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Atta S, Mandal A, Majumdar A. Generation of Thiosulfate, Selenite, Dithiosulfite, Perthionitrite, Nitric Oxide, and Reactive Chalcogen Species by Binuclear Zinc(II)-Chalcogenolato/-Polychalcogenido Complexes. Inorg Chem 2024; 63:15161-15176. [PMID: 39084849 DOI: 10.1021/acs.inorgchem.4c02527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
A comparative bioinspired reactivity study of new binuclear Zn(II) complexes featuring coordinated thiolate, selenolate, trisulfide and diselenide in relation with (i) the generation of reactive sulfur/selenium species (RSS/RSeS), (ii) the oxygen dependent oxidation and disproportionation of polysulfide (Sn2-) to produce sulfite (SO32-), thiosulfate (S2O32-) and sulfide (S2-) by sulfur oxygenase reductase (SOR), and (iii) the reaction of Sn2- with nitrite (NO2-) to generate thionitrite (SNO-), perthionitrite (SSNO-) and nitric oxide (NO), is presented. The binuclear Zn(II)-thiolate/selenolate complexes could react with elemental sulfur to generate RSS/RSeS while similar reactions involving elemental selenium could not generate RSeS. The dizinc(II)-S3 and the dizinc(II)-Se2 complexes could react with dioxygen (O2) to generate binuclear Zn(II) complexes featuring coordinated thiosulfate (S2O32-) and selenite (SeO32-), respectively. Finally, unlike the nonreactive nature of the dizinc(II)-Se2 complex toward NO2-, reaction of the dizinc(II)-S3 complex with NO2- produced a new binuclear Zn(II) complex featuring a coordinated dithiosulfite (S3O2-) along with the formation of perthionitrite (SSNO-), of which the latter subsequently produced nitric oxide (NO) and S42-. The present work, thus, demonstrates the comparative reactivity of a series of binuclear Zn(II)-chalcogenolato/-polychalcogenido complexes for the generation of S2O32-, SeO32-, S3O2-, SSNO-, NO and RSS/RSeS.
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Affiliation(s)
- Sayan Atta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Amit Mandal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
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2
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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.
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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.
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Cryo-electron structures of the extreme thermostable enzymes Sulfur Oxygenase Reductase and Lumazine Synthase. PLoS One 2022; 17:e0275487. [PMID: 36191023 PMCID: PMC9529111 DOI: 10.1371/journal.pone.0275487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/18/2022] [Indexed: 11/05/2022] Open
Abstract
Thermostable enzymes have the potential for use in a wide variety of biotechnological applications. Cryo-electron microscopy (cryo-EM) enables the imaging of biomolecules in their native aqueous environment. Here, we present high resolution cryo-EM structures of two thermostable enzymes that exhibit multimeric cage-like structures arranged into two different point-group symmetries. First, we determined the structure of the Sulfur Oxygenase Reductase (SOR) enzyme that catalyzes both the oxygenation and disproportionation of elemental sulfur in Archea and is composed of 24 homomeric units each of MW ≃ 35 kDa arranged in octahedral symmetry. The structure of SOR from Acidianus ambivalens (7X9W) was determined at 2.78 Å resolution. The active site of each subunit inside the central nanocompartment is composed of Fe3+ coordinated to two water molecules and the three amino acids (H86, H90 and E114). Second, we determined the structure of Lumazine Synthase (LS) from Aquifex aeolicus (7X7M) at 2.33 Å resolution. LS forms a cage-like structure consisting of 60 identical subunits each of MW ≃ 15 kDa arranged in a strict icosahedral symmetry. The LS subunits are interconnected by ion-pair network. Due to their thermostability and relatively easy purification scheme, both SOR and LS can serve as a model for the catalytic and structural characterization of biocatalysts as well as a benchmark for cryo-EM sample preparation, optimization of the acquisition parameters and 3D reconstruction.
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Pal N, Sinha S, Shivani, Chakraborty M. A review on bacterial and archaeal thermostable sulfur oxidoreductases (SORS)-an insight into the biochemical, molecular and in-silico structural comparative analysis of a neglected thermostable enzyme of industrial significance. Arch Microbiol 2022; 204:655. [PMID: 36175582 DOI: 10.1007/s00203-022-03256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
Diverse thermophilic microorganisms with the potential to withstand extreme physiological conditions have long been investigated and explored for human commercial benefit. Thermozymes with distinct functional and structural properties isolated from these thermophiles are known to have high thermostability without significant loss of specific enzyme activity. Thermophiles isolated and characterised from the thermophilic ecological niche of India are well documented. There is a plethora of work in the literature emphasising its industrial significance. However, in-depth knowledge of the thermophilic oxidoreductase group of enzymes (Oxizymes) is restricted. Sulfur Oxygenase Reductases or Sulfur Oxygen-Reductases (SORs) are a group of thermophilic oxizymes reported predominantly from thermophilic and mesophilic archaea and bacteria, which catalyse oxygen-dependent disproportionation reactions of elemental sulfur, producing sulfite, thiosulfate, and sulphide. There have been few reports on isolated and characterised SORs from the Indian geothermal niche. The review article will highlight the SORs reported till date with a concise overview of different archaeal and bacterial species producing the enzymes. Based on the literature available till date, characteristics including physico-chemical properties, amino acid sequence homology, conserved motifs and their 3D structure comparison have been discussed. In-silico sequence and structure level preliminary comparative analysis of various SORs has also been discussed. However, a few SORs whose structural information is not reported in the protein data bank have been modelled to enrich our analysis.
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Affiliation(s)
- Nirmalya Pal
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Sanjana Sinha
- NMR Micro-Imaging and Spectroscopy Laboratory, Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, 500007, Telangana, India
| | - Shivani
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Mitun Chakraborty
- Department of Biotechnology Engineering and Food Technology, University Institute of Engineering, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
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5
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Alain K, Aronson HS, Allioux M, Yvenou S, Amend JP. Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents. Environ Microbiol 2022; 24:2210-2219. [PMID: 35315563 DOI: 10.1111/1462-2920.15975] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/12/2022] [Indexed: 11/28/2022]
Abstract
Sulfur is abundant in different oxidation states in hydrothermal ecosystems, where it plays a central role in microbial energy production. The contribution of microbially catalyzed disproportionation of elemental sulfur (S0 ) to the energy fluxes of this ecosystem is unknown. Indeed, within the current knowledge it is impossible to study this process in a global way due to the lack of specific genetic markers and because of the difficulties in unraveling the isotopic signals from the different reactions of the sulfur cycle. In this context, calculations of the Gibbs energy (∆Gr) of sulfur disproportionation can identify whether this process is thermodynamically favorable and provides sufficient energy yields for growth at the temperatures, pressures, and chemical compositions found in the various niches of the hydrothermal ecosystem. Herein, free energy yield calculations were performed using internally consistent thermodynamic properties and geochemical data from four different hydrothermal systems. These calculations showed that S0 -disproportionation is sufficiently exergonic to allow growth in most niches of the hydrothermal ecosystems, regardless of the geological and geochemical context, and depth; it is most favorable at elevated temperatures and alkaline pH, at low sulfide and sulfate concentrations, and in the presence of sulfide-chelating minerals, which are common in these environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Karine Alain
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Heidi S Aronson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089
| | - Maxime Allioux
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Stéven Yvenou
- Univ Brest, CNRS, Ifremer, Unité Biologie et Ecologie des Ecosystèmes marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, 90089
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6
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Ferreira P, Fernandes P, Ramos M. The archaeal non-heme iron-containing Sulfur Oxygenase Reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Sulfite oxidation by the quinone-reducing molybdenum sulfite dehydrogenase SoeABC from the bacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148279. [DOI: 10.1016/j.bbabio.2020.148279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
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8
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Sato Y, Yabuki T, Adachi N, Moriya T, Arakawa T, Kawasaki M, Yamada C, Senda T, Fushinobu S, Wakagi T. Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100030. [PMID: 32775998 PMCID: PMC7398979 DOI: 10.1016/j.yjsbx.2020.100030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
Sulfur oxygenase reductase (SOR) was biochemically and structurally characterized. High resolution structures of SOR were determined by crystallography and cryo-EM. Twenty-four identical subunits of SOR form a hollow sphere. Catalytic components exhibited different features in the crystal and cryo-EM structures.
Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of S. tokodaii (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.
