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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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Jones S, Santini JM. Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms. Essays Biochem 2023; 67:685-699. [PMID: 37449416 PMCID: PMC10427800 DOI: 10.1042/ebc20220257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.
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Affiliation(s)
- Sarah Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, U.K
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
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Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions. THE ISME JOURNAL 2021; 15:3221-3238. [PMID: 34007059 PMCID: PMC8528912 DOI: 10.1038/s41396-021-00995-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 02/04/2023]
Abstract
Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases.
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Barragán CE, Márquez MA, Dopson M, Montoya D. RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite. Extremophiles 2021; 25:143-158. [PMID: 33616780 DOI: 10.1007/s00792-021-01217-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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Affiliation(s)
- Carlos Eduardo Barragán
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Marco Antonio Márquez
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems EEMiS, Linnaeus University, Kalmar, Sweden
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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Zhan Y, Yang M, Zhang S, Zhao D, Duan J, Wang W, Yan L. Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans. World J Microbiol Biotechnol 2019; 35:60. [PMID: 30919119 DOI: 10.1007/s11274-019-2632-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022]
Abstract
Acidithiobacillus ferrooxidans is a gram-negative, autotrophic and rod-shaped bacterium. It can gain energy through the oxidation of Fe(II) and reduced inorganic sulfur compounds for bacterial growth when oxygen is sufficient. It can be used for bio-leaching and bio-oxidation and contributes to the geobiochemical circulation of metal elements and nutrients in acid mine drainage environments. The iron and sulfur oxidation pathways of A. ferrooxidans play key roles in bacterial growth and survival under extreme circumstances. Here, the electrons transported through the thermodynamically favourable pathway for the reduction to H2O (downhill pathway) and against the redox potential gradient reduce to NAD(P)(H) (uphill pathway) during the oxidation of Fe(II) were reviewed, mainly including the electron transport carrier, relevant operon and regulation of its expression. Similar to the electron transfer pathway, the sulfur oxidation pathway of A. ferrooxidans, related genes and operons, sulfur oxidation mechanism and sulfur oxidase system are systematically discussed.
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Affiliation(s)
- Yue Zhan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Mengran Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Jiangong Duan
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, Gansu Province, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China. .,College of Food Science, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China.
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Razmilic V, Castro JF, Marchant F, Asenjo JA, Andrews B. Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes. Antonie van Leeuwenhoek 2018; 111:1479-1491. [DOI: 10.1007/s10482-018-1031-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/25/2018] [Indexed: 01/16/2023]
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Kernan T, West AC, Banta S. Characterization of endogenous promoters for control of recombinant gene expression in
Acidithiobacillus ferrooxidans. Biotechnol Appl Biochem 2017; 64:793-802. [DOI: 10.1002/bab.1546] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/16/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Timothy Kernan
- Department of Physiology & Cellular Biophysics Columbia University New York NY USA
| | - Alan C. West
- Department of Chemical Engineering Columbia University New York NY USA
| | - Scott Banta
- Department of Chemical Engineering Columbia University New York NY USA
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Dopson M, Holmes DS, Lazcano M, McCredden TJ, Bryan CG, Mulroney KT, Steuart R, Jackaman C, Watkin ELJ. Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions. Front Microbiol 2017; 7:2132. [PMID: 28111571 PMCID: PMC5216662 DOI: 10.3389/fmicb.2016.02132] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022] Open
Abstract
Extremely acidophilic microorganisms (pH optima for growth of ≤3) are utilized for the extraction of metals from sulfide minerals in the industrial biotechnology of “biomining.” A long term goal for biomining has been development of microbial consortia able to withstand increased chloride concentrations for use in regions where freshwater is scarce. However, when challenged by elevated salt, acidophiles experience both osmotic stress and an acidification of the cytoplasm due to a collapse of the inside positive membrane potential, leading to an influx of protons. In this study, we tested the ability of the halotolerant acidophile Acidihalobacter prosperus to grow and catalyze sulfide mineral dissolution in elevated concentrations of salt and identified chloride tolerance mechanisms in Ac. prosperus as well as the chloride susceptible species, Acidithiobacillus ferrooxidans. Ac. prosperus had optimum iron oxidation at 20 g L−1 NaCl while At. ferrooxidans iron oxidation was inhibited in the presence of 6 g L−1 NaCl. The tolerance to chloride in Ac. prosperus was consistent with electron microscopy, determination of cell viability, and bioleaching capability. The Ac. prosperus proteomic response to elevated chloride concentrations included the production of osmotic stress regulators that potentially induced production of the compatible solute, ectoine uptake protein, and increased iron oxidation resulting in heightened electron flow to drive proton export by the F0F1 ATPase. In contrast, At. ferrooxidans responded to low levels of Cl− with a generalized stress response, decreased iron oxidation, and an increase in central carbon metabolism. One potential adaptation to high chloride in the Ac. prosperus Rus protein involved in ferrous iron oxidation was an increase in the negativity of the surface potential of Rus Form I (and Form II) that could help explain how it can be active under elevated chloride concentrations. These data have been used to create a model of chloride tolerance in the salt tolerant and susceptible species Ac. prosperus and At. ferrooxidans, respectively.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
| | - David S Holmes
- Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile; Center for Bioinformatics and Genome Biology, Fundacion Ciencia y VidaSantiago, Chile
| | - Marcelo Lazcano
- Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile; Center for Bioinformatics and Genome Biology, Fundacion Ciencia y VidaSantiago, Chile
| | - Timothy J McCredden
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Christopher G Bryan
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Kieran T Mulroney
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Robert Steuart
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Connie Jackaman
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Elizabeth L J Watkin
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
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Are there multiple mechanisms of anaerobic sulfur oxidation with ferric iron in Acidithiobacillus ferrooxidans ? Res Microbiol 2016; 167:357-66. [DOI: 10.1016/j.resmic.2016.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/17/2022]
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Talla E, Hedrich S, Mangenot S, Ji B, Johnson DB, Barbe V, Bonnefoy V. Insights into the pathways of iron- and sulfur-oxidation, and biofilm formation from the chemolithotrophic acidophile Acidithiobacillus ferrivorans CF27. Res Microbiol 2014; 165:753-60. [PMID: 25154051 DOI: 10.1016/j.resmic.2014.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/29/2014] [Accepted: 08/07/2014] [Indexed: 11/15/2022]
Abstract
The iron-oxidizing acidithiobacilli cluster into at least four groups, three of which (Acidithiobacillus ferrooxidans, Acidithiobacillus ferridurans and Acidithiobacillus ferrivorans) have been designated as separate species. While these have many physiological traits in common, they differ in some phenotypic characteristics including motility, and pH and temperature minima. In contrast to At. ferrooxidans and At. ferridurans, all At. ferrivorans strains analysed to date possess the iro gene (encoding an iron oxidase) and, with the exception of strain CF27, the rusB gene encoding an iso-rusticyanin whose exact function is uncertain. Strain CF27 differs from other acidithiobacilli by its marked propensity to form macroscopic biofilms in liquid media. To identify the genetic determinants responsible for the oxidation of ferrous iron and sulfur and for the formation of extracellular polymeric substances, the genome of At. ferrivorans CF27 strain was sequenced and comparative genomic studies carried out with other Acidithiobacillus spp.. Genetic disparities were detected that indicate possible differences in ferrous iron and reduced inorganic sulfur compounds oxidation pathways among iron-oxidizing acidithiobacilli. In addition, strain CF27 is the only sequenced Acidithiobacillus spp. to possess genes involved in the biosynthesis of fucose, a sugar known to confer high thickening and flocculating properties to extracellular polymeric substances.
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Affiliation(s)
- Emmanuel Talla
- Aix-Marseille Université and Centre National de la Recherche Scientifique, LCB UMR7283, 31 chemin J. Aiguier, 13402 Marseilles Cedex 20, France.
| | - Sabrina Hedrich
- College of Natural Sciences, Bangor University, Brambell Building, Deiniol Road, LL57 2UW Bangor Gwynedd, UK.
| | - Sophie Mangenot
- CEA/IG/Genoscope, Laboratoire de finition, 2 rue Gaston Cremieux, CP5706, 91057 Evry Cedex, France.
| | - Boyang Ji
- Aix-Marseille Université and Centre National de la Recherche Scientifique, LCB UMR7283, 31 chemin J. Aiguier, 13402 Marseilles Cedex 20, France.
| | - D Barrie Johnson
- College of Natural Sciences, Bangor University, Brambell Building, Deiniol Road, LL57 2UW Bangor Gwynedd, UK.
| | - Valérie Barbe
- CEA/IG/Genoscope, Laboratoire de finition, 2 rue Gaston Cremieux, CP5706, 91057 Evry Cedex, France.
| | - Violaine Bonnefoy
- Aix-Marseille Université and Centre National de la Recherche Scientifique, LCB UMR7283, 31 chemin J. Aiguier, 13402 Marseilles Cedex 20, France.
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ten Brink F, Schoepp-Cothenet B, van Lis R, Nitschke W, Baymann F. Multiple Rieske/cytb complexes in a single organism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1392-406. [PMID: 23507620 DOI: 10.1016/j.bbabio.2013.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Most organisms contain a single Rieske/cytb complex. This enzyme can be integrated in any respiratory or photosynthetic electron transfer chain that is quinone-based and sufficiently energy rich to allow for the turnover of three enzymes - a quinol reductase, a Rieske/cytb complex and a terminal oxidase. Despite this universal usability of the enzyme a variety of phylogenetically distant organisms have multiple copies thereof and no reason for this redundancy is obvious. In this review we present an overview of the distribution of multiple copies among species and describe their properties from the scarce experimental results, analysis of their amino acid sequences and genomic context. We discuss the predicted redox properties of the Rieske cluster in relation to the nature of the pool quinone. It appears that acidophilic iron-oxidizing bacteria specialized one of their two copies for reverse electron transfer, archaeal Thermoprotei adapted their three copies to the interaction with different oxidases and several, phylogenetically unrelated species imported a second complex with a putative heme ci that may confer some yet to be determined properties to the complex. These hypothesis and all the more the so far completely unexplained cases call for further studies and we put forward a number of suggestions for future research that we hope to be stimulating for the field. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- F ten Brink
- BIP/UMR7281, FR3479, CNRS/AMU, 13 chemin Joseph Aiguier, 13009 Marseille, France
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Ferrous iron oxidation by sulfur-oxidizing Acidithiobacillus ferrooxidans and analysis of the process at the levels of transcription and protein synthesis. Antonie van Leeuwenhoek 2013; 103:905-19. [DOI: 10.1007/s10482-012-9872-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/24/2012] [Indexed: 11/26/2022]
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Mineral respiration under extreme acidic conditions: from a supramolecular organization to a molecular adaptation in Acidithiobacillus ferrooxidans. Biochem Soc Trans 2012; 40:1324-9. [DOI: 10.1042/bst20120141] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotrophic Gram-negative bacterium that can derive energy from the oxidation of ferrous iron at pH 2 using oxygen as electron acceptor. The study of this bacterium has economic and fundamental biological interest because of its use in the industrial extraction of copper and uranium from ores. For this reason, its respiratory chain has been analysed in detail in recent years. Studies have shown the presence of a functional supercomplex that spans the outer and the inner membranes and allows a direct electron transfer from the extracellular Fe2+ ions to the inner membrane cytochrome c oxidase. Iron induces the expression of two operons encoding proteins implicated in this complex as well as in the regeneration of the reducing power. Most of these are metalloproteins that have been characterized biochemically, structurally and biophysically. For some of them, the molecular basis of their adaptation to the periplasmic acidic environment has been described. Modifications in the metal surroundings have been highlighted for cytochrome c and rusticyanin, whereas, for the cytochrome c oxidase, an additional partner that maintains its stability and activity has been demonstrated recently.
