- Research article
- Open Access
Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans
- Huaqun Yin†1, 2Email author,
- Xian Zhang†1, 2,
- Xiaoqi Li1, 2,
- Zhili He3,
- Yili Liang1, 2,
- Xue Guo1, 2,
- Qi Hu1, 2,
- Yunhua Xiao1, 2,
- Jing Cong1, 2,
- Liyuan Ma1, 2,
- Jiaojiao Niu1, 2 and
- Xueduan Liu1, 2Email author
© Yin et al.; licensee BioMed Central Ltd. 2014
Received: 14 February 2014
Accepted: 19 June 2014
Published: 4 July 2014
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.
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.
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.
Acidithiobacillus thiooxidans (A. thiooxidans), an extremely acidophilic, chemolithoautotrophic, gram-negative, rod-shaped 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 , 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 .
Previous studies showed that the oxidation of elemental sulfur and 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. The studies of oxidation and electron transfer pathways for elemental sulfur or RISCs are more complicated than those for ferrous iron, making the gene prediction and pathway clarification much more difficult . Furthermore, some steps independent of enzymatic catalysis took place spontaneously, which adds the difficulty to modeling the mechanism of such a pathway. Fortunately, the method based on genome sequence analysis could provide the opportunities to predict some of these missing assignments, and also to suggest novel genes involved in the oxidation of elemental sulfur or RISCs such as sulfide, thiosulfate, and tetrathionate .
Elemental sulfur exists in the form of a stable octasulfane ring (S8) in nature, which forms orthorhombic crystals with extremely poor water solubility . An activation prior to oxidation was postulated [6, 8]. The first and critical step of sulfur oxidation could be an opening of the S8 ring by the thiol groups of cysteine residues, resulting in the formation of thiol-bound sulfane sulfur atoms (R-S-SnH) [8, 9]. Subsequently, the R-S-SnH is transported into the periplasm and then oxidized by sulfur dioxygenase (SDO), of which gene(s) has (have) not yet been detected [6, 9, 10].
As sulfide was found to be one of the most common forms of S in the inorganic sulfur compounds, the initial step in RISCs oxidation mainly was the transition of sulfide into S0, forming a conjugated sulfur compound bound to a membrane fraction . Furthermore, the first step of hydrogen sulfide oxidation is its conversion to sulfur or polysulfide in many phototrophic and chemotrophic bacteria by flavocytochrome c (Fcc), or by sulfide quinone reductase (SQR), which are located in the periplasm and the periplasmic surface of the cytoplasmic membrane, respectively [11, 12]. Moreover, Fcc does not exist in various sulfide-oxidizing bacteria and appears to be restricted to certain species which possess the ability of thiosulfate oxidation .
Compared with the enzymes described above, the sulfur oxidizing (Sox) system has been elaborated in facultatively lithoautotrophic Paracoccus pantotrophus (P. pantotrophus). It is located in the periplasm and comprised of SoxXA (both c type cytochromes), SoxYZ (covalently sulfur-binding protein and sulfur compound chelating protein, respectively), SoxB (monomeric, dimanganese-containing protein that is similar to zinc-containing 5′-nucleotidases and considered to act as the sulfate thiol esterase component of the Sox system), and Sox (CD)2 (sulfur dehydrogenase), which mediate hydrogen sulfide-, sulfur-, thiosulfate- and sulfite-dependent cytochrome c reduction [14–17]. In contrast to the P. pantotrophus, the Sox (CD)2 complex is absent in the truncated Sox system of many α-Proteobacteria .
The periplasmic thiosulfate is synthesized spontaneously from sulfite and a sulfur atom , and then catalyzed to generate tetrathionate by thiosulfate:quinone oxidoreductase (TQO), which is constituted of a large subunit (DoxD) and a smaller subunit (DoxA); tetrathionate is then hydrolyzed by tetrathionate hydrolase (TetH) to produce thiosulfate and other uncertain products. TetH was studied previously in A. ferrooxidans, and the tetH gene cluster has been also characterized in Acidithiobacillus caldus (A. caldus) .
In addition, other RISCs oxidation enzymes were identified in Acidithiobacillus spp. including: rhodanese or thiosulfate sulfurtransferase (TST) and heterodisulfide reductase (HDR). The TST widely exists in the cytoplasm of both prokaryotes and eukaryotes. It cleaves the sulfur-sulfur bond of thiosulfate to yield sulfur and sulfite, and then the former is transferred to a thiophilic acceptor such as cyanide and thiol compounds [20, 21]. The cytoplasmic heterodisulfide reductase complex HdrABC was reported to catalyze the reversible reaction of the disulfide bond X-S-S-X reduction accompanied with energy conservation in sulfate reducing archaea and bacteria and methanogenic archaea , while this complex was only speculated from transcriptomics and genomics analysis instead of biochemical experiments in A. ferrooxidans.
Recently, a model of electron transfer pathways involved in the sulfur oxidation of A. ferrooxidans was proposed, in which electrons released from RISC oxidation were transferred either to terminal oxidases to produce proton gradient or to NADH complex I to generate reducing power via the quinol pool (QH2) [2, 6]. However, the lack of genetic manipulation systems has greatly restricted the exploration of the molecular biology and physiology in extreme acidophilic microorganisms, and considerably less information is known about the mechanism by which microorganisms grow, survive and proliferate in extremely acidophilic environments. With the ongoing and rapid development of sequencing technologies and the continuous improvement of bioinformatics-based analytical methods, effective tools have been offered for investigating metabolic and regulatory models . A substantial body of information could be acquired by deep genome analysis, which can assist the laboratory scientists to focus on experimental investigation of several most significant predictions, thus save considerable time and efforts .
To get a better understanding of how these metabolic processes occur and further explore how to make them more efficient in A. thiooxidans, the whole-genome sequencing was carried out. Through bioinformatics analysis of the bioleaching bacterium, A. thiooxidans genome sequence, it is expected that we would predict and validate the genes and conserved gene clusters involved in sulfur oxidation. Subsequently, a further experiment at the transcriptional level was performed via quantitative real-time PCR (qRT-PCR). On the basis of bioinformatics analysis, together with qRT-PCR data, a putative model of sulfur oxidation in A. thiooxidans was proposed.
The strain (A. thiooxidans A01) was obtained from a wastewater of coal dump of Jiangxi, China. This study doesn’t involve any ethical issue.
Bioinformatics analysis of A. thiooxidans genome sequence
A bioinformatics pipeline was used to analyze the genome sequence of A. thiooxidans. The genomic DNA of A. thiooxidans A01 was extracted using TIANamp Bacteria DNA Kit (TIANGEN) according to the manufacturer’s instructions and then sequenced by BGI- Shenzhen (Beijing Genomics Institute) using Illumina HiSeq 2000 for 2 × 100 bp paired-end sequencing (Illumina, Inc. USA). After filtering, with Phred 20 as a cutoff, high quality raw sequences were assembled into longer fragment sequences, contigs and scaffolds, relied on strategy using SOAPdenovo version 2.0 . According to previous data, coding regions detection and potential genes identification were performed using Glimmer . Moreover, RepeatMasker  was used to screen DNA sequences with interspersed repeats and low complexity. The RNAmmer  and tRNAscan-SE  were used to search for rRNA genes and tRNA genes in genomic sequence, respectively.
To further analyze the candidate genes and their predicted protein products, perl scripts written in our laboratory were used to extract the corresponding sequences of previously predicted CDSs. Subsequently, each putative gene was annotated using the BLASTx program (e value, ≤1e-5) against the alternative database such as Non-redundant protein database, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Clusters of Orthologous Groups of proteins (COG).
Media and culture conditions
The strain A. thiooxidans A01 was isolated in this laboratory. The components of 9 K medium  and DSMZ medium 71  corresponding to S0 and Na2S2O3 media respectively were previously described in references. Elemental sulfur (S0) (boiling sterilized, 10 g/L) and Na2S2O3 · 5H2O (sterile filtration, 5 g/L) were added as substrates prior to inoculation. The bacterium was cultivated in 100-ml culture medium with an initial pH 2.0 for 9 K medium and pH 4.4 for DSMZ medium 71. The initial bacterial concentration was 2.5 × 106 cells/ml and the cultivation temperature was 30°C. The shaking speed for liquid cultivation of A. thiooxidans A01 was 170 rpm if not specifically stated. All cultures under the same conditions were manipulated in triplicate.
Quantitative real-time PCR (qRT-PCR)
Primers used in qRT-PCR detection of genes related to sulfur oxidation
Sequence (5′ to 3′)
Subsequently, the total RNA of 2 μg was reversely transcribed using First Strand cDNA Synthesis Kit (TOYOBO) under the following conditions: 30°C for 10 min, 42°C for 20 min, 99°C for 5 min, and 4°C for 5 min. RT reaction products of 1 μl as template in 25 μl reaction volume were used for PCR amplification with specific primers (Table 1) using QuantiFast SYBR Green PCR Kit (QIAGEN). The conditions for the PCR reaction were as follows: 95°C for 5 min followed by 40 cycles at 95°C for 30 s, 56°C for 15 s and 72°C for 25 s in MyiQ Single-Color Real-Time PCR Detection System (BIO-RAD). The transcription reference gene, glyceraldehyde-3-phosphate dehydrogenase gene (gapdh), was used for normalization. The relative fold changes in gene expression were calculated using the 2-ΔΔCT method .
Nucleotide sequence accession numbers
The draft genome sequence of A. thiooxidans A01 was deposited at DDBJ/EMBL/GenBank under the accession number AZMO00000000. The version described in this paper is version AZMO01000000.
Results and discussion
General features of draft genome sequence of A. thiooxidans A01
Total length (bp)
No. of tRNA genes
No. of rRNA operon (5S-16S-23S)
Total number of CDSs
Proteins with known function
Conserved hypothetical proteins
Predicted genes involved in sulfur oxidation
Amino-acid sequence identities of the products encoded by sulfur metabolic genes between A. thiooxidans A01 and other thiobacteria including A. ferrooxidans (CP001132), A. caldus (CP002573) and T. denitrificans (CP000116)
aa identity (%)
Contig6: 1–918 (partial)
Contig175: 463–1311 (partial)
In addition, bioinformatics analysis identified a truncated Sox sulfur oxidizing system in A. thiooxidans A01, which contains two sox gene clusters, sox cluster I (resC-soxAX-resB-hyp-soxBZY) and sox cluster II (soxXYZA-hyp-soxB), and both are quite differ from those of Paracoccus denitrificans, Pseudaminobacter salicylatoxidans and Starkeya novella: soxRSVWXYZABCDEFGH (X79242), soxGTRSVWXYZABCD (AJ404005) and soxFDCBZYAXWV (AF139113) [14, 15, 36, 37]. Comparison of all genes sequences in two sox clusters of A. thiooxidans A01 to those of Thiobacillus denitrificans ATCC 25259 (CP000116) revealed amino-acid sequence identities in the range of 35% to 51%. Unlike the sox cluster II of A. thiooxidans A01, however, there is only additional soxXA in the genome sequence of T. denitrificans ATCC 25259 . Interestingly, significant sequence similarity (52% to 88%) and relatively conserved gene constitution of A. thiooxidans A01 sox gene clusters to those of A. caldus SM-1 (CP002573) indicated the similar functional properties (Figure 2B).
Furthermore, heterodisulfide reductase (HDR) has been postulated to be involved in sulfur oxidation. All genes (hdrA, hdrB and hdrC) of HDR were found in the draft genome of A. thiooxidans A01. The putative HdrA subunit is flavoprotein within a FAD binding domain and a NAD (P)-binding Rossmann-like domain. The HdrB subunit contains the typical cysteine-rich domain and the remaining HdrC subunit contains 4Fe-4S dicluster domain. In addition, all putative Hdr subunits in A. thiooxidans A01 suggested over 90% identities to the respective Hdr subunits compared with A. ferrooxidans and A. caldus (Table 3).
Five genes encoding rhodanese (sequence length 109 aa to 155 aa) were detected and one of them was used to design primer for qRT-PCR (Table 1). The phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase, which consecutively oxidize sulfite to produce sulfate via an indirect pathway, were found in the genome of A. thiooxidans. Two genes encoding APS kinase and three genes encoding PAPS reductase were predicted in the draft genome but their roles in sulfur oxidation remain to be established.
The genome information showed that A. thiooxidans A01 contains two gene clusters potentially encoding components of the NADH quinone-oxidoreductase complex (nuoABCDEFGHIJKLMN) similar to that in A. caldus. In addition, seven copies of bd ubiquinol oxidase genes (cyd AB) and two gene clusters encoding bo 3 ubiquinol oxidase (cyoB ACD) exist in A. thiooxidans A01. However, components of the aa 3 -type cytochrome oxidase genes (cox BACD) only exist in the A. ferrooxidans.
The sulfur oxygenase reductase gene (sor) found in A. thiooxidans
As the initial enzyme in the aerobic sulfur oxidation of thermophilic archaea [38, 39] and acidophilic bacteria [40, 41], the sulfur oxygenase reductase (SOR) has been identified. SOR simultaneously catalyzes elemental sulfur to produce sulfite, thiosulfate, and sulfide [38, 42], which are oxygen-dependent disproportionation reactions. The catalytic reaction has certain characteristics: (1) The enzyme involved in this reaction is soluble and located in cytoplasm ; (2) The optimum pH and temperature for activity are founded to be 7.0 ± 0.5 (Sulfolobus brierleyi) and 65–85°C (Acidianus tengchongensis and Acidianus ambivalens), respectively [44, 45]; and (3) It does not require cofactors or external electron donors/acceptors for activity [46, 47].
So far as we know, the sor gene is for the first time detected and reported in A. thiooxidans. The discovery of sor gene supplies a novel idea that these genome-based predictions can offer new opportunities to detect similar genes in other microorganisms and also provide new markers to explore the metabolic pathways. However, the further biochemical experiments at the transcription and protein levels should be carried out in order to verify the presence or absence of sor gene.
Growth of A. thiooxidans in S0 and Na2S2O3 media
Expression of selected genes involved in sulfur oxidation
Comparison of raw fold changes in gene expression between S 0 and Na 2 S 2 O 3 -grown cells (mid-log phase) obtained by qRT-PCR in this study
Sulfide quinone reductase
4.14 ± 0.09
sulfur oxygenase reductase
Sulfur oxygenase reductase
4.06 ± 0.01
tetrathionate hydrolase operon
Thiosulfate:quinone oxidoreductase subunit
3.19 ± 0.01
0.96 ± 0.06
Heterodisulfide reductase complex operon
Pyridine nucleotide-disulfide oxidoreductase
1.35 ± 0.02
Heterodisulfide reductase subunit B
171.37 ± 0.09
Iron-sulfur cluster-binding protein
49.69 ± 0.02
Sox operon I
Diheme cytochrome c
48.17 ± 0.01
Sulfate thiol esterase
4.98 ± 0.11
Cytochrome c, class I
13.80 ± 0.08
Covalently sulfur-binding protein
3.89 ± 0.01
Sulfur compound-chelating protein
150.12 ± 0.06
Sox operon II
Diheme cytochrome c
1.23 ± 0.04
Sulfate thiol esterase
1.42 ± 0.08
Cytochrome c, class I
1.57 ± 0.07
Covalently sulfur-binding protein
0.83 ± 0.04
Sulfur compound-chelating protein
1.87 ± 0.04
Rhodanese (sulfur transferase)
13.04 ± 0.08
With S0 in the medium, a mass of sulfur atoms (S) and hydrogen sulfide are produced during the activation of S8 and then are used as the substrates of SQR, SOR, TST and HDR in succession. This could be the reason for the higher expression of sqr, sor, rhd and hdrABC in the S0 medium than in the Na2S2O3 medium (Table 4). Our experiments showed that thiosulfate was sufficient at the mid-log phase in the Na2S2O3 medium, thus resulting in the lower expression level of doxD and tetH. The sox operon I but not sox operon II together with a bo 3 ubiquinol oxidase operon gene may make it feasible to regulate and control at their transcriptional level, thus this may be one of the reasons why the expression of the sox operon I was up-regulated in the S0 medium whereas the sox operon II had no obvious changes in these two substrates.
Construction of sulfur oxidation model in A. thiooxidans
Enzyme properties involved in the sulfur oxidation of A. thiooxidans
No. of enzyme
S0 → SO3 2−
Sulfide quinone reductase
H2S → S0
S2O3 2− → S4O6 2−
S4O6 2− → S2O3 2− + SO4 2− + S0
Sulfur oxidizing protein
S2O3 2− → SO4 2− + S0
RSSH → RSH + SO3 2−
Sulfur oxygenase reductase
S0 → H2S + SO3 2− + S2O3 2−
S2O3 2− → SO3 2− + S0
Phosphoadenosine phosphosulfate reductase
SO3 2− → PAPS
PAPS → APS
In addition, sulfite could have pernicious effect on the cell unless it is digested quickly in the organism. So far, the sulfite acceptor oxidoreductase (SAR) that catalyzes sulfite to sulfate has not been identified in the genome of A. thiooxidans A01, neither was the A. thiooxidans DSM 17318 genome . Phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase genes were discovered in A thiooxidans A01, while the sulfate adenylyltransferase dissimilatory-type (SAT) gene that catalyzed adenosine - 5′ - phosphosulfate (APS) to sulfite was not detected (Figure 6). Therefore, another putative pathway based on PAPS reductase and APS kinase that catalyze sulfite to produce sulfate indirectly is proposed: sulfite is catalyzed by PAPS reductase and APS kinase to generate PAPS and APS in succession, while the latter could produce sulfate as the final product via an unknown mechanism.
