Les biotechnologies sont un outil puissant permettant d’emprunter les circuits biologiques pour produire des composés aux applications multiples (médecine, alimentation, industries…). Les cyanobactéries possèdent des propriétés génétiques et trophiques précieuses pour réduire les coûts et l’empreinte environnementale de ces procédés (photosynthèse, fixation du CO₂, sources d’azote assimilables...). Elles produisent aussi naturellement certaines molécules énergétiques comme le H₂ dont pourraient émerger de nouvelles filières propres de biocarburants. Cependant, une compréhension globale et approfondie de leur physiologie est nécessaire pour concevoir un châssis biologique performant à partir de ces organismes. Elles sont aisément manipulables génétiquement mais présentent une versatilité favorisant la fixation de mutations bénéfiques mais aussi délétères pour leur exploitation à grande échelle. Au cours de ma thèse, j’ai construit et étudié des mutants d’un régulateur de l’assimilation du CO₂ dont l’activation est liée à la photosynthèse. J’ai montré que l’activité du cycle de Calvin synchronise les flux du carbone et le statut rédox de Synechocystis et que sa dérégulation se répercute de manière pléiotropique sur son métabolisme. Plus spécifiquement, je me suis intéressé au déséquilibre carbone/azote dans cette espèce et à son métabolisme de l’urée qui présente un intérêt biotechnologique considérable. J’ai démontré que ce dernier était en compétition avec l’hydrogénase pour l’insertion du nickel dans leurs centres catalytiques respectifs. L’insuffisance de ce métal a permis de sélectionner des mutants de l’uréase tolérant une exposition prolongée à l’urée et conservant une forte capacité de production de H₂ en présence de ce substrat azoté. L’ensemble de ces résultats montre que le métabolisme de Synechocystis peut être détourné au profit de certains processus cellulaires. Les approches « omiques » permettent d’identifier globalement les réponses physiologiques induites ainsi que les leviers biologiques de compensation. Ces travaux sont discutés au regard des implications biotechnologiques de l’instabilité génétique et de la nécessité de renforcer notre compréhension de la plasticité métabolique et génomique des cyanobactéries. / Biotechnology is a powerful tool allowing exploitation of biological circuits to produce compounds with multiple uses (medicine, nutrition, industrial…). Cyanobacteria have valuable genetic and trophic properties which could reduce the costs and the environmental footprint of these processes (photosynthesis, CO₂ fixation, assimilation of diverse nitrogen sources…). They also naturally produce energetic molecules such as H₂ from which new and sustainable biofuels sectors may rise. However, a global and fine understanding of their physiology is required in order to design an efficient biological chassis with these organisms. They are genetically manipulable but also exhibit a strong versatility favoring fixation of mutations that can be either beneficial or harmful to their large-scale cultivation. Over the course of my PhD, I constructed and studied mutants of a CO₂ fixation regulator whose activation is linked to photosynthesis. I showed that the Calvin cycle activity synchronizes carbon fluxes and redox status in Synechocystis and that its deregulation affects the metabolism in a pleiotropic manner. I was specifically interested into the carbon/nitrogen balance in this species and its urea metabolism which is of prime interest in biotechnology. I demonstrated that the latter was in competition with the hydrogenase for the insertion of nickel into their respective catalytic centers. Scarcity of this metal leads to selection of mutants thriving upon prolonged exposure to urea that retained a high capacity of H₂ production in presence of this nitrogenic substrate. This work shows that the metabolism of Synechocystis can be altered in favor of other cellular processes. Omics approaches allow global identification of the physiological responses induced as well as the biological compensation mechanisms. These observations are discussed with regards to biotechnological implications of genetic instability and the need to strengthen our understanding of metabolic and genetic plasticity in cyanobacteria.

A 2000 mm long saturated laboratory soil column was used to simulate soil aquifer treatment under saturated conditions to assess the removal of chemical and biochemical oxygen demand (COD and BOD), dissolved organic carbon (DOC), nitrogen and phosphate, using high strength artificial wastewater. The removal rates were determined under a combination of constant hydraulic loading rates (HLR) and variable COD concentrations as well as variable HLR under a constant COD. Within the range of COD concentrations considered (42 mg L(-)(1)-135 mg L(-)(1)) it was found that at fixed hydraulic loading rate, a decrease in the influent concentrations of dissolved organic carbon (DOC), biochemical oxygen demand (BOD), total nitrogen and phosphate improved their removal efficiencies. At the high COD concentrations applied residence times influenced the redox conditions in the soil column. Long residence times were detrimental to the removal process for COD, BOD and DOC as anoxic processes and sulphate reduction played an important role as electron acceptors. It was found that total COD mass loading within the range of 911 mg d(-)(1)-1780 mg d(-)(1) applied as low COD wastewater infiltrated coupled with short residence times would provide better effluent quality than the same mass applied as a COD with higher concentration at long residence times. The opposite was true for organic nitrogen where relatively high concentrations coupled with long residence time gave better removal efficiency.

