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Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.

Yin H, Zhang X, Li X, He Z, Liang Y, Guo X, Hu Q, Xiao Y, Cong J, Ma L, Niu J, Liu X - BMC Microbiol. (2014)

Bottom Line: It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components.Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences.Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. yinhuaqun@gmail.com.

ABSTRACT

Background: Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation.

Results: The genome of A. thiooxidans A01 was sequenced and annotated. It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components. Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences. In addition, another putative pathway was found in the cytoplasm of A. thiooxidans, which catalyzes sulfite to sulfate as the final product by phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase. This differs from its closest relative Acidithiobacillus caldus, which is performed by sulfate adenylyltransferase (SAT). Furthermore, real-time quantitative PCR analysis showed that most of sulfur oxidation genes were more strongly expressed in the S0 medium than that in the Na2S2O3 medium at the mid-log phase.

Conclusion: Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.

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The sulfur oxidation model in A. thiooxidans based on documented models [[2],[6],[9]-[11]], bioinformatics analysis of draft genome sequence. Abbreviations: SDO, sulfur dioxygenase; SQR, sulfide quinone reductase; TQO, thiosulfate:quinone oxidoreductase; TetH, tetrathionate hydrolase; Sox, sulfur oxidizing protein; HDR, heterodisulfide reductase; SOR, sulfur oxygenase reductase; TST, thiosulfate sulfurtransferase; A, phosphoadenosine phosphosulfate reductase; B, adenylylsulfate kinase. As is shown, the sulfur oxidation metabolism in A. thiooxidans A01 contains various sulfur oxidation systems and the electron transfer pathways in different cellular compartments. (i) In the outer membrane, elemental sulfur (S8) in the form of stable octasulfane ring is activated and transported into the periplasm as thiol-bound sulfane sulfur atoms (R-S-SnH); (ii) In the periplasm, R-S-SnH is oxidized by SDO, while tetrathionate is utilized by TetH to produce thiosulfate, and the thiosulfate is sequentially catalyzed by Sox complex; (iii) In the cytoplasmic membrane, SQR and TQO carry out their respective functions with electrons further transferred to terminal oxidase or NADH complex I; and (iv) In the cytoplasm, the particular enzymes perform the catalytic reaction by a sequence of steps that eventually produce sulfate.
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Figure 6: The sulfur oxidation model in A. thiooxidans based on documented models [[2],[6],[9]-[11]], bioinformatics analysis of draft genome sequence. Abbreviations: SDO, sulfur dioxygenase; SQR, sulfide quinone reductase; TQO, thiosulfate:quinone oxidoreductase; TetH, tetrathionate hydrolase; Sox, sulfur oxidizing protein; HDR, heterodisulfide reductase; SOR, sulfur oxygenase reductase; TST, thiosulfate sulfurtransferase; A, phosphoadenosine phosphosulfate reductase; B, adenylylsulfate kinase. As is shown, the sulfur oxidation metabolism in A. thiooxidans A01 contains various sulfur oxidation systems and the electron transfer pathways in different cellular compartments. (i) In the outer membrane, elemental sulfur (S8) in the form of stable octasulfane ring is activated and transported into the periplasm as thiol-bound sulfane sulfur atoms (R-S-SnH); (ii) In the periplasm, R-S-SnH is oxidized by SDO, while tetrathionate is utilized by TetH to produce thiosulfate, and the thiosulfate is sequentially catalyzed by Sox complex; (iii) In the cytoplasmic membrane, SQR and TQO carry out their respective functions with electrons further transferred to terminal oxidase or NADH complex I; and (iv) In the cytoplasm, the particular enzymes perform the catalytic reaction by a sequence of steps that eventually produce sulfate.

Mentions: In order to acquire the functional attributes of cells, it is necessary to understand the structural constitution and characters of cellular metabolic networks [53]. With respect to sulfur oxidation, a bioinformatics analysis of the genome sequence of organism was performed, indicating that various enzymes, enzyme complexes, and the electron transport chain components were located in different cellular compartments. Based on the documented models in other Acidithiobacillus species [2,6,9-11], genome sequence analysis, our current knowledge, and experimental results in this study, a hypothetical model is developed for sulfur oxidation in A. thiooxidans A01 (FigureĀ 6).


Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.

