Biochemical Studies of asoxF-Encoded Monomeric Flavoprotein Purified from the Green Sulfur BacteriumChlorobaculum tepidumThat Stimulatesin VitroThiosulfate Oxidation

Ogawa, Taiji; Furusawa, Toshinari; Shiga, Michiko; Seo, Daisuke; Inoue, Kazuhito

doi:10.1271/bbb.90815

Cited by 17 publications

(18 citation statements)

References 39 publications

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“…However, reconstituted Sox systems of P. pantotrophus have been shown to oxidize different reduced sulfur substrates with different affinities (particularly hydrogen sulfide and sulfite) . Moreover, Ogawa et al report that the Sox component of Chlorobium tepidum, which does not possess a SoxCD complex, could oxidize sulfide and sulfite (33). Mutant strains of C. tepidum devoid of a soxB gene showed partial growth on media containing only sulfide relative to the wild type (34), suggesting that the soxB gene is important for function of the Sox enzyme complex in oxidizing reduced sulfur compounds other than thiosulfate.…”

mentioning

confidence: 99%

Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

Headd

Engel

2013

Appl Environ Microbiol

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The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and soxB genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxB gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the Paracoccus sulfide oxidation pathway (e.g., Bradyrhizobium, Paracoccus, and Rhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g., Chlorobium, Thiothrix, Thiobacillus, Halothiobacillus, and Thiomonas) were identified. Different variations of the soxB genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different soxB gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.

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confidence: 99%

Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

Headd

Engel

2013

Appl Environ Microbiol

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Section: Introductionmentioning

confidence: 99%

“…At whatever point sulfide is produced, it is a prime need to oxidize the sulfide to essential sulfur [1]. Thiosulfate is the main sulfur substrate that is all around oxidized by dominant part of known chemolithotrophic life forms [1]. In our surroundings, a standout amongst the most imperative arrangements of biogeochemical responses are the redox reactions of environmental sulfur compounds and their steady turnover is highly important to adjust a biosystem with sulfur compounds [1].…”

Section: Introductionmentioning

confidence: 99%

Insights from the docked DoxDA Model with Thiosulphate

Ray

Bagchi

2016

Bioinformation

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Redox reaction of inorganic sulphur compound is very essential to maintain a global sulphur cycle. Certain experimental evidences suggest that gamma-proteobacterial Acidothiobacillus thiooxidans; lacking the sulphur-oxidizing (sox) operon, has an alternative thiosulphate oxidation pathway. Dox operon having essentially participating proteins; DoxD and DoxA serves as the central players for this alternative pathway of thiosulphate oxidation. So, to identify their role in thiosulphate oxidation process, functional 3D model of DoxD and DoxA protein’s independently functioning conserved domains were built after the contentment of necessary stereochemical features. After formation of the best suited DoxDA protein-complex, DoxDA was MD simulated in several steps and finally through MD simulation run utilizing GROMACS. Even after running beyond 20ns, 18ns simulated protein complex was the most stable and was selected for further study. Residual binding mode conferred mainly two ionic and twelve Hbonded interactions in DoxDA. Astonishingly, Asp167 and Arg18 from DoxA and DoxD, respectively was observed to hold a pivotal role in 6 H-bonds accompanied by a separate ionic interaction. Interestingly, four residues from DoxD; Trp32, Met33, Lys36 and Asn140 strengthened the DoxD–thiosulphate interaction. Interaction energy (deltaG = (-) 222.016kcal/mol) and net solvent accessibility calculations depicts spontaneous and fervent residual participation in DoxDA, which is essential for thiosulphate interaction and further sulphur oxidation. Conformational flexibility in DoxD with increased coil percentage benefits DoxD and makes its susceptible for the interaction with thiosulphate even after spontaneous interaction with DoxA. Therefore, this study serves as an insight at computational basis for sulphur oxidation even in organisms lacking sox operon.

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“…But is has been clearly noted that the SoxY-Z protein complex often remains in inactive form in sulphur oxidizing micro-organisms. In C. tepidum, the SoxY-Z protein complex is often activated by SoxF protein from Sox operon [5]. SoxF protein has sulfide dehydrogenase activity and is responsible to enhance the thiosulfate oxidation activity [5].…”

Section: Introductionmentioning

confidence: 99%

“…In C. tepidum, the SoxY-Z protein complex is often activated by SoxF protein from Sox operon [5]. SoxF protein has sulfide dehydrogenase activity and is responsible to enhance the thiosulfate oxidation activity [5]. Hydrogenophilus thermoluteolus is a thermophilic facultative chemoautotroph, which lives prevalently in high temperature geothermal niches.…”

Section: Introductionmentioning

confidence: 99%

In-Silico Structural Analysis of SoxF Protein Through Molecular Modelling and Protein-Protein Docking from Hydrogenophilus thermoluteolus: An Approach to Understand the Molecular Mechanism of Thiosulfate Oxidation

Ray

Bagchi

2015

Advances in Intelligent Systems and Computing

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Microbial redox reactions of inorganic sulphur compounds play vital role for recycling of sulphur to maintain environmental sulphur balance. These important reactions are carried out by enzyme system encoded by sox operon. Central player of sulphur oxidation process is SoxY-Z protein complex. Thermophilic betaproteobacterium-Hydrogenophilus thermoluteolus, oxidizes sulphur compounds including thiosulfate with the help of proteins encoded by sox operon. Protein SoxF having sulfide dehydrogenase activity has the ability to reactivate the inactivated SoxY-Z complex. Till date no structural details are available for SoxF protein from H. thermoluteolus. In present work, homology modeling has been used to build 3D structures of SoxY, SoxZ and SoxF of H. thermoluteolus. 3D structure of SoxY-Z-F complex was obtained by ClusPro2.0. Amino acid residues responsible for proteinprotein interaction were identified. Interactions in SoxY-Z-F were found to be mediated through hydrogen bonding. Probable biophysical mechanism of the interactions of SoxF with SoxY-Z complex has been identified.

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Biochemical Studies of asoxF-Encoded Monomeric Flavoprotein Purified from the Green Sulfur BacteriumChlorobaculum tepidumThat Stimulatesin VitroThiosulfate Oxidation

Cited by 17 publications

References 39 publications

Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

Evidence for Niche Partitioning Revealed by the Distribution of Sulfur Oxidation Genes Collected from Areas of a Terrestrial Sulfidic Spring with Differing Geochemical Conditions

Insights from the docked DoxDA Model with Thiosulphate

In-Silico Structural Analysis of SoxF Protein Through Molecular Modelling and Protein-Protein Docking from Hydrogenophilus thermoluteolus: An Approach to Understand the Molecular Mechanism of Thiosulfate Oxidation

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