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Open Access Highly Accessed Research article

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

Huaqun Yin12*, Xian Zhang12, Xiaoqi Li12, Zhili He3, Yili Liang12, Xue Guo12, Qi Hu12, Yunhua Xiao12, Jing Cong12, Liyuan Ma12, Jiaojiao Niu12 and Xueduan Liu12*

Author Affiliations

1 School of Minerals Processing and Bioengineering, Central South University, Changsha, China

2 Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China

3 Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA

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BMC Microbiology 2014, 14:179  doi:10.1186/1471-2180-14-179

Published: 4 July 2014

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.

Keywords:
Acidithiobacillus thiooxidans; Whole genome sequence; Bioinformatics analysis; Real-time quantitative PCR; Sulfur oxidation model