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Key Words
- AaSOR, Acidianus ambivalens SOR
- AqSOR, Aquifex aeolicus SOR
- Archaea
- AtSOR, Acidianus tengchongensis SOR
- CTF, contrast transfer function
- Cryogenic electron microscopy
- DTNB, 5,5′-dithiobis(2-nitrobenzoic acid)
- FSC, Fourier shell correlation
- HnSOR, Halothiobacillus neapolitanus SOR
- Nonheme mononuclear iron center
- PAGE, polyacrylamide gel electrophoresis
- RMSD, root mean square deviation
- SD, standard deviation
- SDS, sodium dodecyl sulfate
- SOR, sulfur oxygenase reductase
- SbSOR, Sulfobacillus thermosulfidooxidans SOR
- StSOR, Sulfurisphaera tokodaii SOR
- Sulfur metabolism
- TpSOR, Thioalkalivibrio paradoxus SOR
- X-ray crystallography
- cryo-EM, cryogenic electron microscopy
- pCMB, p-chloromercuribenzoate
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Affiliation(s)
- Yuta Sato
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Yabuki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Allioux M, Yvenou S, Slobodkina G, Slobodkin A, Shao Z, Jebbar M, Alain K. Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388 T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents. Microorganisms 2020; 8:microorganisms8081132. [PMID: 32727039 PMCID: PMC7463578 DOI: 10.3390/microorganisms8081132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
Marine hydrothermal systems are characterized by a pronounced biogeochemical sulfur cycle with the participation of sulfur-oxidizing, sulfate-reducing and sulfur-disproportionating microorganisms. The diversity and metabolism of sulfur disproportionators are studied to a much lesser extent compared with other microbial groups. Dissulfurirhabdus thermomarina SH388T is an anaerobic thermophilic bacterium isolated from a shallow sea hydrothermal vent. D. thermomarina is an obligate chemolithoautotroph able to grow by the disproportionation of sulfite and elemental sulfur. Here, we present the results of the sequencing and analysis of the high-quality draft genome of strain SH388T. The genome consists of a one circular chromosome of 2,461,642 base pairs, has a G + C content of 71.1 mol% and 2267 protein-coding sequences. The genome analysis revealed a complete set of genes essential to CO2 fixation via the reductive acetyl-CoA (Wood-Ljungdahl) pathway and gluconeogenesis. The genome of D. thermomarina encodes a complete set of genes necessary for the dissimilatory reduction of sulfates, which are probably involved in the disproportionation of sulfur. Data on the occurrences of Dissulfurirhabdus 16S rRNA gene sequences in gene libraries and metagenome datasets showed the worldwide distribution of the members of this genus. This study expands our knowledge of the microbial contribution into carbon and sulfur cycles in the marine hydrothermal environments.
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Affiliation(s)
- Maxime Allioux
- Univ Brest, CNRS, IFREMER, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.A.); (S.Y.); (M.J.)
| | - Stéven Yvenou
- Univ Brest, CNRS, IFREMER, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.A.); (S.Y.); (M.J.)
| | - Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia; (G.S.); (A.S.)
| | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia; (G.S.); (A.S.)
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China;
| | - Mohamed Jebbar
- Univ Brest, CNRS, IFREMER, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.A.); (S.Y.); (M.J.)
| | - Karine Alain
- Univ Brest, CNRS, IFREMER, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.A.); (S.Y.); (M.J.)
- Correspondence:
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10
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Diversity of Sulfur-Oxidizing and Sulfur-Reducing Microbes in Diverse Ecosystems. ADVANCES IN SOIL MICROBIOLOGY: RECENT TRENDS AND FUTURE PROSPECTS 2018. [DOI: 10.1007/978-981-10-6178-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Brzezinski K, Czyrko J, Sliwiak J, Nalewajko-Sieliwoniuk E, Jaskolski M, Nocek B, Dauter Z. S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. Int J Biol Macromol 2017; 104:584-596. [PMID: 28629859 PMCID: PMC7888557 DOI: 10.1016/j.ijbiomac.2017.06.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
Abstract
Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures.
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Affiliation(s)
- Krzysztof Brzezinski
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland.
| | - Justyna Czyrko
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | | | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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12
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Rühl P, Kletzin A. The Sulfur Oxygenase Reductase Activity Assay: Catalyzing a Reaction with Elemental Sulfur as Substrate at High Temperatures. Bio Protoc 2017; 7:e2403. [PMID: 34541134 DOI: 10.21769/bioprotoc.2403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/21/2017] [Accepted: 06/22/2017] [Indexed: 11/02/2022] Open
Abstract
The sulfur oxygenase reductase (SOR) reaction is a dioxygen-dependent disproportionation of elemental sulfur (S0), catalyzed at optimal temperatures between 65 °C and 85 °C. Thiosulfate and sulfite are formed as oxidized products as well hydrogen sulfide as reduced product. External co-factors are not required. Usually, the SOR assay is performed in a milliliter scale in S0-containing Tris-buffer at high temperatures followed by colorimetric product quantification. In order to make the SOR assay more sensitive and better reproducible, several modifications were implemented compared to the original SOR assay (Kletzin, 1989). Here we present the modified SOR assay and the following quantification of the reaction products.
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Affiliation(s)
- Patrick Rühl
- Sulfur Biochemistry and Microbial Bioenergetics, Dept. of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Arnulf Kletzin
- Sulfur Biochemistry and Microbial Bioenergetics, Dept. of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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A Sulfur Oxygenase from the Haloalkaliphilic Bacterium Thioalkalivibrio paradoxus with Atypically Low Reductase Activity. J Bacteriol 2017; 199:JB.00675-16. [PMID: 27920296 DOI: 10.1128/jb.00675-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/28/2016] [Indexed: 01/26/2023] Open
Abstract
Sequence comparisons showed that the sulfur oxygenase reductase (SOR) of the haloalkaliphilic bacterium Thioalkalivibrio paradoxus Arh 1 (TpSOR) is branching deeply within dendrograms of these proteins (29 to 34% identity). A synthetic gene encoding TpSOR expressed in Escherichia coli resulted in a protein 14.7 ± 0.9 nm in diameter and an apparent molecular mass of 556 kDa. Sulfite and thiosulfate were formed from elemental sulfur in a temperature range of 10 to 98°C (optimum temperature ≈ 80°C) and a pH range of 6 to 11.5 (optimum pH ≈ 9; 308 ± 78 U/mg of protein). Sulfide formation had a maximum specific activity of 0.03 U/mg, or <1% of the corresponding activity of other SORs. Hence, reductase activity seems not to be an integral part of the reaction mechanism. TpSOR was most active at NaCl or glycine betaine concentrations of 0 to 1 M, although 0.2% of the maximal activity was detected even at 5 M NaCl and 4 M betaine. The melting point of TpSOR was close to 80°C, when monitored by circular dichroism spectroscopy or differential scanning fluorimetry; however, the denaturation kinetics were slow: 55% of the residual activity remained after 25 min of incubation at 80°C. Site-directed mutagenesis showed that the active-site residue Cys44 is essential for activity, whereas alanine mutants of the two other conserved cysteines retained about 0.5% residual activity. A model of the sulfur metabolism in T. paradoxus is discussed. IMPORTANCE Sulfur oxygenase reductases (SORs) are the only enzymes catalyzing an oxygen-dependent disproportionation of elemental sulfur and/or polysulfides to sulfite, thiosulfate, and hydrogen sulfide. SORs are known from mesophilic and extremophilic archaea and bacteria. All SORs seem to form highly thermostable 24-subunit hollow spheres. They carry a low-potential mononuclear nonheme iron in the active site and an indispensable cysteine; however, their exact reaction mechanisms are unknown. Typically, the reductase activity of SORs is in the range of 5 to 50% of the oxygenase activity, but mutagenesis studies had so far failed to identify residues crucial for the reductase reaction. We describe here the first SOR, which is almost devoid of the reductase reaction and which comes from a haloalkaliphilic bacterium.
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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.
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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.
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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
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Braakman R, Smith E. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PLoS One 2014; 9:e87950. [PMID: 24516572 PMCID: PMC3917532 DOI: 10.1371/journal.pone.0087950] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/05/2014] [Indexed: 11/19/2022] Open
Abstract
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.
