RESUMO
New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic drug discovery is to turn potent biochemical inhibitors of essential bacterial components into effective antimicrobials. This difficulty is underpinned by a lack of methods to investigate the physicochemical properties needed for candidate antibiotics to permeate the bacterial cell envelope and avoid clearance by the action of bacterial efflux pumps. To address these issues, here we used a target engagement assay to measure the equilibrium and kinetic binding parameters of antibiotics targeting dihydrofolate reductase (DHFR) in live bacteria. We also used this assay to identify novel DHFR ligands having antimicrobial activity. We validated this approach using the Gram-negative bacteria Escherichia coli and the emerging human pathogen Mycobacterium abscessus. We expect the use of target engagement assays in bacteria to expedite the discovery and progression of novel, cell-permeable antibiotics with on-target activity.
Assuntos
Antibacterianos , Anti-Infecciosos , Antibacterianos/química , Anti-Infecciosos/farmacologia , Escherichia coli/metabolismo , Bactérias Gram-Negativas , Humanos , Tetra-Hidrofolato Desidrogenase/químicaRESUMO
The Firmicutes bacteria participate extensively in virulence and pathological processes. Enterococcus faecalis is a commensal microorganism; however, it is also a pathogenic bacterium mainly associated with nosocomial infections in immunocompromised patients. Iron-sulfur [Fe-S] clusters are inorganic prosthetic groups involved in diverse biological processes, whose in vivo formation requires several specific protein machineries. Escherichia coli is one of the most frequently studied microorganisms regarding [Fe-S] cluster biogenesis and encodes the iron-sulfur cluster and sulfur assimilation systems. In Firmicutes species, a unique operon composed of the sufCDSUB genes is responsible for [Fe-S] cluster biogenesis. The aim of this study was to investigate the potential of the E. faecalis sufCDSUB system in the [Fe-S] cluster assembly using oxidative stress and iron depletion as adverse growth conditions. Quantitative real-time polymerase chain reaction demonstrated, for the first time, that Gram-positive bacteria possess an OxyR component responsive to oxidative stress conditions, as fully described for E. coli models. Likewise, strong expression of the sufCDSUB genes was observed in low concentrations of hydrogen peroxide, indicating that the lowest concentration of oxygen free radicals inside cells, known to be highly damaging to [Fe-S] clusters, is sufficient to trigger the transcriptional machinery for prompt replacement of [Fe-S] clusters.
Assuntos
Enterococcus faecalis/metabolismo , Proteínas Ferro-Enxofre/genética , Estresse Oxidativo , Vias Biossintéticas , Proteínas Ferro-Enxofre/biossíntese , Modelos Moleculares , Reação em Cadeia da Polimerase em Tempo Real , Especificidade por SubstratoRESUMO
The Firmicutes bacteria participate extensively in virulence and pathological processes. Enterococcus faecalis is a commensal microorganism; however, it is also a pathogenic bacterium mainly associated with nosocomial infections in immunocompromised patients. Iron-sulfur [Fe-S] clusters are inorganic prosthetic groups involved in diverse biological processes, whose in vivo formation requires several specific protein machineries. Escherichia coli is one of the most frequently studied microorganisms regarding [Fe-S] cluster biogenesis and encodes the iron-sulfur cluster and sulfur assimilation systems. In Firmicutes species, a unique operon composed of the sufCDSUB genes is responsible for [Fe-S] cluster biogenesis. The aim of this study was to investigate the potential of the E. faecalis sufCDSUB system in the [Fe-S] cluster assembly using oxidative stress and iron depletion as adverse growth conditions. Quantitative real-time polymerase chain reaction demonstrated, for the first time, that Gram-positive bacteria possess an OxyR component responsive to oxidative stress conditions, as fully described for E. coli models. Likewise, strong expression of the sufCDSUB genes was observed in low concentrations of hydrogen peroxide, indicating that the lowest concentration of oxygen free radicals inside cells, known to be highly damaging to [Fe-S] clusters, is sufficient to trigger the transcriptional machinery for prompt replacement of [Fe-S] clusters.