Yin H, Zhang X, Li X, He Z, Liang Y, Guo X, Hu Q, Xiao Y, Cong J, Ma L, Niu J, Liu X - BMC Microbiol. (2014)

The sulfur oxidation model in A. thiooxidans based on documented models [[2],[6],[9]-[11]], bioinformatics analysis of draft genome sequence. Abbreviations: SDO, sulfur dioxygenase; SQR, sulfide quinone reductase; TQO, thiosulfate:quinone oxidoreductase; TetH, tetrathionate hydrolase; Sox, sulfur oxidizing protein; HDR, heterodisulfide reductase; SOR, sulfur oxygenase reductase; TST, thiosulfate sulfurtransferase; A, phosphoadenosine phosphosulfate reductase; B, adenylylsulfate kinase. As is shown, the sulfur oxidation metabolism in A. thiooxidans A01 contains various sulfur oxidation systems and the electron transfer pathways in different cellular compartments. (i) In the outer membrane, elemental sulfur (S8) in the form of stable octasulfane ring is activated and transported into the periplasm as thiol-bound sulfane sulfur atoms (R-S-SnH); (ii) In the periplasm, R-S-SnH is oxidized by SDO, while tetrathionate is utilized by TetH to produce thiosulfate, and the thiosulfate is sequentially catalyzed by Sox complex; (iii) In the cytoplasmic membrane, SQR and TQO carry out their respective functions with electrons further transferred to terminal oxidase or NADH complex I; and (iv) In the cytoplasm, the particular enzymes perform the catalytic reaction by a sequence of steps that eventually produce sulfate.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 6: The sulfur oxidation model in A. thiooxidans based on documented models [[2],[6],[9]-[11]], bioinformatics analysis of draft genome sequence. Abbreviations: SDO, sulfur dioxygenase; SQR, sulfide quinone reductase; TQO, thiosulfate:quinone oxidoreductase; TetH, tetrathionate hydrolase; Sox, sulfur oxidizing protein; HDR, heterodisulfide reductase; SOR, sulfur oxygenase reductase; TST, thiosulfate sulfurtransferase; A, phosphoadenosine phosphosulfate reductase; B, adenylylsulfate kinase. As is shown, the sulfur oxidation metabolism in A. thiooxidans A01 contains various sulfur oxidation systems and the electron transfer pathways in different cellular compartments. (i) In the outer membrane, elemental sulfur (S8) in the form of stable octasulfane ring is activated and transported into the periplasm as thiol-bound sulfane sulfur atoms (R-S-SnH); (ii) In the periplasm, R-S-SnH is oxidized by SDO, while tetrathionate is utilized by TetH to produce thiosulfate, and the thiosulfate is sequentially catalyzed by Sox complex; (iii) In the cytoplasmic membrane, SQR and TQO carry out their respective functions with electrons further transferred to terminal oxidase or NADH complex I; and (iv) In the cytoplasm, the particular enzymes perform the catalytic reaction by a sequence of steps that eventually produce sulfate.
Mentions: In order to acquire the functional attributes of cells, it is necessary to understand the structural constitution and characters of cellular metabolic networks [53]. With respect to sulfur oxidation, a bioinformatics analysis of the genome sequence of organism was performed, indicating that various enzymes, enzyme complexes, and the electron transport chain components were located in different cellular compartments. Based on the documented models in other Acidithiobacillus species [2,6,9-11], genome sequence analysis, our current knowledge, and experimental results in this study, a hypothetical model is developed for sulfur oxidation in A. thiooxidans A01 (FigureĀ 6).

Bottom Line: It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components.Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences.Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. yinhuaqun@gmail.com.

ABSTRACT

Background: Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation.

Results: The genome of A. thiooxidans A01 was sequenced and annotated. It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components. Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences. In addition, another putative pathway was found in the cytoplasm of A. thiooxidans, which catalyzes sulfite to sulfate as the final product by phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase. This differs from its closest relative Acidithiobacillus caldus, which is performed by sulfate adenylyltransferase (SAT). Furthermore, real-time quantitative PCR analysis showed that most of sulfur oxidation genes were more strongly expressed in the S0 medium than that in the Na2S2O3 medium at the mid-log phase.

Conclusion: Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.

Show MeSH
Related in: MedlinePlus