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Houghton JL, Foustoukos DI, Fike DA. The effect of O 2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila. Geobiology 2019; 17:564-576. [PMID: 31180189 DOI: 10.1111/gbi.12352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur-oxidizing micro-organisms in particular. In this study, the thiosulfate-oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04-1.9 mM) and high pressure (5-10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed-system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2 was 0.25 hr-1 . This is comparable to the μmax (0.28 hr-1 ) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half-saturation constant for O2 ( KO2 ) estimated from this study was 0.2 mM (at a cell density of 105 cells/ml) and was robust at all pressures tested (0.4-10 MPa), consistent with piezotolerant behavior of this strain. The cell-specific KO2 was determined to be 1.5 pmol O2 /cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell-specific KO2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).
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Affiliation(s)
- Jennifer L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, District of Columbia
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
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Grabarczyk DB, Berks BC. Intermediates in the Sox sulfur oxidation pathway are bound to a sulfane conjugate of the carrier protein SoxYZ. PLoS One 2017; 12:e0173395. [PMID: 28257465 PMCID: PMC5336275 DOI: 10.1371/journal.pone.0173395] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/20/2017] [Indexed: 01/04/2023] Open
Abstract
The Sox pathway found in many sulfur bacteria oxidizes thiosulfate to sulfate. Pathway intermediates are covalently bound to a cysteine residue in the carrier protein SoxYZ. We have used biochemical complementation by SoxYZ-conjugates to probe the identity of the intermediates in the Sox pathway. We find that unconjugated SoxYZ and SoxYZ-S-sulfonate are unlikely to be intermediates during normal turnover in disagreement with current models. By contrast, conjugates with multiple sulfane atoms are readily metabolised by the Sox pathway. The most parsimonious interpretation of these data is that the true carrier species in the Sox pathway is a SoxYZ-S-sulfane adduct.
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Affiliation(s)
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Houghton JL, Foustoukos DI, Flynn TM, Vetriani C, Bradley AS, Fike DA. Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry. Environ Microbiol 2016; 18:3057-72. [PMID: 26914243 DOI: 10.1111/1462-2920.13232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 01/17/2016] [Indexed: 11/29/2022]
Abstract
Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.
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Affiliation(s)
- J L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA.
| | - D I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, 20015, USA
| | - T M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA.,Computation Institution, The University of Chicago, Chicago, IL, 60637, USA
| | - C Vetriani
- Department of Biochemistry and Microbiology and Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
| | - D A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
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Kilmartin JR, Maher MJ, Krusong K, Noble CJ, Hanson GR, Bernhardt PV, Riley MJ, Kappler U. Insights into structure and function of the active site of SoxAX cytochromes. J Biol Chem 2011; 286:24872-81. [PMID: 21592966 PMCID: PMC3137062 DOI: 10.1074/jbc.m110.212183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 04/20/2011] [Indexed: 11/06/2022] Open
Abstract
SoxAX cytochromes catalyze the formation of heterodisulfide bonds between inorganic sulfur compounds and a carrier protein, SoxYZ. They contain unusual His/Cys-ligated heme groups with complex spectroscopic signatures. The heme-ligating cysteine has been implicated in SoxAX catalysis, but neither the SoxAX spectroscopic properties nor its catalysis are fully understood at present. We have solved the first crystal structure for a group 2 SoxAX protein (SnSoxAX), where an N-terminal extension of SoxX forms a novel structure that supports dimer formation. Crystal structures of SoxAX with a heme ligand substitution (C236M) uncovered an inherent flexibility of this SoxA heme site, with both bonding distances and relative ligand orientation differing between asymmetric units and the new residue, Met(236), representing an unusual rotamer of methionine. The flexibility of the SnSoxAX(C236M) SoxA heme environment is probably the cause of the four distinct, new EPR signals, including a high spin ferric heme form, that were observed for the enzyme. Despite the removal of the catalytically active cysteine heme ligand and drastic changes in the redox potential of the SoxA heme (WT, -479 mV; C236M, +85 mV), the substituted enzyme was catalytically active in glutathione-based assays although with reduced turnover numbers (WT, 3.7 s(-1); C236M, 2.0 s(-1)). SnSoxAX(C236M) was also active in assays using SoxYZ and thiosulfate as the sulfur substrate, suggesting that Cys(236) aids catalysis but is not crucial for it. The SoxYZ-based SoxAX assay is the first assay for an isolated component of the Sox multienzyme system.
