title: Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. yinhuaqun@gmail.com.
authors.forename: Huaqun
authors.initials: H
authors.lastname: Yin
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Li
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Yili
authors.initials: Y
authors.lastname: Liang
authors.forename: Xue
authors.initials: X
authors.lastname: Guo
authors.forename: Qi
authors.initials: Q
authors.lastname: Hu
authors.forename: Yunhua
authors.initials: Y
authors.lastname: Xiao
authors.forename: Jing
authors.initials: J
authors.lastname: Cong
authors.forename: Liyuan
authors.initials: L
authors.lastname: Ma
authors.forename: Jiaojiao
authors.initials: J
authors.lastname: Niu
authors.forename: Xueduan
authors.initials: X
authors.lastname: Liu
mesh_terms: D013856:Acidithiobacillus thiooxidans / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D016680:Genome, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D017422:Sequence Analysis, DNA; D013455:Sulfur / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D013455:Sulfur