1
|
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.
Collapse
Affiliation(s)
- Tadayoshi Kanao
- Department of Agricultural and Biological Chemistry, Graduate School of Environment, Life, Natural Science, and Technology, Okayama University, Okayama, Japan
| |
Collapse
|
2
|
Han S, Li Y, Gao H. Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria. Antioxidants (Basel) 2022; 11:antiox11122487. [PMID: 36552695 PMCID: PMC9774590 DOI: 10.3390/antiox11122487] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H2S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H2S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H2S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H2S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H2S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H2S/RSS.
Collapse
|
3
|
Nguyen PM, Do PT, Pham YB, Doan TO, Nguyen XC, Lee WK, Nguyen DD, Vadiveloo A, Um MJ, Ngo HH. Roles, mechanism of action, and potential applications of sulfur-oxidizing bacteria for environmental bioremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158203. [PMID: 36044953 DOI: 10.1016/j.scitotenv.2022.158203] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Sulfur (S) is a crucial component in the environment and living organisms. This work is the first attempt to provide an overview and critical discussion on the roles, mechanisms, and environmental applications of sulfur-oxidizing bacteria (SOB). The findings reveal that key enzymes of SOB embarked on oxidation of sulfide, sulfite, thiosulfate, and elemental S. Conversion of reduced S compounds was oxidatively catalyzed by various enzymes (e.g. sulfide: quinone oxidoreductase, flavocytochrome c-sulfide dehydrogenase, dissimilatory sulfite reductase, heterodisulfide reductase-like proteins). Environmental applications of SOB discussed include detoxifying hydrogen sulfide, soil bioremediation, and wastewater treatment. SOB producing S0 engaged in biological S soil amendments (e.g. saline-alkali soil remediation, the oxidation of sulfide-bearing minerals). Biotreatment of H2S using SOB occurred under both aerobic and anaerobic conditions. Sulfide, nitrate, and sulfamethoxazole were removed through SOB suspension cultures and S0-based carriers. Finally, this work presented future perspectives on SOB development, including S0 recovery, SOB enrichment, field measurement and identification of sulfur compounds, and the development of mathematical simulation.
Collapse
Affiliation(s)
- Phuong Minh Nguyen
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Phuc Thi Do
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam; Key Laboratory of Enzyme and Protein Technology (KLEPT), University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Yen Bao Pham
- Key Laboratory of Enzyme and Protein Technology (KLEPT), University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Thi Oanh Doan
- Faculty of Environment, Ha Noi University of Natural Resources and Environment, No 41A, Phu Dien Street, Bac Tu Liem, Ha Noi, Vietnam
| | - Xuan Cuong Nguyen
- Center for Advanced Chemistry, Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam; Faculty of Environmental Chemical Engineering, Duy Tan University, Da Nang 550000, Vietnam.
| | - Woo Kul Lee
- Department of Chemical Engineering, Dankook University, 152 Jukjeonro, Yongin 16890, South Korea
| | - D Duc Nguyen
- Faculty of Environmental and Food Engineering, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 4, HCM City, 755414, Vietnam; Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, South Korea
| | - Ashiwin Vadiveloo
- Algae R & D Centre, Environmental and Conservation Sciences, College of Science, Health, Engineering and Education, 90 South Street, Murdoch, WA 6150, Australia
| | - Myoung-Jin Um
- Department of Civil Engineering, Kyonggi University, Suwon 16227, South Korea
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia.
| |
Collapse
|
4
|
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: 5] [Impact Index Per Article: 1.7] [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.
Collapse
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
| |
Collapse
|
5
|
Mandal S, Rameez MJ, Chatterjee S, Sarkar J, Pyne P, Bhattacharya S, Shaw R, Ghosh W. Molecular mechanism of sulfur chemolithotrophy in the betaproteobacterium Pusillimonas ginsengisoli SBSA. MICROBIOLOGY-SGM 2020; 166:386-397. [PMID: 31999239 DOI: 10.1099/mic.0.000890] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Chemolithotrophic sulfur oxidation represents a significant part of the biogeochemical cycling of this element. Due to its long evolutionary history, this ancient metabolism is well known for its extensive mechanistic and phylogenetic diversification across a diverse taxonomic spectrum. Here we carried out whole-genome sequencing and analysis of a new betaproteobacterial isolate, Pusillimonas ginsengisoli SBSA, which is found to oxidize thiosulfate via the formation of tetrathionate as an intermediate. The 4.7 Mb SBSA genome was found to encompass a soxCDYZAXOB operon, plus single thiosulfate dehydrogenase (tsdA) and sulfite : acceptor oxidoreductase (sorAB) genes. Recombination-based knockout of tsdA revealed that the entire thiosulfate is first converted to tetrathionate by the activity of thiosulfate dehydrogenase (TsdA) and the Sox pathway is not functional in this bacterium despite the presence of all necessary sox genes. The ∆soxYZ and ∆soxXA knockout mutants exhibited a wild-type-like phenotype for thiosulfate/tetrathionate oxidation, whereas ∆soxB, ∆soxCD and soxO::KanR mutants only oxidized thiosulfate up to tetrathionate intermediate and had complete impairment in tetrathionate oxidation. The substrate-dependent O2 consumption rate of whole cells and the sulfur-oxidizing enzyme activities of cell-free extracts, measured in the presence/absence of thiol inhibitors/glutathione, indicated that glutathione plays a key role in SBSA tetrathionate oxidation. The present findings collectively indicate that the potential glutathione : tetrathionate coupling in P. ginsengisoli involves a novel enzymatic component, which is different from the dual-functional thiol dehydrotransferase (ThdT), while subsequent oxidation of the sulfur intermediates produced (e.g. glutathione : sulfodisulfane molecules) may proceed via the iterative action of soxBCD .
