Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes

<p>Abstract</p> <p>Background</p> <p><it>Thiomonas </it>strains are ubiquitous in arsenic-contaminated environments. Differences between <it>Thiomonas </it>strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five <it>Thiomonas </it>strains, that are interesting in terms of arsenic metabolism were selected: <it>T. arsenivorans</it>, <it>Thiomonas </it>spp. WJ68 and 3As are able to oxidise As(III), while <it>Thiomonas </it>sp. Ynys1 and <it>T. perometabolis </it>are not. Moreover, <it>T. arsenivorans </it>and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor.</p> <p>Results</p> <p>The metabolism of carbon and arsenic was compared in the five <it>Thiomonas </it>strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/<it>rpoA </it>gene phylogeny, especially regarding arsenic metabolism. Physiologically, <it>T. perometabolis </it>and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the <it>aox </it>arsenic-oxidising genes and carried only a single <it>ars </it>arsenic resistance operon. <it>Thiomonas arsenivorans </it>belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in <it>T. arsenivorans</it>, the <it>rbc</it>/<it>cbb </it>genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in <it>Thiomonas </it>sp. 3As.</p> <p>Conclusion</p> <p>Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.</p

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans

Background: Arsenic is present in numerous ecosystems and microorganisms have developed various mechanisms to live in such hostile environments. Herminiimonas arsenicoxydans, a bacterium isolated from arsenic contaminated sludge, has acquired remarkable capabilities to cope with arsenic. In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III). Results: Microarrays were designed to compare gene transcription profiles under a temporal As(III) exposure. Transcriptome kinetic analysis demonstrated the existence of two phases in arsenic response. The expression of approximatively 14% of the whole genome was significantly affected by an As(III) early stress and 4% by an As(III) late exposure. The early response was characterized by arsenic resistance, oxidative stress, chaperone synthesis and sulfur metabolism. The late response was characterized by arsenic metabolism and associated mechanisms such as phosphate transport and motility. The major metabolic changes were confirmed by chemical, transcriptional, physiological and biochemical experiments. These early and late responses were defined as general stress response and specific response to As(III), respectively. Conclusion: Gene expression patterns suggest that the exposure to As(III) induces an acute response to rapidly minimize the immediate effects of As(III). Upon a longer arsenic exposure, a broad metabolic response was induced. These data allowed to propose for the first time a kinetic model of the As(III) response in bacteria

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

Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans

<p>Abstract</p> <p>Background</p> <p>Both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. These transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. <it>Herminiimonas arsenicoxydans </it>has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism.</p> <p>Results</p> <p>In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of <it>H. arsenicoxydans </it>to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn<it>5 </it>transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted <it>aoxR </it>and <it>aoxS </it>genes, showing that the <it>aox </it>operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in <it>rpoN </it>coding for the alternative N sigma factor (σ⁵⁴) of RNA polymerase and in <it>dnaJ </it>coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the <it>rpoN </it>and <it>dnaJ </it>gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the <it>aoxAB </it>operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 σ⁵⁴-dependent promoter motif was identified upstream of <it>aoxAB </it>coding sequences.</p> <p>Conclusion</p> <p>These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in <it>H. arsenicoxydans</it>. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.</p

Adaptation in toxic environments: Arsenic genomic islands in the bacterial genus Thiomonas:

Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments

Life in an arsenic-containing gold mine: Genome and physiology of the autotrophic arsenite-oxidizing bacterium Rhizobium sp. NT-26:

Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arseniccontaining goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions. © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution

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

Regulation de la synthese et de l'activite de NifA chez Azospirillum brasilense, a l'etat libre et en association avec le ble

Azospirillum brasilense is a diazotrophic bacterium that associates with the roots of gramineae. The nitrogen fixation genes (nif genes) are expressed only in microaerobiosis and in the absence of ammonia. Expression of the nif genes requires the transcriptional activator NifA. The present work focuses on the regulation of Nifa synthesis and activity. Modulation of NifA activity involves the PII protein. Our results suggest that in the presence of ammonia, the N-terminal domain of NifA plays an inhibitory role, inactivating the rest of the protein. In the absence of ammonia, the PII protein maintains NifA in its active form by preventing inhibition of this domain. NifA is synthesised both in conditions compatible with nitrogen fixation and in the presence of air and ammonia. The ntrbc genes play a minor role in the expression of nifa and mutants of ntrb or ntrc are Nif+. These genes nevertheless play a role in nitrogen fixation, since they are involved in controlling the regulation of nitrogenase activity by ADP-ribosylation (switch-off phenomenon). Regulation of nif gene expression was also studied during association with wheat. We were able to show that the same regulation model applied to bacteria in pure culture and in association with wheat roots. Under the conditions used, NifA is found in the active form.Azospirillum brasilense est une bacterie diazotrophe qui s'associe aux racines de graminees. Les genes de la fixation de l'azote (genes nif) sont exprimes uniquement en microaerobiose et en absence d'ammoniaque. L'expression des genes nif requiert l'activateur transcriptionnel nifa. L'etude de la regulation de la synthese et de l'activite de nifa fait l'objet du travail presente. La modulation de l'activite de nifa fait intervenir la proteine p#i#i. Nos resultats suggerent qu'en presence d'ammoniaque, le domaine n-terminal de nifa joue un role inhibiteur, en inactivant le reste de la proteine. En absence d'ammoniaque, la proteine p#i#i maintient nifa sous sa forme active en empechant l'inhibition de ce domaine. Nifa est synthetisee aussi bien dans des conditions compatibles avec la fixation de l'azote qu'en presence d'air et d'ammoniaque. Les genes ntrbc jouent un role mineur dans l'expression de nifa et des mutants de ntrb ou ntrc sont nif#+. Ces genes jouent tout de meme un role dans la fixation de l'azote, puisqu'ils interviennent dans le controle de la regulation de l'activite de la nitrogenase par adp-ribosylation (phenomene de switch-off). La regulation de l'expression des genes nif a ete etudiee egalement au cours de l'association avec le ble. Nous avons pu montre qu'un meme modele de regulation s'applique aux bacteries en culture pure et en association avec les racines de ble. Dans les conditions utilisees, nifa se trouve sous forme active

Proteomic tools to decipher microbial community structure and functioning

Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented