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Xin Y, Wang Y, Zhang H, Wu Y, Xia Y, Li H, Qu X. Cupriavidus pinatubonensis JMP134 Alleviates Sulfane Sulfur Toxicity after the Loss of Sulfane Dehydrogenase through Oxidation by Persulfide Dioxygenase and Hydrogen Sulfide Release. Metabolites 2023; 13:metabo13020218. [PMID: 36837837 PMCID: PMC9959259 DOI: 10.3390/metabo13020218] [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: 01/11/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
An incomplete Sox system lacking sulfane dehydrogenase SoxCD may produce and accumulate sulfane sulfur when oxidizing thiosulfate. However, how bacteria alleviate the pressure of sulfane sulfur accumulation remains largely unclear. In this study, we focused on the bacterium Cupriavidus pinatubonensis JMP134, which contains a complete Sox system. When soxCD was deleted, this bacterium temporarily produced sulfane sulfur when oxidizing thiosulfate. Persulfide dioxygenase (PDO) in concert with glutathione oxidizes sulfane sulfur to sulfite. Sulfite can spontaneously react with extra persulfide glutathione (GSSH) to produce thiosulfate, which can feed into the incomplete Sox system again and be oxidized to sulfate. Furthermore, the deletion strain lacking PDO and SoxCD produced volatile H2S gas when oxidizing thiosulfate. By comparing the oxidized glutathione (GSSG) between the wild-type and deletion strains, we speculated that H2S is generated during the interaction between sulfane sulfur and the glutathione/oxidized glutathione (GSH/GSSG) redox couple, which may reduce the oxidative stress caused by the accumulation of sulfane sulfur in bacteria. Thus, PDO and H2S release play a critical role in alleviating sulfane sulfur toxicity after the loss of soxCD in C. pinatubonensis JMP134.
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Affiliation(s)
- Yufeng Xin
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence: (Y.X.); (X.Q.); Tel.: +86-15562345068 (Y.X.)
| | - Yaxin Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honglin Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yu Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huanjie Li
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xiaohua Qu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence: (Y.X.); (X.Q.); Tel.: +86-15562345068 (Y.X.)
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2
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Hu L, Wang Y, Ci M, Long Y. Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics. CHEMOSPHERE 2023; 313:137537. [PMID: 36521740 DOI: 10.1016/j.chemosphere.2022.137537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/25/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Hydrogen sulfide (H2S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H2S odor control in landfill management.
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Affiliation(s)
- Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Yuqian Wang
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Manting Ci
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Instrumental Analysis Center, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Instrumental Analysis Center, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
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3
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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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4
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Jeon W, Priscilla L, Park G, Lee H, Lee N, Lee D, Kwon H, Ahn I, Lee C, Lee H, Ahn J. Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKT T. Stand Genomic Sci 2017; 12:54. [PMID: 28904743 PMCID: PMC5588614 DOI: 10.1186/s40793-017-0265-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 08/23/2017] [Indexed: 02/03/2023] Open
Abstract
A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO2 bio-mitigation owing to its ability to convert CO2 into C5H8NO4− at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of S. lithotrophicum 42BKTT comprised of a single chromosome of 2217,891 bp with 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we present its complete genome-sequence information, including information about the genes encoding enzymes involved in CO2 fixation and sulfur oxidation.
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Affiliation(s)
- Wooyoung Jeon
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, South Korea
| | - Lia Priscilla
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Chemical Engineering Study Program, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl.Ganesa No. 10, Bandung, 40132 Indonesia
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, South Korea
| | - Heeseok Lee
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, South Korea
| | - Narae Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576 Singapore
| | - Dongyup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576 Singapore
| | - Hyuksung Kwon
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749 South Korea
| | - Iksung Ahn
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749 South Korea
| | - Changha Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749 South Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, South Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, KRIBB, 40 Yeongudanji-ro, Cheongju, 363-883 South Korea.,Bioprocess Department, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, South Korea
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Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
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6
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Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle. Proc Natl Acad Sci U S A 2015; 112:E7166-75. [PMID: 26655737 DOI: 10.1073/pnas.1506386112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The bacterial Sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. Intermediates in the Sox pathway are covalently attached to the heterodimeric carrier protein SoxYZ through conjugation to a cysteine on a protein swinging arm. We have investigated how the carrier protein shuttles intermediates between the enzymes of the Sox pathway using the interaction between SoxYZ and the enzyme SoxB as our model. The carrier protein and enzyme interact only weakly, but we have trapped their complex by using a "suicide enzyme" strategy in which an engineered cysteine in the SoxB active site forms a disulfide bond with the incoming carrier arm cysteine. The structure of this trapped complex, together with calorimetric data, identifies sites of protein-protein interaction both at the entrance to the enzyme active site tunnel and at a second, distal, site. We find that the enzyme distinguishes between the substrate and product forms of the carrier protein through differences in their interaction kinetics and deduce that this behavior arises from substrate-specific stabilization of a conformational change in the enzyme active site. Our analysis also suggests how the carrier arm-bound substrate group is able to outcompete the adjacent C-terminal carboxylate of the carrier arm for binding to the active site metal ions. We infer that similar principles underlie carrier protein interactions with other enzymes of the Sox pathway.
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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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Kappler U, Maher MJ. The bacterial SoxAX cytochromes. Cell Mol Life Sci 2013; 70:977-92. [PMID: 22907414 PMCID: PMC11113948 DOI: 10.1007/s00018-012-1098-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/09/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
SoxAX cytochromes are heme-thiolate proteins that play a key role in bacterial thiosulfate oxidation, where they initiate the reaction cycle of a multi-enzyme complex by catalyzing the attachment of sulfur substrates such as thiosulfate to a conserved cysteine present in a carrier protein. SoxAX proteins have a wide phylogenetic distribution and form a family with at least three distinct types of SoxAX protein. The types of SoxAX cytochromes differ in terms of the number of heme groups present in the proteins (there are diheme and triheme versions) as well as in their subunit structure. While two of the SoxAX protein types are heterodimers, the third group contains an additional subunit, SoxK, that stabilizes the complex of the SoxA and SoxX proteins. Crystal structures are available for representatives of the two heterodimeric SoxAX protein types and both of these have shown that the cysteine ligand to the SoxA active site heme carries a modification to a cysteine persulfide that implicates this ligand in catalysis. EPR studies of SoxAX proteins have also revealed a high complexity of heme dependent signals associated with this active site heme; however, the exact mechanism of catalysis is still unclear at present, as is the exact number and types of redox centres involved in the reaction.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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9
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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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Drew SC, Reijerse E, Quentmeier A, Rother D, Friedrich CG, Lubitz W. Spectroscopic Characterization of the Molybdenum Cofactor of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus. Inorg Chem 2011; 50:409-11. [DOI: 10.1021/ic102201f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon C. Drew
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
| | - Eduard Reijerse
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
| | - Armin Quentmeier
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Dagmar Rother
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Cornelius G. Friedrich
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
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11
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Kappler U. Bacterial sulfite-oxidizing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1-10. [DOI: 10.1016/j.bbabio.2010.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 11/25/2022]
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12
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Zander U, Faust A, Klink BU, de Sanctis D, Panjikar S, Quentmeier A, Bardischewsky F, Friedrich CG, Scheidig AJ. Structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase SoxCD. J Biol Chem 2010; 286:8349-8360. [PMID: 21147779 DOI: 10.1074/jbc.m110.193631] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six-electron oxidation reaction within the Sox cycle. SoxCD is an α(2)β(2) heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D(1) and D(2). SoxCD(1) misses the heme-2 domain D(2) and is catalytically as active as SoxCD. The crystal structure of SoxCD(1) was solved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys-110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD(1) substrate funnel toward the molybdopterin is narrow and partially shielded by side-chain residues of SoxD(1). For access of the sulfane-sulfur of SoxY-Cys-110 persulfide we propose that (i) the blockage by SoxD-Arg-98 is opened via interaction with the C terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine-bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom that is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Because SoxYZ, SoxXA, and SoxB are already structurally characterized, with SoxCD(1) the structures of all key enzymes of the Sox cycle are known with atomic resolution.
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Affiliation(s)
- Ulrich Zander
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany,; the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany
| | - Annette Faust
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Björn U Klink
- the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany
| | - Daniele de Sanctis
- the Structural Biology Group, European Synchrotron Radiation Facility Grenoble, 6 Rue Jules Horowitz, B.P. 220, 38043 Grenoble Cedex 9, France, and
| | - Santosh Panjikar
- the EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Armin Quentmeier
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Frank Bardischewsky
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany
| | - Cornelius G Friedrich
- the Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, 44221 Dortmund, Germany,.
| | - Axel J Scheidig
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany,; the Department of Biophysics-Structural Biology, Saarland University, 66421 Homburg, Germany,.
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Yamamoto M, Nakagawa S, Shimamura S, Takai K, Horikoshi K. Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1. Environ Microbiol 2010; 12:1144-53. [PMID: 20132283 DOI: 10.1111/j.1462-2920.2010.02155.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular components involved in energy metabolism of deep-sea Epsilonproteobacteria were characterized in the mesophilic hydrogen- and sulfur-oxidizing chemolithoautotroph Sulfurovum sp. NBC37-1. Previous whole-genome analysis of strain NBC37-1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur-reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37-1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep-sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.
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Affiliation(s)
- Masahiro Yamamoto
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
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Sulfite oxidation in Sinorhizobium meliloti. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1516-25. [DOI: 10.1016/j.bbabio.2009.07.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 07/16/2009] [Accepted: 07/16/2009] [Indexed: 11/21/2022]
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15
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Welte C, Hafner S, Krätzer C, Quentmeier A, Friedrich CG, Dahl C. Interaction between Sox proteins of two physiologically distinct bacteria and a new protein involved in thiosulfate oxidation. FEBS Lett 2009; 583:1281-6. [PMID: 19303410 DOI: 10.1016/j.febslet.2009.03.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 03/02/2009] [Accepted: 03/11/2009] [Indexed: 10/21/2022]
Abstract
Organisms using the thiosulfate-oxidizing Sox enzyme system fall into two groups: group 1 forms sulfur globules as intermediates (Allochromatium vinosum), group 2 does not (Paracoccus pantotrophus). While several components of their Sox systems are quite similar, i.e. the proteins SoxXA, SoxYZ and SoxB, they differ by Sox(CD)(2) which is absent in sulfur globule-forming organisms. Still, the respective enzymes are partly exchangeable in vitro: P. pantotrophus Sox enzymes work productively with A. vinosum SoxYZ whereas A. vinosum SoxB does not cooperate with the P. pantotrophus enzymes. Furthermore, A. vinosum SoxL, a rhodanese-like protein encoded immediately downstream of soxXAK, appears to play an important role in recycling SoxYZ as it increases thiosulfate depletion velocity in vitro without increasing the electron yield.
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Affiliation(s)
- Cornelia Welte
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
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16
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Rother D, Ringk J, Friedrich CG. Sulfur oxidation of Paracoccus pantotrophus: the sulfur-binding protein SoxYZ is the target of the periplasmic thiol-disulfide oxidoreductase SoxS. MICROBIOLOGY-SGM 2008; 154:1980-1988. [PMID: 18599826 DOI: 10.1099/mic.0.2008/018655-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The periplasmic thiol-disulfide oxidoreductase SoxS is essential for chemotrophic growth of Paracoccus pantotrophus with thiosulfate. To trap its periplasmic partner, the cysteine residues of the CysXaaXaaCys motif of SoxS (11 kDa) were changed to alanine by site-directed mutagenesis. The disrupted soxS gene of the homogenote mutant G OmegaS was complemented with plasmids carrying the mutated soxS[C13A] or soxS[C16A] gene. Strain G OmegaS(pRD179.6[C16A](S)) displayed a marginal thiosulfate-oxidizing activity, suggesting that Cys13(S) binds the target protein. Evidence is presented that SoxS specifically binds SoxY. (i) Immunoblot analysis using non-reducing SDS gel electrophoresis and anti-SoxS and anti-SoxYZ antibodies identified the respective antigens of strain G OmegaS(pRD179.6[C16A](S)) at the 25 kDa position, suggesting an adduct of about 14 kDa, close to the value expected for SoxY migration. (ii) A mutant unable to produce SoxYZ, such as strain G OmegaX(pRD187.7[C16A](S)), did not form a SoxS(C16A) adduct, while addition of homogeneous SoxYZ resulted in the 25 kDa adduct. (iii) The SoxY and SoxZ subunits were distinguished by site-directed mutagenesis of the cysteine residue in SoxZ. SoxYZ(C53S) formed the 25 kDa adduct with SoxS(C16A). These results demonstrate that the target of SoxS is the sulfur-binding protein SoxY of the SoxYZ complex. As SoxYZ is reversibly inactivated, SoxS may activate SoxYZ as a crucial function for chemotrophy of P. pantotrophus.
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Affiliation(s)
- Dagmar Rother
- Lehrstuhl für Technische Mikrobiologie, Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, D-44221 Dortmund, Germany
| | - Josefina Ringk
- Lehrstuhl für Technische Mikrobiologie, Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, D-44221 Dortmund, Germany
| | - Cornelius G Friedrich
- Lehrstuhl für Technische Mikrobiologie, Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, D-44221 Dortmund, Germany
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Kappler U, Bernhardt PV, Kilmartin J, Riley MJ, Teschner J, McKenzie KJ, Hanson GR. SoxAX cytochromes, a new type of heme copper protein involved in bacterial energy generation from sulfur compounds. J Biol Chem 2008; 283:22206-14. [PMID: 18552405 DOI: 10.1074/jbc.m800315200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SoxAX cytochromes are essential for the function of the only confirmed pathway for bacterial thiosulfate oxidation, the so-called "Sox pathway," in which they catalyze the initial formation of a S-S bond between thiosulfate and the SoxYZ carrier protein. Our work using the Starkeya novella diheme SoxAX protein reveals for the first time that in addition to two active site heme groups, SoxAX contains a mononuclear Cu(II) center with a distorted tetragonal geometry and three to four nitrogen ligands, one of which is a histidine. The Cu(II) center enhanced SoxAX activity in a newly developed, glutathione-based assay system that mimics the natural reaction of SoxAX with SoxYZ. EPR spectroscopy confirmed that the SoxAX Cu(II) center is reduced by glutathione. At pH 7 a K(m) (app) of 0.19+/-0.028 mm and a k(cat) (app) of 5.7+/-0.25s(-1) were determined for glutathione. We propose that SoxAX cytochromes are a new type of heme-copper proteins, with SoxAX-mediated S-S bond formation involving both the copper and heme centers.