Collapse
Affiliation(s)
- Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Prosenjit Pyne
- Present address: National Institute of Cholera and Enteric Diseases (NICED), P- C.I.T. Scheme XM, Beleghata, 33, CIT Rd, Beleghata, Kolkata - 700054, India.,Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | | | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| |
Collapse
|
6
|
Rameez MJ, Pyne P, Mandal S, Chatterjee S, Alam M, Bhattacharya S, Mondal N, Sarkar J, Ghosh W. Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST. Microbiol Res 2019; 230:126345. [PMID: 31585234 DOI: 10.1016/j.micres.2019.126345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/08/2019] [Accepted: 09/21/2019] [Indexed: 02/02/2023]
Abstract
Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy involves direct oxidation of thiosulfate (S2O32-) to sulfate (SO42-) without any free intermediate. This pathway mediated by SoxXAYZBCD is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate(S4O62-)-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process of Paracoccus pantotrophus. Our results reveal a unique case where an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation converting ∼10% of the thiosulfate supplied, whilst ∼90% of the substrate is oxidized via a pathway that produces tetrathionate as an intermediate. Sulfur oxidation kinetics of a deletion mutant showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which in turn is also less efficient than the P. pantotrophus Sox. Deletion of soxB abolished sulfate-formation from thiosulfate/tetrathionate, while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the insertional mutation of a thiol dehydrotransferase (thdT) homolog, together with the absence of sulfite as an intermediate, indicated that SST tetrathionate oxidation is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. The present findings highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.
Collapse
Affiliation(s)
- Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Prosenjit Pyne
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Masrure Alam
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | | | - Nibendu Mondal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
| |
Collapse
|
7
|
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: 105] [Impact Index Per Article: 21.0] [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.
Collapse
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
| |
Collapse
|
8
|
Pyne P, Alam M, Rameez MJ, Mandal S, Sar A, Mondal N, Debnath U, Mathew B, Misra AK, Mandal AK, Ghosh W. Homologs from sulfur oxidation (Sox) and methanol dehydrogenation (Xox) enzyme systems collaborate to give rise to a novel pathway of chemolithotrophic tetrathionate oxidation. Mol Microbiol 2018; 109:169-191. [DOI: 10.1111/mmi.13972] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Prosenjit Pyne
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Masrure Alam
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Moidu Jameela Rameez
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Subhrangshu Mandal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Abhijit Sar
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Nibendu Mondal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Utsab Debnath
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Boby Mathew
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Anup Kumar Misra
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Wriddhiman Ghosh
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| |
Collapse
|
9
|
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: 5] [Impact Index Per Article: 0.8] [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.
Collapse
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
| |
Collapse
|
10
|
Li LF, Fu LJ, Lin JQ, Pang X, Liu XM, Wang R, Wang ZB, Lin JQ, Chen LX. The σ54-dependent two-component system regulating sulfur oxidization (Sox) system in Acidithiobacillus caldus and some chemolithotrophic bacteria. Appl Microbiol Biotechnol 2016; 101:2079-2092. [DOI: 10.1007/s00253-016-8026-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 11/30/2022]
|
11
|
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: 25] [Impact Index Per Article: 3.1] [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.
Collapse
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
| |
Collapse
|
12
|
Lin KH, Liao BY, Chang HW, Huang SW, Chang TY, Yang CY, Wang YB, Lin YTK, Wu YW, Tang SL, Yu HT. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015; 16:1029. [PMID: 26630941 PMCID: PMC4668684 DOI: 10.1186/s12864-015-2230-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2230-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kuei-Han Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ben-Yang Liao
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Hao-Wei Chang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Molecular Microbiology and Microbial Pathogenesis Program, Division of Biology and Biomedical Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Shiao-Wei Huang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Ting-Yan Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, 35053, Taiwan, Republic of China.
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Bin Wang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Yu-Teh Kirk Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan, Republic of China. .,Degree Program of Genome and Systems Biology, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan, Republic of China.
| |
Collapse
|
13
|
Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus. Microorganisms 2015; 3:707-24. [PMID: 27682113 PMCID: PMC5023260 DOI: 10.3390/microorganisms3040707] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/01/2015] [Accepted: 10/10/2015] [Indexed: 12/15/2022] Open
Abstract
The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant.
Collapse
|
14
|
The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
15
|
Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014; 15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. RESULTS Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. CONCLUSIONS Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
Collapse
Affiliation(s)
- Nicholas B Justice
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA USA
| | - Anders Norman
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Section for Infection Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Brown
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Andrea Singh
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Brian C Thomas
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Jillian F Banfield
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| |
Collapse
|
16
|
Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics. J Proteomics 2014; 109:276-89. [DOI: 10.1016/j.jprot.2014.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/16/2022]
|
17
|
Nuñez H, Loyola D, Cárdenas JP, Holmes DS, Johnson DB, Quatrini R. Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Res Microbiol 2014; 165:735-42. [PMID: 25176612 DOI: 10.1016/j.resmic.2014.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 11/30/2022]
Abstract
Phenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes.
