RESUMO
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴠ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴠ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
Assuntos
Fosfatos Açúcares , Humanos , Fosfatos Açúcares/metabolismo , Terpenos/farmacologia , Terpenos/metabolismo , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Eritritol/metabolismoRESUMO
In this work, we implemented for the first time the cycloSaligenyl prodrug strategy to increase the bioavailability of fosmidomycin phosphate analogs in bacteria. Here, we report the synthesis of 34 cycloSaligenyl prodrugs of fosfoxacin and its derivatives. Among them, fifteen double prodrugs efficiently prevented the growth of the non-pathogenic, fast-growing Mycobacterium smegmatis.
Assuntos
Pró-Fármacos , Monofosfato de Citidina , Mycobacterium smegmatis , FosfatosRESUMO
Three α,α-difluorophosphonate derivatives of fosmidomycin were synthesized from diethyl 1,1-difluorobut-3-enylphosphonate and were evaluated on Escherichia coli. Two of them are among the best 1-deoxy-d-xylulose 5-phosphate reductoisomerase inhibitors, with IC50 in the nM range, much better than fosmidomycin, the reference compound. They also showed an enhanced antimicrobial activity against E. coli on Petri dishes in comparison with the corresponding phosphates and the non-fluorinated phosphonate.
Assuntos
Antibacterianos/farmacologia , Fosfomicina/análogos & derivados , Ácidos Hidroxâmicos/farmacologia , Aldose-Cetose Isomerases/antagonistas & inibidores , Aldose-Cetose Isomerases/metabolismo , Farmacorresistência Bacteriana/efeitos dos fármacos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Fosfomicina/síntese química , Fosfomicina/química , Fosfomicina/farmacologia , Testes de Sensibilidade MicrobianaRESUMO
Aryl phosphoramidate prodrugs of fosfoxacin derivatives 15a-b and 8a-b were synthesized and investigated for their ability to target bacteria. No growth inhibition was observed neither for Mycobacterium smegmatis nor for Escherichia coli on solid medium, demonstrating the absence of release of the active compounds in the bacterial cells. Investigation of the stability of the prodrugs and their multienzymatic cleavage in abiotic and biotic conditions showed that the use of aryl phosphoramidate prodrug approach to deliver non-nucleotides compounds is not obvious and might not be appropriate for an antimicrobial drug.
Assuntos
Amidas/síntese química , Monofosfato de Citidina/análogos & derivados , Ácidos Fosfóricos/síntese química , Pró-Fármacos/síntese química , Amidas/química , Monofosfato de Citidina/síntese química , Monofosfato de Citidina/química , Estrutura Molecular , Ácidos Fosfóricos/química , Pró-Fármacos/químicaRESUMO
Graphene oxide (GO) and graphene-based materials (GBMs) have gained over the last two decades considerable attention due to their intrinsic physicochemical properties and their applications. Besides, a lot of concern regarding the potential toxicity of GBMs has emerged. One of the aspects of concern is the interactions between GBMs and different environmental compartments, especially indigenous microbial and, in particular, bacterial communities. Recent research showed that GO and GBMs impacted bacterial pure culture or bacterial communities; therefore, these interactions have to be further studied to better understand and assess the fate of these materials in the environment. Here, we present our opinion and hypotheses related to possible degradation mechanisms of GO that can be used by environmental bacteria. This work is the first attempt to deduce and summarize plausible degradation pathways of GO, from structurally similar recalcitrant and toxic compounds, such as polyaromatic hydrocarbons.
Assuntos
Grafite , Grafite/metabolismo , Bactérias/metabolismoRESUMO
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.
Assuntos
Betaproteobacteria/genética , Evolução Molecular , Genoma Bacteriano/genética , Adaptação Fisiológica/genética , Arsênio/metabolismo , Carbono/metabolismo , Hibridização Genômica Comparativa , Metabolismo Energético/genética , Meio Ambiente , Transferência Genética Horizontal/genética , Genes Bacterianos/genética , Genes Duplicados/genética , Variação Genética , Ilhas Genômicas/genética , Redes e Vias Metabólicas/genética , Plasmídeos/genética , Prófagos/genéticaRESUMO
BACKGROUND: The recycling of the organic matter is a crucial function in any environment, especially in oligotrophic environments such as Acid Mine Drainages (AMDs). Polymer-degrading bacteria might play an important role in such ecosystem, at least by releasing by-products useful for the rest of the community. In this study, physiological, molecular and biochemical experiments were performed to decipher the role of a Paenibacillus strain isolated from the sediment of Carnoulès AMD. RESULTS: Even though Paenibacillus sp. strain Q8 was isolated from an oligotrophic AMD showing an acidic pH, it developed under both acidic and alkaline conditions and showed a heterotrophic metabolism based on the utilization of a broad range of organic compounds. It resisted to numerous metallic stresses, particularly high arsenite (As(III)) concentrations (> 1,800 mg/L). Q8 was also able to efficiently degrade polymers such as cellulose, xylan and starch. Function-based screening of a Q8 DNA-library allowed the detection of 15 clones with starch-degrading activity and 3 clones with xylan-degrading activity. One clone positive for starch degradation carried a single gene encoding a "protein of unknown function". Amylolytic and xylanolytic activities were measured both in growing cells and with acellular extracts of Q8. The results showed the ability of Q8 to degrade both polymers under a broad pH range and high As(III) and As(V) concentrations. Activity measurements allowed to point out the constitutive expression of the amylase genes and the mainly inducible expression of the xylanase genes. PACE demonstrated the endo-acting activity of the amylases and the exo-acting activity of the xylanases. CONCLUSIONS: AMDs have been studied for years especially with regard to interactions between bacteria and the inorganic compartment hosting them. To date, no study reported the role of microorganisms in the recycling of the organic matter. The present work suggests that the strain Q8 might play an important role in the community by recycling the scarce organic matter (cellulose, hemicellulose, starch...), especially when the conditions change. Furthermore, function-based screening of a Q8 DNA library allowed to assign an amylolytic function to a gene previously unknown. AMDs could be considered as a reservoir of genes with potential biotechnological properties.
Assuntos
Compostos Orgânicos/metabolismo , Paenibacillus/metabolismo , Arsenitos/química , Arsenitos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Celulose/metabolismo , Concentração de Íons de Hidrogênio , Mineração , Dados de Sequência Molecular , Amido/metabolismo , Xilanos/metabolismoRESUMO
BACKGROUND: 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. Herminiimonas arsenicoxydans 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. RESULTS: In the present study, a differential transcriptome analysis was used to identify genes, including arsenite oxidase encoding genes, involved in the response of H. arsenicoxydans to As(III). To get insight into the molecular mechanisms of this enzyme activity, a Tn5 transposon mutagenesis was performed. Transposon insertions resulting in a lack of arsenite oxidase activity disrupted aoxR and aoxS genes, showing that the aox operon transcription is regulated by the AoxRS two-component system. Remarkably, transposon insertions were also identified in rpoN coding for the alternative N sigma factor (sigma54) of RNA polymerase and in dnaJ coding for the Hsp70 co-chaperone. Western blotting with anti-AoxB antibodies and quantitative RT-PCR experiments allowed us to demonstrate that the rpoN and dnaJ gene products are involved in the control of arsenite oxidase gene expression. Finally, the transcriptional start site of the aoxAB operon was determined using rapid amplification of cDNA ends (RACE) and a putative -12/-24 sigma54-dependent promoter motif was identified upstream of aoxAB coding sequences. CONCLUSION: These results reveal the existence of novel molecular regulatory processes governing arsenite oxidase expression in H. arsenicoxydans. These data are summarized in a model that functionally integrates arsenite oxidation in the adaptive response to As(III) in this microorganism.
Assuntos
Regulação Bacteriana da Expressão Gênica , Oxalobacteraceae/genética , Oxalobacteraceae/metabolismo , Oxirredutases/genética , Sequência de Aminoácidos , Arsenitos/metabolismo , Arsenitos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Sequência Conservada , Perfilação da Expressão Gênica/métodos , Genes Bacterianos , Redes e Vias Metabólicas , Dados de Sequência Molecular , Mutação , Óperon , Oxalobacteraceae/enzimologia , Oxirredutases/biossíntese , Oxirredutases/metabolismo , Percepção de Quorum/efeitos dos fármacos , Percepção de Quorum/genética , Alinhamento de Sequência , Transcrição Gênica/efeitos dos fármacosRESUMO
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 beta-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.
Assuntos
Arsênio/metabolismo , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Bactérias/genética , Biodegradação Ambiental , Carbono/metabolismo , Farmacorresistência Bacteriana/genética , Metabolismo Energético , Genoma Bacteriano , Metais/farmacologia , Modelos Biológicos , Oxirredução , FilogeniaRESUMO
Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was previously observed that after exposure to arsenite, when grown in a biofilm, some strains of Thiomonas bacteria develop variants that are more resistant to arsenic. Here, we identified the mechanisms involved in the emergence of such variants in biofilms. We found that the percentage of variants generated increased in the presence of high concentrations of arsenite (5.33 mM), especially in the detached cells after growth under biofilm-forming conditions. Analysis of gene expression in the parent strain CB2 revealed that genes involved in DNA repair were upregulated in the conditions where variants were observed. Finally, we assessed the phenotypes and genomes of the subsequent variants generated to evaluate the number of mutations compared to the parent strain. We determined that multiple point mutations accumulated after exposure to arsenite when cells were grown under biofilm conditions. Some of these mutations were found in what is referred to as ICE19, a genomic island (GI) carrying arsenic-resistance genes, also harbouring characteristics of an integrative and conjugative element (ICE). The mutations likely favoured the excision and duplication of this GI. This research aids in understanding how Thiomonas bacteria adapt to highly toxic environments, and, more generally, provides a window to bacterial genome evolution in extreme environments.
Assuntos
Arsenitos/metabolismo , Biofilmes/crescimento & desenvolvimento , Burkholderiales , Genoma Bacteriano/genética , Adaptação Fisiológica/genética , Arseniatos/metabolismo , Arsênio/metabolismo , Burkholderiales/genética , Burkholderiales/crescimento & desenvolvimento , Burkholderiales/metabolismo , Reparo do DNA/genética , Elementos de DNA Transponíveis/genética , Evolução Molecular , Perfilação da Expressão Gênica , Variação Genética/genética , Ilhas Genômicas/genética , Mineração , Sequenciamento Completo do GenomaRESUMO
BACKGROUND: Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor. RESULTS: The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As. CONCLUSION: 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.
Assuntos
Adaptação Fisiológica , Arsênio/metabolismo , Betaproteobacteria/enzimologia , Carbono/metabolismo , Arsenitos/metabolismo , Betaproteobacteria/classificação , Betaproteobacteria/genética , Crescimento Quimioautotrófico/efeitos dos fármacos , Filogenia , Especificidade da EspécieRESUMO
A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.
Assuntos
Arsenitos/metabolismo , Bactérias/enzimologia , Bactérias/genética , Oxirredutases/genética , Sequência de Aminoácidos , Sequência de Bases , Biodiversidade , Crescimento Quimioautotrófico , Sequência Conservada , Primers do DNA , DNA Bacteriano/isolamento & purificação , Genes Bacterianos , Marcadores Genéticos , Variação Genética , Dados de Sequência Molecular , Oxirredução , Filogenia , Reação em Cadeia da Polimerase , Proteobactérias/enzimologia , Proteobactérias/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de DNA , Análise de Sequência de Proteína , Microbiologia do Solo , Poluentes do Solo/metabolismoRESUMO
The original version of this article unfortunately contains a mistake.
RESUMO
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
Assuntos
Adaptação Biológica/genética , Resistência Microbiana a Medicamentos/genética , Genômica , Mineração , Águas Residuárias/microbiologia , Ácidos/farmacologia , Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Bactérias/genética , Bases de Dados Genéticas , Resistência Microbiana a Medicamentos/efeitos dos fármacos , Metais Pesados/farmacologiaAssuntos
Arsenitos/metabolismo , Bactérias/enzimologia , Genes Bacterianos , Oxirredutases/metabolismo , Terminologia como Assunto , Aerobiose , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Regulação Enzimológica da Expressão Gênica , Oxirredução , Oxirredutases/genética , Subunidades ProteicasRESUMO
Pseudomonas xanthomarina S11 is an arsenite-oxidizing bacterium isolated from an arsenic-contaminated former gold mine in Salsigne, France. This bacterium showed high resistance to arsenite and was able to oxidize arsenite to arsenate at concentrations up to 42.72 mM As[III]. The genome of this strain was sequenced and revealed the presence of three ars clusters. One of them is located on a plasmid and is organized as an "arsenic island" harbouring an aio operon and genes involved in phosphorous metabolism, in addition to the ars genes. Neither the aioXRS genes nor a specific sigma-54-dependent promoter located upstream of aioBA genes, both involved in regulation of arsenite oxidase expression in other arsenite-oxidizing bacteria, could be identified in the genome. This observation is in accordance with the fact that no difference was observed in expression of arsenite oxidase in P. xanthomarina S11, whether or not the strain was grown in the presence of As[III].
Assuntos
Arsênio/metabolismo , Proteínas de Bactérias/genética , Oxirredutases/genética , Oxirredutases/metabolismo , Pseudomonas/genética , Arseniatos/metabolismo , Arsênio/farmacologia , ATPases Transportadoras de Arsenito/genética , ATPases Transportadoras de Arsenito/metabolismo , Arsenitos/metabolismo , Arsenitos/farmacologia , Proteínas de Bactérias/metabolismo , Sequência de Bases , DNA Bacteriano , Farmacorresistência Bacteriana , França , Regulação Bacteriana da Expressão Gênica , Mineração , Óperon , Oxirredução , Filogenia , Plasmídeos , Pseudomonas/enzimologia , Pseudomonas/crescimento & desenvolvimento , Pseudomonas/isolamento & purificaçãoRESUMO
The acid mine drainage (AMD) in Carnoulès (France) is characterized by the presence of toxic metals such as arsenic. Several bacterial strains belonging to the Thiomonas genus, which were isolated from this AMD, are able to withstand these conditions. Their genomes carry several genomic islands (GEIs), which are known to be potentially advantageous in some particular ecological niches. This study focused on the role of the "urea island" present in the Thiomonas CB2 strain, which carry the genes involved in urea degradation processes. First, genomic comparisons showed that the genome of Thiomonas sp. CB2, which is able to degrade urea, contains a urea genomic island which is incomplete in the genome of other strains showing no urease activity. The urease activity of Thiomonas sp. CB2 enabled this bacterium to maintain a neutral pH in cell cultures in vitro and prevented the occurrence of cell death during the growth of the bacterium in a chemically defined medium. In AMD water supplemented with urea, the degradation of urea promotes iron, aluminum and arsenic precipitation. Our data show that ureC was expressed in situ, which suggests that the ability to degrade urea may be expressed in some Thiomonas strains in AMD, and that this urease activity may contribute to their survival in contaminated environments.
RESUMO
An efficient, inexpensive microplate colorimetric assay for screening of bacteria which can be used in bioremediation of arsenic was developed. The assay is based on the colorimetric analysis of the precipitates formed upon reaction of silver nitrate with arsenic. The method proved reliable and sensitive for the detection of As[III] oxidizers and As[V] reducers and can be used over a large pH range (5.8-8.4). Seventy-eight bacterial strains isolated from different environments were tested by this method. It also showed agreement with results obtained by high-performance liquid chromatography coupled with inductively coupled plasma atomic emission spectrometry.
Assuntos
Arseniatos/metabolismo , Arsenitos/metabolismo , Bactérias/metabolismo , Técnicas Bacteriológicas , Colorimetria/métodos , Arsênio/metabolismo , Biodegradação Ambiental , Soluções Tampão , Oxirredução , Nitrato de Prata/químicaRESUMO
Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient.