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Gram-negative bacteria use N-acyl homoserine lactones (AHLs) to sense population density and regulate gene expression, including virulent phenotypes. The quorum-quenching AHL lactonase from Bacillus thuringiensis cleaves the lactone ring of AHLs, disabling this mode of gene regulation. Despite the potential applications of this enzyme as an antibacterial weapon, little was known about it's lactone ring-opening mechanism. As a member of the metallo-beta-lactamase superfamily, AHL lactonase requires two divalent metal ions for catalysis. NMR experiments confirm that these metal ions are also involved in proper enzyme folding. The chemical mechanism of ring opening was explored using isotope incorporation studies, and hydrolysis was determined to proceed via a nucleophilic attack by a solvent-derived hydroxide at the carbonyl of the lactone ring. A transient, kinetically significant metal-leaving group interaction was detected in steady-state kinetic assays with AHL lactonase containing alternative divalent metal ions hydrolyzing a sulfur-containing substrate. High-resolution crystal structures implicated two residues in substrate binding and hydrolysis, Tyr194 and Asp108. Site-directed mutagenesis of these residues followed by steady-state kinetic studies with wild-type and mutant enzymes hydrolyzing a spectrum of AHL substrates revealed that mutations Y194F and D108N significantly affect catalysis. Combining these results allows the proposal of a detailed hydrolytic mechanism. The binding site for the N-acyl hydrophobic moiety was probed using steady-state kinetics with a variety of naturally occurring and non-natural AHL substrates, and these studies indicate that AHL lactonase will accept a broad range of homoserine lactone containing substrates. Crystal structures with AHL substrates and non-hydrolyzable analogs reveal two distinct binding sites for this N-acyl group. Based on the ability of this enzyme to accommodate a variety of substrates, AHL lactonase was shown to have the ability to quench quorum sensing regulated by a newly discovered class of homoserine lactone signal molecules possessing an N-aryl group using a bioassay. Steady-state kinetic studies confirm that this class of signal molecules are indeed substrates for AHL lactonase. / text

Chez les Vibrio spp., le QS est impliqué dans de nombreuses fonctions comme la colonisation de niche écologiques, les stratégies de survie ou encore la virulence. Cependant, pour la majorité des espèces de Vibrio, la diversité des AHLs produites reste largement sous-estimée et l'étude du QS est encore limitée à quelques espèces modèles ou pathogènes. Toutefois, dans les environnements aquatiques, ces espèces sont minoritaires et les espèces les plus abondantes ne sont que très peu étudiées. Nos résultats ont révélé une importante diversité d'AHLs mais aussi, de façon surprenante, une hétérogénéité dans les phénotypes de production d'AHL au sein d'une même espèce de Vibrio. Pour la première fois, nous avons mis en évidence qu'une même souche de Vibrio pouvait présenter des phénotypes de production d'AHLs différent au cours du temps et une approche statistique a révélé l'implication de certains déterminants biotiques et abiotiques dans ces variations temporelles. Par ailleurs, une approche à micro-échelle a révélé une structuration des populations de Vibrio en unités fonctionnelles constituées de souches phylogénétiquement proches qui partagent des niches écologiques spécifiques et des comportements sociaux. Nos résultats ont mis en évidence que les modalités de communication pouvaient être hétérogènes suggérant l'absence d'un langage commun au sein de ces unités fonctionnelles. En conclusion, ce travail de thèse a permis d'apporter de nouvelles connaissances sur le QS chez les Vibrio dans l'environnement marin, de la souche à la population, et propose une vision intégrée des mécanismes de régulation de la production d'AHLs dans l'environnement. / Quorum sensing is an important mechanism among Vibrio species and is involved in many vital functions such as niche colonization, survival strategies or virulence. However, AHL diversity still largely underestimated for the majority of Vibrio species and the current knowledge on AHL-mediated QS is limited to a few pathogenic or bioluminescent species. Nonetheless, these species are weakly abundant in seawater while dominant species in the environment are poorly studied. Our results revealed a unexpected diversity of AHL molecules but also a quite surprising intra-species diversity of AHL production phenotypes. For the first time, we showed that different isolates of a single genotype switched between different AHL production phenotypes among time and we revealed the potential involvement of abiotic and biotic parameters in these variations. However, it appears that when studied at a microscale, Vibrio populations are showing a functional structuration in ecological units consisting of phylogenetically close strains sharing habitat and social traits. In this context, it was necessary to determine if these different AHL production phenotypes were associated to different micro-habitats in the water column. We did not demonstrate that a common language was spoken within ecological populations. This thesis work provide new insights on AHL-mediated QS among a broader range of species and among Vibrio populations and depicts the potential impact of multiple aspects of marine environments on AHL production.

Les bactéries sont capables de communiquer entre elles afin de coordonner l’expression de certains gènes en fonction de leur densité de population. Ce système de communication utilise de petites molécules appelées autoinducteurs (AIs) comme messagers chimiques et est connu sous le nom de Quorum Sensing (QS). Chez les bactéries pathogènes, les gènes régulés sont, en particulier, ceux codant pour la production des facteurs de virulence et la structuration des biofilms. Ainsi des inhibiteurs du QS chez ces bactéries pourraient être de nouveaux agents anti-bactériens alternatifs aux antibiotiques actuels. Chez les bactéries à Gram-négatif, les AIs sont très majoritairement des acyl-homosérine lactones (AHLs). Utilisant deux approches, la conception rationnelle et le criblage virtuel, nous avons découvert cinq nouvelles familles d’antagonistes des AHLs, ainsi qu’un certain nombre d’agonistes. Nous avons également préparé des analogues d’antagonistes naturels de la famille des bromo-furanones, afin d’établir une étude structure-activité de ce type de composés. / The bacteria are able to communicate with each other for coordinating gene expression depending on their population density. This communication system use small molecules called autoinducers (AIs) as chemical messengers and is referred to as quorum sensing (QS). In pathogenic bacteria, the regulated genes are, in particular, those coding for the production of virulence factors and biofilms formation. Thus, inhibitors of bacterial QS could be used as new anti-bacterial agents providing an alternative to current antibiotics. In Gram-negative bacteria, the main AIs are acyl-homoserine lactones (AHLs). Using two approaches, rational design and virtual screening, we have discovered five new families of AHLs antagonists, and some agonists. We have also prepared analogues of natural bromo-furanones antagonists, in order to establish a structure-activity study of this type of compounds.