Collapse
Affiliation(s)
| | - David Loyola
- National Center for Genomics, Proteomics and Bioinformatics of Chile, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile
| | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile
| | - D Barrie Johnson
- School of Biological Sciences, University of Wales, LL572UW Bangor, UK
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Andres Bello University, Santiago, Chile.
| |
Collapse
|
18
|
Kanao T, Nakayama H, Kato M, Kamimura K. The sole cysteine residue (Cys301) of tetrathionate hydrolase from Acidithiobacillus ferrooxidans does not play a role in enzyme activity. Biosci Biotechnol Biochem 2014; 78:2030-5. [PMID: 25144400 DOI: 10.1080/09168451.2014.948374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Cysteine residues are absolutely indispensable for the reactions of almost all enzymes involved in the dissimilatory oxidation pathways of reduced inorganic sulfur compounds. Tetrathionate hydrolase from the acidophilic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans (Af-Tth) catalyzes tetrathionate hydrolysis to generate elemental sulfur, thiosulfate, and sulfate. Af-Tth is a key enzyme in the dissimilatory sulfur oxidation pathway in this bacterium. Only one cysteine residue (Cys301) has been identified in the deduced amino acid sequence of the Af-Tth gene. In order to clarify the role of the sole cysteine residue, a site-specific mutant enzyme (C301A) was generated. No difference was observed in the retention volumes of the wild-type and mutant Af-Tth enzymes by gel-filtration column chromatography, and surprisingly the enzyme activities measured in the cysteine-deficient and wild-type enzymes were the same. These results suggest that the sole cysteine residue (Cys301) in Af-Tth is involved in neither the tetrathionate hydrolysis reaction nor the subunit assembly. Af-Tth may thus have a novel cysteine-independent reaction mechanism.
Collapse
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
| | | | | | | |
Collapse
|
19
|
Yin H, Zhang X, Li X, He Z, Liang Y, Guo X, Hu Q, Xiao Y, Cong J, Ma L, Niu J, Liu X. Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiol 2014; 14:179. [PMID: 24993543 PMCID: PMC4109375 DOI: 10.1186/1471-2180-14-179] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/19/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation. RESULTS The genome of A. thiooxidans A01 was sequenced and annotated. It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components. Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences. In addition, another putative pathway was found in the cytoplasm of A. thiooxidans, which catalyzes sulfite to sulfate as the final product by phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase. This differs from its closest relative Acidithiobacillus caldus, which is performed by sulfate adenylyltransferase (SAT). Furthermore, real-time quantitative PCR analysis showed that most of sulfur oxidation genes were more strongly expressed in the S0 medium than that in the Na2S2O3 medium at the mid-log phase. CONCLUSION Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.
Collapse
Affiliation(s)
- Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xiaoqi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Qi Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Jing Cong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
20
|
Guo X, Yin H, Liang Y, Hu Q, Zhou X, Xiao Y, Ma L, Zhang X, Qiu G, Liu X. Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PLoS One 2014; 9:e99417. [PMID: 24940621 PMCID: PMC4062416 DOI: 10.1371/journal.pone.0099417] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/14/2014] [Indexed: 12/21/2022] Open
Abstract
The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus thermosulfidooxidans strain ST was deciphered to obtain a comprehensive insight into the genetic content and to understand the cellular mechanisms necessary for its survival. Furthermore, the expressions of key genes related with iron and sulfur oxidation were verified by semi-quantitative RT-PCR analysis. The draft genome sequence of Sulfobacillus thermosulfidooxidans strain ST, which encodes 3225 predicted coding genes on a total length of 3,333,554 bp and a 48.35% G+C, revealed the high degree of heterogeneity with other Sulfobacillus species. The presence of numerous transposases, genomic islands and complete CRISPR/Cas defence systems testifies to its dynamic evolution consistent with the genome heterogeneity. As expected, S. thermosulfidooxidans encodes a suit of conserved enzymes required for the oxidation of inorganic sulfur compounds (ISCs). The model of sulfur oxidation in S. thermosulfidooxidans was proposed, which showed some different characteristics from the sulfur oxidation of Gram-negative A. ferrooxidans. Sulfur oxygenase reductase and heterodisulfide reductase were suggested to play important roles in the sulfur oxidation. Although the iron oxidation ability was observed, some key proteins cannot be identified in S. thermosulfidooxidans. Unexpectedly, a predicted sulfocyanin is proposed to transfer electrons in the iron oxidation. Furthermore, its carbon metabolism is rather flexible, can perform the transformation of pentose through the oxidative and non-oxidative pentose phosphate pathways and has the ability to take up small organic compounds. It encodes a multitude of heavy metal resistance systems to adapt the heavy metal-containing environments.
