Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans

University of Illinois, Chicago, USA
Hydrometallurgy (Impact Factor: 1.93). 09/2006; 83(1):273-280. DOI: 10.1016/j.hydromet.2006.03.029

ABSTRACT Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as an energy and electron source. Bioinformatic analysis of the A. ferrooxidans draft genome sequence was used to identify putative genes and potential metabolic pathways involved in CO2 fixation, 2P-glycolate detoxification, carboxysome formation and glycogen utilization. Microarray transcript profiling was carried out to compare the relative expression of the predicted genes of these pathways when the microorganism was grown in the presence of iron versus sulfur. Several gene expression patterns were confirmed by real-time PCR. Genes for each of the above-predicted pathways were found to be organized into discrete clusters. Clusters exhibited differential gene expression depending on the presence of iron or sulfur in the medium. Concordance of gene expression within each cluster suggested that they are operons. Most notably, clusters of genes predicted to be involved in CO2 fixation, carboxysome formation, 2P-glycolate detoxification and glycogen biosynthesis were upregulated in sulfur medium, whereas genes involved in glycogen utilization were preferentially expressed in iron medium. These results can be explained in terms of models of gene regulation that suggest how A. ferrooxidans can adjust its central carbon management to respond to changes in its environment.

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Available from: Violaine Bonnefoy, Sep 29, 2015
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    • "These authors detected a series of proteins involved in various cellular functions that are directly related to the different substrates and culture and stress conditions. Microarray transcript profiling of sulfur-and iron-oxidizing cells has been reported, focusing on their carbon (Appia-Ayme et al. 2006) and energy metabolism (Quatrini et al. 2006, 2009), which led to the generalized model of iron and sulfur respiration pathways. Vera et al. (2009) described the different gene expression patterns of planktonic and sessile cells grown on pyrite. "
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    ABSTRACT: In contrast to iron-oxidizing Acidithiobacillus ferrooxidans, A. ferrooxidans from a stationary phase elemental sulfur-oxidizing culture exhibited a lag phase in pyrite oxidation, which is similar to its behaviour during ferrous iron oxidation. The ability of elemental sulfur-oxidizing A. ferrooxidans to immediately oxidize ferrous iron or pyrite without a lag phase was only observed in bacteria obtained from growing cultures with elemental sulfur. However, these cultures that shifted to ferrous iron oxidation showed a low rate of ferrous iron oxidation while no growth was observed. Two-dimensional gel electrophoresis was used for a quantitative proteomic analysis of the adaptation process when bacteria were switched from elemental sulfur to ferrous iron. A comparison of total cell lysates revealed 39 proteins whose increase or decrease in abundance was related to this phenotypic switching. However, only a few proteins were closely related to iron and sulfur metabolism. Reverse-transcription quantitative PCR was used to further characterize the bacterial adaptation process. The expression profiles of selected genes primarily involved in the ferrous iron oxidation indicated that phenotypic switching is a complex process that includes the activation of genes encoding a membrane protein, maturation proteins, electron transport proteins and their regulators.
    Antonie van Leeuwenhoek 01/2013; 103(4). DOI:10.1007/s10482-012-9872-2 · 1.81 Impact Factor
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    • "Bioinformatic analysis of the genome data of A. ferrooxidans has been used to predict the regulation of nitrogen metabolism (Barreto et al. 2003; Levican et al. 2008), sulfur assimilation and its regulatory interplay with nitrogen fixation, hydrogen oxidation and energy metabolism (Valdés et al. 2003), iron homeostasis (references in preceding paragraph), CO 2 fixation (Esparza et al. 2009, 2010) and other aspects of central carbon metabolism (Appia-Ayme et al. 2006). Some of these models have been supported with experimental evidence. "
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    ABSTRACT: This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.
    Applied Microbiology and Biotechnology 10/2010; 88(3):605-20. DOI:10.1007/s00253-010-2795-9 · 3.34 Impact Factor
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    • "The intergenic region between cbbR and cbbL is predicted to harbor binding sites for CbbR [4]. In addition, microarray transcript profiling experiments have detected differential expression of several genes in A. ferrooxidans potentially involved in the CBB cycle depending on the growth substrate used [8]. "
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    ABSTRACT: Acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low pH (pH 1-2). Although a substantial amount of information is available regarding CO2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. Four gene clusters (termed cbb1-4) in the A. ferrooxidans genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson-Bassham (CBB) cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC and the CO2-concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon cbb1 is divergently transcribed from a gene, cbbR, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma70-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N11-A/TNA-N7TNA) were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs) confirmed that purified CbbR is able to bind to the upstream regions of the cbb1, cbb2 and cbb3 operons, demonstrating that the predicted CbbR-binding sites are functional in vitro. However, CbbR failed to bind the upstream region of the cbb4 operon that contains cbbP, encoding phosphoribulokinase (EC Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The cbb3 operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO2 fixation and tryptophan biosynthesis. The presence of a form II RubisCO could promote the ability of A. ferrooxidans to fix CO2 at different concentrations of CO2. A. ferrooxidans has features of cbb gene organization for CO2-assimilating functions that are characteristic of obligate chemolithoautotrophs and distinguish this group from facultative autotrophs. The most conspicuous difference is a separate operon for the cbbP gene. It is hypothesized that this organization may provide greater flexibility in the regulation of expression of genes involved in inorganic carbon assimilation.
    BMC Microbiology 08/2010; 10(1):229. DOI:10.1186/1471-2180-10-229 · 2.73 Impact Factor
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