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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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Comparison of tetH gene cluster (A) and the sox gene clusters (B) between A. thiooxidans A01 and other sulfur oxidizers containing identified or putative genes. Abbreviations: tpase, transposase; rsrR, response regulator (two-component system); rsrS: histidine kinase (two-component system); tetH, tetrathionate hydrolase; doxD, thiosulfate:quinone oxidoreductase; hyp, hypothetical protein; resB, cytochrome c-type biogenesis protein ResB; resC, cytochrome c-type biogenesis protein ResC. The tetH cluster in AT: A. thiooxidans A01, AC: A. caldus SM-1 (CP002573); Two sox clusters in AT: A. thiooxidans A01, AC: A.caldus SM-1 (CP002573), TD: T. denitrificans ATCC 25259 (CP000116). The homology proteins are expressed by the same color, and percentage of amino acid similarity is indicated. The direction of transcription is represented by the arrows.
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Figure 2: Comparison of tetH gene cluster (A) and the sox gene clusters (B) between A. thiooxidans A01 and other sulfur oxidizers containing identified or putative genes. Abbreviations: tpase, transposase; rsrR, response regulator (two-component system); rsrS: histidine kinase (two-component system); tetH, tetrathionate hydrolase; doxD, thiosulfate:quinone oxidoreductase; hyp, hypothetical protein; resB, cytochrome c-type biogenesis protein ResB; resC, cytochrome c-type biogenesis protein ResC. The tetH cluster in AT: A. thiooxidans A01, AC: A. caldus SM-1 (CP002573); Two sox clusters in AT: A. thiooxidans A01, AC: A.caldus SM-1 (CP002573), TD: T. denitrificans ATCC 25259 (CP000116). The homology proteins are expressed by the same color, and percentage of amino acid similarity is indicated. The direction of transcription is represented by the arrows.

Mentions: Other enzymes reported to be involved in sulfur oxidation are TQO and TetH. Our sequence analysis revealed that the homolog of doxDA existed in the draft genome of A. thiooxidans A01, and it is predicted to encode a thiosulfate:quinone oxidoreductase (TQO), and also has a conserved DoxD domain (pfam04173) and a conserved DoxA domain (pfam07680). There is a fusion of separate DoxD- and DoxA–like subunits that were reported previously in A. ferrooxidans DoxD [6]. The putative TetH of A. thiooxidans shares 60% and 77% identity with TetH in A. ferrooxidans and A. caldus respectively, indicating their high similarity in orthologous relationship. Our analysis also indicates that TetH of all sequenced Acidithiobacillus spp. has a conserved pyrrolo-quinoline quinone (PQQ) domain (pfam01011). Although TetH was predicted to be external membrane proteins, experimental evidence showed that it was a soluble periplasmic homo-dimer with an optimum pH of 3 in A. caldus[35]. Previous studies have revealed that there is a tetH gene cluster in A. caldus[19], which is comprised of five cotranscribed genes, tpase1, rsrR, rsrS, tetH and doxD. While in the draft genome sequence of A. thiooxidans A01, only tetH and doxD located at the upstream constitute the tetH cluster (Figure 2A).


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)

Comparison of tetH gene cluster (A) and the sox gene clusters (B) between A. thiooxidans A01 and other sulfur oxidizers containing identified or putative genes. Abbreviations: tpase, transposase; rsrR, response regulator (two-component system); rsrS: histidine kinase (two-component system); tetH, tetrathionate hydrolase; doxD, thiosulfate:quinone oxidoreductase; hyp, hypothetical protein; resB, cytochrome c-type biogenesis protein ResB; resC, cytochrome c-type biogenesis protein ResC. The tetH cluster in AT: A. thiooxidans A01, AC: A. caldus SM-1 (CP002573); Two sox clusters in AT: A. thiooxidans A01, AC: A.caldus SM-1 (CP002573), TD: T. denitrificans ATCC 25259 (CP000116). The homology proteins are expressed by the same color, and percentage of amino acid similarity is indicated. The direction of transcription is represented by the arrows.
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Figure 2: Comparison of tetH gene cluster (A) and the sox gene clusters (B) between A. thiooxidans A01 and other sulfur oxidizers containing identified or putative genes. Abbreviations: tpase, transposase; rsrR, response regulator (two-component system); rsrS: histidine kinase (two-component system); tetH, tetrathionate hydrolase; doxD, thiosulfate:quinone oxidoreductase; hyp, hypothetical protein; resB, cytochrome c-type biogenesis protein ResB; resC, cytochrome c-type biogenesis protein ResC. The tetH cluster in AT: A. thiooxidans A01, AC: A. caldus SM-1 (CP002573); Two sox clusters in AT: A. thiooxidans A01, AC: A.caldus SM-1 (CP002573), TD: T. denitrificans ATCC 25259 (CP000116). The homology proteins are expressed by the same color, and percentage of amino acid similarity is indicated. The direction of transcription is represented by the arrows.
Mentions: Other enzymes reported to be involved in sulfur oxidation are TQO and TetH. Our sequence analysis revealed that the homolog of doxDA existed in the draft genome of A. thiooxidans A01, and it is predicted to encode a thiosulfate:quinone oxidoreductase (TQO), and also has a conserved DoxD domain (pfam04173) and a conserved DoxA domain (pfam07680). There is a fusion of separate DoxD- and DoxA–like subunits that were reported previously in A. ferrooxidans DoxD [6]. The putative TetH of A. thiooxidans shares 60% and 77% identity with TetH in A. ferrooxidans and A. caldus respectively, indicating their high similarity in orthologous relationship. Our analysis also indicates that TetH of all sequenced Acidithiobacillus spp. has a conserved pyrrolo-quinoline quinone (PQQ) domain (pfam01011). Although TetH was predicted to be external membrane proteins, experimental evidence showed that it was a soluble periplasmic homo-dimer with an optimum pH of 3 in A. caldus[35]. Previous studies have revealed that there is a tetH gene cluster in A. caldus[19], which is comprised of five cotranscribed genes, tpase1, rsrR, rsrS, tetH and doxD. While in the draft genome sequence of A. thiooxidans A01, only tetH and doxD located at the upstream constitute the tetH cluster (Figure 2A).

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