Collapse
Affiliation(s)
- Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Qi Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xishu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
21
|
Yu Y, Liu X, Wang H, Li X, Lin J. Construction and characterization of tetH overexpression and knockout strains of Acidithiobacillus ferrooxidans. J Bacteriol 2014; 196:2255-64. [PMID: 24727223 PMCID: PMC4054192 DOI: 10.1128/jb.01472-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/28/2014] [Indexed: 11/20/2022] Open
Abstract
Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for bioleaching. It can obtain energy from the oxidation of Fe(2+), H2, S(0), and various reduced inorganic sulfur compounds (RISCs). Tetrathionate is a key intermediate during RISC oxidation, hydrolyzed by tetrathionate hydrolase (TetH), and used as sole energy source. In this study, a tetH knockout (ΔtetH) mutant and a tetH overexpression strain were constructed and characterized. The tetH overexpression strain grew better on sulfur and tetrathionate and possessed a higher rate of tetrathionate utilization and TetH activity than the wild type. However, its cell yields on tetrathionate were much lower than those on sulfur. The ΔtetH mutant could not grow on tetrathionate but could proliferate on sulfur with a lower cell yield than the wild type's, which indicated that tetrathionate hydrolysis is mediated only by TetH, encoded by tetH. The ΔtetH mutant could survive in ferrous medium with an Fe(2+) oxidation rate similar to that of the wild type. For the tetH overexpression strain, the rate was relatively higher than that of the wild type. The reverse transcription-quantitative PCR (qRT-PCR) results showed that tetH and doxD2 acted synergistically, and doxD2 was considered important in thiosulfate metabolism. Of the two sqr genes, AFE_0267 seemed to play as important a role in sulfide oxidation as AFE_1792. This study not only provides a substantial basis for studying the function of the tetH gene but also may serve as a model to clarify other candidate genes involved in sulfur oxidation in this organism.
Collapse
Affiliation(s)
- Yangyang Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Xiangmei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Huiyan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Xiuting Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Jianqun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| |
Collapse
|
22
|
Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One 2013; 8:e78237. [PMID: 24250794 PMCID: PMC3826726 DOI: 10.1371/journal.pone.0078237] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. PRINCIPAL FINDINGS Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. SIGNIFICANCE For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
Collapse
Affiliation(s)
- Lillian G. Acuña
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | | | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingenieria, Universidad de Talca, Talca, Chile
| | | | - Jorge Valdés
- Center for Systems Biotechnology, Fraunhofer Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Douglas E. Rawlings
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - David S. Holmes
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
23
|
Kanao T, Kosaka M, Yoshida K, Nakayama H, Tamada T, Kuroki R, Yamada H, Takada J, Kamimura K. Crystallization and preliminary X-ray diffraction analysis of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:692-4. [PMID: 23722856 PMCID: PMC3668597 DOI: 10.1107/s1744309113013419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
Tetrathionate hydrolase (4THase) from the iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans catalyses the disproportionate hydrolysis of tetrathionate to elemental sulfur, thiosulfate and sulfate. The gene encoding 4THase (Af-tth) was expressed as inclusion bodies in recombinant Escherichia coli. Recombinant Af-Tth was activated by refolding under acidic conditions and was then purified to homogeneity. The recombinant protein was crystallized in 20 mM glycine buffer pH 10 containing 50 mM sodium chloride and 33%(v/v) PEG 1000 using the hanging-drop vapour-diffusion method. The crystal was a hexagonal cylinder with dimensions of 0.2 × 0.05 × 0.05 mm. X-ray crystallographic analysis showed that the crystal diffracted to 2.15 Å resolution and belongs to space group P3(1) or P3(2), with unit-cell parameters a = b = 92.1, c = 232.6 Å.
Collapse
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
| | - Megumi Kosaka
- Department of Instrumental Analysis, Advanced Science Research Center, Okayama University, 3-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kyoya Yoshida
- 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
| | - Taro Tamada
- Molecular Biology Research Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4, Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Ryota Kuroki
- Molecular Biology Research Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4, Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Hidenori Yamada
- Department of Instrumental Analysis, Advanced Science Research Center, Okayama University, 3-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Jun Takada
- Department of Material Chemistry, Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, 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
| |
Collapse
|
24
|
Kinetic enrichment of 34S during proteobacterial thiosulfate oxidation and the conserved role of SoxB in S-S bond breaking. Appl Environ Microbiol 2013; 79:4455-64. [PMID: 23686269 DOI: 10.1128/aem.00956-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria Paracoccus pantotrophus, Tetrathiobacter kashmirensis, and Thiomicrospira crunogena rendered steady enrichment of (34)S in the end product sulfate, with overall fractionation ranging between -4.6‰ and +5.8‰. The fractionation kinetics of T. crunogena was essentially similar to that of P. pantotrophus, albeit the former had a slightly higher magnitude and rate of (34)S enrichment. In the case of T. kashmirensis, the only significant departure of its fractionation curve from that of P. pantotrophus was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical (34)S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine S-thiosulfonates, as well as cysteine S-sulfonates, in P. pantotrophus) in the actively sulfate-producing cells of all three species. The inducible expression of soxB during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by T. kashmirensis is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such T. kashmirensis proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate- or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.
