangold S, Dopson M, Valenzuela PD, Holmes DS (2009) Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the Acidithiobacillus genus. J Bacteriol 191:614–622

    Article  CAS  Google Scholar 

  • Valenzuela L, Beard S, Guiliani N, Jerez CA (2005) Differencial expression proteomics of Acidithiobacillus ferrooxidans grown in different oxidizable substrates: study of the sulfate/thiosulfate/molybdate binding proteins. In: Harrison STL, Rawlings DE, Petersen J (eds) 16th International biohydrometallurgy symposium. Compress Cape Town, South Africa, Cape Town, South Africa, pp 773–780

    Google Scholar 

  • Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA (2006) Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol Adv 24:197–211

    Article  PubMed  CAS  Google Scholar 

  • Valenzuela S, Banderas A, Jerez CA, Guiliani N (2007) Cell-cell communication in bacteria. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Dordrecht, The Netherlands, pp 253–264

    Chapter  Google Scholar 

  • Varela P, Jerez CA (1992) Identification and characterization of GroEL and DnaK homologues in Thiobacillus ferrooxidans. FEMS Microbiol Lett 77:149–153

    Article  PubMed  CAS  Google Scholar 

  • Vera M, Guiliani N, Jerez CA (2003) Proteomic and genomic analysis of the phosphate starvation response of Acidithiobacillus ferrooxidans. Hydrometallurgy 71:125–132

    Article  CAS  Google Scholar 

  • Vera M, Rohwerder T, Bellenberg S, Sand W, Denis Y, Bonnefoy V (2009) Characterization of biofilm formation by the bioleaching acidophilic bacterium Acidithiobacillus ferrooxidans by a microarray transcriptome analysis. Adv Mat Res 71–73:175–178

    Article  Google Scholar 

  • Wilmes P, Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 6:911–920

    Article  PubMed  CAS  Google Scholar 

  • Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14:92–97

    Article  PubMed  CAS  Google Scholar 

  • Yarzábal A, Brasseur G, Bonnefoy V (2002a) Cytochromes c of Acidithiobacillus ferrooxidans. FEMS Microbiol Lett 209:189–195

    PubMed  Google Scholar 

  • Yarzábal A, Brasseur G, Ratouchniak J, Lund K, Lemesle-Meunier D, DeMoss JA, Bonnefoy V (2002b) The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. J Bacteriol 184:313–317

    Article  PubMed  Google Scholar 

  • Yarzábal A, Appia-Ayme C, Ratouchniak J, Bonnefoy V (2004) Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150:2113–2123

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

The author acknowledges DS Holmes (Universidad Andres Bello, Santiago, Chile) and N Guiliani (Universidad de Chile, Santiago, Chile) to give her access to information before publication.

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Correspondence to Violaine Bonnefoy .

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Bonnefoy, V. (2010). Bioinformatics and Genomics of Iron- and Sulfur-Oxidizing Acidophiles. In: Barton, L., Mandl, M., Loy, A. (eds) Geomicrobiology: Molecular and Environmental Perspective. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9204-5_8

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