A estase de secreção salivar e alimentos deglutidos na luz esofágica de pacientes com megaesôfago chagásico traz como consequências: (1) supercrescimento bacteriano na luz do órgão, (2) episódios de aspiração pulmonar e infecções respiratórias de repetição, (3) aumento do risco dos procedimentos terapêuticos cirúrgicos ou endoscópicos em caso de perfuração pela maior possibilidade de contaminação, (4) desenvolvimento de processos inflamatórios crônicos na mucosa esofágica, que podem predispor ao aparecimento de displasia e câncer. Apesar disto, a microbita esofágica no megaesôfago nunca foi estudado. Esse estudo teve o objetivo de analisar qualitativa e quantitativamente a microbiota presente no líquido de estase esofágico de pacientes portadores de megaesôfago chagásico, comparando-a com a existente em indivíduos sadios. Foram estudados prospectivamente 25 pacientes (10 homens e 15 mulheres) com idades variando de 24 a 74 anos ( &#61507; = 49,1a). Quinze pacientes eram portadores de esofagopatia chagásica, sendo 5 portadores de mega grau I (MG1), 5 portadores de mega grau II (MG2) e 5 portadores de mega grau III (MG3), segundo a classificação de Rezende; e 10 indivíduos sadios, agrupados no Grupo Controle (GC). Utilizou-se método de coleta que permitia aspiração de líquido através de sonda de Levine diretamente da luz esofágica, evitando-se a contaminação com microrganismos da orofaringe. Após análise microbiológica qualitativa e quantitativa, foi feita a descrição dos microrganismos encontrados nos vários grupos e sua classificação em aeróbios Gram positivos, aeróbios Gram negativos, anaeróbios e fungos. A análise estatística visou avaliar diferenças quantitativas entre os microrganismos nos diferentes grupos, sendo para tanto utilizado o teste não paramétrico de Kruskal-Wallis, com nível de rejeição menor 0,05 (5%). A positividade das culturas no Grupo Controle foi 40%, com predomínio do gênero Streptococcus sp, em concentrações que variaram de 101 a 102 ufc/ml. No Grupo Megaesôfago 93,3% da culturas foram positivas, com grande variedade de bactérias, mas predomínio de aeróbios Gram positivos (Streptococcus sp. foi o mais comum) e anaeróbios (Veillonella sp foi a mais freqüente) em concentrações que variaram de 101 a 105 ufc/ml. As concentrações foram geralmente mais elevadas em MG3, quando comparado com MG1, MG2 e GC (p<0,05). Concluiu-se que no megoesôfago, diferentemente dos indivíduos sadios, existe a presença de rica microflora bacteriana, constituída principalmente por aeróbios Gram positivos e anaeróbios, em concentrações tanto maiores quanto maior o seu grau de dilatação. Parte desta microbiota tem capacidade de metabolizar nitratos, etapa importante na formação de nitrosaminas. / The stasis of saliva and swallowed food in the esophageal lumen of patients with chagasic megaesophagus causes: (1) bacterial overgrowth in the esophageal lumen, (2) recurring pulmonary aspirations and respiratory infections, (3) increased risk of surgical or endoscopic procedures if perforation occurs by the major possibility of contamination, and (4) the development of chronic inflammatory process in esophageal mucosa, that can predispose to the development of dysplasia and cancer. In spite of this, esophageal microbiota in the megaesophagus has never been studied. The aim of this study was to analyze qualitatively and quantitatively the microbiota in chagasic megaesophagus in comparison to the normal esophagus. Twenty-five patients (10 men and 15 women) were prospectively studied, with ages varying from 24 to 74 years (&#61507;=49,1), from March to September 2000. Fifteen patients with chagasic megaesophagus (MG), were divided into three sub- groups according to the grade of esophageal dilation: MG1 – 5 patients with megaesophagus grade I; MG2- 5 patients with megaesophagus grade II; MG3- 5 patients with megaesophagus grade III. Another group of ten patients without any esophageal disease was constituted in the Control Group (CG). The sample collection was performed using a method specially developed to avoid contamination with microorganisms of the oral cavity and oropharynx. After qualitative and quantitative analysis, the microorganisms found were described and classified as Gram positive aerobes, Gram negative aerobes, anaerobes and fungus. Statistical analysis using Kruskal-Wallis non-parametric test was performed in order to find quantitative differences of microorganisms in the different groups. In CG 40% of the cultures were positive with predominance of the genus Streptococcus sp, in concentrations that varied from 101 to 102 cfu/ml. In MG, 93,3% of the cultures were positive, with great bacterial variability and predominance of a variety of aerobic Gram-positive (Streptococcus sp was the most common) and anaerobic bacteria (Veillonella sp was the most frequent), in concentrations that varied from 101 to 105 cfu/ml. The bacterial concentrations were generally more elevated in MG3 in comparison to MG1, MG2 and CG (p<0,05). It was concluded that patients with megaesophagus present a varied microbiota constituted mostly of aerobic Gram positive and anaerobic bacteria, in concentrations that vary with the megaesophagus dilatation degree. Some of the bacteria found in MG are able to metabolize nitrates intro nitrites, an important step in the formation of nitrosamines.

Although considered as a poison for long time, the importance of selenium as an essential trace element is now well recognized. In proteins, the redox active selenium moiety is incorportated as selenocysteine (Sec), the 21st amino acid. In mammals, selenium exerts its redox activities through several selenocysteine-containing enzymes, which include glutathione peroxidase (GPx), iodothyronine deiodinase (ID) and thioredoxin reductase (TrxR). Although these enzymes have Sec in their active sites, they catalyze completely different reactions and their substrate specificity and cofactor or co-substrate systems are significantly different. The most widely studied selenoenzyme GPx protects various organisms from oxidative stresses by catalyzing the reduction of hydroperoxides by using glutathione (GSH) as cofactor. The chemical aspects of the reduction of hydroperoxide by GPx have been extensively studied with the help of synthetic selenium and tellurium compounds. For example, 2-phenyl, 1, 2-benzoisoselenazol-3(2H)-one, commonly known as ebselen exhibits significant GPx activity by using GSH as cofactor. The anti-inflammatory, antiatherosclerotic and cytoprotective properties of ebselen have led to the design and synthesis of nex GPx mimics for potential therapeutic applications. In the first chapter, the importance of selenium in biochemistry in general and the function of selenoenzyme GPx and its synthetic mimics in particular are discussed. In the second chapter, the importance of ebselen as a GPx mimic and how thiol exchange reaction in the selenenyl sulfide intermediate deactivates its catalytic cycle and the possible ways to overcome thiol exchange reaction are described. The third chapter deals with the first synthetic chemical model that effectively mimics the unusual cyclization of sulfenic acid to a sulfenyl amide in protein Tyrosien Phosphatase 1B(PTP1B). PTP1B is a cysteine containing enzyme where the sulfenic acid (PTP1B-SOH) intermediate produced in response to its oxidation by H2O2 is rapidly converted into a sulfenyl amide species, in which sulfur atom of the catalytic cysteine is covalently bonded to the main chain nitrogen of an adjacent serine residue. This unusual protein modification in PTP1B has been proposed to protect the sulfur centre from irreversible oxidation to sulfinic acid and and sulfonic acids. In the fourth chapter, it is shown that not only the catalytic efficiency of ebselen but also its phosphatase like behavior is important for its antioxidant activity. Ebselen is regenerated from selenenic acid (R-SeOH) under a verity of conditions, which protects its selenium centre from irreversible oxidation and thus reduces its toxicity. The fifth chapter deals with spirodizaselenurane and Spirodiazatellurane. Although the chemistry of spirodioxyselenuranes and spirodiazasulfuranes has been studied extensively due to their interesting structural and stereochemical properties, there is no example of stable spirodiazaselenurane and its tellurium analogues. In the fifth chapter, the synthesis, structure and GPx-like activity of the spirodizzaselenurane and spirodiazatellurane are discussed. In summary, the synthetic sulfenic acids and seleneric acids undergo cyclization to their corresponding sulfenyl amides and selenenyl amides and thus protect their sulfur and selenium centers from irreversible inactivation. We have also observed that selenoxides and telluroxides with nearby amide moieties undergo cyclization to their corresponding cyclic spiro compounds. This unusual transformation of sulfenic acids has been recently discovered in PTP1B. As the redox regulation cycle of PTP1B and the catalytic cycle of GPx are similar we believe that GPx may involve a selenenyl amide intermediate in its catalytic cycle.

A estase de secreção salivar e alimentos deglutidos na luz esofágica de pacientes com megaesôfago chagásico traz como consequências: (1) supercrescimento bacteriano na luz do órgão, (2) episódios de aspiração pulmonar e infecções respiratórias de repetição, (3) aumento do risco dos procedimentos terapêuticos cirúrgicos ou endoscópicos em caso de perfuração pela maior possibilidade de contaminação, (4) desenvolvimento de processos inflamatórios crônicos na mucosa esofágica, que podem predispor ao aparecimento de displasia e câncer. Apesar disto, a microbita esofágica no megaesôfago nunca foi estudado. Esse estudo teve o objetivo de analisar qualitativa e quantitativamente a microbiota presente no líquido de estase esofágico de pacientes portadores de megaesôfago chagásico, comparando-a com a existente em indivíduos sadios. Foram estudados prospectivamente 25 pacientes (10 homens e 15 mulheres) com idades variando de 24 a 74 anos ( &#61507; = 49,1a). Quinze pacientes eram portadores de esofagopatia chagásica, sendo 5 portadores de mega grau I (MG1), 5 portadores de mega grau II (MG2) e 5 portadores de mega grau III (MG3), segundo a classificação de Rezende; e 10 indivíduos sadios, agrupados no Grupo Controle (GC). Utilizou-se método de coleta que permitia aspiração de líquido através de sonda de Levine diretamente da luz esofágica, evitando-se a contaminação com microrganismos da orofaringe. Após análise microbiológica qualitativa e quantitativa, foi feita a descrição dos microrganismos encontrados nos vários grupos e sua classificação em aeróbios Gram positivos, aeróbios Gram negativos, anaeróbios e fungos. A análise estatística visou avaliar diferenças quantitativas entre os microrganismos nos diferentes grupos, sendo para tanto utilizado o teste não paramétrico de Kruskal-Wallis, com nível de rejeição menor 0,05 (5%). A positividade das culturas no Grupo Controle foi 40%, com predomínio do gênero Streptococcus sp, em concentrações que variaram de 101 a 102 ufc/ml. No Grupo Megaesôfago 93,3% da culturas foram positivas, com grande variedade de bactérias, mas predomínio de aeróbios Gram positivos (Streptococcus sp. foi o mais comum) e anaeróbios (Veillonella sp foi a mais freqüente) em concentrações que variaram de 101 a 105 ufc/ml. As concentrações foram geralmente mais elevadas em MG3, quando comparado com MG1, MG2 e GC (p<0,05). Concluiu-se que no megoesôfago, diferentemente dos indivíduos sadios, existe a presença de rica microflora bacteriana, constituída principalmente por aeróbios Gram positivos e anaeróbios, em concentrações tanto maiores quanto maior o seu grau de dilatação. Parte desta microbiota tem capacidade de metabolizar nitratos, etapa importante na formação de nitrosaminas. / The stasis of saliva and swallowed food in the esophageal lumen of patients with chagasic megaesophagus causes: (1) bacterial overgrowth in the esophageal lumen, (2) recurring pulmonary aspirations and respiratory infections, (3) increased risk of surgical or endoscopic procedures if perforation occurs by the major possibility of contamination, and (4) the development of chronic inflammatory process in esophageal mucosa, that can predispose to the development of dysplasia and cancer. In spite of this, esophageal microbiota in the megaesophagus has never been studied. The aim of this study was to analyze qualitatively and quantitatively the microbiota in chagasic megaesophagus in comparison to the normal esophagus. Twenty-five patients (10 men and 15 women) were prospectively studied, with ages varying from 24 to 74 years (&#61507;=49,1), from March to September 2000. Fifteen patients with chagasic megaesophagus (MG), were divided into three sub- groups according to the grade of esophageal dilation: MG1 – 5 patients with megaesophagus grade I; MG2- 5 patients with megaesophagus grade II; MG3- 5 patients with megaesophagus grade III. Another group of ten patients without any esophageal disease was constituted in the Control Group (CG). The sample collection was performed using a method specially developed to avoid contamination with microorganisms of the oral cavity and oropharynx. After qualitative and quantitative analysis, the microorganisms found were described and classified as Gram positive aerobes, Gram negative aerobes, anaerobes and fungus. Statistical analysis using Kruskal-Wallis non-parametric test was performed in order to find quantitative differences of microorganisms in the different groups. In CG 40% of the cultures were positive with predominance of the genus Streptococcus sp, in concentrations that varied from 101 to 102 cfu/ml. In MG, 93,3% of the cultures were positive, with great bacterial variability and predominance of a variety of aerobic Gram-positive (Streptococcus sp was the most common) and anaerobic bacteria (Veillonella sp was the most frequent), in concentrations that varied from 101 to 105 cfu/ml. The bacterial concentrations were generally more elevated in MG3 in comparison to MG1, MG2 and CG (p<0,05). It was concluded that patients with megaesophagus present a varied microbiota constituted mostly of aerobic Gram positive and anaerobic bacteria, in concentrations that vary with the megaesophagus dilatation degree. Some of the bacteria found in MG are able to metabolize nitrates intro nitrites, an important step in the formation of nitrosamines.

Le lin cultivé (Linum usitatissimum L.) est l’une des principales sources de lignanes, faisant de cette plante un modèle d’étude de cette voie du métabolisme spécialisé. Les principaux lignanes de lin dérivent de composés optiquement actifs, en particuliers les stéréoisomères du sécoisolaricirésinol qui sont synthétisés à partir de pinorésinol via laricirésinol. Les principales enzymes impliquées dans la synthèse de ces stéréoisomères sont deux isoformes de pinorésinol-laricirésinol réductases (PLR) déjà caractérisées et possédant des énantiospécificitées opposées. Néanmoins l'action de ces deux réductases bifonctionnelles ne permet pas d'expliquer les profils d'accumulation complexes notamment de laricirésinol et ses dérivés observés dans les graines, tiges et suspensions cellulaires de lin. Afin de mieux comprendre les mécanismes mis en oeuvre menant à ces profils d’accumulation de lignanes chez cette plante, la recherche de nouvelles PLRs a révélé l’existence de deux nouvelles isoformes. L’analyse de l'expression des gènes ainsi que l'activité enzymatique in vitro de ces deux nouvelles PLR putatives, LuPLR3 et LuPLR4 ont été élucidées. LuPLR4, in vitro, présente une activité réductase uniquement du pinorésinol. Ce type d’activité est ici décrit pour la première fois en dehors de la famille Brassicées et permet d’expliquer en partie les profils d’accumulation complexes observés chez le lin. De par leurs propriétés biocides, les lignanes sont suspectés jouer un rôle dans les mécanismes de défense des plantes. Dans le cadre de ce travail, suite à une élicitation fongique à l’aide d’extraits de Fusarium oxysporum spp. linii, un agent pathogène commun du lin, l’analyse de l’expression des différents gènes codant les isoformes de PLRs a révélées une induction globale et coordonnée. En particulier, dans le cas de l’isoforme LuPLR1, des délétions et mutations dans la région promotrice de son gène ont permis de mettre en évidence une région impliquée dans la régulation de la réponse à l’élicitation par F. oxysporum. Cette région contient plusieurs boîtes W, sites de liaison putatifs pour des facteurs de transcription de type WRKY. Les facteurs de transcription WRKY jouent un rôle dans les réponses aux stress biotique et abiotique. Un facteur de transcription candidat LuWRKY36 a été isolé à partir de suspensions cellulaires traitées avec des éliciteurs de F. oxysporum ou de l'acide abscissique. En particulier, les expériences de gel-retard et DPI-ELISA ont montré la capacité de liaison de LuWRKY36 à la boîte W3 présente du promoteur du gène LuPLR1. Cette régulation a ensuite été confirmée in vivo. Nous rapportons également l'impact différentiel de l'élicitation par des extraits de F. oxysporum sur l’expression des gènes LuWRKY36 et LuPLR1 ainsi que la production de sécoisolaricirésinol dans les variétés de lin sensible (Barbara) et résistante (Baïkal) à la fusariose. Enfin, la pleine exploitation des nombreux effets bénéfiques (en santé humaine ou cosmétique notamment) du sécoisolaricirésinol et des autres composés phénoliques accumulés dans les graines de lin nécessitent la mise au point de procédés d’extraction “verts”, efficaces voir sélectifs. Nous rapportons ici que l’utilisation de solvants eutectiques de type NADES (Natural Deep Eutectic Solvent) qui couplée à une extraction assistée par ultrasons, dans le cadre d’un procédé de type cracking, utilisant comme matériel de départ un coproduit d’extraction de l’huile de lin produit de manière innovante, permet d’obtenir des rendements d’extraction élevés et sélectifs de ces différents composés d’intérêt dans le cadre d’une démarche d’éco-extraction. / L. usitatissimum is one of the richest sources of lignans. Main flax lignan is optically active secoisolariciresinol that is synthesized from pinoresinol via lariciresinol. Key enzymes involved in the synthesis of this lignans are two isoforms of pinoresinol-lariciresinol reductases with opposite enantiospecificity. The action of bifunctional reductase does not allow for an explanation for the accumulation of lariciresinol and its derivates in seeds, stem and cell suspension. To try and better understand complex lignan profile we report expression and activity of two new putative PLRs, LuPLR3 and LuPLR4. LuPLR4 in vitro acts only as pinoresinol reductase what has only been seen in Brassicaceae family until now. Lignans play a role in plant defense. All PLRs are upregulated following Fusarium oxysporum attack, a common flax pathogen. Promoter deletions and mutation evidenced region involved in regulation of LuPLR1 gene response to Fusarium. The region contains several W boxes, putative binding sites for WRKY transcription factors. WRKY transcription factors play a role in response to biotic and abiotic stress. We have isolated LuWRKY36 from two cell suspension treated with Fusarium oxysporum or abscisic acid. Gel-shift assay and DPI-ELISA showed binding of LuWRKY36 to W box present in the LuPLR1 gene promoter. This regulation was also confirmed in vivo. We also report the differential impact of F. oxysporum elicitation on LuWRKY36 and LuPLR1 gene expression and secoisolariciresinol production in flax cultivars Barbara (Fusarium sensitive) and Baikal (Fusarium tolerant). Many beneficial effects of secoisolariciresinol and other phenolic compounds found in flax require “green” extraction and sometimes targeted purification of a specific compound. We report here that natural deep eutectic solvents using ultrasound assisted extraction can extract phenolic compounds from flax seed coat and that results indicate that by tuning different parameters of extraction we can target purification of desired plant product.

Orientador: Marcos Pereira Marinho Aidar / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T19:18:09Z (GMT). No. of bitstreams: 1 Marchiori_NidiaMara_M.pdf: 3439360 bytes, checksum: 8e5d49e665742675abd331ec9cff9ba4 (MD5) Previous issue date: 2012 / Resumo: O Nitrogênio é um nutriente essencial para o crescimento das plantas e produtividade de um ecossistema, visto sua ação como limitante para a fotossíntese ou relação com a reflectância da luz (albedo). Além disso, detém importância ecológica por ser uma ferramenta para a categorização de espécies em classes sucessionais baseado na utilização de suas formas disponíveis. Dessa forma, a compreensão da fisiologia do uso de N é essencial, especialmente em florestas tropicais, onde existem poucos estudos com essa abordagem. A Mata Atlântica (MA) é originalmente a segunda maior floresta tropical do continente americano, contudo grande parte de sua área e biodiversidade foi perdida e atualmente essa Floresta é definida como um "hotspot" para conservação da biodiversidade. O conhecimento e entendimento da estrutura e do funcionamento de ecossistemas complexos como os que compõem a MA é de suma importância para a discussão de temas atuais como o balanço de carbono global, nutrição vegetal e mudanças climáticas. Dentre os principais objetivos foram: a caracterização fitossociológica e estrutural de um trecho de Floresta Ombrófila Densa Montana (FODM), elucidar as estratégias de utilização de nitrogênio pelas plantas e avaliar através de parâmetros foliares, as respostas das plantas frente à mudança da estação do ano e a sazonalidade intrínseca. A área de coleta estava localizada na microbacia Ribeirão Casa de Pedra, Núcleo Santa Virgínia/Parque Estadual da Serra do Mar- São Luiz do Paraitinga, SP. Quanto à estrutura e composição do trecho de FODM estudado pode-se verificar uma floresta em estádio secundário inicial de regeneração avançando para uma condição mais tardia, sendo essa definição baseada tanto no histórico de utilização da área, quanto na composição de espécies e fisiologia do uso de nitrogênio. Assim, os resultados indicaram que em FODM há intensa diversidade biológica e diversidade funcional. Importante ressaltar também que esse projeto de mestrado foi parte integrante do Projeto Temático "Carbon tracker and water availability: controls of land use and climate changes" (Clima - FAPESP 08/58120-3; período de 2009-2013; coordenação Humberto Ribeiro da Rocha), cujo objetivo principal foi a quantificação à longo prazo da dinâmica dos fluxos de água, energia e CO2 em Biomas de Cerrado e Mata Atlântica no sudeste do Brasil / Abstract: Nitrogen is an essencial nutrient for plant growth and ecosystem productivity, either by limiting photosynthesis or related to the light reflectance (albedo). In addition, N has an ecological importance because it can be a tool for the categorization of species in ecological succession and functional types based on the use of its available forms. Thus, understanding the physiology of N use is essential, especially in tropical forests, where despite the impending increase of this element as a result of intensive fertilization or atmospheric deposition there are few studies using this approach. The Atlantic Forest (AF) is originally the second largest rainforest at the America continent, but much of its area and biodiversity has been lost and now the forest is defined as a "hotspot" for biodiversity conservation. The knowledge and understanding of the structure and functioning of complex ecosystems such as those that comprise the AF is of paramount importance for the discussion of current issues as the global carbon balance, plant nutrition and climate change. The main aims were: phytosociological and structural characterization of the tree component in a Montane Tropical Rainforest, understand the strategies of nitrogen use by plants and assess through leaf parameters, the response of plants to the change of season and intrinsic seasonality. The study area of the three chapters that follow are inserted in the watershed Ribeirão Casa de Pedra, Núcleo Santa Virginia Parque Estadual da Serra do Mar, located in São Luiz do Paraitinga-SP. The results indicated that Montane Tropical Rainforest was in initial secondary stage of regeneration evolving to a climax condition, based on the past human disturbance in the area, species composition and physiology of N use. Also indicated that this forest has many species and functional diversity. It is also important to note that this Master's project is part of the Thematic Project "Carbon tracker and water availability: controls of land use and climate changes" (Climate - FAPESP 08/58120-3; period 2009-2013; coordinated by Humberto Ribeiro da Rocha), whose main objective is to quantify the long-term dynamics of fluxes of water, CO2, energy at Cerrado and Atlantic Forest biomes in southeastern Brazil / Mestrado / Biologia Vegetal / Mestra em Biologia Vegetal

Ribonucleotide reductases (RNR) are essential enzymes that catalyze the reduction of ribonucleotides to 2'-deoxyribonucleotides, which is a critical step that produces precursors for DNA replication and repair. The inactivation of RNR, logically, would discontinue producing the precursors of the DNA of viral or cancer cells, which then would consequently end the cycle of DNA replication. Among different compounds that were found to be inhibitors of RNR, 2'-azido-2'-deoxynucleotide diphosphates (N3NDPs) have been investigated in depth as potent inhibitors of RNR. Decades of investigation has suggested that the inactivation of RNR by N3NDPs is a result of the formation of a nitrogen-centered radical (N•) that is covalently attached to the nucleotide at C3' and cysteine molecule C225 [3'-C(R-S-N•-C-OH)]. Biomimetic simulation reactions for the generation of the nitrogen-centered radicals similar to the one observed during the inactivation of the RNR by azionuclotides was investigated. The study included several modes: (i) theoretical calculation that showed the feasibility of the ring closure reaction between thiyl radicals and azido group; (ii) synthesis of the model azido nucleosides with a linker attached to C3' or C5' having a thiol or vicinal dithiol functionality; (iii) generation of the thiyl radical under both physiological and radiolysis conditions whose role is important in the initiation on RNR cascades; and (iv) analysis of the nitrogen-centered radical species formed during interaction between the thiyl radical and azido group by electron paramagnetic resonance spectroscopy (EPR). Characterization of the aminyl radical species formed during one electron attachment to the azido group of 2'-azido-2'-deoxyuridine and its stereospecifically labelled 1'-, 2'-, 3'-, 4'- or 5,6-[2H2]-analogues was also examined. This dissertation gave insight toward understanding the mechanism of the formation of the nitrogen-centered radical during the inactivation of RNRs by azidonucleotides as well as the mechanism of action of RNRs that might provide key information necessary for the development of the next generation of antiviral and anticancer drugs.

Les voies métaboliques les plus importantes dans le contrôle du stress oxydant chez la plante restent à élucider. Celles liées au glutathion jouent un rôle important. Cependant, les réactions responsables de l'oxydation du glutathion (du GSH en GSSG) n'ont pas encore été clairement identifiées. L’analyse des données biochimiques, transcriptomiques et génétiques soulèvent des questions pour mieux comprendre comment la régulation redox liée au stress pourrait influer sur la signalisation hormonale chez les plantes. Par une approche de génétique inverse utilisant, notamment, le mutant photorespiratoire conditionnel cat2, nous avons étudié la réponse et l'importance fonctionnelle de trois voies potentielles, médiées par les glutathion S-transférases, les peroxirédoxines dépendant de la glutarédoxine et les déhydroascorbate réductases (DHARs) chez Arabidopsis. Ainsi, l'interaction entre les DHARs semble être nécessaire pour coupler les pools d'ascorbate et de glutathion lors d’un stress oxydant. En complément à l'approche expérimentale, une modélisation mécaniste a permis d'étudier la production de H2O2 et son métabolisme, en lien avec l'activité catalase et la voie ascorbate-glutathion. Le modèle révèle que la catalase et l'ascorbate peroxydase prennent en charge de concert le traitement de H2O2, y compris dans les conditions optimales de croissance. Nos simulations suggèrent que la disponibilité en NADPH peut déterminer l'oxydation du glutathion via la monodéshydroascorbate réductase. Nos résultats expérimentaux et le modèle cinétique valident que la sensibilité du statut du glutathion au stress oxydant constitue un senseur approprié des augmentations du H2O2. / The most important metabolic pathways in the control of oxidative stress remain to be elucidated in plants. Those linked to glutathione play an important role. However, the reactions responsible for its oxidation have not been clearly identified. Here, analysis based on available biochemical, transcriptomic and genetic data emphasized likely important questions to be elucidated for a full understanding of how stress-related redox regulation might impinge on phytohormone-related signaling pathways. Using a reverse genetics approach and the photorespiratory conditional cat2 mutant, we studied the response and functional importance of three potential routes for glutathione oxidation pathways mediated by glutathione S-transferases, glutaredoxin dependent peroxiredoxins, and dehydroascorbate reductases (DHAR) in Arabidopsis during oxidative stress. Hence, interplay between different DHARs appears to be necessary to couple ascorbate and glutathione pools and to allow glutathione-related signaling during enhanced H2O2 metabolism. In addition to experimental work, modelling is another way to investigate H2O2 production and its metabolism related to catalase activity and ascorbate glutathione pathway. This approach led to major conclusions, that catalase and ascorbate peroxidase can share the load in H2O2 processing even in optimal growth conditions. Furthermore, simulations propose that NADPH availability may determine glutathione oxidation through its influence on monodehydroascorbate reduction. Taken together, experimental results and our kinetic model strengthen that the sensitivity of glutathione status to oxidative stress acts as a suitable sensor of increased H2O2.

Cette étude a pour objectif la mise en évidence, chez les basidiomycetes du genre Pycnoporus, de nouvelles oxydo-réductases impliquées dasn la dégradation de la biomasse végétale: de l'expression des gènes aux applications biotechnologiques. Les champs d'application visés concernent essentiellement le domaine de la chimie verte, dans le cadre du projet européen BIORENEW. Le travail s'est articulé autour de trois axes principaux. Le premier a concerné l'exploration de la biodiversité naturelle en particulier tropicale, pour la sélection de souches productrices de nouvelles laccases de haut potentiel d'oxydo-réduction. Le gène codant pour la laccase Lac1 chez Pycnoporus a été utilisé comme marqueur moléculaire d'identification et de relation phylogénie-fonction, mettant en évidence une distribution des souches fortement corrélée avec leur écozone. Le deuxième axe a porté sur l'isolement de trois nouvelles laccases issues de P.sanguineus et P. coccineus qui exhibent des caractéristiques biochimiques complémentaires: haute thermostabilité, résistance aux solvants, au pH, constantes catalytiques et potentiels rédox élevés. Ces enzymes constituent de bons modèles pour des applications en biotechnologies blanches:décoloration de colorants polyphénoliques, oxydation de composés modèles de type lignine non-phénolique, oligomérisation de flavonoides naturels adaptés aux applications cosmétiques et pharmaceutiques. Enfin, dans le cadre de l'annotation du génome des souches monocaryotiques P. cinnabarinus BRFM 137 et P; sanguineus BRFM 1264, dont le séquençage a été réalisé par notre Unité, un regard tout à fait nouveau est porté sur le système lignolytique du genre Pycnoporus, longtemps décrit comme produisant que de la laccase comme enzyme du système lignolytique. Pour la première fois, nous avons montré la présence de gènes codant pour tout l'arsenal enzymatique de dégradation des lignines, c'est à dire plusieurs laccases mais surtout de nombreuses peroxydases et des enzymes auxilliaires génératrices d'H2O2 comme les glyoxal oxydases. Ces nouvelles enzymes ont été caractérisées in silico. Pour la première fois également, la sécrétion effective de peroxydases, de glyoxal oxydases et d'autres FOLymes dans nos conditions de culture a également pu être démontrée par analyse protéomique. / The purpose of this work was to prospect, in the genus Pycnoporus, for new oxido-reductases involved in the degradation of lignocellulosic biomass: from gene expression to biotechnological applications. This research was conducted in the framework of green chemistry applications according to BIORENEW European Project. The study was divided in three main research axes. Firstly, the exploration of natural biodiversity, especially tropical biodiversity, for the selection of new high redox potential-laccase producing strains. These strains were repositionned in a context of phylogenomic/function through the lac1 gene. Molecular clustering based on lac1 sequences enabled the distribution of P. sanguineus and P. coccineus through four distinct, well supported clades and subclades. This distribution was highly correlated with ecozones. The second part of the work deals with the biochemical and molecular characterization of three novel laccases from P. coccineus and P. sanguineus, and their applicability on natural or model phenolic substrates. The three laccases showed complementary biochemical features: high thermo- and pH stability, high catalytic efficiency and resistance to organic solvents. The three novel laccases proved to be suitable models for white biotechnology processes: polyphenolic dye decolourization, non-phenolic lignin model compound oxidation, and synthesis of new oligomers from natural flavonoids suitable for cosmetic or pharmaceutical applications. Finally, annotation of genomic data from the monocaryotic strains P. cinnabarinus BRFM 137 and P. sanguineus BRFM 1264 (genomes sequenced by the UMR1163 BCF ) was performed for lignolytic enzymes. For the first time, new oxidases (peroxidases, glyoxal oxidases and other FOLymes) were evidenced in Pycnoporus and in silico characterized. Moreover, the active secretion of several of these enzymes has been demonstrated in our culture conditions by 1D-proteomic analysis

A Análise de Acoplamentos Estatísticos é uma técnica computacional capaz de identificar resíduos importantes para a estrutura e função de proteínas em uma família por meio da quantificação de conservação posicional, correlação entre posições e identificação de grupos de resíduos correlacionados entre si. Neste trabalho, a análise de acoplamentos estatísticos foi implementada e aplicada ao estudo das proteínas tirosina fosfatases. Em conjunto com as proteínas tirosina quinases (PTKs), que adicionam um grupo fosforil a um resíduo de tirosina em uma proteína, as proteínas tirosina fosfatases (PTPs), que o removem, são responsáveis por diversos processos de sinalização celular. Elas são um caso de evolução convergente, onde um subgrupo (as proteínas tirosina fosfatases de baixo peso molecular) não apresenta homologia às chamadas PTPs \"clássicas\", capazes de defosforilar apenas resíduos de tirosina, e às fosfatases de especifidicade dupla, capazes de defosforilar também resíduos de serina e treonina, além de substratos não-protéicos. Em comum, as três subfamílias apresentam apenas o motivo CX5R, característico para todas as PTPs. Através do estudo das três subfamílias utilizando a análise de acoplamentos estatísticos, foi possível obter uma descrição detalhada de suas características conservadas e correlacionadas, relacionando-as ao conhecimento acumulado sobre proteínas tirosina fosfatases e a questões em aberto como a regulação por dimerização, a especificidade e mutações relacionadas a patologias. Foi possível também apresentar um método capaz de distinguir proteínas tirosina fosfatases de baixo peso molecular das arsenato redutases, derivadas das primeiras por evolução divergente. Adicionalmente, a técnica foi aplicada ao estudo das hexoquinases, às superóxido dismutases e às peroxidases. A tese descreve também estudos desenvolvidos pelo autor na área de cristalografia de proteínas a determinação das estruturas da Transtirretina humana em complexo com genisteína, da holo-Hexoquinase PI de S. cerevisae, do complexo IL-22/IL-22R1 e da Laminarinase de R. marinus. / The statistical coupling analysis is a computational technique which can identify important residues for the structure and function of proteins in a family by quantifying positional conservation, correlation between positions and identifying groups of self-correlating residues. Its implementation in this research group was applied to the study of the protein tyrosine phosphatases. Together with the protein tyrosine kinases (PTKs), which add a phosphoryl group to a tyrosine residue in proteins, the protein tyrosine phosphatases (PTPs), which remove it, are responsible for a variety of cell signaling processes. They are a case of convergent evolution, since one subgroup (the low molecular weight protein tyrosine phosphatases) are not homologous to the classical phosphatases, which can only dephosphorilate tyrosine residues, and the dual-specificity phosphatases, which can also dephosphorilate serine and threonine residues, and also non-proteinaceous substrates. All three sub-families have, in common, the CX5R motif, a characteristic of all PTPs. By applying the statistical coupling analysis to the study of the three sub-families, it was possible to obtain a detailed depiction of their conserved and correlated characteristics, relating them to the accumulated knowledge on protein tyrosine phosphatases and open questions such as protein regulation by dimerization, specificity and disease-related mutations. It was also possible to present a method to distinguish between low molecular weight phosphatases and arsenate reductases, which are derived by the former by divergent evolution. In addition, the technique was applied to the study of hexokinases, superoxide dismutases and peroxidases. The thesis also describe studies developed by the author in the field of protein crystallography the structure determination of human transthyretin in complex with genistein, holo-hexokinase PI from S. cerevisae, the IL-22/IL-22R1 complex and the laminarinase from R. marinus.

La mucoviscidose est la maladie génétique la plus fréquente dans la population caucasienne. Le genre Scedosporium se situe au deuxième rang parmi les champignons filamenteux isolés des expectorations dans ce contexte. Au niveau pulmonaire, les colonisations/infections entraînent le recrutement de phagocytes qui induisent un stress oxydatif normalement délétère pour les pathogènes. Pour se défendre, ceux-ci ont développé des systèmes antioxydants, notamment diverses enzymes. Ce travail de thèse visait à étudier la réponse au stress oxydatif chez Scedosporium. Tout d’abord, la capacité à germer en présence d’oxydants a été évaluée. Par la suite, trente-trois gènes potentiellement impliqués dans la défense contre le stress oxydatif ont été identifiés. Leur expression en présence d’oxydants et en co-cultures avec des phagocytes suggère un rôle majeur, notamment pour une catalase, une peroxyrédoxine et deux thiorédoxine réductases. Par ailleurs, un mutant défectif pour un gène codant une superoxyde dismutase (SOD) pariétale et spécifique des spores a été produit. L’auranofin, un inhibiteur des thiorédoxine réductases, présente une activité vis-à-vis des Scedosporium et un effet additif avec des triazolés. Un test ELISA a été développé pour le sérodiagnostic des scédosporioses, utilisant une catalase et une Cu/Zn-SOD recombinantes. Ce test sensible et spécifique permet de distinguer les infections à Scedosporium de celles à Aspergillus fumigatus et des colonisations à Scedosporium. Au final, ces résultats indiquent un rôle majeur des enzymes antioxydantes chez Scedosporium, qui pourraient être de véritables facteurs de virulence et donc de nouvelles cibles thérapeutiques. / Cystic fibrosis (CF) is the most common genetic disease in Caucasian populations. The Scedosporium genus ranks the second among the filamentous fungi colonizing the airways of CF patients. In the respiratory tract, colonizations/infections lead to the recruitment of phagocytes which produce an oxidative stress, usually deleterious for pathogens. To defend themselves, pathogens have developed protective antioxidant systems, especially various enzymes. This thesis aimed to study the oxidative stress response in Scedosporium species. First, capacity of several Scedosporium isolates to germinate upon oxidative stress conditions was evaluated. Then, thirty-three genes potentially involved in protection against the oxidative stress were identified. Their overexpression in response to oxidants and in co-cultures with phagocytes suggested a crucial role, especially for one catalase, one peroxiredoxin and the two thioredoxin reductases. A mutant defective for the gene encoding a superoxide dismutase (SOD) anchored to the cell wall and specific for the conidia was produced. Auranofin, a thioredoxin reductase inhibitor, exhibits little anti-Scedosporium activity and an additive effect with triazole drugs. An ELISA was developed for serodiagnosis of scedosporiosis, using recombinant proteins derived from one catalase and a Cu/Zn-SOD. This sensitive and specific assay allows to differentiate Scedosporium infections from Aspergillus fumigatus infections and Scedosporium colonizations. Finally, these results indicate a crucial role of antioxidant enzymes in Scedosporium species, which could therefore be considered as virulence factors and as possible new therapeutic targets.