Collapse
|
25
|
Bobadilla Fazzini RA, Cortés MP, Padilla L, Maturana D, Budinich M, Maass A, Parada P. Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans. Biotechnol Bioeng 2013; 110:2242-51. [PMID: 23436458 DOI: 10.1002/bit.24875] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 11/09/2022]
Abstract
The prokaryotic oxidation of reduced inorganic sulfur compounds (RISCs) is a topic of utmost importance from a biogeochemical and industrial perspective. Despite sulfur oxidizing bacterial activity is largely known, no quantitative approaches to biological RISCs oxidation have been made, gathering all the complex abiotic and enzymatic stoichiometry involved. Even though in the case of neutrophilic bacteria such as Paracoccus and Beggiatoa species the RISCs oxidation systems are well described, there is a lack of knowledge for acidophilic microorganisms. Here, we present the first experimentally validated stoichiometric model able to assess RISCs oxidation quantitatively in Acidithiobacillus thiooxidans (strain DSM 17318), the archetype of the sulfur oxidizing acidophilic chemolithoautotrophs. This model was built based on literature and genomic analysis, considering a widespread mix of formerly proposed RISCs oxidation models combined and evaluated experimentally. Thiosulfate partial oxidation by the Sox system (SoxABXYZ) was placed as central step of sulfur oxidation model, along with abiotic reactions. This model was coupled with a detailed stoichiometry of biomass production, providing accurate bacterial growth predictions. In silico deletion/inactivation highlights the role of sulfur dioxygenase as the main catalyzer and a moderate function of tetrathionate hydrolase in elemental sulfur catabolism, demonstrating that this model constitutes an advanced instrument for the optimization of At. thiooxidans biomass production with potential use in biohydrometallurgical and environmental applications.
Collapse
|
26
|
Chen L, Ren Y, Lin J, Liu X, Pang X, Lin J. Acidithiobacillus caldus sulfur oxidation model based on transcriptome analysis between the wild type and sulfur oxygenase reductase defective mutant. PLoS One 2012; 7:e39470. [PMID: 22984393 PMCID: PMC3440390 DOI: 10.1371/journal.pone.0039470] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus (A. caldus) is widely used in bio-leaching. It gains energy and electrons from oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs) for carbon dioxide fixation and growth. Genomic analyses suggest that its sulfur oxidation system involves a truncated sulfur oxidation (Sox) system (omitting SoxCD), non-Sox sulfur oxidation system similar to the sulfur oxidation in A. ferrooxidans, and sulfur oxygenase reductase (SOR). The complexity of the sulfur oxidation system of A. caldus generates a big obstacle on the research of its sulfur oxidation mechanism. However, the development of genetic manipulation method for A. caldus in recent years provides powerful tools for constructing genetic mutants to study the sulfur oxidation system. RESULTS An A. caldus mutant lacking the sulfur oxygenase reductase gene (sor) was created and its growth abilities were measured in media using elemental sulfur (S(0)) and tetrathionate (K(2)S(4)O(6)) as the substrates, respectively. Then, comparative transcriptome analysis (microarrays and real-time quantitative PCR) of the wild type and the Δsor mutant in S(0) and K(2)S(4)O(6) media were employed to detect the differentially expressed genes involved in sulfur oxidation. SOR was concluded to oxidize the cytoplasmic elemental sulfur, but could not couple the sulfur oxidation with the electron transfer chain or substrate-level phosphorylation. Other elemental sulfur oxidation pathways including sulfur diooxygenase (SDO) and heterodisulfide reductase (HDR), the truncated Sox pathway, and the S(4)I pathway for hydrolysis of tetrathionate and oxidation of thiosulfate in A. caldus are proposed according to expression patterns of sulfur oxidation genes and growth abilities of the wild type and the mutant in different substrates media. CONCLUSION An integrated sulfur oxidation model with various sulfur oxidation pathways of A. caldus is proposed and the features of this model are summarized.
Collapse
Affiliation(s)
- Linxu Chen
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Yilin Ren
- School of Life Science, Shandong Normal University, Jinan, China
| | - Jianqun Lin
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Xiangmei Liu
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Xin Pang
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| | - Jianqiang Lin
- State Key Lab of Microbial Technology, Shandong University, Jinan, China
| |
Collapse
|
27
|
You XY, Guo X, Zheng HJ, Zhang MJ, Liu LJ, Zhu YQ, Zhu B, Wang SY, Zhao GP, Poetsch A, Jiang CY, Liu SJ. Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation. J Genet Genomics 2011; 38:243-52. [DOI: 10.1016/j.jgg.2011.04.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 04/14/2011] [Accepted: 04/20/2011] [Indexed: 11/25/2022]
|
28
|
|
29
|
Protze J, Müller F, Lauber K, Naß B, Mentele R, Lottspeich F, Kletzin A. An Extracellular Tetrathionate Hydrolase from the Thermoacidophilic Archaeon Acidianus Ambivalens with an Activity Optimum at pH 1. Front Microbiol 2011; 2:68. [PMID: 21747790 PMCID: PMC3128947 DOI: 10.3389/fmicb.2011.00068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 03/25/2011] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The thermoacidophilic and chemolithotrophic archaeon Acidianus ambivalens is routinely grown with sulfur and CO(2)-enriched air. We had described a membrane-bound, tetrathionate (TT) forming thiosulfate:quinone oxidoreductase. Here we describe the first TT hydrolase (TTH) from Archaea. RESULTS A. ambivalens cells grown aerobically with TT as sole sulfur source showed doubling times of 9 h and final cell densities of up to 8 × 10(8)/ml. TTH activity (≈0.28 U/mg protein) was found in cell-free extracts of TT-grown but not of sulfur-grown cells. Differential fractionation of freshly harvested cells involving a pH shock showed that about 92% of the TTH activity was located in the pseudo-periplasmic fraction associated with the surface layer, while 7.3% and 0.3% were present in the soluble and membrane fractions, respectively. The enzyme was enriched 54-fold from the cytoplasmic fraction and 2.1-fold from the pseudo-periplasmic fraction. The molecular mass of the single subunit was 54 kDa. The optimal activity was at or above 95°C at pH 1. Neither PQQ nor divalent cations had a significant effect on activity. The gene (tth1) was identified following N-terminal sequencing of the protein. Northern hybridization showed that tth1 was transcribed in TT-grown cells in contrast to a second paralogous tth2 gene. The deduced amino acid sequences showed similarity to the TTH from Acidithiobacillus and other proteins from the PQQ dehydrogenase superfamily. It displayed a β-propeller structure when being modeled, however, important residues from the PQQ-binding site were absent. CONCLUSION The soluble, extracellular, and acidophilic TTH identified in TT-grown A. ambivalens cells is essential for TT metabolism during growth but not for the downstream processing of the TQO reaction products in S°-grown cells. The liberation of TTH by pH shock from otherwise intact cells strongly supports the pseudo-periplasm hypothesis of the S-layer of Archaea.