Hydrogenasen sind komplexe Enzyme, die die reversible Oxidation von molekularem Wasserstoff zu Protonen und Elektronen katalysieren. Diese Enzyme erlauben ihrem Wirtsorganismus das Wachstum unter chemolithoautotrophen Bedingungen. Der Modellorganismus Ralstonia eutropha besitzt drei gut charakterisierte Hydrogenasen der [NiFe]-Klasse, die sich durch ihre Sauerstofftoleranz auszeichnen. Ihr aktives Zentrum besteht aus einer komplexen prosthetischen Gruppe, welche aus einem Nickel- und einem Eisenatom besteht. Letzteres koordiniert drei diatomare Liganden, zwei Cyanide und ein CO. Die Synthese der gesamten Ni(SR)2(µ-SR)2Fe(CN)2(CO)-Gruppe ist ein komplexer Prozess. Die sogenannte Maturation benötigt wenigstens sechs akzessorische Proteine, die sogenannten Hyp-Proteine. Das umfassende Verständnis dieser Maturationsprozesse ermöglicht eine Vielzahl von biotechnologischen Anwendungen. Die vorliegende Arbeit untersucht die Maturation unter verschiedenen Gesichtspunkten. Zentrale, offene Fragen sind die Herkunft des Carbonylliganden sowie die Prozesse, die zur Ligandierung des katalytischen Eisens führen. Dazu wurden molekularbiologische, biochemische und spektroskopische Methoden in Verbindung mit Isotopenmarkierung eingesetzt. Unter anderem konnte dabei gezeigt werden, dass das katalytische Eisen alle seine Liganden bereits im HypCD-Komplex, dem zentralen Element der Maturation, erhält. Ferner konnte in dieser Arbeit, erstmalig für [NiFe]-Hydrogenasen, eine konkrete Biosynthese des seltenen und toxischen diatomaren CO-Liganden beschrieben werden. Ausgehend vom Alpha-Kohlenstoff von Glycin wird der Tetrahydrofolat (THF)-abhängige C1-Metabolismus mit C1-Einheiten versorgt. Durch die enzymatische Aktivität von HypX wird die Formylgruppe von N10-Formyl-THF zu CO umgesetzt. / Hydrogenases are complex enzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons. These enzymes allow their host organism to grow under chemolithoautotrophic conditions. The model organism Ralstonia eutropha has three well-characterized [NiFe]-hydrogenases, which exhibit an extraordinary high oxygen tolerance. Its active center is a complex prosthetic group which consists of a nickel and iron atom. The latter coordinates three diatomic ligands, two cyanides and one CO. The biosynthesis of the whole Ni(SR)2(μ-SR)2Fe(CN)2(CO)-group is a complex process. This so-called maturation process needs the activity of at least six accessory proteins, the Hyp-proteins. Understanding the maturation allows a variety of biotechnological applications. The present study examines the maturation of [NiFe]-hydrogenases under different aspects. The major questions concern the origin of the carbonyl ligand as well as the processes that lead to ligandation of the designated catalytic iron. To adress these tasks, molecular biological, biochemical and spectroscopic methods in combination with isotopic labeling were employed. Inter alia, it could be shown that the catalytic iron in the HypCD-complex, the central element of the maturation process, contains all three diatomic ligands. Furthermore, this study describes, for the first time in [NiFe]-hydrogenases, a specific biosynthetic route of the rare and toxic diatomic CO-ligand. Starting from the alpha-carbon of glycine the tetrahydrofolate (THF)-dependent one-carbon metabolism is replenished with one-carbon units. Subsequently the formyl group from N10-formyl-THF is hydrolyzed by the enzymatic activity from HypX and further converted to carbon monoxide as determined by isotopic labeling and infrared spectroscopy.

