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Espada‐Hinojosa S, Karthäuser C, Srivastava A, Schuster L, Winter T, de Oliveira AL, Schulz F, Horn M, Sievert S, Bright M. Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative. Mol Ecol Resour 2024; 24:e13889. [PMID: 38010882 PMCID: PMC10952691 DOI: 10.1111/1755-0998.13889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/31/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.
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Affiliation(s)
| | - Clarissa Karthäuser
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Abhishek Srivastava
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Lukas Schuster
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Deakin UniversityBurwoodAustralia
| | - Teresa Winter
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - André Luiz de Oliveira
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Frederik Schulz
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Present address:
DOE Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Matthias Horn
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Stefan Sievert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Monika Bright
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
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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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3
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Sand W, Schippers A, Hedrich S, Vera M. Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A. Appl Microbiol Biotechnol 2022; 106:6933-6952. [PMID: 36194263 PMCID: PMC9592645 DOI: 10.1007/s00253-022-12168-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Abstract Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia. Key points • Leaching of metal sulfides is strongly enhanced by microorganisms • Biofilm formation and extracellular polymer production influences bioleaching • Cell interactions in mixed bioleaching cultures are key for process optimization
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Affiliation(s)
- Wolfgang Sand
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany. .,Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.
| | - Axel Schippers
- Bundesanstalt für Geowissenschaften und Rohstoffe (BGR), Hannover, Germany
| | - Sabrina Hedrich
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Mario Vera
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Departamento de Ingeniería Hidráulica y Ambiental, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Pal N, Sinha S, Shivani, Chakraborty M. A review on bacterial and archaeal thermostable sulfur oxidoreductases (SORS)-an insight into the biochemical, molecular and in-silico structural comparative analysis of a neglected thermostable enzyme of industrial significance. Arch Microbiol 2022; 204:655. [PMID: 36175582 DOI: 10.1007/s00203-022-03256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
Diverse thermophilic microorganisms with the potential to withstand extreme physiological conditions have long been investigated and explored for human commercial benefit. Thermozymes with distinct functional and structural properties isolated from these thermophiles are known to have high thermostability without significant loss of specific enzyme activity. Thermophiles isolated and characterised from the thermophilic ecological niche of India are well documented. There is a plethora of work in the literature emphasising its industrial significance. However, in-depth knowledge of the thermophilic oxidoreductase group of enzymes (Oxizymes) is restricted. Sulfur Oxygenase Reductases or Sulfur Oxygen-Reductases (SORs) are a group of thermophilic oxizymes reported predominantly from thermophilic and mesophilic archaea and bacteria, which catalyse oxygen-dependent disproportionation reactions of elemental sulfur, producing sulfite, thiosulfate, and sulphide. There have been few reports on isolated and characterised SORs from the Indian geothermal niche. The review article will highlight the SORs reported till date with a concise overview of different archaeal and bacterial species producing the enzymes. Based on the literature available till date, characteristics including physico-chemical properties, amino acid sequence homology, conserved motifs and their 3D structure comparison have been discussed. In-silico sequence and structure level preliminary comparative analysis of various SORs has also been discussed. However, a few SORs whose structural information is not reported in the protein data bank have been modelled to enrich our analysis.
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Affiliation(s)
- Nirmalya Pal
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Sanjana Sinha
- NMR Micro-Imaging and Spectroscopy Laboratory, Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, 500007, Telangana, India
| | - Shivani
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Mitun Chakraborty
- Department of Biotechnology Engineering and Food Technology, University Institute of Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
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5
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Ferreira P, Fernandes P, Ramos M. The archaeal non-heme iron-containing Sulfur Oxygenase Reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Narayanan M, Natarajan D, Kandasamy S, Chinnathambi A, Ali Alharbi S, Karuppusamy I, Kathirvel B. Pyrite biomining proficiency of sulfur dioxygenase (SDO) enzyme extracted from Acidithiobacillus thiooxidans. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Sato Y, Yabuki T, Adachi N, Moriya T, Arakawa T, Kawasaki M, Yamada C, Senda T, Fushinobu S, Wakagi T. Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100030. [PMID: 32775998 PMCID: PMC7398979 DOI: 10.1016/j.yjsbx.2020.100030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
Sulfur oxygenase reductase (SOR) was biochemically and structurally characterized. High resolution structures of SOR were determined by crystallography and cryo-EM. Twenty-four identical subunits of SOR form a hollow sphere. Catalytic components exhibited different features in the crystal and cryo-EM structures.
Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of S. tokodaii (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.
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Key Words
- AaSOR, Acidianus ambivalens SOR
- AqSOR, Aquifex aeolicus SOR
- Archaea
- AtSOR, Acidianus tengchongensis SOR
- CTF, contrast transfer function
- Cryogenic electron microscopy
- DTNB, 5,5′-dithiobis(2-nitrobenzoic acid)
- FSC, Fourier shell correlation
- HnSOR, Halothiobacillus neapolitanus SOR
- Nonheme mononuclear iron center
- PAGE, polyacrylamide gel electrophoresis
- RMSD, root mean square deviation
- SD, standard deviation
- SDS, sodium dodecyl sulfate
- SOR, sulfur oxygenase reductase
- SbSOR, Sulfobacillus thermosulfidooxidans SOR
- StSOR, Sulfurisphaera tokodaii SOR
- Sulfur metabolism
- TpSOR, Thioalkalivibrio paradoxus SOR
- X-ray crystallography
- cryo-EM, cryogenic electron microscopy
- pCMB, p-chloromercuribenzoate
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Affiliation(s)
- Yuta Sato
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Yabuki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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8
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Buetti-Dinh A, Herold M, Christel S, El Hajjami M, Delogu F, Ilie O, Bellenberg S, Wilmes P, Poetsch A, Sand W, Vera M, Pivkin IV, Friedman R, Dopson M. Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics 2020; 21:23. [PMID: 31964336 PMCID: PMC6975020 DOI: 10.1186/s12859-019-3337-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. METHODS We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. RESULTS The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. CONCLUSIONS The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.
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Affiliation(s)
- Antoine Buetti-Dinh
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | | | - Francesco Delogu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Oslo, Norway
| | - Olga Ilie
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Sören Bellenberg
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- Center for Marine and Molecular Biotechnology, QNLM, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wolfgang Sand
- Faculty of Chemistry, Essen, Germany
- College of Environmental Science and Engineering, Donghua University, Shanghai, People’s Republic of China
- Mining Academy and Technical University Freiberg, Freiberg, Germany
| | - Mario Vera
- Institute for Biological and Medical Engineering. Schools of Engineering, Medicine & Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Hydraulic & Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Igor V. Pivkin
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
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Yin Z, Feng S, Tong Y, Yang H. Adaptive mechanism of Acidithiobacillus thiooxidans CCTCC M 2012104 under stress during bioleaching of low-grade chalcopyrite based on physiological and comparative transcriptomic analysis. ACTA ACUST UNITED AC 2019; 46:1643-1656. [DOI: 10.1007/s10295-019-02224-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/07/2019] [Indexed: 11/27/2022]
Abstract
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is often used for sulfur-bearing ores bioleaching, but its adaptive mechanism to harsh environments remains unclear. Here, we explored the adaptive mechanism of A. thiooxidans in the process of low-grade chalcopyrite bioleaching based on the physiology and comparative transcriptome analysis. It was indicated that A. thiooxidans maintains intracellular pH homeostasis by regulating unsaturated fatty acids, especially cyclopropane fatty acids, intracellular ATP, amino acid metabolism, and antioxidant factors. Comparative transcriptome analysis indicated that the key genes involved in sulfur oxidation, sor and soxABXYZ, were significantly up-regulated, generating more energy to resist extreme environmental stress by more active sulfur metabolism. Confocal laser scanning microscope analysis found that down-regulation of flagellar-related genes was likely to promote the biofilm formation. System-level understanding of leaching microorganisms under extreme stress can contribute to the evolution of these extremophiles via genetic engineering modification work, which further improves bioleaching in future.
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Affiliation(s)
- Zongwei Yin
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
| | - Yanjun Tong
- grid.258151.a 0000 0001 0708 1323 State Key Laboratory of Food Science and Technology Jiangnan University Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Food Science and Technology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
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10
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Buetti-Dinh A, Galli V, Bellenberg S, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M. Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. ACTA ACUST UNITED AC 2019; 22:e00321. [PMID: 30949441 PMCID: PMC6430008 DOI: 10.1016/j.btre.2019.e00321] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022]
Abstract
Deep learning has become widely used in different fields of computer science such as face recognition, but also in biology, for example to detect malignant skin cancers based on images. Deep learning applied to microscopy images of biofilm colonization patterns accurately characterized its bacterial composition. Deep learning applications only rarely outperform human experts in classification tasks. Here however, deep learning reached an accuracy of 90%, therefore clearly outperforming human experts (50% accurate). Our method provides an accurate alternative to standard, time-consuming biochemical methods, using visual information only.
Background Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases. Methods The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles. Results A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts. Conclusions Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods.
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Affiliation(s)
- Antoine Buetti-Dinh
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera italiana, Lugano, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author.
| | - Vanni Galli
- Institute for Information Systems and Networking, University of Applied Sciences of Southern Switzerland, Manno, Switzerland
| | - Sören Bellenberg
- Fakultät für Chemie, Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
| | - Olga Ilie
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera italiana, Lugano, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mariia Boretska
- Fakultät für Chemie, Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
| | - Igor V. Pivkin
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera italiana, Lugano, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Wolfgang Sand
- Fakultät für Chemie, Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
- College of Environmental Science and Engineering, Donghua University, Shanghai, People's Republic of China
- Mining Academy and Technical University Freiberg, Freiberg, Germany
| | - Mario Vera
- Institute for Biological and Medical Engineering. Schools of Engineering, Medicine & Biological Sciences, Department of Hydraulic & Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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11
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Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX. Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp. Front Microbiol 2019; 9:3290. [PMID: 30687275 PMCID: PMC6335251 DOI: 10.3389/fmicb.2018.03290] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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12
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Christel S, Herold M, Bellenberg S, Buetti-Dinh A, El Hajjami M, Pivkin IV, Sand W, Wilmes P, Poetsch A, Vera M, Dopson M. Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching. Front Microbiol 2018; 9:3059. [PMID: 30631311 PMCID: PMC6315122 DOI: 10.3389/fmicb.2018.03059] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidic ores that provides a more environmentally friendly alternative to many traditional metal extraction methods, such as roasting or smelting. Industrial interest is steadily increasing and today, circa 15-20% of the world's copper production can be traced back to this method. However, bioleaching of the world's most abundant copper mineral chalcopyrite suffers from low dissolution rates, often attributed to passivating layers, which need to be overcome to use this technology to its full potential. To prevent these passivating layers from forming, leaching needs to occur at a low oxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult and costly. As an alternative, selected weak iron-oxidizers could be employed that are incapable of scavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onset of bioleaching, but not high enough to allow for the occurrence of passivation. In this study, we report that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications. Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole iron oxidizer exhibited significantly lower redox potentials and higher release of copper compared to communities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic response to single and co-culture of these two iron oxidizers was studied and revealed a greatly decreased number of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured in the presence of L. ferriphilum. This allowed for the identification of genes potentially responsible for S. thermosulfidooxidans' weaker iron oxidation to be studied in the future, as well as underlined the need for new mechanisms to control the microbial population in bioleaching heaps.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Sören Bellenberg
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Aquatic Biotechnology, Universität Duisburg-Essen, Essen, Germany
| | - Antoine Buetti-Dinh
- Faculty of Informatics, Institute of Computational Science, Università della Svizzera Italiana, Lugano, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Igor V Pivkin
- Faculty of Informatics, Institute of Computational Science, Università della Svizzera Italiana, Lugano, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Wolfgang Sand
- Aquatic Biotechnology, Universität Duisburg-Essen, Essen, Germany.,College of Environmental Science and Engineering, Donghua University, Shanghai, China.,Mining Academy and Technical University Freiberg, Freiberg, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom
| | - Mario Vera
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Hydraulic and Environmental Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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13
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Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Balmer L, Frutschi M, Sommer G, Bernier-Latmani R. Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 2018; 9:2129. [PMID: 30245678 PMCID: PMC6137086 DOI: 10.3389/fmicb.2018.02129] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Louise Balmer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Guillaume Sommer
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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14
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Feng S, Lin X, Tong Y, Huang X, Yang H. Biodesulfurization of sulfide wastewater for elemental sulfur recovery by isolated Halothiobacillus neapolitanus in an internal airlift loop reactor. BIORESOURCE TECHNOLOGY 2018; 264:244-252. [PMID: 29843112 DOI: 10.1016/j.biortech.2018.05.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The biodesulfurization of sulfide wastewater for elemental sulfur recovery by isolated Halothiobacillus neapolitanus in an internal airlift loop reactor (IALR) was investigated. The flocculant producer Pseudomonas sp. strain N1-2 was used to deposit the produced elemental sulfur during biodesulfurization. The functional group analysis indicated that biofloculation was closely associated with NH and CO. The biodesulfurization system performed well under moderate water quality fluctuations (1.29-3.88 kg·m-3·d-1 COD; 1.54-3.08 kg·m-3·d-1·S2-) as it maintained stable S2- removal and sulfur flocculation rates. Meanwhile, the qRT-PCR analysis indicated that the transcriptional level of cbbL decreased in the presence of organic carbon, while the expressions of sqr, sat, and cytochrome C3 increased under higher sulfide stress. Moreover, the relative proportions of Halothiobacillus was strengthened via microbial intervention of the LJN1-3 strain. The S2- removal efficiency and elemental sulfur production was further improved by 32.5% and 28.2%, respectively, in an IALR.
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Affiliation(s)
- Shoushuai Feng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, People's Republic of China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, People's Republic of China; School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xu Lin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, People's Republic of China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, People's Republic of China; School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yanjun Tong
- National Engineering Research Center for Functional Food, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xing Huang
- WUXI City Environmental Technology Co., Ltd, People's Republic of China
| | - Hailin Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, People's Republic of China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, People's Republic of China; School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.
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15
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Rühl P, Haas P, Seipel D, Becker J, Kletzin A. Persulfide Dioxygenase From Acidithiobacillus caldus: Variable Roles of Cysteine Residues and Hydrogen Bond Networks of the Active Site. Front Microbiol 2018; 9:1610. [PMID: 30072973 PMCID: PMC6060420 DOI: 10.3389/fmicb.2018.01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/27/2018] [Indexed: 12/16/2022] Open
Abstract
Persulfide dioxygenases (PDOs) are abundant in Bacteria and also crucial for H2S detoxification in mitochondria. One of the two pdo-genes of the acidophilic bacterium Acidithiobacillus caldus was expressed in Escherichia coli. The protein (AcPDO) had 0.77 ± 0.1 Fe/subunit and an average specific sulfite formation activity of 111.5 U/mg protein (Vmax) at 40°C and pH 7.5 with sulfur and GSH following Michaelis-Menten kinetics. KM for GSH and Kcat were 0.5 mM and 181 s-1, respectively. Glutathione persulfide (GSSH) as substrate gave a sigmoidal curve with a Vmax of 122.3 U/mg protein, a Kcat of 198 s-1 and a Hill coefficient of 2.3 ± 0.22 suggesting positive cooperativity. Gel permeation chromatography and non-denaturing gels showed mostly tetramers. The temperature optimum was 40-45°C, the melting point 63 ± 1.3°C in thermal unfolding experiments, whereas low activity was measurable up to 95°C. Site-directed mutagenesis showed that residues located in the predicted GSH/GSSH binding site and in the central hydrogen bond networks including the iron ligands are essential for activity. Among these, the R139A, D141A, and H171A variants were inactive concomitant to a decrease of their melting points by 3-8 K. Other variants were inactivated without significant melting point change. Two out of five cysteines are likewise essential, both of which lie presumably in close proximity at the surface of the protein (C87 and C224). MalPEG labeling experiments suggests that they form a disulfide bridge. The reducing agent Tris(2-carboxyethyl)phosphine was inhibitory besides N-ethylmaleimide and iodoacetamide suggesting an involvement of cysteines and the disulfide in catalysis and/or protein stabilization. Mass spectrometry revealed modification of C87, C137, and C224 by 305 mass units equivalent to GSH after incubation with GSSH and with GSH in case of the C87A and C224A variants. The results of this study suggest that disulfide formation between the two essential surface-exposed cysteines and Cys-S-glutathionylation serve as a protective mechanism against uncontrolled thiol oxidation and the associated loss of enzyme activity.
