Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

<p>Abstract</p> <p>Background</p> <p><it>Acidithiobacillus ferrooxidans </it>gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different <it>A. ferrooxidans </it>strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of <it>A. ferrooxidans </it>in order to comprehend the full metabolic potential of the pangenome of the genus.</p> <p>Results</p> <p>Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in <it>A. ferrooxidans </it>ATCC23270. These include for iron oxidation: <it>cup </it>(copper oxidase-like), <it>ctaABT </it>(heme biogenesis and insertion), <it>nuoI </it>and <it>nuoK </it>(NADH complex subunits), <it>sdrA1 </it>(a NADH complex accessory protein) and <it>atpB </it>and <it>atpE </it>(ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (<it>rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB</it>) encoding three sulfurtransferases and a heterodisulfide reductase complex, <it>sat </it>potentially encoding an ATP sulfurylase and <it>sdrA2 </it>(an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (<it>ctaRUS</it>) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome <it>aa</it>₃oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool.</p> <p>Conclusion</p> <p>Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in <it>A. ferrooxidans </it>and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.</p

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes

The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (&lt;10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth

Structure, Function, and Evolution of the Thiomonas spp. Genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live

Etude des opérons petI et petII codant pour deux complexes bc1 chez la bactérie acidophile chimioautotrophe stricte Acidithiobacillus ferrooxidans

AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

Caractérisation de "Thiomonas arsenitoxydans" et étude de la régulation des gènes codant pour l'arsénite oxydase

Thiomonas sp. 3As, bactérie isolée d'eaux de drainage de mine (Carnoulès, France) contaminées par l'arsenic, a la capacité d'oxyder l'arsenic. Nous l'avons caractérisée aux niveaux physiologique et chimiotaxonomique, ce qui a montré qu'il s'agit d'une nouvelle espèce : "Thiomonas arsenitoxudans". L'arsénite axydase catalyse l'oxydation de l'arsénite (As(III)) en arséniate (As(V)), moins soluble et toxique. Nous avons montré chez cette bactérie que les gènes aoxAB codant pour les 2 sous-unités de cette enzyme sont co-transcrits ArsR/SmtB. Cet opéron est transcrit en présence d'As(III) et d'As(V). Nos résultats indiquent qu'ArsR-like (1) est stabilisé par l'As(III) ou l'As(V). Nos résultats suggèrent qu'ArsR-like a un mécanisme d'action différent de celui établi pour les autres membres de la famille ArsR/SmtBThiamonas sp. 3As, a bacterium isolated from acid mine drainage waters heavily loaded with arsenic (Carnoulès, France), has the capacity to oxidize arsenic. We characterized it both at the physiological and chemotaxonomical levels, which showed that it belongs to a new species : "thiomonas arsenitoxydans". The arsenite oxidase catalyses the oxidation of arsenite (As(III)) to arsenate (As(V)), less soluble and toxic. We showed that the genes aoxAB encoding the 2 sub-units of this enzyme are co-transcribed with the genes coding for 2 cytochromes c and a metalloregulator ArsR-like of the ArsR/SmtB family in "Tm. arsenitoxydans". This operon is transcribed in the presence of As(III)) or As(V). Our results indicaded that ArsR-like (1) is stabilized by As(III) or As(V), and (2) binds on the regulatory sequence of the aox operon in the presence of As(III) or As(V). From oour results, we suggest that the mechanism of ArsR-like is different from that of the other members of the ArsR/SmtB familyAIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

Energy Acquisition in Low pH Environments

International audienceExtreme acidophiles thriving in acidic habitats are characterised by low organic substrate inputs and high concentrations in inorganic substances, in particular sulfur compounds and iron. Their strategies for harvesting energy for growth in these harsh environments are described in this chapter. An overview of the general concepts on bioenergetics is given to highlight the particular challenges faced by extreme acidophiles. Pathways involved in oxidation and reduction of iron and sulfur compounds are presented and discussed. From the available data, it is obvious that, for the same electron donor and acceptor, the metabolic pathways differ sufficiently between different prokaryotes to suggest independent origins followed by diversification and horizontal gene transfer

Rôle des bactéries dans la bioremédiation de l'arsenic dans les eaux acides de drainage de la mine de Carnoulès

AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

Etude pour la mise au point d'un biocapteur à arsénite

Afin de diminuer les problèmes de santé dûe à l arsenic, il est nécessaire de créer un biocapteur spécifique de l'arsénite. L arsénite oxydase pourrait être utilisée pour un biocapteur ampérométrique. Le criblage de 60 bactéries a permis de sélectionner 3 bactéries ayant une activité arsénite oxydase élevée dans différentes conditions : Thiomonas sp., Herminiimonas arsenicoxydans et Ralstonia solanacearum str. S22. Les gènes des bactéries T. sp. et H. arsenicoxydans, codant pour l arsénite oxydase ont été clonés dans un vecteur d'expression. Les enzymes recombinantes obtenues formaient des corps d inclusion et ne possédaient pas d activité arsénite oxydase dans les conditions utilisées. Nous avons purifié partiellement l arsénite oxydase et un cytochrome c qui pourrait être son partenaire physiologique de la bactérie S22. Nous avons détecté une activité sulfite oxydase ce qui suggère que l arsénite oxydase de S22 n est pas spécifique de l arsénite.AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF