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Huang S, Li H, Ma L, Liu R, Li Y, Wang H, Lu X, Huang X, Wu X, Liu X. Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus. BMC Genomics 2023; 24:282. [PMID: 37231368 DOI: 10.1186/s12864-023-09372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. RESULTS In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. CONCLUSIONS This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.
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Affiliation(s)
- Shanshan Huang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Huiying Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Yiran Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Hongmei Wang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xiaolu Lu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
| | - Xinhong Wu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
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2
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Miklovics N, Duzs Á, Balogh F, Paragi G, Rákhely G, Tóth A. Quinone binding site in a type VI sulfide:quinone oxidoreductase. Appl Microbiol Biotechnol 2022; 106:7505-7517. [PMID: 36219222 DOI: 10.1007/s00253-022-12202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
Monotopic membrane-bound flavoproteins, sulfide:quinone oxidoreductases (SQRs), have a variety of physiological functions, including sulfide detoxification. SQR enzymes are classified into six groups. SQRs use the flavin adenine dinucleotide (FAD) cofactor to transfer electrons from sulfide to quinone. A type VI SQR of the photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina (TrSqrF), has been previously characterized, and the mechanism of sulfide oxidation has been proposed. This paper reports the characterization of quinone binding site (QBS) of TrSqrF composed of conserved aromatic and apolar amino acids. Val331, Ile333, and Phe366 were identified near the benzoquinone ring of enzyme-bound decylubiquinone (dUQ) using the TrSqrF homology model. In silico analysis revealed that Val331 and Ile333 alternately connected with the quinone head group via hydrogen bonds, and Phe366 and Trp369 bound the quinones via hydrophobic interactions. TrSqrF variants containing alanine (V331A, I333A, F366A) and aromatic amino acid (V331F, I333F, F366Y), as well as a C-terminal α-helix deletion (CTD) mutant were generated. These amino acids are critical for quinone binding and, thus, catalysis. Spectroscopic analyses proved that all mutants contained FAD. I333F replacement resulted in the lack of the charge transfer complex. In summary, the interactions described above maintain the quinone molecule's head in an optimal position for direct electron transfer from FAD. Surprisingly, the CTD mutant retained a relatively high level of specific activity while remaining membrane-anchored. This is a unique study because it focuses on the QBS and the oxidative stage of a type VI sulfide-dependent quinone reduction. KEY POINTS: • V331, I333, F366, and W369 were shown to interact with decylubiquinone in T. roseopersicina SqrF • These amino acids are involved in proper positioning of quinones next to FAD • I333 is essential in formation of a charge transfer complex from FAD to quinone.
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Affiliation(s)
- Nikolett Miklovics
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Fanni Balogh
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Paragi
- Institute of Physics, University of Pécs, Pécs, Hungary
- Department of Theoretical Physics, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary.
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
| | - András Tóth
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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3
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Duzs Á, Miklovics N, Paragi G, Rákhely G, Tóth A. Insights into the catalytic mechanism of type VI sulfide:quinone oxidoreductases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148337. [PMID: 33202220 DOI: 10.1016/j.bbabio.2020.148337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Sulfide oxidation is catalyzed by ancient membrane-bound sulfide:quinone oxidoreductases (SQR) which are classified into six different types. For catalysis of sulfide oxidation, all SQRs require FAD cofactor and a redox-active centre in the active site, usually formed between conserved essential cysteines. SQRs of different types have variation in the number and position of cysteines, highlighting the potential for diverse catalytic mechanisms. The photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina contains a type VI SQR enzyme (TrSqrF) having unusual catalytic parameters and four cysteines likely involved in the catalysis. Site-directed mutagenesis was applied to identify the role of cysteines in the catalytic process of TrSqrF. Based on biochemical and kinetic characterization of these TrSqrF variants, Cys121 is identified as crucial for enzyme activity. The cofactor is covalently bound via a heterodisulfide bridge between Cys121 and the C8M group of FAD. Mutation of another cysteine present in all SQRs (Cys332) causes remarkably decreased enzyme activity (14.6% of wild type enzyme) proving important, but non-essential role of this residue in enzyme catalysis. The sulfhydril-blocking agent, iodoacetamide can irreversibly inactivate TrSqrF but only if substrates are present and the enzyme is actively catalyzing its reaction. When the enzyme is inhibited by iodoacetamide, the FAD cofactor is released. The inhibition studies support a mechanism that entails opening and reforming of the heterodisulfide bridge during the catalytic cycle of TrSqrF. Our study thus reports the first detailed structure-function analysis of a type VI SQR enzyme which enables the proposal of a distinct mechanism of sulfide oxidation for this class.
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Affiliation(s)
- Ágnes Duzs
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Nikolett Miklovics
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary; Doctoral School in Biology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
| | - Gábor Paragi
- Institute of Physics, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary; MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Dóm square 8, H-6720 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary.
| | - András Tóth
- Institute of Biophysics, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary; Department of Biotechnology, University of Szeged, Közép fasor 52., H-6726 Szeged, Hungary
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4
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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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Sensitive detection of low-concentration sulfide based on the synergistic effect of rGO, np-Au, and recombinant microbial cell. Biosens Bioelectron 2020; 151:111985. [DOI: 10.1016/j.bios.2019.111985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/09/2019] [Accepted: 12/22/2019] [Indexed: 11/17/2022]
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6
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Lencina AM, Gennis RB, Schurig-Briccio LA. The oligomeric state of the Caldivirga maquilingensis type III sulfide:Quinone Oxidoreductase is required for membrane binding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148132. [PMID: 31816290 DOI: 10.1016/j.bbabio.2019.148132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/11/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022]
Abstract
Sulfide:quinone oxidoreductase (SQR) is a monotopic membrane flavoprotein present in all domains of life, with multiple roles including sulfide detoxification, homeostasis and energy generation by providing electrons to respiratory or photosynthetic electron transport chains. A type III SQR from the hyperthermophilic archeon Caldivirga maquilingensis has been previously characterized, and its C-terminal amphipathic helices were demonstrated to be responsible for membrane binding. Here, the oligomeric state of this protein was experimentally evaluated by size exclusion chromatography, native gels and crosslinking, and found to be a monomer-dimer-trimer equilibrium. Remarkably, mutant and truncated variants unable to bind to the membrane are able to maintain their oligomeric association. Thus, unlike other related monotopic membrane proteins, the region involved in membrane binding does not influence oligomerization. Furthermore, by studying heterodimers between the WT and mutants, it was concluded that membrane binding requires an oligomer with at least two copies of the protein with intact C-terminal amphipathic helices. A structural homology model of the C. maquilingensis SQR was used to define the flavin- and quinone-binding sites. CmGly12, CmGly16, CmAla77 and CmPro44 were determined to be important for flavin binding. Unexpectedly, CmGly299 is only important for quinone reduction despite its proximity to bound FAD. CmPhe337 and CmPhe362 are also important for quinone binding apparently by direct interaction with the quinone ring, whereas CmLys359, postulated to hydrogen bond to the quinone, seems to have a more structural role. The results presented differentiate the Type III CmSQR from some of its counterparts classified as Type I, II and V.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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7
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Shen Y, Chen J, Shen W, Chen C, Lin Z, Li C. Molecular characterization of a novel sulfide:quinone oxidoreductase from the razor clam Sinonovacula constricta and its expression response to sulfide stress. Comp Biochem Physiol B Biochem Mol Biol 2020; 239:110367. [DOI: 10.1016/j.cbpb.2019.110367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/10/2019] [Accepted: 10/03/2019] [Indexed: 01/16/2023]
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8
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Landry AP, Moon S, Kim H, Yadav PK, Guha A, Cho US, Banerjee R. A Catalytic Trisulfide in Human Sulfide Quinone Oxidoreductase Catalyzes Coenzyme A Persulfide Synthesis and Inhibits Butyrate Oxidation. Cell Chem Biol 2019; 26:1515-1525.e4. [PMID: 31591036 DOI: 10.1016/j.chembiol.2019.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 09/17/2019] [Indexed: 01/09/2023]
Abstract
Mitochondrial sulfide quinone oxidoreductase (SQR) catalyzes the oxidation of H2S to glutathione persulfide with concomitant reduction of CoQ10. We report herein that the promiscuous activity of human SQR supported the conversion of CoA to CoA-SSH (CoA-persulfide), a potent inhibitor of butyryl-CoA dehydrogenase, and revealed a molecular link between sulfide and butyrate metabolism, which are known to interact. Three different CoQ1-bound crystal structures furnished insights into how diverse substrates access human SQR, and provided snapshots of the reaction coordinate. Unexpectedly, the active site cysteines in SQR are configured in a bridging trisulfide at the start and end of the catalytic cycle, and the presence of sulfane sulfur was confirmed biochemically. Importantly, our study leads to a mechanistic proposal for human SQR in which sulfide addition to the trisulfide cofactor eliminates 201Cys-SSH, forming an intense charge-transfer complex with flavin adenine dinucleotide, and 379Cys-SSH, which transfers sulfur to an external acceptor.
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Affiliation(s)
- Aaron P Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Sojin Moon
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pramod K Yadav
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arkajit Guha
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Bonanata J, Coitiño EL. Understanding the mechanism of H 2S oxidation by flavin-dependent sulfide oxidases: a DFT/IEF-PCM study. J Mol Model 2019; 25:308. [PMID: 31502063 DOI: 10.1007/s00894-019-4197-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022]
Abstract
In the last years, H2S has been recognized as a signaling molecule in mammals, which can synthesize and catabolize (by oxidation) such species. The latter process is accelerated by a sulfide:quinone oxidoreductase (SQR, E.C. 1.8.5.4), a flavin-dependent sulfide oxidase (FDSO). FDSOs catalyze electron transfer from H2S to an acceptor in catalytic cycles involving two phases: (I) reduction of FAD by H2S (SH-) and (II) electron transfer from FADH- to the electron acceptor. The first step of FAD reduction consists on the reaction of SH- with a catalytic disulfide at the active site of the enzyme, to yield a thiolate and a persulfide in the protein. This step is ca. 106 times faster than the analogous reaction with low-molecular-weight disulfides (LMWDs) and the causes of such extraordinary acceleration remain unknown. Using the IEF-PCM(ε ≈ 10)/M06-2X-D3/6-31+G(d,p) level of theory, we have modeled the reaction of SH- with a disulfide as located in a representative model of the active site extracted from a prokaryotic SQR, assessing the effects of partial covalent interactions (PCIs) between the leaving sulfur atom and flavin ring on the activation Gibbs free-energy barrier at 298 K (∆‡G298K). To also evaluate the importance of entropic penalties on the first step, we have modeled at the same level of theory the reaction of (bis)hydroxyethyl disulfide in aqueous solution, a LMWD for which experimental data is available. Our results show that PCIs between the leaving sulfur atom and the flavin group only have a minor effect (∆‡G298K reduced by 1.6 kcal mol-1) while compensating entropic penalties could have a much larger effect (up to 8.3 kcal mol-1). Finally, we also present here a first model of some of further steps in the phase I of the catalytic cycle as in mammalian FDSOs, providing some light about their detailed mechanism. Graphical abstract .
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias and Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
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10
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Zhan Y, Yang M, Zhang S, Zhao D, Duan J, Wang W, Yan L. Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans. World J Microbiol Biotechnol 2019; 35:60. [PMID: 30919119 DOI: 10.1007/s11274-019-2632-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022]
Abstract
Acidithiobacillus ferrooxidans is a gram-negative, autotrophic and rod-shaped bacterium. It can gain energy through the oxidation of Fe(II) and reduced inorganic sulfur compounds for bacterial growth when oxygen is sufficient. It can be used for bio-leaching and bio-oxidation and contributes to the geobiochemical circulation of metal elements and nutrients in acid mine drainage environments. The iron and sulfur oxidation pathways of A. ferrooxidans play key roles in bacterial growth and survival under extreme circumstances. Here, the electrons transported through the thermodynamically favourable pathway for the reduction to H2O (downhill pathway) and against the redox potential gradient reduce to NAD(P)(H) (uphill pathway) during the oxidation of Fe(II) were reviewed, mainly including the electron transport carrier, relevant operon and regulation of its expression. Similar to the electron transfer pathway, the sulfur oxidation pathway of A. ferrooxidans, related genes and operons, sulfur oxidation mechanism and sulfur oxidase system are systematically discussed.