Introdução - Os hábitos alimentares e os nutrientes da via metabólica do folato e homocisteína possuem grande importância na manutenção da saúde. Objetivo - Investigar a relação entre padrões alimentares (PAs) e os nutrientes envolvidos nessa via metabólica, com medidas antropométricas do recém-nascido, duração da infecção por HPV em homens e concentrações de homocisteína (Hcy) em adultos. Métodos - Foram utilizados dados dos estudos de coorte ProcriAr (Influência dos fatores nutricionais e poluentes atmosféricos urbanos na saúde pulmonar de crianças: um estudo de coorte com gestantes da zona oeste do município de São Paulo, n=299); e HIM (História natural da infecção por HPV em homens, n=1.194); e do estudo transversal ISA-Capital 2008 (Inquérito de saúde do estado de São Paulo, n=281). Os padrões alimentares foram derivados por análise fatorial por componentes principais nos estudos ProcriAr e ISA-Capital 2008 e utilizando reduced rank regression (RRR) no estudo HIM. Modelos multivariados de regressão de Poisson e lineares foram utilizados nos estudos ProcriAr e HIM para identificar a relação entre PAs e medidas antropométricas do recém-nascido e duração da infecção por HPV em homens, respectivamente. Utilizando modelo de equação estrutural, investigou-se a relação entre PAs, concentrações bioquímicas de folato, vitamina B12 e ácido docosahexaenoico (DHA) e concentrações de homocisteína em adultos do estudo ISA-Capital, considerando polimorfismo da enzima metilenotetrahidrofolato redutase (MTHFR 677C>T). Os três estudos utilizaram questionário de frequência alimentar para avaliação do consumo alimentar. Resultados - No estudo ProcriAr, a maior adesão materna ao PA \"Snacks, sanduíches, doces e refrigerantes\", rico em energia, gordura, e folato sintético, esteve diretamente associada a ter um filho pequeno ao nascer (peso e/ou comprimento ao nascer, ajustado pela idade gestacional, abaixo do percentil 10 - INTERGOWTH-21st) (RR: 2,01; IC 95%: 1.13-3.57). No estudo HIM, homens com maior adesão ao \"PA3\" tiveram, em média, um aumento de 1,15 (IC95% 0,09-2,21) à 1,18 (IC95% 0,11-2,24) meses na duração da infecção por HPV. O \"PA3\" esteve positivamente correlacionado com vitamina B6 (r = 0,59), vitamina B12 (0,27) e DFE (0,07) e negativamente correlacionado com DHA (-0,37). No estudo ISA-Capital o PA \"Prudente\" esteve inversamente associado à concentração de Hcy (β = -0,12). O DHA esteve diretamente associado ao PA \"Prudente\"; composto por verduras e legumes, peixe, frutas, frango, suco natural e batata/mandioca/polenta (cozida ou assada). Conclusões - Os PAs estão associados às medidas antropométricas do recém-nascido, à duração da infecção por HPV em homens e às concentrações de homocisteína em adultos. Estes resultados reforçam a importância de estudos sobre alimentação e nutrição que considerem não somente nutrientes, mas principalmente o consumo de alimentos e suas combinações, servindo como base para a elaboração de estratégias e políticas públicas de promoção à saúde. / Introduction - The dietary habits and nutrients involved in one-carbon metabolism are of great importance in health. Objective - To investigate the relationship between dietary patterns (DP) and the nutrients involved in this metabolism, with newborn\'s anthropometric measurements, duration of HPV infection in men, and homocysteine (Hcy) levels in adults. Methods - Data from the cohort studies ProcriAr (Influence of nutritional factors and urban air pollutants on the pulmonary health of children: a cohort study with pregnant women from the western region of the city of São Paulo, n=299); and HIM (Natural history of HPV infection in men, n=1,194); and the cross-sectional study ISA-Capital 2008 (São Paulo State Health Survey, n=281) were used. The DP were estimated using factor analysis with principal component\'s estimation in ProcriAr and ISA-Capital 2008 studies and using reduced rank regression (RRR) in HIM study. Multivariate Poisson and linear regression models were used in the ProcriAr and HIM studies to identify the relationship between DP and newborn\'s anthropometric measurements and duration of HPV infection in men, respectively. Using a structural equation model, the relationship between DP, biochemical levels of folate, vitamin B12 and docosahexaenoic acid (DHA) and homocysteine levels was investigated in adults from the ISA-Capital 2008 study, considering the polymorphism of the enzyme methylenetetrahydrofolate reductase (MTHFR 677C>T). The three studies used a