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-13T13:06:45Z (GMT). No. of bitstreams: 1 Pomini_ArmandoMateus_D.pdf: 4501241 bytes, checksum: 249f7514962993874b22ddcad9831cc8 (MD5) Previous issue date: 2009 / As bactérias Gram-positivas e Gram-negativas possuem um mecanismo de comunicação química intra-específico conhecido como ¿quorum-sensing¿, regulando a expressão de uma vasta gama de atividades biológicas. As bactérias Gram-negativas utilizam acil-homosserina lactonas (acil-HSLs) como principais substâncias sinalizadoras. Na presente tese, relatamos a determinação da configuração absoluta do raro metabólito (S)-(-)-N-heptanoil-HSL produzida pela bactéria fitopatogênica Pantoea ananatis. A configuração absoluta desta substância foi determinada através da técnica de cromatografia gasosa com detecção por ionização em chama com coluna quiral, através de comparações de tempo de retenção e co-injeção com padrões sintetizados. Avaliou-se também a importância da configuração absoluta para a atividade antimicrobiana de acil-HSLs contra bactérias Gram-positivas (Bacillus subtilis, Bacillus cereus e Staphylococcus aureus). Curiosamente, o enantiômero não natural (R)-N-3-oxo-octanoil-HSL foi tão ativo quanto o produto natural (S). Estudou-se também as interações da (S)-N-3-oxo-octanoil-HSL com células de Agrobacterium tumefaciens NTL4(pZLR4) através da técnica de ressonância magnética nuclear de hidrogênio por diferença de transferência de saturação (STD-RMN), revelando que o primeiro evento de interação da substância com a célula ocorre com a região lipídica da membrana celular externa. Finalmente, realizou-se o estudo químico das substâncias sinalizadoras produzidas pela bactéria Methylobacterium mesophilicum, que ocorre simbioticamente com a bactéria Xylella fastidiosa nos vasos condutores de laranjeiras atacadas pela clorose variegada dos citros. Entre os vários resultados inéditos, reportamos a caracterização e síntese do produto natural inédito (S)-N-(2E)-dodecenoil-HSL e a primeira síntese do metabólito (S)-N-(2E, 7Z)-tetradecadienil-HSL. Outrossim, reportamos a primeira caracterização da configuração absoluta de cinco acil-HSLs naturais de cadeia longa. Realizou-se também estudos relacionados aos efeitos das acil-HSLs sintéticas contra bactérias Gram-positivas endofíticas da laranjeira. Adicionalmente, caracterizou-se a secreção de defesa do opilião Hoplobunus mexicanus. O repertório de defesa deste animal é composto por dois componentes voláteis de alta irritabilidade (2,5-dimetil-fenol e 2-metil-5-etil-fenol), além da tanatose e emissão de sons, uma característica inédita em opiliões / Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. In general, Gram-negative bacteria use acylated homoserine lactones (acyl-HSLs) as autoinducers, and Gram-positive bacteria use processed oligo-peptides. In the present work, we relate the absolute configuration determination of the rare metabolite (S)-(-)-N-heptanoyl-HSL produced by the phytopathogen Pantoea ananatis. The absolute configuration was determined by gas chromatography coupled to flame ionization detection with chiral column, through retention time comparison and co-injections with synthetic products. The importance of the absolute configuration for the antimicrobial activity of acyl-HSL against Gram-positive bacteria (Bacillus subtilis, Bacillus cereus and Staphylococcus aureus) was assessed. Curiously, non-natural (R)-N-3-oxo-octanoyl-HSL was as active as the natural product with (S) absolute configuration. The interaction of (S)-N-3-oxo-octanoil-HSL with Agrobacterium tumefaciens NTL4(pZLR4) cells was further studied using hydrogen nuclear magnetic resonance experiments with saturation transfer difference (STD-NMR) revealing that the first binding event is the diffusion through the lipidic part of the outer membrane. Finally, we have investigated the chemical study of the signaling substances produced by Methylobacterium mesophilicum, which co-occurs with Xylella fastidiosa in orange trees affected by the citrus variegated chlorosis disease. Among several results, we report herein the characterization and synthesis of a new natural product [(S)-N-(2E)-dodecenoyl-HSL], the first synthetic procedure for the rare (S)-N-(2E,7Z)-tetradecadienyl-HSL and the occurrence of a rare long, odd chain representative (N-tridecanoyl-HSL) in trace amounts. We report the first absolute configuration determination for five natural acyl-HSLs. We have also studied the effects of synthetic acyl-HSLs on Gram positive bacteria isolated from orange tissues. Additionally, the defensive secretion produced by the harvestman Hoplobunus mexicanus was characterized. The defensive repertory of this arachnid includes two irritating and volatile components (2,5-dimethyl-phenol and 2-methyl-5-ethyl-phenol), besides thanatosis and sound emission, a new behavioral artifice in opilionids / Doutorado / Quimica Organica / Doutor em Ciências

Codakia orbicularis est un mollusque bivalve appartenant à la famille des Lucinidae et établissant des symbioses avec des bactéries sulfo-oxydantes (symbiotes) au sein de ses branchies. Dans l’hypothèse où toute symbiose nécessite une régulation par des molécules de dialogue, une étude chimique exhaustive pourrait aboutir à la mise en évidence des métabolites impliqués. Le travail de ce manuscrit porte donc sur l'isolement de métabolites secondaires à partir des branchies de ce bivalve et sur l'évaluation de l'activité antibactérienne des molécules isolées. Douze composés ont été isolés des branchies de Codakia orbicularis et leurs structures ont été déterminées par les méthodes spectroscopiques usuelles. Parmi ces molécules, une seule est nouvelle et a été nommée orbicularisine. Elle présente un squelette indolone spirotetracyclique inédit. Parmi les molécules isolées, seules quatre d’entre elles présentent une activité antibactérienne à savoir le soufre S8, la 4-hydroxybenzaldéhyde et deux monoglycérolipides. L'orbicularisine s'est révélée inactive contre un panel de lignées cellulaires cancéreuses et de kinases. Le nouveau squelette de l’orbicularisine pourrait permettre d'aboutir à une nouvelle famille de molécules par synthèse organique et ainsi accroître la diversité moléculaire autour de ce motif inédit. Il sera également intéressant de déterminer l'origine des molécules isolées et de connaître leur(s) implication(s) dans la régulation des symbiotes du bivalve. Les résultats chimiques obtenus sur C. orbicularis et sur les Lucinidae en général sont intéressants puisque les espèces côtières appartenant aux bivalves ont été peu exploitées en chimie jusqu’à ce jour. / Codakia orbicularis is a bivalve mollusc belonging to the family Lucinidae and establishing symbiosis with sulfooxidizing bacteria (symbionts) within its gills. In the hypothesis that any symbiosis requires a regulation by molecules of dialogue, an exhaustive chemical study could lead to the demonstration of the metabolites involved. The work of this manuscript focuses on the isolation of secondary metabolites from the gills of this bivalve and on the evaluation of the antibacterial activity of the isolated molecules. Twelve compounds were isolated from the gills of Codakia orbicularis and their structures were determined by the usual spectroscopic methods. Of these molecules, only one is new and has been named orbicularisin. It presents an indolone spirotetracyclic skeleton unpublished. Among the isolated molecules, only four of them have antibacterial activity, namely sulfur S8, 4-hydroxybenzaldehyde and two monoglycerolipids. Orbicularisin has been shown to be inactive against a panel of cancer cell lines and kinases. The new skeleton of orbicularisin could lead to a new family of molecules by organic synthesis and thus increase the molecular diversity around this original motif. It will also be interesting to determine the origin of the isolated molecules and know their involvement (s) in the regulation of the bivalve symbionts. The chemical results obtained on C. orbicularis and on Lucinidae in general are interesting because the coastal species belonging to bivalves have been little exploited in chemistry to date.

The black band disease (BBD) microbial consortium often causes mortality of reef-building corals. Microbial chemical interactions (i.e., quorum sensing (QS) and antimicrobial production) may be involved in the BBD disease process. Culture filtrates (CFs) from over 150 bacterial isolates from BBD and the surface mucopolysaccharide layer (SML) of healthy and diseased corals were screened for acyl homoserine lactone (AHL) and Autoinducer-2 (AI-2) QS signals using bacterial reporter strains. AHLs were detected in all BBD mat samples and nine CFs. More than half of the CFs (~55%) tested positive for AI-2. Approximately 27% of growth challenges conducted among 19 isolates showed significant growth inhibition. These findings demonstrate that QS is actively occurring within the BBD microbial mat and that culturable bacteria from BBD and the coral SML are able to produce QS signals and antimicrobial compounds. This is the first study to identify AHL production in association with active coral disease.

The tumor microenvironment is a well-recognized contributor to cancer progression in solid tumors. Cancer cell interactions with abnormal extracellular matrix, tumor associated immune and stromal cells, and aberrant fluid flow all contribute to cancer progression. Breast tumors are often characterized by a dense collagenous stroma and a hypoxic core. A recently identified and little understood component of the breast tumor microenvironment is the breast microbiome. The work described here elaborates on the importance of the tumor microenvironment in cancer progression and demonstrates the importance of studying cancer-microbiome interactions in the context of tumor microenvironmental stimuli. / Master of Science

Yes / Bacteria sense their own population size, tune the expression of responding genes, and behave accordingly to environmental stimuli by secreting signaling molecules. This phenomenon is termed as quorum sensing (QS). By exogenously manipulating the signal transduction bacterial population behaviors could be controlled, which may be done through quorum quenching (QQ). QS related regulatory networks have been proven their involvement in regulating many virulence determinants in pathogenic bacteria in the course of infections. Interfering with QS signaling system could be a novel strategy against bacterial infections and therefore requires more understanding of their fundamental mechanisms. Here we review the development of studies specifically on the inhibition of production of N-acyl-homoserine lactone (AHL), a common proteobacterial QS signal. The opportunistic pathogen, Pseudomonas aeruginosa, equips the alkylquinolone (AQ)-mediated QS which also plays crucial roles in its pathogenicity. The studies in QQ targeting on AQ are also discussed. / University of Malaya High Impact Research Grants (UMC/625/1/HIR/MOHE/CHAN/01, A-000001-50001,and UMC/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027)