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Affiliation(s)
- Yue Zhan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Mengran Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Jiangong Duan
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, Gansu Province, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China. .,College of Food Science, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China.
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11
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Duzs Á, Tóth A, Németh B, Balogh T, Kós PB, Rákhely G. A novel enzyme of type VI sulfide:quinone oxidoreductases in purple sulfur photosynthetic bacteria. Appl Microbiol Biotechnol 2018; 102:5133-5147. [PMID: 29680900 DOI: 10.1007/s00253-018-8973-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/23/2018] [Accepted: 03/28/2018] [Indexed: 11/24/2022]
Abstract
Sulfide detoxification can be catalyzed by ancient membrane-bound flavoproteins, sulfide:quinone oxidoreductases (Sqr), which have important roles in sulfide homeostasis and sulfide-dependent energy conservation processes by transferring electrons from sulfide to respiratory or photosynthetic membrane electron flow. Sqr enzymes have been categorized into six groups. Several members of the groups I, II, III, and V are well-known, but type IV and VI Sqrs are, as yet, uncharacterized or hardly characterized at all. Here, we report detailed characterization of a type VI sulfide:quinone oxidoreductase (TrSqrF) from a purple sulfur bacterium, Thiocapsa roseopersicina. Phylogenetic analysis classified this enzyme in a special group composed of SqrFs of endosymbionts, while a weaker relationship could be observed with SqrF of Chlorobaculum tepidum which is the only type VI enzyme characterized so far. Directed mutagenesis experiments showed that TrSqrF contributed substantially to the sulfide:quinone oxidoreductase activity of the membranes. Expression of the sqrF gene could be induced by sulfide. Homologous recombinant TrSqrF protein was expressed and purified from the membranes of a SqrF-deleted T. roseopersicina strain. The purified protein contains redox-active covalently bound FAD cofactor. The recombinant TrSqrF enzyme catalyzes sulfur-dependent quinone reduction and prefers ubiquinone-type quinone compounds. Kinetic parameters of TrSqrF show that the affinity of the enzyme is similar to duroquinone and decylubiquinone, but the reaction has substantially lower activation energy with decylubiquinone, indicating that the quinone structure has an effect on the catalytic process. TrSqrF enzyme affinity for sulfide is low, therefore, in agreement with the gene expressional analyis, SqrF could play a role in energy-conserving sulfide oxidation at high sulfide concentrations. TrSqrF is a good model enzyme for the subgroup of type VI Sqrs of endosymbionts and its characterization might provide deeper insight into the molecular details of the ancient, anoxic, energy-gaining processes using sulfide as an electron donor.
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Affiliation(s)
- Ágnes Duzs
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - András Tóth
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Brigitta Németh
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Tímea Balogh
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Péter B Kós
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary. .,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary.
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12
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Sousa FM, Pereira JG, Marreiros BC, Pereira MM. Taxonomic distribution, structure/function relationship and metabolic context of the two families of sulfide dehydrogenases: SQR and FCSD. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:742-753. [PMID: 29684324 DOI: 10.1016/j.bbabio.2018.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/28/2018] [Accepted: 04/15/2018] [Indexed: 12/26/2022]
Abstract
Hydrogen sulfide (H2S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H2S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H2S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H2S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Juliana G Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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Liu Z, Ma H, Sun H, Gao R, Liu H, Wang X, Xu P, Xun L. Nanoporous gold-based microbial biosensor for direct determination of sulfide. Biosens Bioelectron 2017. [DOI: 10.1016/j.bios.2017.06.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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