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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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Multiple sequence alignment of SORs between A. thiooxidans and other species. Protein sequences were aligned by the DNAMAN multiple sequence alignment program. The putative domains in SOR were boxed by the rectangle. And the conserved domains V-G-P-K-V-C32, H87-E-E-M-H91 and C102-XX-C105 were indicated by the rectangleA, B, C, respectively. Abbreviations: A. thiooxidans, Acidithiobacillus thiooxidans; A. caldus, Acidithiobacillus caldus (WP_004871908); A. ferrivorans, Acidithiobacillus ferrivorans (YP_004785009); A. ambivalens, Acidianus ambivalens (P29082); A. tengchongensis, Acidianus tengchongensis (AAK58572); S. tokodaii, Sulfolobus tokodaii (NP_377053); S. thermosulfidooxidans, Sulfobacillus thermosulfidooxidans (WP_020375642).
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Figure 4: Multiple sequence alignment of SORs between A. thiooxidans and other species. Protein sequences were aligned by the DNAMAN multiple sequence alignment program. The putative domains in SOR were boxed by the rectangle. And the conserved domains V-G-P-K-V-C32, H87-E-E-M-H91 and C102-XX-C105 were indicated by the rectangleA, B, C, respectively. Abbreviations: A. thiooxidans, Acidithiobacillus thiooxidans; A. caldus, Acidithiobacillus caldus (WP_004871908); A. ferrivorans, Acidithiobacillus ferrivorans (YP_004785009); A. ambivalens, Acidianus ambivalens (P29082); A. tengchongensis, Acidianus tengchongensis (AAK58572); S. tokodaii, Sulfolobus tokodaii (NP_377053); S. thermosulfidooxidans, Sulfobacillus thermosulfidooxidans (WP_020375642).

Mentions: In addition, homology searches showed that the nucleotide sequence of this putative gene in A. thiooxidans and its predicted amino acid sequence have high similarities to other species. Multiple sequence alignment of SORs from A. thiooxidans and other species was carried out (FigureĀ 4). It is demonstrated that three cysteine residues located in two separately conserved domains, C32 at V-G-P-K-V-C32 and C102 and C105 at C102-X-X-C105, are essential to its activity [50]. In addition, the conserved motif H87-X3-H91-X23-E115, which is considered to be iron binding site [47], is detected in SOR from A. thiooxidans. The crystal structure of the SOR in A. ambivalens is demonstrated to be a large homo-multimer composed of 24 identical monomers of 308 residues, forming a large hollow sphere [51,52]. The active sites of SOR are constituted of a mononuclear non-heme iron site and three conserved cysteine residues [45]. Furthermore, the structural analysis has been performed to study the potential functions of the cysteine residues in A. tengchongensis. It is proposed that C32 residue constitutes most possibly the substrate binding site and that C102 and C105, together with the iron binding motif H87-X3-H91-X23-E115, probably form the catalytic site.


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)

Multiple sequence alignment of SORs between A. thiooxidans and other species. Protein sequences were aligned by the DNAMAN multiple sequence alignment program. The putative domains in SOR were boxed by the rectangle. And the conserved domains V-G-P-K-V-C32, H87-E-E-M-H91 and C102-XX-C105 were indicated by the rectangleA, B, C, respectively. Abbreviations: A. thiooxidans, Acidithiobacillus thiooxidans; A. caldus, Acidithiobacillus caldus (WP_004871908); A. ferrivorans, Acidithiobacillus ferrivorans (YP_004785009); A. ambivalens, Acidianus ambivalens (P29082); A. tengchongensis, Acidianus tengchongensis (AAK58572); S. tokodaii, Sulfolobus tokodaii (NP_377053); S. thermosulfidooxidans, Sulfobacillus thermosulfidooxidans (WP_020375642).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4109375&req=5

Figure 4: Multiple sequence alignment of SORs between A. thiooxidans and other species. Protein sequences were aligned by the DNAMAN multiple sequence alignment program. The putative domains in SOR were boxed by the rectangle. And the conserved domains V-G-P-K-V-C32, H87-E-E-M-H91 and C102-XX-C105 were indicated by the rectangleA, B, C, respectively. Abbreviations: A. thiooxidans, Acidithiobacillus thiooxidans; A. caldus, Acidithiobacillus caldus (WP_004871908); A. ferrivorans, Acidithiobacillus ferrivorans (YP_004785009); A. ambivalens, Acidianus ambivalens (P29082); A. tengchongensis, Acidianus tengchongensis (AAK58572); S. tokodaii, Sulfolobus tokodaii (NP_377053); S. thermosulfidooxidans, Sulfobacillus thermosulfidooxidans (WP_020375642).
Mentions: In addition, homology searches showed that the nucleotide sequence of this putative gene in A. thiooxidans and its predicted amino acid sequence have high similarities to other species. Multiple sequence alignment of SORs from A. thiooxidans and other species was carried out (FigureĀ 4). It is demonstrated that three cysteine residues located in two separately conserved domains, C32 at V-G-P-K-V-C32 and C102 and C105 at C102-X-X-C105, are essential to its activity [50]. In addition, the conserved motif H87-X3-H91-X23-E115, which is considered to be iron binding site [47], is detected in SOR from A. thiooxidans. The crystal structure of the SOR in A. ambivalens is demonstrated to be a large homo-multimer composed of 24 identical monomers of 308 residues, forming a large hollow sphere [51,52]. The active sites of SOR are constituted of a mononuclear non-heme iron site and three conserved cysteine residues [45]. Furthermore, the structural analysis has been performed to study the potential functions of the cysteine residues in A. tengchongensis. It is proposed that C32 residue constitutes most possibly the substrate binding site and that C102 and C105, together with the iron binding motif H87-X3-H91-X23-E115, probably form the catalytic site.

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