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Ouyang J, Liu Q, Li B, Ao J, Chen X. Proteomic Analysis of Differential Protein Expression in Acidithiobacillus ferrooxidans Grown on Ferrous Iron or Elemental Sulfur. Indian J Microbiol 2012; 53:56-62. [PMID: 24426079 DOI: 10.1007/s12088-012-0322-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 10/16/2012] [Indexed: 01/23/2023] Open
Abstract
In this study, a proteomic analysis of Acidithiobacillus ferrooxidans by two-dimensional electrophoresis identified 24 proteins that were differentially expressed when the cells were grown on ferrous iron (Fe(2+)) or elemental sulfur (S°). Sixteen of these proteins were upregulated by growth on S° or downregulated by growth on Fe(2+), including four proteins involved in disulfide bond reduction such as pyridine nucleotide-disulfide oxidoreductase, heterodisulfide reductase subunit B, thioredoxin-disulfide reductase, and cysteine desulfurase IscS, and three proteins involved in saccharide metabolism. A total of eight proteins were upregulated by growth on Fe(2+) or downregulated by S°. Northern blots further confirmed the differences in transcription for these differentially expressed proteins. We functionally characterized cysteine desulfurase IscS, and found that its overexpression in E. coli promoted the growth of the cells in LB containing 2.5 % sodium thiosulfate. Our results provide new insights into the molecular basis for S° and Fe(2+) oxidation by this extreme acidophile.
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Affiliation(s)
- Jianping Ouyang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography State Oceanic Administration, 184 Daxue Road, Xiamen, 361005 People's Republic of China
| | - Qian Liu
- School of Resource Processing and Bioengineering, Central South University, Hunan, People's Republic of China
| | - Bo Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography State Oceanic Administration, 184 Daxue Road, Xiamen, 361005 People's Republic of China
| | - Jingqun Ao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography State Oceanic Administration, 184 Daxue Road, Xiamen, 361005 People's Republic of China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography State Oceanic Administration, 184 Daxue Road, Xiamen, 361005 People's Republic of China
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Ilbert M, Bonnefoy V. Insight into the evolution of the iron oxidation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:161-75. [PMID: 23044392 DOI: 10.1016/j.bbabio.2012.10.001] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 01/01/2023]
Abstract
Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O(2). This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Marianne Ilbert
- Aix-Marseille Université, CNRS, BIP UMR7281,13009, Marseille, France.
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Kucera J, Bouchal P, Cerna H, Potesil D, Janiczek O, Zdrahal Z, Mandl M. Kinetics of anaerobic elemental sulfur oxidation by ferric iron in Acidithiobacillus ferrooxidans and protein identification by comparative 2-DE-MS/MS. Antonie van Leeuwenhoek 2011; 101:561-73. [PMID: 22057833 DOI: 10.1007/s10482-011-9670-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/27/2011] [Indexed: 11/25/2022]
Abstract
Elemental sulfur oxidation by ferric iron in Acidithiobacillus ferrooxidans was investigated. The apparent Michaelis constant for ferric iron was 18.6 mM. An absence of anaerobic ferric iron reduction ability was observed in bacteria maintained on elemental sulfur for an extended period of time. Upon transition from ferrous iron to elemental sulfur medium, the cells exhibited similar kinetic characteristics of ferric iron reduction under anaerobic conditions to those of cells that were originally maintained on ferrous iron. Nevertheless, a total loss of anaerobic ferric iron reduction ability after the sixth passage in elemental sulfur medium was demonstrated. The first proteomic screening of total cell lysates of anaerobically incubated bacteria resulted in the detection of 1599 protein spots in the master two-dimensional electrophoresis gel. A set of 59 more abundant and 49 less abundant protein spots that changed their protein abundances in an anaerobiosis-dependent manner was identified and compared to iron- and sulfur-grown cells, respectively. Proteomic analysis detected a significant increase in abundance under anoxic conditions of electron transporters, such as rusticyanin and cytochrome c(552), involved in the ferrous iron oxidation pathway. Therefore we suggest the incorporation of rus-operon encoded proteins in the anaerobic respiration pathway. Two sulfur metabolism proteins were identified, pyridine nucleotide-disulfide oxidoreductase and sulfide-quinone reductase. The important transcription regulator, ferric uptake regulation protein, was anaerobically more abundant. The anaerobic expression of several proteins involved in cell envelope formation indicated a gradual adaptation to elemental sulfur oxidation.
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Affiliation(s)
- Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
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Merino M, Andrews B, Asenjo J. Stoichiometric model and metabolic flux analysis for Leptospirillum ferrooxidans. Biotechnol Bioeng 2010; 107:696-706. [DOI: 10.1002/bit.22851] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes DS, Bonnefoy V. Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 2009; 10:394. [PMID: 19703284 PMCID: PMC2754497 DOI: 10.1186/1471-2164-10-394] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Accepted: 08/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus. Results Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa3 oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool. Conclusion Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.
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Affiliation(s)
- Raquel Quatrini
- Center for Bioinformatics and Genome Biology, MIFAB, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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Nieto PA, Covarrubias PC, Jedlicki E, Holmes DS, Quatrini R. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol Biol 2009; 10:63. [PMID: 19555508 PMCID: PMC2713239 DOI: 10.1186/1471-2199-10-63] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 06/25/2009] [Indexed: 01/14/2023] Open
Abstract
Background Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis and for the validation of microarray profiling data in microbial systems. The choice and use of reference genes that are stably expressed across samples, experimental conditions and designs is a key consideration for the accurate interpretation of gene expression data. Results Here, we evaluate a carefully selected set of reference genes derived from previous microarray-based transcriptional profiling experiments performed on Acidithiobacillus ferrooxidans and identify a set of genes with minimal variability under five different experimental conditions that are frequently used in Acidithiobacilli research. Suitability of these and other previously reported reference genes to monitor the expression of four selected target genes from A. ferrooxidans grown with different energy sources was investigated. Utilization of reference genes map, rpoC, alaS and era results in improved interpretation of gene expression profiles in A. ferrooxidans. Conclusion This investigation provides a validated set of reference genes for studying A. ferrooxidans gene expression under typical biological conditions and an initial point of departure for exploring new experimental setups in this microorganism and eventually in other closely related Acidithiobacilli. The information could also be of value for future transcriptomic experiments in other bacterial systems.
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Hold C, Andrews B, Asenjo J. A stoichiometric model ofAcidithiobacillus ferrooxidansATCC 23270 for metabolic flux analysis. Biotechnol Bioeng 2009; 102:1448-59. [DOI: 10.1002/bit.22183] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 2008; 9:597. [PMID: 19077236 PMCID: PMC2621215 DOI: 10.1186/1471-2164-9-597] [Citation(s) in RCA: 325] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 12/11/2008] [Indexed: 11/10/2022] Open
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, gamma-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.
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Affiliation(s)
- Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile.
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Energetic problems faced by micro-organisms growing or surviving on parsimonious energy sources and at acidic pH: I. Acidithiobacillus ferrooxidans as a paradigm. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1471-9. [DOI: 10.1016/j.bbabio.2008.08.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 08/20/2008] [Accepted: 08/25/2008] [Indexed: 11/24/2022]
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Chi A, Valenzuela L, Beard S, Mackey AJ, Shabanowitz J, Hunt DF, Jerez CA. Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis. Mol Cell Proteomics 2007; 6:2239-51. [PMID: 17911085 PMCID: PMC4631397 DOI: 10.1074/mcp.m700042-mcp200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile capable of obtaining energy by oxidizing ferrous iron or sulfur compounds such as metal sulfides. Some of the proteins involved in these oxidations have been described as forming part of the periplasm of this extremophile. The detailed study of the periplasmic components constitutes an important area to understand the physiology and environmental interactions of microorganisms. Proteomics analysis of the periplasmic fraction of A. ferrooxidans ATCC 23270 was performed by using high resolution linear ion trap-FT MS. We identified a total of 131 proteins in the periplasm of the microorganism grown in thiosulfate. When possible, functional categories were assigned to the proteins: 13.8% were transport and binding proteins, 14.6% were several kinds of cell envelope proteins, 10.8% were involved in energy metabolism, 10% were related to protein fate and folding, 10% were proteins with unknown functions, and 26.1% were proteins without homologues in databases. These last proteins are most likely characteristic of A. ferrooxidans and may have important roles yet to be assigned. The majority of the periplasmic proteins from A. ferrooxidans were very basic compared with those of neutrophilic microorganisms such as Escherichia coli, suggesting a special adaptation of the chemolithoautotrophic bacterium to its very acidic environment. The high throughput proteomics approach used here not only helps to understand the physiology of this extreme acidophile but also offers an important contribution to the functional annotation for the available genomes of biomining microorganisms such as A. ferrooxidans for which no efficient genetic systems are available to disrupt genes by procedures such as homologous recombination.
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Affiliation(s)
- An Chi
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Lissette Valenzuela
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology and Cell Dynamics and Biotechnology Institute, Faculty of Sciences, University of Chile, Santiago 7800024, Chile
| | - Simon Beard
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology and Cell Dynamics and Biotechnology Institute, Faculty of Sciences, University of Chile, Santiago 7800024, Chile
| | - Aaron J. Mackey
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
- Department of Pathology, University of Virginia, Charlottesville, Virginia 22908
| | - Carlos A. Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology and Cell Dynamics and Biotechnology Institute, Faculty of Sciences, University of Chile, Santiago 7800024, Chile
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Bruscella P, Appia-Ayme C, Levicán G, Ratouchniak J, Jedlicki E, Holmes DS, Bonnefoy V. Differential expression of two bc1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation. MICROBIOLOGY-SGM 2007; 153:102-10. [PMID: 17185539 DOI: 10.1099/mic.0.2006/000067-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three strains of the strict acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans, including the type strain ATCC 23270, contain a petIIABC gene cluster that encodes the three proteins, cytochrome c1, cytochrome b and a Rieske protein, that constitute a bc1 electron-transfer complex. RT-PCR and Northern blotting show that the petIIABC cluster is co-transcribed with cycA, encoding a cytochrome c belonging to the c4 family, sdrA, encoding a putative short-chain dehydrogenase, and hip, encoding a high potential iron-sulfur protein, suggesting that the six genes constitute an operon, termed the petII operon. Previous results indicated that A. ferrooxidans contains a second pet operon, termed the petI operon, which contains a gene cluster that is similarly organized except that it lacks hip. Real-time PCR and Northern blot experiments demonstrate that petI is transcribed mainly in cells grown in medium containing iron, whereas petII is transcribed in cells grown in media containing sulfur or iron. Primer extension experiments revealed possible transcription initiation sites for the petI and petII operons. A model is presented in which petI is proposed to encode the bc1 complex, functioning in the uphill flow of electrons from iron to NAD(P), whereas petII is suggested to be involved in electron transfer from sulfur (or formate) to oxygen (or ferric iron). A. ferrooxidans is the only organism, to date, to exhibit two functional bc1 complexes.
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Affiliation(s)
- Patrice Bruscella
- CNRS, Institut de Biologie Structurale et de Microbiologie, Laboratoire de Chimie Bactérienne, 31 chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
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Ouchane S, Nitschke W, Bianco P, Vermeglio A, Astier C. Multiple Rieske genes in prokaryotes: exchangeable Rieske subunits in the cytochrome bc-complex of Rubrivivax gelatinosus. Mol Microbiol 2005; 57:261-75. [PMID: 15948965 DOI: 10.1111/j.1365-2958.2005.04685.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial cytochrome bc1-complex encoded by the petABC operon consists of three subunits, the Rieske iron-sulphur protein, the b-type cytochrome, and the c1-type cytochrome. Disruption of the petA gene of Rubrivivax gelatinosus is not lethal under photosynthetic growth conditions. However, deletion of both petA and petB results in a photosynthesis-deficient strain, suggesting the presence of a second gene encoding a Rieske protein and rescuing a functional cytochrome bc1-complex in the PETA1 mutant. The corresponding petA2 gene was identified and the PETA2 mutant could also grow under photosynthetic conditions. The double mutant PETA12, however, was unable to grow photosynthetically. The presence of a photo-induced cyclic electron transfer was tested by monitoring the kinetics of cytochrome photo-oxidation on intact cells; the data confirm the capacity of petA2 to replace petA1 in the bc1-complex to support photosynthesis. Soluble forms of both PetA1 and PetA2 Rieske proteins were purified from Escherichia coli and found to contain correctly inserted [2Fe-2S] clusters. Electron paramagnetic resonance (EPR) spectroscopy and midpoint potential measurements showed typical [2Fe-2S] signals and E(m) values of +275 mV for both Rieske proteins. The high amino acid sequence similarity and the obtained midpoint potential values argue for a functional role of these proteins in the cytochrome bc1-complex. The presence of duplicated Rieske genes is not restricted to R. gelatinosus. Phylogenetic trees of Rieske genes from Rubrivivax and other proteobacteria as well as from cyanobacteria were reconstructed. On the basis of the phylogenetic analyses, differing evolutionary origins of duplicated Rieske genes in proteo- and cyanobacteria are proposed.
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Affiliation(s)
- Soufian Ouchane
- Centre de Génétique Moléculaire CNRS (UPR-2167) associéà l'Université Pierre et Marie Curie et Paris XI, France.
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Barreto M, Jedlicki E, Holmes DS. Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2005; 71:2902-9. [PMID: 15932984 PMCID: PMC1151869 DOI: 10.1128/aem.71.6.2902-2909.2005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cluster of five genes, proposed to be involved in the formation of extracellular polysaccharide (EPS) precursors via the Leloir pathway, have been identified in the acidophilic autotroph Acidithiobacillus ferrooxidans. The order of the genes is luxA-galE-galK-pgm-galM, encoding a LuxA-like protein, UDP-glucose 4-epimerase, galactokinase, phosphoglucomutase, and galactose mutarotase, respectively. The gal cluster forms a single transcriptional unit and is therefore an operon. Two other putative genes of the Leloir pathway, galU, potentially encoding UDP-glucose pyrophosphorylase, and a gene designated galT-like, which may encode a galactose-1-phosphate uridylyltransferase-like activity, were found unlinked in the genome. Using semiquantitative reverse transcription-PCR, the genes of the gal operon were shown to be expressed more during growth in iron medium than in growth in sulfur medium. The functions of galE, pgm, galU, and the galT-like gene were validated by complementation of Escherichia coli mutants and by in vitro enzyme assays. The data suggest that A. ferrooxidans is capable of synthesizing the EPS precursors UDP-glucose and UDP-galactose. In addition, genes rfbA, -B, -C, and -D were identified in the genome of A. ferrooxidans, suggesting that it can also synthesize the EPS precursor dTDP-rhamnose. Since EPSs constitute the major bulk of biofilms, this study may provide an initial model for the metabolic pathways involved in biofilm formation in A. ferrooxidans and aid in understanding the role of biofilms in mineral leaching and the formation of acid mine drainage.
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Affiliation(s)
- Marlen Barreto
- Laboratory of Bioinformatics and Genome Biology, Andres Bello University and Millennium Institute of Fundamental and Applied Biology, Santiago, Chile
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Brasseur G, Levican G, Bonnefoy V, Holmes D, Jedlicki E, Lemesle-Meunier D. Apparent redundancy of electron transfer pathways via bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1656:114-26. [PMID: 15178473 DOI: 10.1016/j.bbabio.2004.02.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 02/16/2004] [Accepted: 02/16/2004] [Indexed: 11/19/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotrophic bacterium that can grow in the presence of either the weak reductant Fe(2+), or reducing sulfur compounds that provide more energy for growth than Fe(2+). We have previously shown that the uphill electron transfer pathway between Fe(2+) and NAD(+) involved a bc(1) complex that functions only in the reverse direction [J. Bacteriol. 182, (2000) 3602]. In the present work, we demonstrate both the existence of a bc(1) complex functioning in the forward direction, expressed when the cells are grown on sulfur, and the presence of two terminal oxidases, a bd and a ba(3) type oxidase expressed more in sulfur than in iron-grown cells, besides the cytochrome aa(3) that was found to be expressed only in iron-grown cells. Sulfur-grown cells exhibit a branching point for electron flow at the level of the quinol pool leading on the one hand to a bd type oxidase, and on the other hand to a bc(1)-->ba(3) pathway. We have also demonstrated the presence in the genome of transcriptionally active genes potentially encoding the subunits of a bo(3) type oxidase. A scheme for the electron transfer chains has been established that shows the existence of multiple respiratory routes to a single electron acceptor O(2). Possible reasons for these apparently redundant pathways are discussed.
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Affiliation(s)
- G Brasseur
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, CNRS, 31 Chemin J. Aiguier 13402 Marseille Cedex 20, France
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Yarzábal A, Appia-Ayme C, Ratouchniak J, Bonnefoy V. Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology (Reading) 2004; 150:2113-2123. [PMID: 15256554 DOI: 10.1099/mic.0.26966-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The regulation of the expression of the rus operon, proposed to encode an electron transfer chain from the outer to the inner membrane in the obligate acidophilic chemolithoautroph Acidithiobacillus ferrooxidans, has been studied at the RNA and protein levels. As observed by Northern hybridization, real-time PCR and reverse transcription analyses, this operon was more highly expressed in ferrous iron- than in sulfur-grown cells. Furthermore, it was shown by immunodetection that components of this respiratory chain are synthesized in ferrous iron- rather than in sulfur-growth conditions. Nonetheless, weak transcription and translation products of the rus operon were detected in sulfur-grown cells at the early exponential phase. The results strongly support the notion that rus-operon expression is induced by ferrous iron, in agreement with the involvement of the rus-operon-encoded products in the oxidation of ferrous iron, and that ferrous iron is used in preference to sulfur.
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Affiliation(s)
- Andrés Yarzábal
- Laboratorio de Organización y Expresión del Gen, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Corinne Appia-Ayme
- Laboratoire de Chimie Bactérienne, CNRS, IBSM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Jeanine Ratouchniak
- Laboratoire de Chimie Bactérienne, CNRS, IBSM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, CNRS, IBSM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Brasseur G, Bruscella P, Bonnefoy V, Lemesle-Meunier D. 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? BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:37-43. [PMID: 12206888 DOI: 10.1016/s0005-2728(02)00251-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithotrophic bacterium that can grow in the presence of either a weak reductant, Fe(2+), or reducing sulfur compounds that provide more energy for growth than Fe(2+). Here we first review the latest findings about the uphill electron transfer pathway established in iron-grown A. ferrooxidans, which has been found to involve a bc(1) complex. We then provide evidence that this bc(1) complex cannot function in the forward direction (exergonic reaction), even with an appropriate substrate. A search for the sequence of the three redox subunits of the A. ferrooxidans bc(1) complex (strain ATCC 19859) in the complete genome sequence of the A. ferrooxidans ATCC 23270 strain showed the existence of two different bc(1) complexes in A. ferrooxidans. Cytochrome b and Rieske protein sequence comparisons allowed us to point out some sequence particularities of these proteins in A. ferrooxidans. Lastly, we discuss the possible reasons for the existence of two different "classical" bc(1) complexes and put forward some suggestions as to what role these putative complexes may play in this acidophilic chemolithotrophic bacterium.
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Affiliation(s)
- Gaël Brasseur
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie, CNRS, Marseille, France.
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Abstract
The chemolithoautotrophic Gram-negative bacterium Acidithiobacillus ferrooxidans is versatile and can grow on a number of electron donors and acceptors. In the A. ferrooxidans ATCC 23270 genome, computer analysis identified 11 genes encoding putative cytochromes c. At least eight putative cytochromes c were differentiated on gels in ATCC 33020 cells grown on ferrous iron or sulfur. All these cytochromes were associated with the inner or the outer membranes. Lower levels of total cytochromes c were observed in sulfur- than in ferrous iron-grown cells. One cytochrome c was specific for sulfur conditions while three were specific for iron conditions, suggesting that cytochrome c synthesis is modulated depending on the electron donor.
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Affiliation(s)
- Andrés Yarzábal
- Laboratoire de Chimie Bactérienne, I.B.S.M, C.N.R.S, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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