Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in <i>Acidithiobacillus thiooxidans</i>

Fazzini, Roberto A. Bobadilla; Cortés, María Paz; Padilla, Leandro; Maturana, Daniel; Budinich, Marko; Maass, Alejandro; Parada, Pilar

doi:10.1002/bit.24875

Cited by 41 publications

(35 citation statements)

References 59 publications

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“…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 [10]. 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).…”

Section: Resultsmentioning

confidence: 99%

“…Thiosulfate could be directly catalyzed by the incomplete Sox complex to generate sulfate [10]. 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].…”

Section: Resultsmentioning

confidence: 99%

“…The first and critical step of sulfur oxidation could be an opening of the S 8 ring by the thiol groups of cysteine residues, resulting in the formation of thiol-bound sulfane sulfur atoms (R-S-S n H) [8,9]. Subsequently, the R-S-S n H 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]. …”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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“…[34][35][36] Briey, 10 (AE1) g packing materials were immersed within 10 mL 0.2 M NaOH in a 50 mL centrifuge tube, incubated at 100 C for 10 min, and were then ultrasonicated at 40 kHz for 10 min. Filter-material-free solution with biolm inside was centrifuged at 12 000 rpm for 10 min, whose supernatant was then discarded.…”

Section: Elemental Sulfur Extraction and Analysismentioning

confidence: 99%

Biofilms formed within the acidic and the neutral biotrickling filters for treating H₂S-containing waste gases

Guo

Yang

et al. 2017

RSC Adv.

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Biofiltration of waste gases relies heavily on the biofilm on the surface of packing materials, whose formation has been believed to be associated with various environmental factors. In this study, we characterized two types of biofilms that are developed within an acidic and a neutral biotrickling filter (BTF), respectively. Both BTFs obtained near 100% removal efficiency when the H 2 S inlet loading rate was lower than 12.5 g m À3 h À1. As the rate was increased to 25 g m À3 h À1, however, the performance of the neutral BTF seemed to be compromised, with a decrease of 12.2% in removal efficiency, compared with a slight drop of 0.4% in the acidic one. The biomass in the neutral BTF ranged from 2.13 to 5.76 mg VSS g packing À1, which was higher than that seen in the acidic BTF (from 1.22 to 4.64 mg VSS g packing À1).Based on what was observed, we inferred that the stability of biofilms was influenced by the inlet loading rate and pH fluctuations. Besides, the ratio of planktonic cells : biofilm for the acidic BTF were higher than those of the neutral BTF, and polysaccharide was the dominant component of EPS. The maximum amounts of polysaccharide were 28.4 mg g VSS À1 for the neutral BTF and 156.2 mg g VSS À1 for the acidic one, while the corresponding protein amounts were only 11.2 and 5.4 mg g VSS À1, indicating that the polysaccharide in the EPS may play an important role in maintaining the mechanical stability of biofilm in extremely acidic conditions. Finally, we sampled some biofilms from the BTFs, whose three-dimensional structures were visualized by a confocal laser scanning microscopy (CLSM), and showed that the innermost layer of all biofilms exhibited the highest bacterial viabilities.

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“…This is the same as free-living, symbiotic (Kleiner et al, 2012a;Muyzer et al, 2011a,b) and phototrophic SOB (Friedrich et al, 2005;Ogawa et al, 2008). The complete Sox system yields 8 electrons per thiosulfate molecule, but the loss of the soxCD enzyme results in just 2 electrons being generated and the formation of sulfur globules (Fazzini et al, 2013). As AqS1 likely belongs to the family Ectothiorhodospiraceae , it is characteristic that the sulfur globules are exported from the cell (Garrity et al, 2007).…”

Section: Chemoautotrophic Metabolismmentioning

confidence: 93%

Modelling sponge-symbiont metabolism

Watson¹

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Marine sponges are increasingly being recognised for their nutrient cycling ecosystem services, linking pelagic nutrients with the benthic ecosystem. Furthermore, sponges are the most prolific producers of bioactive secondary metabolites in the marine environment. Despite their ecological and commercial value, little is know about the metabolic processes that are responsible. The inability to produce sufficient sponge biomass, and thus specific bioactive compounds, has been repeatedly identified as a major bottleneck towards commercialising sponge holobiont derived drugs. Likewise, nutrient cycling by sponges has been a relatively recent advancement in marine ecology and the scale of this process is unknown. This thesis takes a systems approach to understanding sponge-symbiont metabolic processes by utilising the genomic resources available for the demosponge Amphimedon queenslandica and its bacterial symbiont AqS1. Specifically, I undertake genome-scale modelling and metabolic flux analyses to investigate the metabolic networks present in this sponge as well as its associated vertically-transmitted microbial symbiont. The goal of this thesis is to generate the data required for, and subsequently develop, a dual-species genome-scale metabolic model for A. queenslandica and AqS1. This will provide a framework to further our understanding of how sponges produce their biomass while living in an oligotrophic, tropical reef environment.To develop a genome-scale metabolic model, the biochemical composition of the organism must first be determined. Knowledge of the relative quantities of macromolecules and their respective building blocks (e.g. protein and amino acids) is vital, as each requires different substrates, enzymes and cofactors for their synthesis. I adapted and developed methods to characterise the composition and abundance of DNA, RNA, protein, lipids and carbohydrates in a marine sponge. These methods are described in detail that allows them to be easily transferred to other, non-model, large marine organisms. This is followed by a detailed analysis of A. queenslandica's macromolecular, amino acid, fatty acid and sterol composition. The biochemical data from this chapter was used to generate a biomass equation that represent the average composition of adult A. queenslandica in the metabolic model. 3To understand how the metabolic network may work towards producing more biomass, it must be considered in the context of the environmental conditions that naturally constrain growth. The dominant environmental constraint on growth on an oligotrophic reef system is nutrient availability.The abundance of key elements, such as carbon and nitrogen, were quantified throughout the course of a year. To investigate effects on the sponge of any changes in nutrient availability, I concurrently sampled sponges and analysed their biochemical composition to the macromolecular level. Chapter 4 presents these data and discusses a number of trends and correlations in the biochemical composition of the sponges with chan...

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Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans

Cited by 41 publications

References 59 publications

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

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

Biofilms formed within the acidic and the neutral biotrickling filters for treating H₂S-containing waste gases

Modelling sponge-symbiont metabolism

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Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans

Cited by 41 publications

References 59 publications

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

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

Biofilms formed within the acidic and the neutral biotrickling filters for treating H2S-containing waste gases

Modelling sponge-symbiont metabolism

Contact Info

Product

Resources

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Biofilms formed within the acidic and the neutral biotrickling filters for treating H₂S-containing waste gases