Another putative pathway of sulfur oxidation is that the periplasmic sulfite combines with sulfur atom to form thiosulfate spontaneously, without enzymatic catalysis. Thiosulfate:quinone oxidoreductase (TQO) located in the cytomembrane is responsible for the catalysis of thiosulfate to produce tetrathionate. The thiosulfate oxidation catalyzed by TQO was illustrated previously in A. ambivalens: DoxD catalyzes thiosulfate to tetrathionate and simultaneously produces two electrons, and then DoxA transfers electrons to the quinone . Tetrathionate hydrolase (TetH), a soluble periplasmic enzyme, is able to catalyze the hydrolysis of tetrathionate . The documented hydrolysates of tetrathionate in A. thiooxidans are thiosulfate and sulfate . Furthermore, sulfur atoms (S) may be also one of important hydrolysates, which explains why the expression level of sor gene was higher in S0 medium.
Thiosulfate could be directly catalyzed by the incomplete Sox complex to generate sulfate . As to the truncated Sox system which is absent of Sox (CD)2, the well-studied pathways were provided from some valuable references [9, 17, 56, 57]. Initially, the SoxXA complex oxidatively couples the sulfane sulfur of thiosulfate to a SoxY-cysteine-sulfhydryl group of the SoxYZ complex to form SoxY-thiocysteine-S-sulfate (SoxYZ-S-S-SO3 −). Subsequently, the terminal sulfone (−SO3 −) group is released as sulfate by the activity of the SoxB component to produce S-thiocysteine (SoxYZ-S-S−). Due to the lack of the sulfur dehydrogenase Sox (CD)2 component, the sulfur atom of the sulfane intermediate (SoxYZ-S-S−) is plausibly dropped from SoxYZ or oxidized by the alternative sulfur dioxygenase (SDO) to generate SoxYZ-cysteine-S-sulfate (SoxYZ-S-SO3 −) . Eventually, the sulfonate moiety of SoxYZ-S-SO3 − is again hydrolyzed by SoxB, regenerating SoxYZ in the process. In addition, other forms of sulfur except for thiosulfate could participate in the Sox pathway via either enzymatic (such as HS−) or nonenzymatic (such as S8) conjugation to SoxY at the proper intermediate state .
There is a strong connection between the expression of the sox cluster genes and the terminal oxidase genes. The hypothetical electron pathway is that electrons from the Sox system are transferred via QH2 to the terminal oxidases (bd and bo 3 ) and the NADH complex (Figure 6).
To date, little is known about electron transfer chains in A. thiooxidans, but it has been elaborated in A. ferrooxidans. One of the electron transfer chains in A. ferrooxidans is that electrons from ferrous iron oxidation flow through Cyc2 to rusticyanin, and then be transferred to oxygen via c-cytochrome Cyc1 to aa 3 cytochrome oxidase (downhill electron pathway) or to NAD+ via c-cytochrome CycA1 → bc 1 complex → ubiquinone pool → NADH dehydrogenase (uphill electron pathway) [2, 6, 58]. Another is that electrons from elemental sulfur or RISCs are transferred via the quinol pool (QH2) either (1) directly to terminal oxidases bd or bo 3, or indirectly to a bc 1 complex and a cytochrome c (CycA2) or a high potential iron-sulfur protein (HiPIP), whose gene iro was identified to be associated with the pet II gene cluster thought to be involved in sulfur oxidation, probably to the aa 3 oxidase to produce a proton gradient or (2) to NADH complex I to generate reducing power [2, 6]. However, A. thiooxidans has only the sulfur oxidation system and annotated results showed that bo 3-type terminal oxidases and bd-type terminal oxidases exist in the draft genome of A. thiooxidans A01. Thus, the hypothesized electron transfer chain in A. thiooxidans A01 is proposed: electrons from SQR, TQO, Sox compounds and HDR are transferred through the QH2 either to terminal oxidase (bd and bo 3) to produce proton gradient, or to NADH complex I to generate reducing power.
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. Based on our analysis and available documented data, a hypothetical model for sulfur oxidation and electron transportation is proposed with several distinguished features. The elemental sulfur (S8) in the outer membrane is activated and transported into the periplasm as thiol-bound sulfane sulfur atoms (R-S-SnH). And then, the R-S-SnH is further oxidized in the periplasm where SDO, TetH, and Sox system perform their functions. The cytoplasmic membrane involving SQR and TQO is the third region with electrons transferring. In the cytoplasm, the sulfur-containing metabolites are catalyzed to eventually produce sulfate by a series of enzymes. Therefore, this study provides novel insights and more instructive guides into sulfur oxidation metabolism in A. thiooxidans. However, many fundamental questions remain unanswered. For example, some genes involved in the sulfur oxidation, such as sor gene, need to be further verified via biochemical experiments, and it is critical to determine the features of key metabolic enzymes involved in sulfur oxidation mechanism, which warrants further investigations of this organism in the future.
The work was supported by the National Basic Research Program (973 Program, No. 2010CB630901).
- Hallberg KB, González-Toril E, Johnson DB: Acidithiobacillus ferrivorans, sp. nov.; facultatively anaerobic, psychrotolerant iron-, and sulfur-oxidizing acidophiles isolated from metal mine-impacted environments. Extremophiles. 2010, 14 (1): 9-19.View ArticlePubMedGoogle Scholar
- Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes DS, Bonnefoy V: Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics. 2009, 10: 394-PubMed CentralView ArticlePubMedGoogle Scholar
- Rohwerder T, Gehrke T, Kinzler K, Sand W: Bioleaching review part A: progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation. Appl Microbiol Biotechnol. 2003, 63: 239-248.View ArticlePubMedGoogle Scholar
- Holmes DS, Bonnefoy V: Genetic And Bioinformatic Insights Into Iron And Sulfur Oxidation Mechanisms Of Bioleaching Organisms. Biomining. Edited by: Rawlings DE, Johnson DB. 2007, Berlin: Springer, 281-307.View ArticleGoogle Scholar
- Pronk JT, Meulenberg R, Hazeu W, Bos P, Kuenen JG: Oxidation of reduced inorganic sulphur compounds by acidophilic thiobacilli. FEMS Microbiol Lett. 1990, 75 (2–3): 293-306.View ArticleGoogle Scholar
- Valdes J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS: Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics. 2008, 9: 597-PubMed CentralView ArticlePubMedGoogle Scholar
- Steudel R: The Chemical Sulfur Cycle. Environmental Technologies to Treat Sulfur Pollution. Edited by: Lens PNL, Pol LH. 2000, IWA Publishing: London, 1-31.Google Scholar
- Rohwerder T, Sand W: The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology. 2003, 149 (7): 1699-1710.View ArticlePubMedGoogle Scholar
- Chen L, Ren Y, Lin J, Liu X, Pang X, Lin J: Acidithiobacillus caldus sulfur oxidation model based on transcriptome analysis between the wild type and sulfur oxygenase reductase defective mutant. PLoS One. 2012, 7 (9): e39470-PubMed CentralView ArticlePubMedGoogle Scholar
- Bobadilla Fazzini RA, Cortés MP, Padilla L, Maturana D, Budinich M, Maass A, Parada P: Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans. Biotechnol Bioeng. 2013, 110 (8): 2242-2251.View ArticlePubMedGoogle Scholar
- Mangold S, Valdes J, Holmes DS, Dopson M: Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus. Front Microbiol. 2011, 2: 17-PubMed CentralView ArticlePubMedGoogle Scholar
- Schütz M, Maldener I, Griesbeck C, Hauska G: Sulfide-quinone reductase from Rhodobacter capsulatus: requirement for growth, periplasmic localization, and extension of gene sequence analysis. J Bacteriol. 1999, 181: 6516-6523.PubMed CentralPubMedGoogle Scholar
- Friedrich CG: Physiology And Genetics Of Bacterial Sulfur Oxidation. Advances in Microbial Physiology. Edited by: Poole RK. 1997, Amsterdam: Elsevier, 235-289.Google Scholar
- Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J: Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?. Appl Environ Microbiol. 2001, 67 (7): 2873-2882.PubMed CentralView ArticlePubMedGoogle Scholar
- Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H: Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol. 2000, 182 (17): 4677-4687.PubMed CentralView ArticlePubMedGoogle Scholar
- Rother D, Henrich H, Quentmeier A, Bardischewsky F, Friedrich CG: Novel genes of the sox gene cluster, mutagenesis of the flavoprotein SoxF, and evidence for a general sulfur-oxidizing system in Paracoccus pantotrophus GB17. J Bacteriol. 2001, 183 (15): 4499-4508.PubMed CentralView ArticlePubMedGoogle Scholar
- Ghosh W, Dam B: Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev. 2009, 33 (6): 999-1043.View ArticlePubMedGoogle Scholar
- de Jong GAH, Hazeu W, Bos P, Kuenen JG: Polythionate degradation by tetrathionate hydrolase of Thiobacillus ferrooxidans. Microbiology. 1997, 143 (part 2): 499-504.View ArticleGoogle Scholar
- Rzhepishevska OI, Valdes J, Marcinkeviciene L, Gallardo CA, Meskys R, Bonnefoy V, Holmes DS, Dopson M: Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds. Appl Environ Microbiol. 2007, 73 (22): 7367-7372.PubMed CentralView ArticlePubMedGoogle Scholar
- Gardner MN, Rawlings DE: Production of rhodanese by bacteria present in bio-oxidation plants used to recover gold from arsenopyrite concentrates. J Appl Microbiol. 2000, 89 (1): 185-190.View ArticlePubMedGoogle Scholar
- Yoch DC, Lindstrom ES: Survey of the photosynthetic bacteria for rhodanese (thiosulfate: cyanide sulfur transferase) activity. J Bacteriol. 1971, 106 (2): 700-701.PubMed CentralPubMedGoogle Scholar
- Valdés J, Pedroso I, Quatrini R, Holmes DS: Comparative genome analysis of Acidithiobacillus ferrooxidans. A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology. Hydrometallurgy. 2008, 94 (1–4): 180-184.View ArticleGoogle Scholar
- Quatrini R, Valdès J, Jedlicki E, Holmes DS: The Use Of Bioinformatics And Genome Biology To Advance Our Understanding Of Bioleaching Microorganisms. Microbial Processing of Metal Sulfides. Edited by: Quatrini R, Valdès J, Jedlicki E, Holmes DS. 2007, Berlin: Springer, 221-239.View ArticleGoogle Scholar
- Huang X, Zhao M, Liu W, Guan Y, Shi Y, Wang Q, Wu S, He M: Gigabase-scale transcriptome analysis on four species of pearl oysters. Mar Biotechnol. 2013, 15 (3): 253-264.View ArticlePubMedGoogle Scholar
- Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27 (23): 4636-4641.PubMed CentralView ArticlePubMedGoogle Scholar
- Bedell JA, Korf I, Gish W: MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000, 16 (11): 1040-1041.View ArticlePubMedGoogle Scholar
- Lagesen K, Hallin P, Rødland EA, Stærfeldt H, Rognes T, Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007, 35 (9): 3100-3108.PubMed CentralView ArticlePubMedGoogle Scholar
- Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 2003, 25 (5): 955-964.View ArticleGoogle Scholar
- Silverman MP, Lundgren DG: Studies on the chemoautotrophic iron bacterium Ferrobacillus ferrooxidans: An improved medium and a harvesting procedure for securing high cell yields. J Bacteriol. 1959, 77 (5): 642-647.PubMed CentralPubMedGoogle Scholar
- Ramírez P, Guiliani N, Valenzuela L, Beard S, Jerez CA: Differential protein expression during growth of Acidithiobacillus ferrooxidans on ferrous iron, sulfur compounds, or metal sulfides. Appl Environ Microbiol. 2004, 70 (8): 4491-4498.PubMed CentralView ArticlePubMedGoogle Scholar
- Simms D, Cizdziel P, Chomczynski P: TRIzolTM: A new reagent for optimal single-step isolation of RNA. Focus. 1993, 15 (4): 99-102.Google Scholar
- Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001, 25 (4): 402-408.View ArticlePubMedGoogle Scholar
- Suzuki I: Oxidation of inorganic sulfur compounds: chemical and enzymatic reactions. Can J Microbiol. 1999, 45 (2): 97-105.View ArticleGoogle Scholar
- Zhang L, Liu X, Liu J, Zhang Z: Characteristics and function of sulfur dioxygenase in echiuran worm Urechis unicinctus. PLoS One. 2013, 8 (12): e81885-PubMed CentralView ArticlePubMedGoogle Scholar
- Bugaytsova Z, Lindström EB: Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus. Eur J Biochem. 2004, 271 (2): 272-280.View ArticlePubMedGoogle Scholar
- Wodara C, Kostka S, Egert M, Kelly DP, Friedrich CG: Identification and sequence analysis of the soxB gene essential for sulfur oxidation of Paracoccus denitrificans GB17. J Bacteriol. 1994, 176 (20): 6188-6191.PubMed CentralPubMedGoogle Scholar
- Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP: The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol. 2006, 188 (4): 1473-1488.PubMed CentralView ArticlePubMedGoogle Scholar
- Kletzin A: Molecular characterization of the sor gene, which encodes the sulfur oxygenase/reductase of the thermoacidophilic Archaeum Desulfurolobus ambivalens. J Bacteriol. 1992, 174 (18): 5854-5859.PubMed CentralPubMedGoogle Scholar
- He Z, Li Y, Zhou P, Liu S: Cloning and heterologous expression of a sulfur oxygenase/reductase gene from the thermoacidophilic archaeon Acidianus sp. S5 in Escherichia coli. FEMS Microbiol Lett. 2000, 193 (2): 217-221.View ArticlePubMedGoogle Scholar