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Affiliation(s)
- Rogier Braakman
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - Eric Smith
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America
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Site-specific mutagenesis and functional analysis of active sites of sulfur oxygenase reductase from Gram-positive moderate thermophile Sulfobacillus acidophilus TPY. Microbiol Res 2013; 168:654-60. [PMID: 23726793 DOI: 10.1016/j.micres.2013.04.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/03/2013] [Accepted: 04/13/2013] [Indexed: 11/23/2022]
Abstract
Sequence alignments revealed that the conserved motifs of SORSa which formed an independent branch between archaea and Gram-negative bacteria SORs according to the phylogenetic relationship were similar with the archaea and Gram-negative bacteria SORs. In order to investigate the active sites of SORSa, cysteines 31, 101 and 104 (C31, C101, C104), histidines 86 and 90 (H86 and H90) and glutamate 114 (E114) of SORSa were chosen as the target amino acid residues for site-specific mutagenesis. The wild type and six mutant SORs were expressed in E. coli BL21, purified and confirmed by SDS-PAGE and Western blotting analysis. Enzyme activity determination revealed that the active sites of SORSa were identical with the archaea and Gram-negative bacteria SORs reported. Replacement of any cysteine residues reduced SOR activity by 53-100%, while the mutants of H86A, H90A and E114A lost their enzyme activities largely, only remaining 20%, 19% and 32% activity of the wild type SOR respectively. This study will enrich our awareness for active sites of SOR in a Gram-positive bacterium.
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Guiral M, Prunetti L, Aussignargues C, Ciaccafava A, Infossi P, Ilbert M, Lojou E, Giudici-Orticoni MT. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv Microb Physiol 2013; 61:125-94. [PMID: 23046953 DOI: 10.1016/b978-0-12-394423-8.00004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.
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Affiliation(s)
- Marianne Guiral
- Unité de Bioénergétique et Ingénierie des Protéines, UMR7281-FR3479, CNRS, Aix-Marseille Université, Marseille, France.
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Guiral M, Aussignargues C, Prunetti L, Infossi P, Ilbert M, Giudici-Orticoni M. The energy sulfur metabolism of the hyperthermophilic bacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [DOI: 10.1016/j.bbabio.2012.06.407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Aussignargues C, Giuliani MC, Infossi P, Lojou E, Guiral M, Giudici-Orticoni MT, Ilbert M. Rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism. J Biol Chem 2012; 287:19936-48. [PMID: 22496367 DOI: 10.1074/jbc.m111.324863] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
How microorganisms obtain energy is a challenging topic, and there have been numerous studies on the mechanisms involved. Here, we focus on the energy substrate traffic in the hyperthermophilic bacterium Aquifex aeolicus. This bacterium can use insoluble sulfur as an energy substrate and has an intricate sulfur energy metabolism involving several sulfur-reducing and -oxidizing supercomplexes and enzymes. We demonstrate that the cytoplasmic rhodanese SbdP participates in this sulfur energy metabolism. Rhodaneses are a widespread family of proteins known to transfer sulfur atoms. We show that SbdP has also some unusual characteristics compared with other rhodaneses; it can load a long sulfur chain, and it can interact with more than one partner. Its partners (sulfur reductase and sulfur oxygenase reductase) are key enzymes of the sulfur energy metabolism of A. aeolicus and share the capacity to use long sulfur chains as substrate. We demonstrate a positive effect of SbdP, once loaded with sulfur chains, on sulfur reductase activity, most likely by optimizing substrate uptake. Taken together, these results lead us to propose a physiological role for SbdP as a carrier and sulfur chain donor to these key enzymes, therefore enabling channeling of sulfur substrate in the cell as well as greater efficiency of the sulfur energy metabolism of A. aeolicus.
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Affiliation(s)
- Clément Aussignargues
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée-CNRS, Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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The sulfur oxygenase reductase from the mesophilic bacterium Halothiobacillus neapolitanus is a highly active thermozyme. J Bacteriol 2011; 194:677-85. [PMID: 22139503 DOI: 10.1128/jb.06531-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium Halothiobacillus neapolitanus (HnSOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The HnSOR purified from Escherichia coli after heterologous gene expression had a temperature range of activity of 10 to 99°C with an optimum at 80°C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the HnSOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile Acidianus ambivalens (AaSOR). The melting point of the HnSOR was ≈20°C lower than that of the AaSOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere.
