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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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Phylogenetic dendrogram based on the SORs from A. thiooxidans and its close homologs from other species. It was constructed using the neighbor-joining algorithm implemented in the MEGA version 5.05, and its reliability was evaluated by 1,000 bootstrap replicates.
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Figure 3: Phylogenetic dendrogram based on the SORs from A. thiooxidans and its close homologs from other species. It was constructed using the neighbor-joining algorithm implemented in the MEGA version 5.05, and its reliability was evaluated by 1,000 bootstrap replicates.

Mentions: The sulfur oxidation system based on the sulfur oxygenase reductase was only reported in several acidophilic and thermophilic archaea (e.g., A. ambivalens, A. tengchongensis) or bacteria (e.g., A. caldus), but not in the species of A. ferrooxidans and A. thiooxidans[9,17,41,48]. However, our annotations show that a potential gene encoding SOR with very similar amino acid sequence in A. caldus, was detected in A. thiooxidans A01. Interestingly, the sor gene was not found in the draft genome sequence of A. thiooxidans ATCC 19377 [49]. To date, it is unclear whether sor gene exists or not in A. thiooxidans ATCC 19377 unless the complete genome sequence is obtained. Subsequently, homology search was performed with BLASTx, and sequence analysis indicated that the putative enzyme of A. thiooxidans A01 shared 80% identity to the SOR of A. caldus. Moreover, the phylogenetic tree, which included almost all homologs of SOR derived from BLASTp search showed that SOR from A. thiooxidans was detected to be closest to that isolated from A. caldus. High bootstrap values insure the reliability of clustering (FigureĀ 3).


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)

Phylogenetic dendrogram based on the SORs from A. thiooxidans and its close homologs from other species. It was constructed using the neighbor-joining algorithm implemented in the MEGA version 5.05, and its reliability was evaluated by 1,000 bootstrap replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4109375&req=5

Figure 3: Phylogenetic dendrogram based on the SORs from A. thiooxidans and its close homologs from other species. It was constructed using the neighbor-joining algorithm implemented in the MEGA version 5.05, and its reliability was evaluated by 1,000 bootstrap replicates.
Mentions: The sulfur oxidation system based on the sulfur oxygenase reductase was only reported in several acidophilic and thermophilic archaea (e.g., A. ambivalens, A. tengchongensis) or bacteria (e.g., A. caldus), but not in the species of A. ferrooxidans and A. thiooxidans[9,17,41,48]. However, our annotations show that a potential gene encoding SOR with very similar amino acid sequence in A. caldus, was detected in A. thiooxidans A01. Interestingly, the sor gene was not found in the draft genome sequence of A. thiooxidans ATCC 19377 [49]. To date, it is unclear whether sor gene exists or not in A. thiooxidans ATCC 19377 unless the complete genome sequence is obtained. Subsequently, homology search was performed with BLASTx, and sequence analysis indicated that the putative enzyme of A. thiooxidans A01 shared 80% identity to the SOR of A. caldus. Moreover, the phylogenetic tree, which included almost all homologs of SOR derived from BLASTp search showed that SOR from A. thiooxidans was detected to be closest to that isolated from A. caldus. High bootstrap values insure the reliability of clustering (FigureĀ 3).

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