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

Huaqun Yin,Xueduan Liu,Yili Liang,Qi Hu,Liyuan Ma,Zhili He,Xue Guo,Yunhua Xiao,Xiaoqi Li,Xian Zhang,Jiaojiao Niu,Jing Cong

doi:10.1186/1471-2180-14-179

Huaqun Yin, Xueduan Liu + Show 10 more

Open Access

https://doi.org/10.1186/1471-2180-14-179

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Abstract

BackgroundAcidithiobacillus 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.ResultsThe 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.ConclusionSulfur 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.

Highlights

Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper
Previous studies showed that the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs) was found in various strains of Acidithiobacillus ferrooxidans (A. ferrooxidans) through the detection of several enzymatic activities [3,4], but some of these activities were not associated with specific genes
Bioinformatics analysis of the genome sequence of A. thiooxidans A01 provides a valuable platform for gene discovery and functional prediction that is much important given the difficulties in performing standard genetic research in this microorganism

Summary

Introduction

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). 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. Acidithiobacillus thiooxidans (A. thiooxidans), an extremely acidophilic, chemolithoautotrophic, gram-negative, rodshaped microorganism, which are typically related to copper mining operations (bioleaching), has been well studied for industry applications. A. thiooxidans grows and survives by autotrophically utilizing elemental sulfur and reduced inorganic sulfur compounds (RISCs) as energy source [1], but it cannot use energy or electrons acquired from the oxidation of ferrous iron (Fe (II)) for carbon dioxide fixation as well as other anabolic processes [2]. The method based on genome sequence analysis could provide the opportunities to predict some of these missing assignments, and to suggest novel genes involved in the oxidation of elemental sulfur or RISCs such as sulfide, thiosulfate, and tetrathionate [6]

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