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Affiliation(s)
| | | | | | | | - Arnulf Kletzin
- Department of Biology, Sulfur Biochemistry and Microbial Bioenergetics, Technische Universität Darmstadt, Darmstadt, Germany
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16
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Diversity of Sulfur-Oxidizing and Sulfur-Reducing Microbes in Diverse Ecosystems. ADVANCES IN SOIL MICROBIOLOGY: RECENT TRENDS AND FUTURE PROSPECTS 2018. [DOI: 10.1007/978-981-10-6178-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Urbieta MS, Rascovan N, Vázquez MP, Donati E. Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities. BMC Genomics 2017; 18:445. [PMID: 28587624 PMCID: PMC5461723 DOI: 10.1186/s12864-017-3828-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potential and metabolic pathways involved in the biomining activity of this group, we sequenced the genome of Acidianus copahuensis ALE1 strain, a novel thermoacidophilic crenarchaeon (optimum growth: 75 °C, pH 3) isolated from the volcanic geothermal area of Copahue at Neuquén province in Argentina. Previous experimental characterization of A. copahuensis revealed a high biomining potential, exhibited as high oxidation activity of sulfur and sulfur compounds, ferrous iron and sulfide minerals (e.g.: pyrite). This strain is also autotrophic and tolerant to heavy metals, thus, it can grow under adverse conditions for most forms of life with a low nutrient demand, conditions that are commonly found in mining environments. Results In this work we analyzed the genome of Acidianus copahuensis and describe the genetic pathways involved in biomining processes. We identified the enzymes that are most likely involved in growth on sulfur and ferrous iron oxidation as well as those involved in autotrophic carbon fixation. We also found that A. copahuensis genome gathers different features that are only present in particular lineages or species from the order Sulfolobales, some of which are involved in biomining. We found that although most of its genes (81%) were found in at least one other Sulfolobales species, it is not specifically closer to any particular species (60–70% of proteins shared with each of them). Although almost one fifth of A. copahuensis proteins are not found in any other Sulfolobales species, most of them corresponded to hypothetical proteins from uncharacterized metabolisms. Conclusion In this work we identified the genes responsible for the biomining metabolisms that we have previously observed experimentally. We provide a landscape of the metabolic potentials of this strain in the context of Sulfolobales and propose various pathways and cellular processes not yet fully understood that can use A. copahuensis as an experimental model to further understand the fascinating biology of thermoacidophilic biomining archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3828-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina. .,, Calle 50, entre 115 y 116, N° 227, La Plata, Buenos Aires, Argentina.
| | - Nicolás Rascovan
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Martín P Vázquez
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Edgardo Donati
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina
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18
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Straub CT, Zeldes BM, Schut GJ, Adams MWW, Kelly RM. Extremely thermophilic energy metabolisms: biotechnological prospects. Curr Opin Biotechnol 2017; 45:104-112. [DOI: 10.1016/j.copbio.2017.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
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