Thèse de doctorat : Chimie : Evry-Val d'Essonne : 2008. / Titre provenant de l'écran-titre.

Modification of proteins by lipid structure is relatively common post-translational modification that affects the properties of proteins directly and has a forthright effect on the binding of modified proteins to cell membranes. Some lipoproteins play key role in various pathological processes. Before the proteomic analysis of these proteins, the sample of interest is digested using a protease. The resulting hydrolysate contains both unmodified peptides and peptides bearing a lipid modification. During the subsequent chromatographic separation, the lipopeptides differ significantly from the unmodified peptides. For this reason, the analysis of lipopeptides, lipoproteins respectively, is problematic in terms of separation and detection. The subject of the study of this diploma thesis was the optimization of the method of lipoprotein analysis using liquid chromatography and mass spectrometry. The procedures were tested on lipoprotein Cya A (bifunctional adenylate-cyclase toxin from Bordetella pertussis) and MMTV (matrix protein of mouse mammary tumour virus). First, various sample preparation procedures involving proteolytic cleavage were tested. When enzymatic digestion using trypsin on filter (eFASP) was used, the lipid modification was detected with high degree of reliability. In the next step,...

Les enzymes sont des protéines aux propriétés catalytiques exceptionnelles mais leur disponibilité et stabilité parfois limitées incitent à développer par ailleurs des systèmes catalytiques plus simples, moins coûteux et plus modulables. Une approche biomimétique consiste ainsi à concevoir des systèmes organocatalytiques en se basant sur la structure des enzymes et sur leur mode d'action. Le chapitre I est une mise au point bibliographique sur la conception de catalyseurs bio-inspirés essentiellement basée sur la création de cavités hydrophobes et sur l'introduction d'acides aminés dans les structures. Le chapitre II présente ensuite la synthèse de lipopeptides amphiphiles comme catalyseurs biomimétiques ainsi que leurs propriétés d'auto-assemblage. Ces molécules sont constituées d'une part d'une chaîne lipophile et d'autre part d'une séquence tripeptidique contenant généralement les motifs glycine et histidine. Ils sont obtenus par réaction de Schotten-Baumann et par couplage peptidique en solution. Le caractère amphiphile des lipopeptides induit leur auto-assemblage en milieu aqueux. Ceci a été mis en évidence dans un second temps par tensiométrie et fluorimétrie tandis que des mesures de diffusion des rayonnements (lumière, neutrons) et des observations par microscopie électronique ont pu apporter des informations sur la taille et la géométrie des agrégats formés. Les lipopeptides forment des objets globulaires dans le cas des chaînes hydrophobes les plus courtes tandis qu'on observe des réseaux de fibres pour les composés plus hydrophobes. Dans une troisième partie, l'activité catalytique des lipopeptides a été évaluée vis-à-vis de l'hydrolyse d'un ester modèle. Ainsi, l'hydrolyse du p-nitrophénylacétate en milieu aqueux a été suivie par spectrophotométrie UV-visible. La variation des structures utilisées en catalyse (séquence peptidique, longueur de chaîne) a notamment permis de mettre en évidence le rôle positif de l'histidine sur la catalyse. L'influence de l'auto-organisation a également été étudiée et une différence de comportements entre monomères et agrégats a été observée : les lipopeptides sont de meilleurs catalyseurs en tant que monomères que sous forme d'agrégats. Cela montre qu'un ajustement adéquat des propriétés hydrophobes des lipopeptides mène à une activité catalytique contrôlée vis-à-vis de l'hydrolyse d'esters. Les propriétés hydrolytiques des lipopeptides ont ensuite été étendues au clivage d'un ADN. Le chapitre IV présente ainsi l'étude de l'activité catalytique de ces différents lipopeptides vis-à-vis du clivage d'un ADN plasmidique. Dans un premier temps, des sondes de fluorescence spécifiques (bromure d'éthidium, Hoechst 33342 et pyrène) ont été utilisées pour étudier les interactions entre les lipopeptides et l'ADN et pour suivre respectivement les phénomènes d'intercalation, de liaison dans le petit sillon ou d'auto-organisation des lipopeptides. Une association entre ADN et lipopeptides a ainsi pu être observée et l'intervention de l'histidine et de la chaîne hydrophobe dans ces processus d'interaction a notamment été mise en évidence. Enfin, l'hydrolyse de l'ADN en présence des lipopeptides a été révélée par électrophorèse sur gel d'agarose puis quantifiée par photodensitométrie. Les lipopeptides à base d'histidine ont révélé une activité hydrolytique significative vis-à-vis du plasmide et le rôle positif de l'hydrophobie des composés a également été constaté. / Enzymes are proteins with remarkable catalytic properties but their stability and availability may sometimes become a limitation to their use. This is why simpler, cheaper and more tunable catalytic systems are developed in the meantime. Therefore, a biomimetic approach consists in designing organocatalysts based on enzymes' structure and mechanism. Chapter I is a bibliographic review about the design of bio-inspired organocatalysts, essentially based on the incorporation of hydrophobic cavities and the introduction of amino acids into their structures. Then, chapter II presents the synthesis of amphiphilic lipopeptides as biomimetic catalysts and their self-assembly properties. These compounds contain a lipophilic tail and a tripeptidic sequence generally consisting of glycine and histidine moieties. They are obtained thanks to Schotten-Baumann reaction and solution-phase peptide synthesis. The amphiphilic properties of the lipopeptides induce their self-assembly in aqueous media. This was evidenced afterwards by tensiometry and fluorimetry, while scattering technics (light, neutrons) and electronic microscopy observations gave information about the size and geometry of the obtained aggregates. Lipopeptides can form globular objects in the case of the shortest hydrophobic tails while fibrillar networks were observed for more hydrophobic compounds. In a third part, the catalytic activity of the lipopeptides was studied regarding the hydrolysis of a model ester. In this way, the hydrolysis of p-nitrophenyl acetate in aqueous media was monitored by UV-vis at 406 nm. Variation of the structures (peptidic sequence, hydrophobic length) evidenced the positive contribution of histidine regarding catalysis. The influence of the self-organization was also studied and different behaviors were observed depending on monomer or aggregated state: lipopeptides seemed to be better catalysts as monomer than aggregates. It showed that an adapted tuning of the hydrophobic properties of the lipopeptides leads to a controlled catalytic activity. Hydrolytic properties of the lipopeptides were further extended to DNA cleavage. Chapter IV presents the study of the catalytic activity of these different lipopeptides regarding DNA cleavage. First, specific fluorescent probes (ethidium bromide, Hoechst 33342 and pyrene) were used to study the interactions between the lipopeptides and DNA and to follow respectively intercalation, minor groove binding and self-assembly of the lipopeptides. Association between DNA and lipopeptides was evidenced as well as the role played by histidine and the hydrophobic part during the interaction process. Then, the hydrolysis of DNA in the presence of lipopeptides was revealed by gel electrophoresis and quantified using photodensitometry. Histidine-based lipopeptides showed a significant hydrolytic activity regarding plasmid DNA while a positive contribution of hydrophobicity was also evidenced.

The complexity of cell membranes is far from being only a simple assembly of lipids and proteins separating cells from the surrounding environment. Each of the thousands of different membrane components performs its specific role in cellular functions, since a multitude of biological processes is mediated by membranes. The understanding of the molecular basis of these processes is one of the important aims of current biological research. Our research employing single- molecule fluorescence methods (e.g. FCS, FCCS, FLIM-FRET) has made a contribution to the knowledge of membrane lateral organization or mechanism of membrane fusion. Furthermore, we revealed the mechanism of membrane activity of a small natural compound. As native cell membranes are very complex structures, we performed the experiments on simplified model lipid membranes that allow studying lipid-lipid or lipid-protein interactions at the molecular level in a controlled way. The first part of this thesis deals with the mode of action of a membrane active secondary metabolite didehydroroflamycoin (DDHR). We demonstrated that DDHR is a pore-forming agent and that this activity is influenced by the presence of cholesterol. Direct visualization of intrinsic fluorescence of DDHR revealed its preferential partitioning into membrane areas...

The complexity of cell membranes is far from being only a simple assembly of lipids and proteins separating cells from the surrounding environment. Each of the thousands of different membrane components performs its specific role in cellular functions, since a multitude of biological processes is mediated by membranes. The understanding of the molecular basis of these processes is one of the important aims of current biological research. Our research employing single- molecule fluorescence methods (e.g. FCS, FCCS, FLIM-FRET) has made a contribution to the knowledge of membrane lateral organization or mechanism of membrane fusion. Furthermore, we revealed the mechanism of membrane activity of a small natural compound. As native cell membranes are very complex structures, we performed the experiments on simplified model lipid membranes that allow studying lipid-lipid or lipid-protein interactions at the molecular level in a controlled way. The first part of this thesis deals with the mode of action of a membrane active secondary metabolite didehydroroflamycoin (DDHR). We demonstrated that DDHR is a pore-forming agent and that this activity is influenced by the presence of cholesterol. Direct visualization of intrinsic fluorescence of DDHR revealed its preferential partitioning into membrane areas...

Reproduction de : Thèse doctorat : Pharmacie. Biologie cellulaire et moléculaire : Reims : 2007. / Titre provenant de l'écran-titre. Bibliographie f.108-124.

Cationic antimicrobial peptides (CAMPs) are produced by plants, animals and bacteria to protect their host against antagonistic microbes. The antitheses of selective antibiotics, these peptides are drawn by electrostatic and hydrophobic interactions to targets as diverse as the bacterial membrane, nucleic acids and serum proteins. This lack of specificity is their greatest strength, as mutations to single genes rarely lead to bacterial resistance. Resistance may be conferred by large scale alterations in cell envelope composition, which generally reduces bacterial fitness in the absence of peptide. Clinical applications of natural CAMPs are limited, as the peptides are toxic to mammalian cells and rapidly inactivated in vivo by serum albumin and proteases. Faced with these challenges we have prepared a number of CAMP analogues, with the goal of creating lead compounds for further development of antibacterial therapeutics. Much of our work has focused on ultrashort lipopeptides and lipopeptoids, which have properties similar to natural CAMPs and extremely abbreviated sequences. The simple structure of these scaffolds allows rapid creation of CAMP analogues in a brief period of time, allowing us to rapidly explore the structural requirements for CAMP activity. The balance of this work focuses on imparting CAMP-like behaviour to known antibiotics, in order to expand their spectrum of susceptible bacteria and combat the development of drug-resistant bacteria. In particular, the aminoglycosides neomycin and tobramycin have been fused to phenolic disinfectants such as triclosan and biclotymol, in order to improve their diffusion across the bacterial envelope and activity against Gram-negative bacteria.

Cationic antimicrobial peptides (CAMPs) are produced by plants, animals and bacteria to protect their host against antagonistic microbes. The antitheses of selective antibiotics, these peptides are drawn by electrostatic and hydrophobic interactions to targets as diverse as the bacterial membrane, nucleic acids and serum proteins. This lack of specificity is their greatest strength, as mutations to single genes rarely lead to bacterial resistance. Resistance may be conferred by large scale alterations in cell envelope composition, which generally reduces bacterial fitness in the absence of peptide. Clinical applications of natural CAMPs are limited, as the peptides are toxic to mammalian cells and rapidly inactivated in vivo by serum albumin and proteases. Faced with these challenges we have prepared a number of CAMP analogues, with the goal of creating lead compounds for further development of antibacterial therapeutics. Much of our work has focused on ultrashort lipopeptides and lipopeptoids, which have properties similar to natural CAMPs and extremely abbreviated sequences. The simple structure of these scaffolds allows rapid creation of CAMP analogues in a brief period of time, allowing us to rapidly explore the structural requirements for CAMP activity. The balance of this work focuses on imparting CAMP-like behaviour to known antibiotics, in order to expand their spectrum of susceptible bacteria and combat the development of drug-resistant bacteria. In particular, the aminoglycosides neomycin and tobramycin have been fused to phenolic disinfectants such as triclosan and biclotymol, in order to improve their diffusion across the bacterial envelope and activity against Gram-negative bacteria.

Dans le lagon de Moorea, en Polynésie Française, nous avons identifié un écosystème constitué de deux producteurs primaires (les cyanobactéries filamenteuses Lyngbya majuscula et Anabaena cf. torulosa), trois mollusques herbivores (Stylocheilus striatus, S. longicauda, et Bulla orientalis), un nudibranche carnivore (Gymnodoris ceylonica) et un crabe carnivore (Thalamita coerulipes). L. majuscula et A. cf torulosa prolifèrent sur de vastes zones jusqu’à épiphyter les coraux ; elles sont des producteurs importants de métabolites secondaires, principalement des lipopeptides cycliques, qui peuvent être toxiques ou répulsifs. Cependant, ces composés n’empêchent pas le lièvre de mer S. striatus de consommer les cyanobactéries. S. striatus, décrit comme un prédateur spécialiste de L. majuscula, est connu pour séquestrer et/ou biotransformer les métabolites secondaires de L. majuscula. Cependant nous avons également observé S. striatus, sur A. cf torulosa où il semble moins exposé à la prédation du nudibranch G. ceylonica que quand il est sur L. majuscula. Dans cet écosystème modèle, nous avons combiné le profilage des métabolomes des deux cyanobactéries et des expériences en écologie dans le but d’étudier le rôle des médiateurs chimiques dans la structuration de cet écosystème ; nous avons complété la caractérisation des profils métaboliques des deux cyanobactéries, étudié les transmissions verticale et horizontale des métabolites secondaires produits par les cyanobactéries le long de la chaine trophique, et étudié le rôle de ces composés dans les relations prédateurs-proies. De A. cf torulosa, nous avons isolé cinq analogues acyliques et deux analogues cyliques des laxaphycines que nous avons caractérisés par RMN (1D et 2D RMN : COSY, TOCSY, HSQC, HMBC, NOESY), spectrométrie de masse (spectrométrie de masse à haute résolution et fragmentation en MSn), ainsi que par dégradation chimique avec la méthode de Marfey. La présence de laxaphycines acycliques n’a jamais été décrite auparavant. Nous avons montré que les peptides de L. majuscula sont séquestrés sans biotransformation par les herbivores, alors que les herbivores présents sur A. cf torulosa biotransforment deux laxaphycines en quatre composés nouveaux que nous avons caractérisés. Il ne semble pas que la séquestration et la biotransformation soient opérées dans le but d’améliorer les défenses chimiques des herbivores mais plutôt comme un mécanisme de tolérance. Nous avons également montré que les mollusques herbivores utilisent les composés produits par les cyanobactéries comme signaux chimiques pour détecter à distance les cyanobactéries et pour le choix de leur nourriture. Ces expériences de choix semblent indiquer que S. striatus et B. orientalis sont des herbivores généralistes bien que l’influence des molécules des cyanobactéries suggère un comportement adaptatif permettant au mollusque de retrouver l’hôte sur lequel il a été prélevé. / In the lagoon of Moorea in French Polynesia, we have identified a relatively simple tropical marine ecosystem consisting of two primary producers (two filamentous cyanobacteria, Lyngbya majuscula and Anabaena cf. torulosa), three herbivorous molluscs (Stylocheilus striatus, S. longicauda and Bulla orientalis), a carnivorous nudibranch (Gymnodoris ceylonica) and a carnivorous crab (Thalamita coerulipes). L. majuscula and A. cf torulosa, that bloom ephemerally across wide sandy areas and even on corals, are prolific producers of secondary metabolites, mainly cyclic lipopeptides, which may either be toxic or act as feeding deterrents to potential consumers. However, these compounds do not prevent the sea hare S. striatus, feeding on cyanobacteria. S. striatus, considered as L. majuscula specialist, is known to sequester and transform some secondary metabolites produced by L. majuscula,. However we found also S. striatus feeding on A. cf torulosa and in this case it was less susceptible to predation by the nudibranch G. ceylonicasa than when it fed on L. majuscula. In the study of this model ecosystem, we combine cyanobacterial metabolome profiling and ecological bioassays in order to study the cascading effects of chemical mediators in multi-trophic relationships; we completed the metabolic profile characterization of the two cyanobacteria, we studied vertical and horizontal transmissions of the cyanobacterial secondary metabolites along the trophic web, and studied the role of these compounds in predator-prey relationships. Focusing our attention on A. cf torulosa we isolated seven new lipopeptides, derived from the known laxaphycins, and characterized them using extensive NMR experiments (1D and 2D NMR: COSY, TOCSY, HSQC, HMBC, NOESY), mass spectrometry (HR-MS and fragmentation by MSn) and Marfey’s advanced method. It is the first time that acyclic analogs of laxaphycins have been described. Although the peptides from L. majuscula are found intact in herbivores, some lipopeptides from A. cf torulosa are biotransformed by sea hares into four new compounds we characterized. The sequestration and biotransformation by the herbivores may be considered as a tolerance mechanism rather than a defense mechanism. We demonstrate also that the herbivores use cyanobacterial compounds as chemical cues for cyanobacteria tracking and feeding choice. Our experiments suggest that S. striatus and B. orientalis are generalist consumers, although the influence of cyanobacterial chemical cues on their foraging preferences may suggest an adaptive behavior enabling the mollusc to track their host of origin.

Orientador: Ranulfo Monte Alegre / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-24T00:10:15Z (GMT). No. of bitstreams: 1 Piedrahita-Aguirre_CesarAugusto_D.pdf: 6150918 bytes, checksum: bfd7a30fcb69bbbfa8cbba5856d068f5 (MD5) Previous issue date: 2013 / Resumo: Este trabalho se propôs a estudar a produção da iturina A por Bacillus subtilis em fermentação semi-sólida em biorreatores de leito empacotado. O trabalho foi desenvolvido em quatro partes. Em uma primeira parte foi feito um screening com cepas silvestres e seus mutantes obtidos a partir da exposição de luz UV e acridina laranja. A cepa Bacillus subtilis subsp. subtilis NRRL NRS-1270 foi a que apresentou maior atividade antagônica contra os fungos Aspergillus fumigatus Fresenius NRRL 164, Aspergillus fumigatus Fresenius NRRL 166 e Aspergillus flavus var. oryzae NRRL 484. O extrato metanólico obtido da fermentação semi-sólida do Bacillus subtilis subsp. subtilis NRRL NRS-1270 foi analisado através da espectrometria de massas encontrando-se lipopeptídeos com massa molecular entre m/z 1021,43 e m/z 1087,48, mas sem a presença da iturina A. Em uma segunda etapa a cepa Bacillus Iso 1 foi isolada a partir das raízes de soja, e ante a dificuldade de identificar a iturina A através da cromatografia liquida de alta eficiência (HPLC), foi desenvolvida a metodologia de purificação da iturina A utilizando a cromatografia em coluna de vidro preenchida com sílica gel 60. A iturina A foi eluída com três sistemas de solventes compostos por 20 mL de clorofórmio-metanol-água (65:25:4,v/v/v), fração 1, seguido de 20 mL de clorofórmio-metanol-água (30:50:10, v/v/v), fração 2, e a fração final composta por 10 mL de clorofórmio-metanol-água (20:60:15, v/v/v). As frações obtidas foram analisadas através da HPLC e da espectrometria de massa, identificando 5 isômeros da iturina A (C13-C16). Na terceira etapa, foi feito um delineamento composto central rotacional (DCCR) para avaliar o efeito da casca de arroz como suporte inerte e da vazão volumétrica de ar na produção de iturina A; como substratos foram utilizados o farelo de soja desengordurado e o farelo de trigo. Nenhuma variável do DCCR foi estatisticamente significativa, mas operacionalmente foram importantes, devido à redução da oxigenação do Bacillus Iso 1 pela baixa vazão de ar e menor concentração de casca de arroz, favorecendo a produção de iturina; nestas condições obteve-se 6,88 g/kg de substrato seco de iturina A.Esta é a maior quantidade de iturina A produzida em biorreatores de leito empacotado (coluna) com aeração forçada até hoje. Na quarta etapa, a partir dos resultados obtidos no DCCR foram estudados os parâmetros do processo: queda de pressão, consumo de oxigênio e perfis de temperatura, visando entender o comportamento da fermentação a 0,4 L/min e 0,8 L/min. A máxima produção de iturina obtida foi 5,58 g/kg de substrato seco com a vazão de 0,4 L/min. O incremento na queda de pressão é ocasionado não unicamente pelo incremento da vazão volumétrica, mas também pela produção do biopolímero ?-PGA o qual ocupa os espaços livres entre as partículas, dificultando o fluxo normal de ar através do leito, reduzindo o consumo de oxigênio. A baixa oxigenação favoreceu a alta produção da iturina A e gerou baixo calor metabólico (5,75 W/kg-dry substrato·min). Os resultados obtidos podem ser úteis na elaboração de estratégias para ampliação de escala do processo em fermentadores aerados de leito empacotado / Abstract: This work covers a study of the production of iturin A by Bacillus by solid-state fermentation in packed bed bioreactors. The study was conducted in four parts. At first a screening was conducted with wild strains and their mutants obtained from exposure to UV light and mutagenic agent acridine orange. The strain Bacillus subtilis subsp subtilis NRRL NRS 1270 showed the highest antagonistic activity against Aspergillus fumigatus NRRL 164, Aspergillus fumigatus NRRL 166 and Aspergillus flavus var . oryzae NRRL 484. A methanolic extract obtained by solid state fermentation of Bacillus subtilis subsp subtilis NRRL NRS 1270 was analyzed with mass spectrometry showing lipopeptides with molecular mass between m/z 1021.43 and m/z 1087.48, but without the presence of iturin A. In the second stage, the strain Bacillus Iso 1 was isolated from soybean roots. Given the difficulty of identifying iturin A by high performance liquid chromatography (HPLC), a iturin A purification methodology was developed using glass column chromatography packed with activated Silica gel 60 and alumina. This methodology involved three solvent systems for elution of the iturin A from the column. A first fraction consisted of 20 ml of chloroform-methanol-water (65:25:4 , v/v/v) and was followed by 20 ml of chloroform - methanol- water (30:50 : 10, v/v/v), that was then followed by a final fraction consisting of 10 ml of chloroform-methanol-water (20:60:15, v/v/v). The fractions obtained of fermentation were analyzed by both HPLC and mass spectrometry, identifying five iturin A isomers (C13-C16). In the third stage of the study, an experimental design was constructed in the form of a central composite rotational design (CCRD) to evaluate the effect of rice husk as an inert support and air flow rates to the iturin A production, using defatted soybean meal and wheat bran as substrate. Although none of the studied variables showed statistical significance, the operational importance of reduction of oxygenation of the Bacillus Iso 1 fermentation due to the low concentration of rice husk and air flow rate was observed to favor the production of iturin; in these conditions high productivity was obtained reaching 6.88 g/kg-dry substrate of iturin A. Concluding from available literature, this is the highest concentration of iturin A ever produced in packed bed bioreactor (column) with forced aeration to date. In the fourth stage, in order to understand the behavior of the fermentation under aeration conditions between 0.4 L/min and 0.8 L/min, the following process parameters were studied, based on the results obtained from the CCRD: pressure drop, oxygen consumption and temperature profiles. The maximum production of iturin obtained was 5.58 g/kg-dry substrate with the air flow rate at 0.4 L/. The increase of the pressure gradients is caused not only by increasing the volumetric air flow rate but also by the production of biopolymer ?-PGA by Bacillus iso 1, which occupies the free interparticle space, hindering or preventing the normal flow of air through the bed and thus leading to reduced oxygen consumption. The low oxygenation favored the high iturin A production and resulted in low metabolic heat generation (5.75 W/kg-dry substrate.min). The results of this work are expected to be conducive for designing strategies to scale up the process in aerated packed bed bioreactors / Doutorado / Engenharia de Alimentos / Doutor em Engenharia de Alimentos