- Pelletier N, Leroy G, Guiral M, Giudici-Orticoni M, Aubert C: First characterisation of the active oligomer form of sulfur oxygenase reductase from the bacterium Aquifex aeolicus. Extremophiles. 2008, 12 (2): 205-215.View ArticlePubMedGoogle Scholar
- Chen ZW, Liu YY, Wu JF, She Q, Jiang CY, Liu SJ: Novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates. Appl Microbiol Biotechnol. 2007, 74 (3): 688-698.View ArticlePubMedGoogle Scholar
- Kletzin A: Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: purification and properties of a sulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. J Bacteriol. 1989, 171 (3): 1638-1643.PubMed CentralPubMedGoogle Scholar
- Kletzin A, Urich T, Müller F, Bandeiras TM, Gomes CM: Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. J Bioenerg Biomembr. 2004, 36 (1): 77-91.View ArticlePubMedGoogle Scholar
- Emmel T, Sand W, König WA, Bock E: Evidence for the existence of a sulphur oxygenase in Sulfolobus brierleyi. Microbiology. 1986, 132 (12): 3415-3420.View ArticleGoogle Scholar
- Li M, Chen Z, Zhang P, Pan X, Jiang C, An X, Liu S, Chang W: Crystal structure studies on sulfur oxygenase reductase from Acidianus tengchongensis. Biochem Biophys Res Commun. 2008, 369 (3): 919-923.View ArticlePubMedGoogle Scholar
- Urich T, Bandeiras TM, LEAL SS, Rachel R, Albrecht T, Zimmermann P, Scholz C, Teixeira M, Gomes CM, Kletzin A: The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Biochem J. 2004, 381: 137-146.PubMed CentralView ArticlePubMedGoogle Scholar
- Urich T, Kroke A, Bauer C, Seyfarth K, Reuff M, Kletzin A: Identification of core active site residues of the sulfur oxygenase reductase from Acidianus ambivalens by site-directed mutagenesis. FEMS Microbiol Lett. 2005, 248 (2): 171-176.View ArticlePubMedGoogle Scholar
- Valdes J, Quatrini R, Hallberg K, Dopson M, Valenzuela PDT, Holmes DS: Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus. J Bacteriol. 2009, 191 (18): 5877-5878.PubMed CentralView ArticlePubMedGoogle Scholar
- Valdes J, Ossandon F, Quatrini R, Dopson M, Holmes DS: Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus. J Bacteriol. 2011, 193 (24): 7003-7004.PubMed CentralView ArticlePubMedGoogle Scholar
- Chen Z, Jiang C, She Q, Liu S, Zhou P: Key role of cysteine residues in catalysis and subcellular localization of sulfur oxygenase-reductase of Acidianus tengchongensis. Appl Environ Microbiol. 2005, 71 (2): 621-628.PubMed CentralView ArticlePubMedGoogle Scholar
- Urich T, Gomes CM, Kletzin A, Frazão C: X-ray structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science. 2006, 311 (5763): 992-996.View ArticleGoogle Scholar
- Urich T, Coelho R, Kletzina A, Frazao C: The sulfur oxygenase reductase from Acidianus ambivalens is an icosatetramer as shown by crystallization and Patterson analysis. BBA-Proteins Proteomics. 2005, 1747 (2): 267-270.View ArticlePubMedGoogle Scholar
- Schilling CH, Palsson BO: Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol. 2000, 203 (3): 249-283.View ArticlePubMedGoogle Scholar
- Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A: Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol. 2004, 53 (4): 1147-1160.View ArticlePubMedGoogle Scholar
- Tano T, Kitaguchi H, Harada M, Nagasawa T, Sugio T: Purification and some properties of a tetrathionate decomposing enzyme from Thiobacillus thiooxidans. Biosci Biotechnol Biochem. 1996, 60: 224-227.View ArticleGoogle Scholar
- Meyer B, Imhoff JF, Kuever J: Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria – evolution of the Sox sulfur oxidation enzyme system. Environ Microbiol. 2007, 9 (12): 2957-2977.View ArticlePubMedGoogle Scholar
- Ghosh W, Mallick S, DasGupta SK: Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins. Res Microbiol. 2009, 160 (6): 409-420.View ArticlePubMedGoogle Scholar
- Brasseur G, Levican G, Bonnefoy V, Holmes D, Jedlicki E, Lemesle-Meunier D: Apparent redundancy of electron transfer pathways via bc 1 complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans. Biochim Biophys Acta-Bioenerg. 2004, 1656 (2–3): 114-126.View ArticleGoogle Scholar
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