Collapse
Affiliation(s)
- Jonas Protze
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Fabian Müller
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Karin Lauber
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Bastian Naß
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | | | | | - Arnulf Kletzin
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| |
Collapse
|
30
|
Mangold S, Valdés J, Holmes DS, Dopson M. Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. Front Microbiol 2011; 2:17. [PMID: 21687411 PMCID: PMC3109338 DOI: 10.3389/fmicb.2011.00017] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/25/2011] [Indexed: 12/20/2022] Open
Abstract
Given the challenges to life at low pH, an analysis of inorganic sulfur compound (ISC) oxidation was initiated in the chemolithoautotrophic extremophile Acidithiobacillus caldus. A. caldus is able to metabolize elemental sulfur and a broad range of ISCs. It has been implicated in the production of environmentally damaging acidic solutions as well as participating in industrial bioleaching operations where it forms part of microbial consortia used for the recovery of metal ions. Based upon the recently published A. caldus type strain genome sequence, a bioinformatic reconstruction of elemental sulfur and ISC metabolism predicted genes included: sulfide-quinone reductase (sqr), tetrathionate hydrolase (tth), two sox gene clusters potentially involved in thiosulfate oxidation (soxABXYZ), sulfur oxygenase reductase (sor), and various electron transport components. RNA transcript profiles by semi quantitative reverse transcription PCR suggested up-regulation of sox genes in the presence of tetrathionate. Extensive gel based proteomic comparisons of total soluble and membrane enriched protein fractions during growth on elemental sulfur and tetrathionate identified differential protein levels from the two Sox clusters as well as several chaperone and stress proteins up-regulated in the presence of elemental sulfur. Proteomics results also suggested the involvement of heterodisulfide reductase (HdrABC) in A. caldus ISC metabolism. A putative new function of Hdr in acidophiles is discussed. Additional proteomic analysis evaluated protein expression differences between cells grown attached to solid, elemental sulfur versus planktonic cells. This study has provided insights into sulfur metabolism of this acidophilic chemolithotroph and gene expression during attachment to solid elemental sulfur.
Collapse
Affiliation(s)
| | - Jorge Valdés
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
- Departamento de Ciencias Biologicas, Andrés Bello UniversitySantiago, Chile
| | - Mark Dopson
- Center for Bioinformatics and Genome Biology, Fundación Ciencia para VidaSantiago, Chile
| |
Collapse
|
31
|
Kanao T, Matsumoto C, Shiraga K, Yoshida K, Takada J, Kamimura K. Recombinant tetrathionate hydrolase from Acidithiobacillus ferrooxidans requires exposure to acidic conditions for proper folding. FEMS Microbiol Lett 2010; 309:43-7. [PMID: 20546308 DOI: 10.1111/j.1574-6968.2010.02019.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur metabolism in the acidophilic chemolithoautotrophic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. We have already identified the gene encoding 4THase (Af-tth) in this bacterium. The heterologous expression of Af-tth in Escherichia coli resulted in the formation of inclusion bodies of the protein in an inactive form. The recombinant protein (Af-Tth) was successfully activated after an in vitro refolding treatment. The specific activity of the refolded Af-Tth obtained was 21.0+/-9.4 U mg(-1) when the protein solubilized from inclusion bodies by 6 M guanidine hydrochloride solution was refolded in a buffer containing 10 mM beta-alanine, 2 mM dithiothreitol, 0.4 M ammonium sulfate, and 30% v/v glycerol with the pH adjusted to 4.0 by sulfuric acid for 14 h at 4 degrees C. The in vitro refolding experiments revealed that Af-Tth required exposure to an acidic environment during protein folding for activation. This property reflects a physiological characteristic of the Af-Tth localized in the outer membrane of the acidophilic A. ferrooxidans. No cofactor such as pyrroloquinoline quinone (PQQ) was required during the refolding process in spite of the similarity in the primary structure of Af-Tth to the PQQ family of proteins.
Collapse
Affiliation(s)
- Tadayoshi Kanao
- Department of Instrumental Analysis, Advanced Science Research Center, Okayama University, Kita-ku, Okayama, Japan.
| | | | | | | | | | | |
Collapse
|
32
|
Identification of components of electron transport chains in the extremely thermoacidophilic crenarchaeon Metallosphaera sedula through iron and sulfur compound oxidation transcriptomes. Appl Environ Microbiol 2008; 74:7723-32. [PMID: 18931292 DOI: 10.1128/aem.01545-08] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The crenarchaeal order Sulfolobales collectively contain at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. While specific respiratory complexes in certain Sulfolobales have been characterized previously as proton pumps for maintaining intracellular pH and generating proton motive force, their contribution to sulfur and iron biooxidation has not been considered. For M. sedula growing in the presence of ferrous iron and reduced inorganic sulfur compounds (RISCs), global transcriptional analysis was used to track the response of specific genes associated with these complexes, as well as other known and putative respiratory electron transport chain elements. Open reading frames from all five terminal oxidase or bc(1)-like complexes were stimulated on one or more conditions tested. Components of the fox (Msed0467 to Msed0489) and soxNL-cbsABA (Msed0500 to Msed0505) terminal/quinol oxidase clusters were triggered by ferrous iron, while the soxABCDD' terminal oxidase cluster (Msed0285 to Msed0291) were induced by tetrathionate and S(0). Chemolithotrophic electron transport elements, including a putative tetrathionate hydrolase (Msed0804), a novel polysulfide/sulfur/dimethyl sulfoxide reductase-like complex (Msed0812 to Msed0818), and a novel heterodisulfide reductase-like complex (Msed1542 to Msed1550), were also stimulated by RISCs. Furthermore, several hypothetical proteins were found to have strong responses to ferrous iron or RISCs, suggesting additional candidates in iron or sulfur oxidation-related pathways. From this analysis, a comprehensive model for electron transport in M. sedula could be proposed as the basis for examining specific details of iron and sulfur oxidation in this bioleaching archaeon.
Collapse
|
33
|
Construction of arsB and tetH mutants of the sulfur-oxidizing bacterium Acidithiobacillus caldus by marker exchange. Appl Environ Microbiol 2008; 74:5686-94. [PMID: 18658286 DOI: 10.1128/aem.01235-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acidithiobacillus caldus is a moderately thermophilic, acidophilic bacterium that has been reported to be the dominant sulfur oxidizer in stirred-tank processes used to treat gold-bearing arsenopyrite ores. It is also widely distributed in heap reactors used for the extraction of metals from ores. Not only are these bacteria commercially important, they have an interesting physiology, the study of which has been restricted by the nonavailability of defined mutants. A recently reported conjugation system based on the broad-host-range IncW plasmids pSa and R388 was used to transfer mobilizable narrow-host-range suicide plasmid vectors containing inactivated and partially deleted chromosomal genes from Escherichia coli to A. caldus. Through the dual use of a selectable kanamycin resistance gene and a hybridization probe made from a deleted portion of the target chromosomal gene, single- and double-recombinant mutants of A. caldus were isolated. The functionality of the gene inactivation system was shown by the construction of A. caldus arsB and tetH mutants, and the effects of these mutations on cell growth in the presence of arsenic and by means of tetrathionate oxidation were demonstrated.
Collapse
|
34
|
Rzhepishevska OI, Valdés J, Marcinkeviciene L, Gallardo CA, Meskys R, Bonnefoy V, Holmes DS, Dopson M. Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds. Appl Environ Microbiol 2007; 73:7367-72. [PMID: 17873067 PMCID: PMC2168230 DOI: 10.1128/aem.01497-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 09/07/2007] [Indexed: 11/20/2022] Open
Abstract
Acidithiobacillus caldus has been proposed to play a role in the oxidation of reduced inorganic sulfur compounds (RISCs) produced in industrial biomining of sulfidic minerals. Here, we describe the regulation of a new cluster containing the gene encoding tetrathionate hydrolase (tetH), a key enzyme in the RISC metabolism of this bacterium. The cluster contains five cotranscribed genes, ISac1, rsrR, rsrS, tetH, and doxD, coding for a transposase, a two-component response regulator (RsrR and RsrS), tetrathionate hydrolase, and DoxD, respectively. As shown by quantitative PCR, rsrR, tetH, and doxD are upregulated to different degrees in the presence of tetrathionate. Western blot analysis also indicates upregulation of TetH in the presence of tetrathionate, thiosulfate, and pyrite. The tetH cluster is predicted to have two promoters, both of which are functional in Escherichia coli and one of which was mapped by primer extension. A pyrrolo-quinoline quinone binding domain in TetH was predicted by bioinformatic analysis, and the presence of an o-quinone moiety was experimentally verified, suggesting a mechanism for tetrathionate oxidation.
Collapse
|
35
|
Kanao T, Kamimura K, Sugio T. Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans. J Biotechnol 2007; 132:16-22. [PMID: 17904676 DOI: 10.1016/j.jbiotec.2007.08.030] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 07/26/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Tetrathionate is one of the most important intermediates in dissimilatory sulfur oxidation and can itself be utilized as a sole energy source by some sulfur-oxidizing microorganisms. Tetrathionate hydrolase (4THase) plays a significant role in tetrathionate oxidation and should catalyze the initial step in the oxidative dissimilation when sulfur-oxidizing bacteria are grown on tetrathionate. 4THase activity was detected in tetrathionate-grown Acidithiobacillus ferrooxidans ATCC 23270 cells but not in iron-grown cells. A 4THase having a dimeric structure of identical 50kDa polypeptides was purified from tetrathionate-grown cells. The 4THase showed the maximum activity at pH 3.0 and high stability under acidic conditions. An open reading frame (ORF) encoding the N-terminal amino acid sequence of the purified 4THase was identified by a BLAST search using the database for the A. ferrooxidans ATCC 23270 genome. Heterologous expression of the gene in Escherichia coli resulted in the formation of inclusion bodies of the protein in an inactive form. Antisera against the recombinant protein clearly recognized the purified native 4THase, indicating that the ORF encoded the 4THase.
Collapse
Affiliation(s)
- Tadayoshi Kanao
- Department of Instrumental Analysis, Advanced Science Research Center, Okayama University, 3-1-1 Tsushima-Naka, Okayama 700-8530, Japan.
| | | | | |
Collapse
|
36
|
Dam B, Mandal S, Ghosh W, Das Gupta SK, Roy P. The S4-intermediate pathway for the oxidation of thiosulfate by the chemolithoautotroph Tetrathiobacter kashmirensis and inhibition of tetrathionate oxidation by sulfite. Res Microbiol 2007; 158:330-8. [PMID: 17509837 DOI: 10.1016/j.resmic.2006.12.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 10/17/2006] [Accepted: 12/15/2006] [Indexed: 10/23/2022]
Abstract
Chemolithotrophic oxidation of reduced sulfur compounds was studied in the betaproteobacterium Tetrathiobacter kashmirensis in correlation with its transposon (Tn5-mob)-inserted mutants impaired in sulfur oxidation (Sox(-)) and found to be carried out via the tetrathionate intermediate (S(4)I) pathway. The group of physiologically identical Sox(-) mutant strains presently examined could fully oxidize thiosulfate supplied in the media to equivalent amounts of tetrathionate but could only convert 5-10% of the latter to equivalent amounts of sulfite (equivalences in terms of mug atoms of S ml(-1)). These mutants were found to possess intact thiosulfate dehydrogenase, but defunct sulfite dehydrogenase, activities. Single copies of Tn5-mob in the genomes of the Sox(-) mutants were found inserted within the moeA gene, responsible for molybdopterin cofactor biosynthesis. This explained the inactivity of sulfite dehydrogenase. Chemolithotrophic oxidation of tetrathionate and sulfite by T. kashmirensis was found to be inhibited by 12 mM tungstate, whose effect could however be reversed by further addition of 15 mM molybdate. In mixotrophic medium, the mutants showed uninterrupted utilization of maltose but inhibition of tetrathionate utilization due to accumulation of sulfite. When sulfite was added to wild type cultures growing on tetrathionate-containing chemolithoautotrophic medium, it was found to render concentration-dependent inhibition of oxidation of tetrathionate. Our findings indicate that sulfite molecules negatively regulate their own synthesis by plausible inhibitory interaction(s) with enzyme(s) responsible for the oxidation of tetrathionate to sulfite; thereby clearly suggesting that one of the control mechanisms of chemolithotrophic sulfur oxidation could be at the level of sulfite.
Collapse
Affiliation(s)
- Bomba Dam
- Department of Microbiology, Bose Institute, P-1/12, C. I. T. Scheme VII-M, Kolkata 700054, India
| | | | | | | | | |
Collapse
|
37
|
Kamimura K, Higashino E, Kanao T, Sugio T. Effects of inhibitors and NaCl on the oxidation of reduced inorganic sulfur compounds by a marine acidophilic, sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH. Extremophiles 2004; 9:45-51. [PMID: 15375674 DOI: 10.1007/s00792-004-0420-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Accepted: 08/24/2004] [Indexed: 11/25/2022]
Abstract
The effect of NaCl and the pathways of the oxidation of reduced inorganic sulfur compounds were studied using resting cells and cell-free extracts of Acidithiobacillus thiooxidans strain SH. This isolate specifically requires NaCl for growth. The oxidation of sulfur and sulfite by resting cells was strongly inhibited by 2-heptyl-4-hydroxyquinoline-N-oxide. Carbonylcyanide m-chlorophenyl-hydrazone and monensin were also relatively strong inhibitors. Thiosulfate-oxidizing activity was not inhibited by these uncouplers. Valinomycin did not inhibit the oxidation of sulfur compounds. NaCl stimulated the sulfur- and sulfite-oxidizing activities in resting cells but not in cell-free extracts. The tetrathionate-oxidizing activity in resting cells was slightly stimulated by NaCl, whereas it did not influence the thiosulfate-oxidizing activity. Sulfide oxidation was biphasic, suggesting the formation of intermediate sulfur. The initial phase of sulfide oxidation was not affected by NaCl, whereas the subsequent oxidation of sulfur in the second phase was Na+-dependent. A model is proposed for the role of NaCl in the metabolism of reduced sulfur compounds in A. thiooxidans strain SH.
Collapse
Affiliation(s)
- Kazuo Kamimura
- Department of Biological Function, Faculty of Agriculture, Okayama University, 1-1-1 Tsushima-Naka, Okayama 700-8530, Japan.
| | | | | | | |
Collapse
|