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Affiliation(s)
- James R. Kilmartin
- From the Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, and
| | - Megan J. Maher
- the Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia
- the School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia, and
| | - Kuakarun Krusong
- the Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Christopher J. Noble
- the Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Graeme R. Hanson
- the Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Paul V. Bernhardt
- From the Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, and
| | - Mark J. Riley
- From the Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, and
| | - Ulrike Kappler
- From the Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, and
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Sakurai H, Ogawa T, Shiga M, Inoue K. Inorganic sulfur oxidizing system in green sulfur bacteria. Photosynth Res 2010; 104:163-176. [PMID: 20143161 DOI: 10.1007/s11120-010-9531-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 01/16/2010] [Indexed: 05/28/2023]
Abstract
Green sulfur bacteria use various reduced sulfur compounds such as sulfide, elemental sulfur, and thiosulfate as electron donors for photoautotrophic growth. This article briefly summarizes what is known about the inorganic sulfur oxidizing systems of these bacteria with emphasis on the biochemical aspects. Enzymes that oxidize sulfide in green sulfur bacteria are membrane-bound sulfide-quinone oxidoreductase, periplasmic (sometimes membrane-bound) flavocytochrome c sulfide dehydrogenase, and monomeric flavocytochrome c (SoxF). Some green sulfur bacteria oxidize thiosulfate by the multienzyme system called either the TOMES (thiosulfate oxidizing multi-enzyme system) or Sox (sulfur oxidizing system) composed of the three periplasmic proteins: SoxB, SoxYZ, and SoxAXK with a soluble small molecule cytochrome c as the electron acceptor. The oxidation of sulfide and thiosulfate by these enzymes in vitro is assumed to yield two electrons and result in the transfer of a sulfur atom to persulfides, which are subsequently transformed to elemental sulfur. The elemental sulfur is temporarily stored in the form of globules attached to the extracellular surface of the outer membranes. The oxidation pathway of elemental sulfur to sulfate is currently unclear, although the participation of several proteins including those of the dissimilatory sulfite reductase system etc. is suggested from comparative genomic analyses.
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Affiliation(s)
- Hidehiro Sakurai
- Research Institute for Photosynthetic Hydrogen Production, Kanagawa University, Hiratsuka, Kanagawa, Japan
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Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 2009; 33:999-1043. [PMID: 19645821 DOI: 10.1111/j.1574-6976.2009.00187.x] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.
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Affiliation(s)
- Wriddhiman Ghosh
- Department of Microbiology, University of Burdwan, West Bengal, India.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Quentmeier A, Li L, Friedrich CG. Identification of two inactive forms of the central sulfur cycle protein SoxYZ of Paracoccus pantotrophus. FEBS Lett 2008; 582:3701-4. [PMID: 18834882 DOI: 10.1016/j.febslet.2008.09.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 09/19/2008] [Accepted: 09/22/2008] [Indexed: 11/30/2022]
Abstract
The central protein of the sulfur-oxidizing enzyme system of Paracoccus pantotrophus, SoxYZ, reacts with three different Sox proteins. Its active site Cys110(Y) is on the carboxy-terminus of the SoxY subunit. SoxYZ "as isolated" consisted mainly of the catalytically inactive SoxY-Y(Z)(2) heterotetramer linked by a Cys110(Y)-Cys110(Y) interprotein disulfide. Sulfide activated SoxYZ "as isolated" 456-fold, reduced the disulfide, and yielded an active SoxYZ heterodimer. The reductant tris(2-carboxyethyl)phosphine (TCEP) inactivated SoxYZ. This form was not re-activated by sulfide, which identified it as a different inactive form. In analytical gel filtration, the elution of "TCEP-treated" SoxYZ was retarded compared to active SoxYZ, indicating a conformational change. The possible enzymes involved in the re-activation of each inactive form of SoxYZ are discussed.
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Affiliation(s)
- Armin Quentmeier
- Lehrstuhl Technische Mikrobiologie, Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, Emil-Figge-Strasse 66, D-44221 Dortmund, Germany
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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 (Reading) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kelly DP. Stable sulfur isotope fractionation and discrimination between the sulfur atoms of thiosulfate during oxidation by Halothiobacillus neapolitanus. FEMS Microbiol Lett 2008; 282:299-306. [DOI: 10.1111/j.1574-6968.2008.01146.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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