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Affiliation(s)
- Ulrike Kappler
- School of Molecular & Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Bardischewsky F, Fischer J, Höller B, Friedrich CG. SoxV transfers electrons to the periplasm of Paracoccus pantotrophus - an essential reaction for chemotrophic sulfur oxidation. MICROBIOLOGY-SGM 2006; 152:465-472. [PMID: 16436434 DOI: 10.1099/mic.0.28523-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The soxVW genes are located upstream of the sox gene cluster encoding the sulfur-oxidizing ability of Paracoccus pantotrophus. SoxV is highly homologous to CcdA, which is involved in cytochrome c maturation of P. pantotrophus. SoxV was shown to function in reduction of the periplasmic SoxW, which shows a CysXaaXaaCys motif characteristic for thioredoxins. From strain GBOmegaV, which carries an Omega-kanamycin-resistance-encoding interposon in soxV, and complementation analysis it was evident that SoxV but not the periplasmic SoxW was essential for lithoautotrophic growth of P. pantotrophus with thiosulfate. However, the thiosulfate-oxidizing activities of cell extracts from the wild-type and from strain GBOmegaV were similar, demonstrating that the low thiosulfate-oxidizing activity of strain GBOmegaV in vivo was not due to a defect in biosynthesis or maturation of proteins of the Sox system and suggesting that SoxV is part of a regulatory or catalytic system of the Sox system. Analysis of DNA sequences available from different organisms harbouring a Sox system revealed that soxVW genes are exclusively present in sox operons harbouring the soxCD genes, encoding sulfur dehydrogenase, suggesting that SoxCD might be a redox partner of SoxV. No complementation of the ccdA mutant P. pantotrophus TP43 defective in cytochrome c maturation was achieved by expression of soxV in trans, demonstrating that the high identity of SoxV and CcdA does not correspond to functional homology.
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Affiliation(s)
- Frank Bardischewsky
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, D-44221 Dortmund, Germany
| | - Jörg Fischer
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, D-44221 Dortmund, Germany
| | - Bettina Höller
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, D-44221 Dortmund, Germany
| | - Cornelius G Friedrich
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Bio- und Chemieingenieurwesen, Universität Dortmund, D-44221 Dortmund, Germany
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Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ. Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation. J Struct Biol 2005; 152:229-34. [PMID: 16297640 DOI: 10.1016/j.jsb.2005.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 09/12/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus pantotrophus is composed of several proteins, which together oxidize hydrogen sulfide, sulfur, thiosulfate or sulfite and transfers the gained electrons to the respiratory chain. The hetero-dimeric cytochrome c complex SoxXA functions as heme enzyme and links covalently the sulfur substrate to the thiol of the cysteine-138 residue of the SoxY protein of the SoxYZ complex. Here, we report the crystal structure of the c-type cytochrome complex SoxXA. The structure could be solved by molecular replacement and refined to a resolution of 1.9A identifying the axial heme-iron coordination involving an unusual Cys-251 thiolate of heme2. Distance measurements between the three heme groups provide deeper insight into the electron transport inside SoxXA and merge in a better understanding of the initial step of the aerobic sulfur oxidation process in chemotrophic bacteria.
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Affiliation(s)
- Tresfore Dambe
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, D-44225 Dortmund, Germany
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Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J. Prokaryotic sulfur oxidation. Curr Opin Microbiol 2005; 8:253-9. [PMID: 15939347 DOI: 10.1016/j.mib.2005.04.005] [Citation(s) in RCA: 315] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 04/20/2005] [Indexed: 11/28/2022]
Abstract
Recent biochemical and genomic data differentiate the sulfur oxidation pathway of Archaea from those of Bacteria. From these data it is evident that members of the Alphaproteobacteria harbor the complete sulfur-oxidizing Sox enzyme system, whereas members of the beta and gamma subclass and the Chlorobiaceae contain sox gene clusters that lack the genes encoding sulfur dehydrogenase. This indicates a different pathway for oxidation of sulfur to sulfate. Acidophilic bacteria oxidize sulfur by a system different from the Sox enzyme system, as do chemotrophic endosymbiotic bacteria.
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Affiliation(s)
- Cornelius G Friedrich
- Department of Biochemical and Chemical Engineering, University of Dortmund, D-44221 Dortmund, Germany.
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