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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 among the SDO sequences from various species. Conserved metal ion binding sites and potential GSH binding site are indicated by * and ■, respectively. The signature motif of metallo-beta-lactamase superfamily is marked with a red rectangle. GenBank accession number: Homo sapiens (NP_055112); Mus musculus (NP_075643); Urechis unicinctus (AEV92813); Caenorhabditis elegans (NP_501684); Apis mellifera (XP_393510); Acidovorax delafieldii (ZP_04761469); Acidithiobacillus caldus (YP_004749948); Nitrosococcus watsonii (YP_003760989); Methylobacter tundripaludum (ZP_08782165).
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Figure 1: Multiple sequence alignment among the SDO sequences from various species. Conserved metal ion binding sites and potential GSH binding site are indicated by * and ■, respectively. The signature motif of metallo-beta-lactamase superfamily is marked with a red rectangle. GenBank accession number: Homo sapiens (NP_055112); Mus musculus (NP_075643); Urechis unicinctus (AEV92813); Caenorhabditis elegans (NP_501684); Apis mellifera (XP_393510); Acidovorax delafieldii (ZP_04761469); Acidithiobacillus caldus (YP_004749948); Nitrosococcus watsonii (YP_003760989); Methylobacter tundripaludum (ZP_08782165).

Mentions: The first documented step in elemental sulfur oxidation is the transition of sulfur to thiosulfate, which is catalyzed by SDO. In A. thiooxidans, three putative sdo orthologs located at the draft genome sequence (contig8: 62452–63315, contig50: 14318–15058 and contig97: 6229–6966) belong to the large and considerably variable metallo-beta-lactamase superfamily (cl00446), which have the signature motif H-X-H-X-D-H (Figure 1). Previous research revealed that SDO in Urechis unicinctus (AEV92813) possessed the conserved metal I binding sites (H113, H115, H169 and D188), metal II binding sites (D117, H118, H169 and H229) and potential glutathione (GSH) binding sites (R197, Y231, M279 and I283) [34]. As is depicted in Figure 1, their conserved sites in At-SDO are much similar to AEV92813, and the possible reason why GSH binding sites between them is slightly different may be their distant relationship. Thus, the conserved regions observed with U. unicinctus as well as SDOs from other species possibly indicate the similar functional properties. However, the properties of SDO-like protein in A. thiooxidans are required further studies. Another gene encoding sulfide quinone reductase (SQR) was detected in the draft genome sequence of A. thiooxidans A01, and the product of sqr gene shares 79% and 72% identity with other sqr ortholog identified in A. ferrooxidans and A. caldus, respectively (Table 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)

Multiple sequence alignment among the SDO sequences from various species. Conserved metal ion binding sites and potential GSH binding site are indicated by * and ■, respectively. The signature motif of metallo-beta-lactamase superfamily is marked with a red rectangle. GenBank accession number: Homo sapiens (NP_055112); Mus musculus (NP_075643); Urechis unicinctus (AEV92813); Caenorhabditis elegans (NP_501684); Apis mellifera (XP_393510); Acidovorax delafieldii (ZP_04761469); Acidithiobacillus caldus (YP_004749948); Nitrosococcus watsonii (YP_003760989); Methylobacter tundripaludum (ZP_08782165).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Multiple sequence alignment among the SDO sequences from various species. Conserved metal ion binding sites and potential GSH binding site are indicated by * and ■, respectively. The signature motif of metallo-beta-lactamase superfamily is marked with a red rectangle. GenBank accession number: Homo sapiens (NP_055112); Mus musculus (NP_075643); Urechis unicinctus (AEV92813); Caenorhabditis elegans (NP_501684); Apis mellifera (XP_393510); Acidovorax delafieldii (ZP_04761469); Acidithiobacillus caldus (YP_004749948); Nitrosococcus watsonii (YP_003760989); Methylobacter tundripaludum (ZP_08782165).
Mentions: The first documented step in elemental sulfur oxidation is the transition of sulfur to thiosulfate, which is catalyzed by SDO. In A. thiooxidans, three putative sdo orthologs located at the draft genome sequence (contig8: 62452–63315, contig50: 14318–15058 and contig97: 6229–6966) belong to the large and considerably variable metallo-beta-lactamase superfamily (cl00446), which have the signature motif H-X-H-X-D-H (Figure 1). Previous research revealed that SDO in Urechis unicinctus (AEV92813) possessed the conserved metal I binding sites (H113, H115, H169 and D188), metal II binding sites (D117, H118, H169 and H229) and potential glutathione (GSH) binding sites (R197, Y231, M279 and I283) [34]. As is depicted in Figure 1, their conserved sites in At-SDO are much similar to AEV92813, and the possible reason why GSH binding sites between them is slightly different may be their distant relationship. Thus, the conserved regions observed with U. unicinctus as well as SDOs from other species possibly indicate the similar functional properties. However, the properties of SDO-like protein in A. thiooxidans are required further studies. Another gene encoding sulfide quinone reductase (SQR) was detected in the draft genome sequence of A. thiooxidans A01, and the product of sqr gene shares 79% and 72% identity with other sqr ortholog identified in A. ferrooxidans and A. caldus, respectively (Table 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