Assuntos
Enterococcus faecalis/metabolismo , Proteínas Ferro-Enxofre/genética , Estresse Oxidativo , Vias Biossintéticas , Proteínas Ferro-Enxofre/biossíntese , Modelos Moleculares , Reação em Cadeia da Polimerase em Tempo Real , Especificidade por SubstratoRESUMO
Iron-sulfur clusters (ISC) ([Fe-S]) are evolutionarily ancient and ubiquitous inorganic prosthetic groups present in almost all living organisms, whose biosynthetic assembly is dependent on complex protein machineries. [Fe-S] clusters are involved in biologically important processes, ranging from electron transfer catalysis to transcriptional regulatory roles. Three different systems involved in [Fe-S] cluster assembly have already been characterized in Proteobacteria, namely, the nitrogen fixation system, the ISC system and the sulfur assimilation system. Although they are well described in various microorganisms, these machineries are poorly characterized in members of the Firmicutes phylum, to which several groups of pathogenic bacteria belong. Recently, several research groups have made efforts to elucidate the biogenesis of [Fe-S] clusters at the molecular level in Firmicutes, and many important characteristics have been described. Considering the pivotal role of [Fe-S] clusters in a number of biological processes, the review presented here focuses on the description of the biosynthetic machineries for [Fe-S] cluster biogenesis in prokaryotes, followed by a discussion on recent results observed for Firmicutes [Fe-S] cluster assembly.
Assuntos
Coenzimas/biossíntese , Bactérias Gram-Positivas/metabolismo , Ferro/metabolismo , Redes e Vias Metabólicas , Enxofre/metabolismo , Proteínas de Bactérias/metabolismo , Enzimas/metabolismoRESUMO
Iron-sulfur [Fe-S] clusters are inorganic prosthetic groups that play essential roles in all living organisms. In vivo [Fe-S] cluster biogenesis requires enzymes involved in iron and sulfur mobilization, assembly of clusters, and delivery to their final acceptor. In these systems, a cysteine desulfurase is responsible for the release of sulfide ions, which are incorporated into a scaffold protein for subsequent [Fe-S] cluster assembly. Although three machineries have been shown to be present in Proteobacteria for [Fe-S] cluster biogenesis (NIF, ISC, and SUF), only the SUF machinery has been found in Firmicutes. We have recently described the structural similarities and differences between Enterococcus faecalis and Escherichia coli SufU proteins, which prompted the proposal that SufU is the scaffold protein of the E. faecalis sufCDSUB system. The present work aims at elucidating the biological roles of E. faecalis SufS and SufU proteins in [Fe-S] cluster assembly. We show that SufS has cysteine desulfurase activity and cysteine-365 plays an essential role in catalysis. SufS requires SufU as activator to [4Fe-4S] cluster assembly, as its ortholog, IscU, in which the conserved cysteine-153 acts as a proximal sulfur acceptor for transpersulfurization reaction.
Assuntos
Liases de Carbono-Enxofre/metabolismo , Cisteína/metabolismo , Enterococcus faecalis/enzimologia , Proteínas Ferro-Enxofre/fisiologia , Enxofre/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Liases de Carbono-Enxofre/química , Liases de Carbono-Enxofre/genética , Liases de Carbono-Enxofre/isolamento & purificação , Clonagem Molecular , Cisteína/química , Enterococcus faecalis/química , Enterococcus faecalis/genética , Enterococcus faecalis/metabolismo , Ativação Enzimática , Proteínas Ferro-Enxofre/química , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/metabolismo , Modelos Moleculares , Ligação Proteica , Especificidade por Substrato , Enxofre/químicaRESUMO
Iron-sulfur [Fe-S] clusters are inorganic prosthetic groups that play essential roles in all living organisms. Iron and sulfur mobilization, formation of [Fe-S] clusters, and delivery to its final protein targets involves a complex set of specific protein machinery. Proteobacteria has three systems of [Fe-S] biogenesis, designated NIF, ISC, and SUF. In contrast, the Firmicutes system is not well characterized and has only one system, formed mostly by SUF homologs. The Firmicutes phylum corresponds to a group of pathological bacteria, of which Enterococcus faecalis is a clinically relevant representative. Recently, the E. faecalis sufCDSUB [Fe-S] cluster biosynthetic machinery has been identified, although there is no further information available about the similarities and/or variations of Proteobacteria and Firmicutes systems. The aim of the present work was to compare the ability of the different Proteobacteria and Firmicutes systems to complement the Azotobacter vinelandii and Escherichia coli ISC and SUF systems. Indeed, E. faecalis sufCDSUB is able to complement the E. coli SUF system, allowing viable mutants of both sufABCDSE and iscRSU-hscBA-fdx systems. The presence of all E. faecalis SUF factors enables proper functional interactions, which would not otherwise occur in proteins from different systems.
Assuntos
Proteínas de Bactérias/genética , Enterococcus faecalis/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Proteínas Ferro-Enxofre/genética , Proteínas de Bactérias/metabolismo , Enterococcus faecalis/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Teste de Complementação Genética , Proteínas Ferro-Enxofre/metabolismoRESUMO
INTRODUCTION: Listeria monocytogenes is a ubiquitous microorganism in nature and is responsible for listeriosis, an infectious disease caused by consumption of contaminated food. METHODS: Molecular characterization was performed on 19 strains of Listeria monocytogenes (serovars 1/2a, 1/2b, 4b and 4c), isolated from dairy products in Rio Grande do Sul, Brazil. The molecular techniques applied were random amplification of polymorphic DNA and restriction enzyme analysis. In addition to the molecular analysis, the antimicrobial resistance profile was determined. RESULTS: The strains studied showed a low degree of diversity. In relation to the antimicrobial resistance profile of those microorganisms from the samples analyzed, all of them were susceptible to the antimicrobials tested. CONCLUSIONS: The molecular techniques that were used presented good discriminatory power for the strains studied. Furthermore, all of the samples that were analyzed were susceptible to the antimicrobials tested.
Assuntos
Laticínios/microbiologia , Microbiologia de Alimentos , Listeria monocytogenes/genética , Antibacterianos/farmacologia , Brasil , Enzimas de Restrição do DNA , Listeria monocytogenes/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Técnica de Amplificação ao Acaso de DNA PolimórficoRESUMO
INTRODUCTION: Listeria monocytogenes is a ubiquitous microorganism in nature and is responsible for listeriosis, an infectious disease caused by consumption of contaminated food. METHODS: Molecular characterization was performed on 19 strains of Listeria monocytogenes (serovars 1/2a, 1/2b, 4b and 4c), isolated from dairy products in Rio Grande do Sul, Brazil. The molecular techniques applied were random amplification of polymorphic DNA and restriction enzyme analysis. In addition to the molecular analysis, the antimicrobial resistance profile was determined. RESULTS: The strains studied showed a low degree of diversity. In relation to the antimicrobial resistance profile of those microorganisms from the samples analyzed, all of them were susceptible to the antimicrobials tested. CONCLUSIONS: The molecular techniques that were used presented good discriminatory power for the strains studied. Furthermore, all of the samples that were analyzed were susceptible to the antimicrobials tested.
INTRODUÇÃO: Listeria monocytogenes é um microrganismo que se encontra disseminado na natureza, sendo responsável por causar listeriose, uma doença infecciosa causada pelo consumo de alimentos contaminados. MÉTODOS: A análise molecular de 19 linhagens de Listeria monocytogenes, sorovares 1/2a, 1/2b, 4b, 4c, isoladas de produtos lácteos do Rio Grande do Sul, Brasil. As técnicas moleculares aplicadas foram: Amplificação Randômica do DNA Polimórfico e Análise por Enzimas de Restrição. Além da análise molecular foi realizado o perfil de resistência antimicrobiana. RESULTADOS: As linhagens estudadas mostraram baixo grau de diversidade, em relação ao perfil de resistência antimicrobiana desses microrganismos das amostras analisadas todas foram susceptíveis aos antimicrobianos testados. CONCLUSÕES: As técnicas moleculares estudadas apresentaram um bom poder de discriminação para as linhagens estudadas. Além disso, todas as amostras analisadas foram susceptíveis aos antimicrobianos analisados.
Assuntos
Laticínios/microbiologia , Microbiologia de Alimentos , Listeria monocytogenes/genética , Antibacterianos/farmacologia , Brasil , Enzimas de Restrição do DNA , Listeria monocytogenes/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Técnica de Amplificação ao Acaso de DNA PolimórficoRESUMO
Fifty-six Enterococcus spp. strains were isolated from foods in Southern Brazil, confirmed by PCR and classified as Enterococcus faecalis (27), Enterococcus faecium (23) and Enterococcus spp(6). Antimicrobial susceptibility tests showed resistance phenotypes to a range of antibiotics widely administrated in humans such as gentamycin, streptomycin, ampicillin and vancomycin.
Cinqüenta e seis cepas de Enterococcus spp. foram isoladas de alimentos no Sul do Brasil, confirmados por PCR e classificadas como Enterococcus faecalis (27), Enterococcus faecium (23) e Enterococcus spp. (6). Testes de susceptibilidade aos antimicrobianos demonstraram fenótipos de resistência a uma gama de antibióticos administrados em humanos, como gentamicina, estreptomicina, ampicilina e vancomicina.
Assuntos
Humanos , Resistência Microbiana a Medicamentos , Enterococcus/genética , Enterococcus/isolamento & purificação , Predisposição Genética para Doença , Gentamicinas/análise , Técnicas In Vitro , Fenótipo , Amostras de Alimentos , Métodos , MétodosRESUMO
BACKGROUND: Iron-sulfur clusters are ubiquitous and evolutionarily ancient inorganic prosthetic groups, the biosynthesis of which depends on complex protein machineries. Three distinct assembly systems involved in the maturation of cellular Fe-S proteins have been determined, designated the NIF, ISC and SUF systems. Although well described in several organisms, these machineries are poorly understood in Gram-positive bacteria. Within the Firmicutes phylum, the Enterococcus spp. genus have recently assumed importance in clinical microbiology being considered as emerging pathogens for humans, wherein Enterococcus faecalis represents the major species associated with nosocomial infections. The aim of this study was to carry out a phylogenetic analysis in Enterococcus faecalis V583 and a structural and conformational characterisation of it SufU protein. RESULTS: BLAST searches of the Enterococcus genome revealed a series of genes with sequence similarity to the Escherichia coli SUF machinery of [Fe-S] cluster biosynthesis, namely sufB, sufC, sufD and SufS. In addition, the E. coli IscU ortholog SufU was found to be the scaffold protein of Enterococcus spp., containing all features considered essential for its biological activity, including conserved amino acid residues involved in substrate and/or co-factor binding (Cys50,76,138 and Asp52) and, phylogenetic analyses showed a close relationship with orthologues from other Gram-positive bacteria. Molecular dynamics for structural determinations and molecular modeling using E. faecalis SufU primary sequence protein over the PDB:1su0 crystallographic model from Streptococcus pyogenes were carried out with a subsequent 50 ns molecular dynamic trajectory. This presented a stable model, showing secondary structure modifications near the active site and conserved cysteine residues. Molecular modeling using Haemophilus influenzae IscU primary sequence over the PDB:1su0 crystal followed by a MD trajectory was performed to analyse differences in the C-terminus region of Gram-positive SufU and Gram-negative orthologous proteins, in which several modifications in secondary structure were observed. CONCLUSION: The data describe the identification of the SUF machinery for [Fe-S] cluster biosynthesis present in the Firmicutes genome, showing conserved sufB, sufC, sufD and sufS genes and the presence of the sufU gene coding for scaffold protein, instead of sufA; neither sufE nor sufR are present. Primary sequences and structural analysis of the SufU protein demonstrated its structural-like pattern to the scaffold protein IscU nearby on the ISC machinery. E. faecalis SufU molecular modeling showed high flexibility over the active site regions, and demonstrated the existence of a specific region in Firmicutes denoting the Gram positive region (GPR), suggested as a possible candidate for interaction with other factors and/or regulators.