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Kanao T. Tetrathionate hydrolase from the acidophilic microorganisms. Front Microbiol 2024; 15:1338669. [PMID: 38348185 PMCID: PMC10859504 DOI: 10.3389/fmicb.2024.1338669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Tetrathionate hydrolase (TTH) is a unique enzyme found in acidophilic sulfur-oxidizing microorganisms, such as bacteria and archaea. This enzyme catalyzes the hydrolysis of tetrathionate to thiosulfate, elemental sulfur, and sulfate. It is also involved in dissimilatory sulfur oxidation metabolism, the S4-intermediate pathway. TTHs have been purified and characterized from acidophilic autotrophic sulfur-oxidizing microorganisms. All purified TTHs show an optimum pH in the acidic range, suggesting that they are localized in the periplasmic space or outer membrane. In particular, the gene encoding TTH from Acidithiobacillus ferrooxidans (Af-tth) was identified and recombinantly expressed in Escherichia coli cells. TTH activity could be recovered from the recombinant inclusion bodies by acid refolding treatment for crystallization. The mechanism of tetrathionate hydrolysis was then elucidated by X-ray crystal structure analysis. Af-tth is highly expressed in tetrathionate-grown cells but not in iron-grown cells. These unique structural properties, reaction mechanisms, gene expression, and regulatory mechanisms are discussed in this review.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Agricultural and Biological Chemistry, Graduate School of Environment, Life, Natural Science, and Technology, Okayama University, Okayama, Japan
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2
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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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Kanao T, Kunihisa T, Ohgimoto S, Ito M, Murakami C, Nakayama H, Tamura T, Kamimura K. Recombinant expression using the tetrathionate hydrolase promoter in Acidithiobacillus ferrooxidans. J Biosci Bioeng 2023; 135:176-181. [PMID: 36635106 DOI: 10.1016/j.jbiosc.2022.12.005] [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: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023]
Abstract
In the iron- and sulfur-oxidizing acidophilic chemolithoautotrophic bacterium, Acidithiobacillus ferrooxidans, tetrathionate hydrolase gene (Af-tth) is highly expressed during tetrathionate growth. The expression levels of Af-tth were specifically determined by quantitative reverse transcription-polymerase chain reaction and the expression ratios of S0/Fe2+ and S4O62-/Fe2+ were found to be 68 ± 21 and 181 ± 5, respectively. The transcriptional start site was identified by primer extension. Promoter regions of Af-tth were cloned into the expression shuttle vector pMPJC and GFP gene was under the direction of the regions. Green fluorescence was observed by UV irradiation in recombinant A. ferrooxidans harboring the plasmid colonies grown on tetrathionate. Furthermore, His-tagged Af-Tth was synthesized in the recombinant cells grown on tetrathionate. Recombinant, His-tagged Af-Tth in an active form, was rapidly purified through metal-affinity column chromatography, although recombinant Af-Tth was synthesized in the inclusion bodies of Escherichia coli and acid-refolding treatment was necessary to recover the activity. The specific activity of purified Af-Tth from recombinant A. ferrooxidans (2.2 ± 0.37 U mg-1) was similar to that of acid-refolded Af-Tth from recombinant E. coli (2.5 ± 0.18 U mg-1). This method can be applied not only to heterologous expression but also to homologous expression of target genes for modification or specific mutation in A. ferrooxidans cells.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan.
| | - Tomoki Kunihisa
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Shuji Ohgimoto
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Megumi Ito
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Chisa Murakami
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hisayuki Nakayama
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuo Kamimura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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4
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Chen J, Liu Y, Diep P, Mahadevan R. Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129456. [PMID: 35777147 DOI: 10.1016/j.jhazmat.2022.129456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.
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5
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Yamada S, Suzuki Y, Kouzuma A, Watanabe K. Development of a CRISPR interference system for selective gene knockdown in Acidithiobacillus ferrooxidans. J Biosci Bioeng 2021; 133:105-109. [PMID: 34865958 DOI: 10.1016/j.jbiosc.2021.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus ferrooxidans is an iron-oxidizing chemolithotroph used for bioleaching of precious metals and is also regarded as a potential host for bioelectrochemical production of value-added chemicals. Despite its industrial utility, however, it is difficult to genetically engineer A. ferrooxidans due to low transformation and recombination efficiencies. Here, we developed a clustered regularly interspaced short palindromic repeats interference (CRISPRi) system that can selectively repress the expression of a target gene in A. ferrooxidans. The mutated gene encoding a nuclease-deactivated Cas9 protein was cloned into the broad-host-range plasmid pBBR1-MCS2, and the applicability of the CRISPRi system was examined using the nitrogenase nifH gene as a knockdown target. Introduction of the CRISPRi plasmid into A. ferrooxidans resulted in decreased nifH transcription and retarded cell growth in the absence of nitrogen sources, demonstrating that the CRISPRi system altered the phenotype of this bacterium via selective gene knockdown. We suggest that the CRISPRi system developed in this study provides an efficient technique for constructing A. ferrooxidans knockdown mutants that are useful for the genetic dissection of this bacterium.
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Affiliation(s)
- Shohei Yamada
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yusuke Suzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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6
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Jung H, Inaba Y, Banta S. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans. Trends Biotechnol 2021; 40:677-692. [PMID: 34794837 DOI: 10.1016/j.tibtech.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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7
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Inaba Y, Kernan T, West AC, Banta S. Dispersion of sulfur creates a valuable new growth medium formulation that enables earlier sulfur oxidation in relation to iron oxidation in Acidithiobacillus ferrooxidans cultures. Biotechnol Bioeng 2021; 118:3225-3238. [PMID: 34086346 DOI: 10.1002/bit.27847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 01/19/2023]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that is commonly reported to exhibit diauxic population growth behavior where ferrous iron is oxidized before elemental sulfur when both are available, despite the higher energy content of sulfur. We have discovered sulfur dispersion formulations that enables sulfur oxidation before ferrous iron oxidation. The oxidation of dispersed sulfur can lower the culture pH within days below the range where aerobic ferrous iron oxidation can occur. Thus, ferric iron reduction can be observed quickly which had previously been reported over extended incubation periods with untreated sulfur. Therefore, we demonstrate that this substrate utilization pattern is strongly dependent on the cell loading in relation to sulfur concentration, sulfur surface hydrophobicity, and the pH of the culture. Our dispersed sulfur formulation, lig-sulfur, can be used to support the rapid antibiotic selection of plasmid-transformed cells, which is not possible in liquid cultures where ferrous iron is the main source of energy for these acidophiles. Furthermore, we find that media containing lig-sulfur supports higher production of green fluorescent protein compared to media containing ferrous iron. The use of dispersed sulfur is a valuable new tool for the development of engineered A. ferrooxidans strains and it provides a new method to control iron and sulfur oxidation behaviors.
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Affiliation(s)
- Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Timothy Kernan
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Alan C West
- Department of Chemical Engineering, Columbia University, New York, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, USA
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8
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Wu P, Wang Z, Zhu Q, Xie Z, Mei Y, Liang Y, Chen Z. Stress preadaptation and overexpression of rpoS and hfq genes increase stress resistance of Pseudomonas fluorescens ATCC13525. Microbiol Res 2021; 250:126804. [PMID: 34144508 DOI: 10.1016/j.micres.2021.126804] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/17/2021] [Accepted: 06/02/2021] [Indexed: 01/06/2023]
Abstract
Pseudomonas fluorescens ATCC13525 is an important growth-promoting rhizobacteria (PGPR) and plant disease biocontrol bacterium. However, due to poor stress resistance, it is prone to be inactivated by preparation, drying and storage. In this study, we investigated the effects of different stress preadaptation methods (2.0∼3.0 wt% NaCl, 0.01∼0.20 wt% H2O2, and 35∼44 °C) and two stress adaptation genes (rpoS, and hfq) on the stress resistance of P. fluorescens ATCC13525 (PF-WT). After stress preadaptation with low stress of 3.0 wt% NaCl, 0.05 wt% H2O2, and 41 °C for 30 min, the tolerance of PF-WT toward high lethal stress environments (20.0 wt% NaCl, 1.00 wt% H2O2, and 47 °C) were significantly improved. Moreover, knockout of rpoS and hfq genes resulted in slower culture growth than PF-WT under the sublethal stress culture conditions (5.0 wt% NaCl, 0.08 wt% H2O2, and 35 °C), whereas rpoS and hfq overexpressed strains (PF-pBBR2-rpoS and PF-pBBR2-hfq) obviously grew better than the control strain PF-pBBR2. Further, we prepared biocontrol agents (BACs) of different strains after different stress preadaptation treatments. Compared to PF-WT without stress preadaptation, preadaptation by 0.05 wt% H2O2 for 30 min resulted in 5.65 times higher survival rate, while treatment with 3.0 wt% NaCl for 30 min of PF-pBBR2-rpoS led to 5.60 times higher survival rate. This finding provides the simple and effective protection methods for P. fluorescens ATCC13525 BACs preparation by stress preadaptation and overexpression of stress adaptation genes.
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Affiliation(s)
- Pengyu Wu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhaopu Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qiuyan Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhixiong Xie
- College of Life Science, Wuhan University, Wuhan, 430072, PR China.
| | - Yuxia Mei
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yunxiang Liang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhenmin Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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Kanao T, Hase N, Nakayama H, Yoshida K, Nishiura K, Kosaka M, Kamimura K, Hirano Y, Tamada T. Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:328-338. [PMID: 33103311 PMCID: PMC7784748 DOI: 10.1002/pro.3984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022]
Abstract
Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur oxidation in the acidophilic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. The structure of recombinant 4THase from A. ferrooxidans (Af-Tth) was determined by X-ray crystallography to a resolution of 1.95 Å. Af-Tth is a homodimer, and its monomer structure exhibits an eight-bladed β-propeller motif. Two insertion loops participate in dimerization, and one loop forms a cavity with the β-propeller region. We observed unexplained electron densities in this cavity of the substrate-soaked structure. The anomalous difference map generated using diffraction data collected at a wavelength of 1.9 Å indicated the presence of polymerized sulfur atoms. Asp325, a highly conserved residue among 4THases, was located near the polymerized sulfur atoms. 4THase activity was completely abolished in the site-specific Af-Tth D325N variant, suggesting that Asp325 plays a crucial role in the first step of tetrathionate hydrolysis. Considering that the Af-Tth reaction occurs only under acidic pH, Asp325 acts as an acid for the tetrathionate hydrolysis reaction. The polymerized sulfur atoms in the active site cavity may represent the intermediate product in the subsequent step.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Naruki Hase
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Hisayuki Nakayama
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kyoya Yoshida
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kazumi Nishiura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Megumi Kosaka
- Department of Instrumental Analysis, Advanced Science Research CenterOkayama UniversityOkayamaJapan
| | - Kazuo Kamimura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Yu Hirano
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
| | - Taro Tamada
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
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10
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Inaba Y, West AC, Banta S. Enhanced microbial corrosion of stainless steel by
Acidithiobacillus ferrooxidans
through the manipulation of substrate oxidation and overexpression of
rus. Biotechnol Bioeng 2020; 117:3475-3485. [DOI: 10.1002/bit.27509] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Yuta Inaba
- Department of Chemical Engineering Columbia University New York New York
| | - Alan C. West
- Department of Chemical Engineering Columbia University New York New York
| | - Scott Banta
- Department of Chemical Engineering Columbia University New York New York
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Sensitive detection of low-concentration sulfide based on the synergistic effect of rGO, np-Au, and recombinant microbial cell. Biosens Bioelectron 2020; 151:111985. [DOI: 10.1016/j.bios.2019.111985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/09/2019] [Accepted: 12/22/2019] [Indexed: 11/17/2022]
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12
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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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13
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Microbially Influenced Corrosion of Stainless Steel by Acidithiobacillus ferrooxidans Supplemented with Pyrite: Importance of Thiosulfate. Appl Environ Microbiol 2019; 85:AEM.01381-19. [PMID: 31444204 DOI: 10.1128/aem.01381-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/19/2019] [Indexed: 11/20/2022] Open
Abstract
Microbially influenced corrosion (MIC) results in significant damage to metallic materials in many industries. Anaerobic sulfate-reducing bacteria (SRB) have been well studied for their involvement in these processes. Highly corrosive environments are also found in pulp and paper processing, where chloride and thiosulfate lead to the corrosion of stainless steels. Acidithiobacillus ferrooxidans is a critically important chemolithotrophic acidophile exploited in metal biomining operations, and there is interest in using A. ferrooxidans cells for emerging processes such as electronic waste recycling. We explored conditions under which A. ferrooxidans could enable the corrosion of stainless steel. Acidic medium with iron, chloride, low sulfate, and pyrite supplementation created an environment where unstable thiosulfate was continuously generated. When combined with the chloride, acid, and iron, the thiosulfate enabled substantial corrosion of stainless steel (SS304) coupons (mass loss, 5.4 ± 1.1 mg/cm2 over 13 days), which is an order of magnitude higher than what has been reported for SRB. There results were verified in an abiotic flow reactor, and the importance of mixing was also demonstrated. Overall, these results indicate that A. ferrooxidans and related pyrite-oxidizing bacteria could produce aggressive MIC conditions in certain environmental milieus.IMPORTANCE MIC of industrial equipment, gas pipelines, and military material leads to billions of dollars in damage annually. Thus, there is a clear need to better understand MIC processes and chemistries as efforts are made to ameliorate these effects. Additionally, A. ferrooxidans is a valuable acidophile with high metal tolerance which can continuously generate ferric iron, making it critical to copper and other biomining operations as well as a potential biocatalyst for electronic waste recycling. New MIC mechanisms may expand the utility of these cells in future metal resource recovery operations.
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Yang CL, Chen XK, Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Lin JQ, Chen LX. Essential Role of σ Factor RpoF in Flagellar Biosynthesis and Flagella-Mediated Motility of Acidithiobacillus caldus. Front Microbiol 2019; 10:1130. [PMID: 31178842 PMCID: PMC6543871 DOI: 10.3389/fmicb.2019.01130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/03/2019] [Indexed: 12/04/2022] Open
Abstract
Acidithiobacillaceae, an important family of acidophilic and chemoautotrophic sulfur or iron oxidizers, participate in geobiochemical circulation of the elements and drive the release of heavy metals in mining associated habitats. Because of their environmental adaptability and energy metabolic systems, Acidithiobacillus spp. have become the dominant bacteria used in bioleaching for heavy metal recovery. Flagella-driven motility is associated with bacterial chemotaxis and bacterial responses to environmental stimuli. However, little is known about how the flagellum of Acidithiobacillus spp. is regulated and how the flagellum affects the growth of these chemoautotrophic bacteria. In this study, we analyzed the flagellar gene clusters in Acidithiobacillus strains and uncovered the close relationship between flagella and the sulfur-oxidizing systems (Sox system). The σ28 gene (rpoF) knockout and overexpression strains of Acidithiobacillus caldus were constructed. Scanning electron microscopy shows that A. caldus ΔrpoF cells lacked flagella, indicating the essential role of RpoF in regulating flagella synthesis in these chemoautotrophic bacteria. Motility analysis suggests that the deletion of rpoF resulted in the reduction of swarming capability, while this capability was enhanced in the rpoF overexpression strain. Both static cultivation and low concentration of energy substrates (elemental sulfur or tetrathionate) led to weak growth of A. caldus ΔrpoF cells. The deletion of rpoF promoted bacterial attachment to the surface of elemental sulfur in static cultivation. The absence of RpoF caused an obvious change in transcription profile, including genes in flagellar cluster and those involved in biofilm formation. These results provide an understanding on the regulation of flagellar hierarchy and the flagellar function in these sulfur or iron oxidizers.
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Affiliation(s)
- Chun-Long Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xian-Ke Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - 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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15
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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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16
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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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17
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Transposase-Mediated Chromosomal Integration of Exogenous Genes in Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2018; 84:AEM.01381-18. [PMID: 30143507 DOI: 10.1128/aem.01381-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
The development of Acidithiobacillus ferrooxidans as a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used to identify the insertion sites of the KDC gene in several mutants, leading to the identification of a region on the chromosome that may be suitable for future genetic insertions. These results demonstrate that functional exogenous metabolic genes have been chromosomally integrated into A. ferrooxidans, and this advance will facilitate the future development of these cells for new biotechnology applications.IMPORTANCE Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph and is a key member of the microbial consortia used in industrial biomining applications. There is interest in exploiting these cells for other metal recovery applications as well as in developing them as unique nonmodel microbial cell factories. Plasmid-driven expression of exogenous genes has been reported, and homologous recombination has been used to knock out some gene expression. Here, new selection protocols facilitated the development of a transposition method for chromosomal integration of exogenous genes into A. ferrooxidans This greatly expands the available genetic toolbox, which will open the door to greater metabolic engineering efforts for these cells.
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Biofilm Formation by the Acidophile Bacterium Acidithiobacillus thiooxidans Involves c-di-GMP Pathway and Pel exopolysaccharide. Genes (Basel) 2018; 9:genes9020113. [PMID: 29466318 PMCID: PMC5852609 DOI: 10.3390/genes9020113] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 01/08/2023] Open
Abstract
Acidophile bacteria belonging to the Acidithiobacillus genus are pivotal players for the bioleaching of metallic values such as copper. Cell adherence to ores and biofilm formation, mediated by the production of extracellular polymeric substances, strongly favors bioleaching activity. In recent years, the second messenger cyclic diguanylate (c-di-GMP) has emerged as a central regulator for biofilm formation in bacteria. C-di-GMP pathways have been reported in different Acidithiobacillus species; however, c-di-GMP effectors and signal transduction networks are still largely uncharacterized in these extremophile species. Here we investigated Pel exopolysaccharide and its role in biofilm formation by sulfur-oxidizing species Acidithiobacillusthiooxidans. We identified 39 open reading frames (ORFs) encoding proteins involved in c-di-GMP metabolism and signal transduction, including the c-di-GMP effector protein PelD, a structural component of the biosynthesis apparatus for Pel exopolysaccharide production. We found that intracellular c-di-GMP concentrations and transcription levels of pel genes were higher in At. thiooxidans biofilm cells compared to planktonic ones. By developing an At. thiooxidans ΔpelD null-mutant strain we revealed that Pel exopolysaccharide is involved in biofilm structure and development. Further studies are still necessary to understand how Pel biosynthesis is regulated in Acidithiobacillus species, nevertheless these results represent the first characterization of a c-di-GMP effector protein involved in biofilm formation by acidophile species.
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Gumulya Y, Boxall NJ, Khaleque HN, Santala V, Carlson RP, Kaksonen AH. In a quest for engineering acidophiles for biomining applications: challenges and opportunities. Genes (Basel) 2018; 9:E116. [PMID: 29466321 PMCID: PMC5852612 DOI: 10.3390/genes9020116] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/27/2022] Open
Abstract
Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.
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Affiliation(s)
- Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Naomi J Boxall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Himel N Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology (TUT), Tampere, 33101, Finland.
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University (MSU), Bozeman, MT 59717, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.
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20
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Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T. Appl Environ Microbiol 2018; 84:AEM.02091-17. [PMID: 29150517 PMCID: PMC5772234 DOI: 10.1128/aem.02091-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 11/20/2022] Open
Abstract
Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilum T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilum T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.
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21
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Kanao T, Onishi M, Kajitani Y, Hashimoto Y, Toge T, Kikukawa H, Kamimura K. Characterization of tetrathionate hydrolase from the marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH. Biosci Biotechnol Biochem 2018; 82:152-160. [PMID: 29303046 DOI: 10.1080/09168451.2017.1415128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tetrathionate hydrolase (4THase), a key enzyme of the S4-intermediate (S4I) pathway, was partially purified from marine acidophilic bacterium, Acidithiobacillus thiooxidans strain SH, and the gene encoding this enzyme (SH-tth) was identified. SH-Tth is a homodimer with a molecular mass of 97 ± 3 kDa, and contains a subunit 52 kDa in size. Enzyme activity was stimulated in the presence of 1 M NaCl, and showed the maximum at pH 3.0. Although 4THases from A. thiooxidans and the closely related Acidithiobacillus caldus strain have been reported to be periplasmic enzymes, SH-Tth seems to be localized on the outer membrane of the cell, and acts as a peripheral protein. Furthermore, both 4THase activity and SH-Tth proteins were detected in sulfur-grown cells of strain SH. These results suggested that SH-Tth is involved in elemental sulfur-oxidation, which is distinct from sulfur-oxidation in other sulfur-oxidizing strains such as A. thiooxidans and A. caldus.
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Affiliation(s)
- Tadayoshi Kanao
- a Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| | - Moe Onishi
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | | | - Yuki Hashimoto
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | - Tatsuya Toge
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | | | - Kazuo Kamimura
- a Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
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22
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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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23
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Metals and minerals as a biotechnology feedstock: engineering biomining microbiology for bioenergy applications. Curr Opin Biotechnol 2017; 45:144-155. [PMID: 28371651 DOI: 10.1016/j.copbio.2017.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/04/2017] [Accepted: 03/10/2017] [Indexed: 01/06/2023]
Abstract
Developing new feedstocks for the efficient production of biochemicals and biofuels will be a critical challenge as we diversify away from petrochemicals. One possible opportunity is the utilization of sulfide-based minerals in the Earth's crust. Non-photosynthetic chemolithoautotrophic bacteria are starting to be developed to produce biochemicals from CO2 using energy obtained from the oxidation of inorganic feedstocks. Biomining of metals like gold and copper already exploit the native metabolism of these bacteria and these represent perhaps the largest-scale bioprocesses ever developed. The metabolic engineering of these bacteria could be a desirable alternative to classical heterotrophic bioproduction. In this review, we discuss biomining operations and the challenges and advances in the engineering of associated chemolithoautotrophic bacteria for biofuel production. The co-generation of biofuels integrated with mining operations is a largely unexplored opportunity that will require advances in fundamental microbiology and the development of new genetic tools and techniques for these organisms. Although this approach is presently in its infancy, the production of biochemicals using energy from non-petroleum mineral resources is an exciting new biotechnology opportunity.
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24
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Application of β-glucuronidase (GusA) as an effective reporter for extremely acidophilic Acidithiobacillus ferrooxidans. Appl Microbiol Biotechnol 2017; 101:3283-3294. [DOI: 10.1007/s00253-017-8116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/20/2016] [Accepted: 12/29/2016] [Indexed: 10/20/2022]
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25
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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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26
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Wang ZB, Li YQ, Lin JQ, Pang X, Liu XM, Liu BQ, Wang R, Zhang CJ, Wu Y, Lin JQ, Chen LX. The Two-Component System RsrS-RsrR Regulates the Tetrathionate Intermediate Pathway for Thiosulfate Oxidation in Acidithiobacillus caldus. Front Microbiol 2016; 7:1755. [PMID: 27857710 PMCID: PMC5093147 DOI: 10.3389/fmicb.2016.01755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/19/2016] [Indexed: 01/10/2023] Open
Abstract
Acidithiobacillus caldus (A. caldus) is a common bioleaching bacterium that possesses a sophisticated and highly efficient inorganic sulfur compound metabolism network. Thiosulfate, a central intermediate in the sulfur metabolism network of A. caldus and other sulfur-oxidizing microorganisms, can be metabolized via the tetrathionate intermediate (S4I) pathway catalyzed by thiosulfate:quinol oxidoreductase (Tqo or DoxDA) and tetrathionate hydrolase (TetH). In A. caldus, there is an additional two-component system called RsrS-RsrR. Since rsrS and rsrR are arranged as an operon with doxDA and tetH in the genome, we suggest that the regulation of the S4I pathway may occur via the RsrS-RsrR system. To examine the regulatory role of the two-component system RsrS-RsrR on the S4I pathway, ΔrsrR and ΔrsrS strains were constructed in A. caldus using a newly developed markerless gene knockout method. Transcriptional analysis of the tetH cluster in the wild type and mutant strains revealed positive regulation of the S4I pathway by the RsrS-RsrR system. A 19 bp inverted repeat sequence (IRS, AACACCTGTTACACCTGTT) located upstream of the tetH promoter was identified as the binding site for RsrR by using electrophoretic mobility shift assays (EMSAs) in vitro and promoter-probe vectors in vivo. In addition, ΔrsrR, and ΔrsrS strains cultivated in K2S4O6-medium exhibited significant growth differences when compared with the wild type. Transcriptional analysis indicated that the absence of rsrS or rsrR had different effects on the expression of genes involved in sulfur metabolism and signaling systems. Finally, a model of tetrathionate sensing by RsrS, signal transduction via RsrR, and transcriptional activation of tetH-doxDA was proposed to provide insights toward the understanding of sulfur metabolism in A. caldus. This study also provided a powerful genetic tool for studies in A. caldus.
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Affiliation(s)
- Zhao-Bao Wang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Ya-Qing Li
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | | | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Yan Wu
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University Jinan, China
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Christel S, Fridlund J, Buetti-Dinh A, Buck M, Watkin EL, Dopson M. RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans. FEMS Microbiol Lett 2016; 363:fnw057. [PMID: 26956550 DOI: 10.1093/femsle/fnw057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 01/08/2023] Open
Abstract
Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Antoine Buetti-Dinh
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Moritz Buck
- National Bioinformatics Infrastructure Sweden and Evolutionary Biology Center, Uppsala University, 751 05 Uppsala, Sweden
| | - Elizabeth L Watkin
- CHIRI Biosciences, School of Biomedical Sciences, Curtin University, Perth 6845, Australia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
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Esparza M, Jedlicki E, Dopson M, Holmes DS. Expression and activity of the Calvin–Benson–Bassham cycle transcriptional regulator CbbR fromAcidithiobacillus ferrooxidansinRalstonia eutropha. FEMS Microbiol Lett 2015; 362:fnv108. [DOI: 10.1093/femsle/fnv108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 11/14/2022] Open
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29
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Electroactive bacteria—molecular mechanisms and genetic tools. Appl Microbiol Biotechnol 2014; 98:8481-95. [DOI: 10.1007/s00253-014-6005-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
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