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Veith A, Urich T, Seyfarth K, Protze J, Frazão C, Kletzin A. Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens. Front Microbiol 2011; 2:37. [PMID: 21747782 PMCID: PMC3128934 DOI: 10.3389/fmicb.2011.00037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 02/17/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The sulfur oxygenase reductase (SOR) is the initial enzyme of the sulfur oxidation pathway in the thermoacidophilic Archaeon Acidianus ambivalens. The SOR catalyzes an oxygen-dependent sulfur disproportionation to H(2)S, sulfite and thiosulfate. The spherical, hollow, cytoplasmic enzyme is composed of 24 identical subunits with an active site pocket each comprising a mononuclear non-heme iron site and a cysteine persulfide. Substrate access and product exit occur via apolar chimney-like protrusions at the fourfold symmetry axes, via narrow polar pores at the threefold symmetry axes and via narrow apolar pores within in each subunit. In order to investigate the function of the pores we performed site-directed mutagenesis and inhibitor studies. RESULTS Truncation of the chimney-like protrusions resulted in an up to sevenfold increase in specific enzyme activity compared to the wild type. Replacement of the salt bridge-forming Arg(99) residue by Ala at the threefold symmetry axes doubled the activity and introduced a bias toward reduced reaction products. Replacement of Met(296) and Met(297), which form the active site pore, lowered the specific activities by 25-55% with the exception of an M(296)V mutant. X-ray crystallography of SOR wild type crystals soaked with inhibitors showed that Hg(2+) and iodoacetamide (IAA) bind to cysteines within the active site, whereas Zn(2+) binds to a histidine in a side channel of the enzyme. The Zn(2+) inhibition was partially alleviated by mutation of the His residue. CONCLUSIONS The expansion of the pores in the outer shell led to an increased enzyme activity while the integrity of the active site pore seems to be important. Hg(2+) and IAA block cysteines in the active site pocket, while Zn(2+) interferes over a distance, possibly by restriction of protein flexibility or substrate access or product exit.
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Affiliation(s)
- Andreas Veith
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Tim Urich
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany,Structural Biology Laboratory, Macromolecular Crystallography Unit, ITQB-UNLOeiras, Portugal
| | - Kerstin Seyfarth
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Jonas Protze
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany
| | - Carlos Frazão
- Structural Biology Laboratory, Macromolecular Crystallography Unit, ITQB-UNLOeiras, Portugal
| | - Arnulf Kletzin
- Institute of Microbiology and Genetics, Technische Universität DarmstadtDarmstadt, Germany,*Correspondence: Arnulf Kletzin, Institute of Microbiology and Genetics, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany. e-mail:
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Prunetti L, Infossi P, Brugna M, Ebel C, Giudici-Orticoni MT, Guiral M. New functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium Aquifex aeolicus. J Biol Chem 2010; 285:41815-26. [PMID: 20971847 DOI: 10.1074/jbc.m110.167841] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. It was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (H(2)S) to molecular oxygen. H(2)S is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. We have purified and characterized a novel membrane-bound multienzyme supercomplex that brings together all the molecular components involved in this bioenergetic chain. Our results indicate that this purified structure consists of one dimeric bc(1) complex (complex III), one cytochrome c oxidase (complex IV), and one or two sulfide quinone reductases as well as traces of the monoheme cytochrome c(555) and quinone molecules. In addition, this work strongly suggests that the cytochrome c oxidase in the supercomplex is a ba(3)-type enzyme. The supercomplex has a molecular mass of about 350 kDa and is enzymatically functional, reducing O(2) in the presence of the electron donor, H(2)S. This is the first demonstration of the existence of such a respirasome carrying a sulfide oxidase-oxygen reductase activity. Moreover, the kinetic properties of the sulfide quinone reductase change slightly when integrated in the supercomplex, compared with the free enzyme. We previously purified a complete respirasome involved in hydrogen oxidation and sulfur reduction from Aquifex aeolicus. Thus, two different bioenergetic pathways (sulfur reduction and sulfur oxidation) are organized in this bacterium as supramolecular structures in the membrane. A model for the energetic sulfur metabolism of Aquifex aeolicus is proposed.
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Affiliation(s)
- Laurence Prunetti
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036, IMM, IFR88-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Guiral M, Prunetti L, Lignon S, Lebrun R, Moinier D, Giudici-Orticoni MT. New Insights into the Respiratory Chains of the Chemolithoautotrophic and Hyperthermophilic Bacterium Aquifex aeolicus. J Proteome Res 2009; 8:1717-30. [DOI: 10.1021/pr8007946] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marianne Guiral
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Laurence Prunetti
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Sabrina Lignon
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Régine Lebrun
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Danielle Moinier
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Service de Microséquençage et de Spectrométrie de Masse, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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