food frequency questionnaire to evaluate dietary intake. Results - In the ProcriAr study, the higher maternal adherence to the \"Snacks, sandwiches, sweets and soft drinks\" DP, which is a DP rich in energy, fat, and synthetic folate, was directly associated with having a child small at birth (weight and/or birth length by gestational age and sex below the 10th percentile - INTERGOWTH-21st) (RR: 2.01, 95% CI: 1.13-3.57). In the HIM study, men with higher adherence to \"DP3\" had, on average, an increase from 1.15 (95% CI 0.09-2.21) to 1.18 (95% CI 0.11-2.24) months in the duration of HPV infection. \"DP3\" was positively correlated with vitamin B6 (r = 0.59), vitamin B12 (0.27) and DFE (0.07) and negatively correlated with DHA (-0.37). In the ISA-Capital study, the \"Prudent\" DP was inversely associated with Hcy levels (β = -0.12). DHA was directly associated with \"Prudent\" DP; composed of vegetables, fish, fruits, chicken, natural juice and potato/cassava/polenta (cooked or roasted). Conclusions - Dietary patterns are associated with newborn\'s anthropometric measurements, duration of HPV infection in men, and Hcy levels in adults. These results reinforce the importance of studies on food and nutrition that consider not only nutrients, but mainly the consumption of foods and their combinations, serving as a basis for the elaboration of public health promotion strategies and policies.

Neisseria meningitidis (Nm) est un germe commensal du rhinopharynx ayant pour seul hôte l’homme. Malgré un portage asymptomatique largement répandu, et pour des raisons encore inconnues, elle peut échapper au système immunitaire de l’hôte et devenir pathogène provoquant ainsi méningite et septicémie pouvant être mortelles principalement chez les enfants. Au cours du processus infectieux, Nm alterne entre des phases de colonisation et de dissémination, et se retrouve alors confrontée à différents environnements. L’adaptation rapide à ces variations, par modulation de l’expression des gènes de virulence, représente un facteur important dans sa pathogénie. Les facteurs qui contribuent à la virulence de Nm sont essentiellement des structures présentes à la surface de la bactérie parmi lesquelles les pili et la capsule. Les gènes codant ces facteurs sont sous le contrôle de la protéine CrgA, régulateur transcriptionnel de la famille LysR qui intervient lors de l’adhésion de Nm aux cellules humaines. La protéine CrgA régule négativement sa propre expression ainsi de celle des gènes impliqués dans la synthèse de la capsule (sia) et des pili (pilE et pilC1). Par ailleurs, le PTS est un système de transduction du signal qui intervient, par phosphorylation ou via des interactions protéine/protéine, dans le transport des sucres et dans la régulation du métabolisme du carbone. Chez Nm, ce système est incomplet (constitué des protéines EI, HPr, et deux EIIA), il n’est donc pas fonctionnel pour le transport des sucres mais aurait pu conserver ses fonctions régulatrices. Nous avons montré que les protéines du PTS de Nm étaient actives in vitro et in vivo et que la cascade de phosphorylation du PTS était fonctionnelle. Nous avons également montré que l’inactivation du gène ptsH, codant la protéine HPr, entrainait une diminution significative de la synthèse de la capsule, une augmentation de l’adhésion du mutant aux cellules épithéliales humaines et une augmentation de l’expression de crgA. De ce fait, l’absence de l’HPr semble empêcher la répression de crgA et par conséquent celle des gènes sia. Par ailleurs, des expériences de co-immunoprécipitation, nous ont permis de mettre en évidence que l’HPr interagissait directement avec la protéine CrgA in vitro et in vivo. Ces résultats suggèrent que la protéine HPr interviendrait dans la régulation de l’expression des gènes de virulence de Nm via la régulation de l’expression de crgA. Ainsi, un lien entre métabolisme du carbone et virulence a été mis en évidence chez Nm. / Neisseria meningitidis (Nm) is a commensal bacterium of the nasopharynx, which only colonizes humans. Despite a large number of asymptomatic carriers, and for reasons so far unknown, Nm occasionally becomes virulent, escaping the host’s immune system and causing septicaemia and meningitis, the latter being potentially lethal, mostly in children.During the infectious process, Nm alternates between phases of colonization and dissemination, each time facing different environments. This rapid adaptation to the changing environment occurs via the modulation of the expression of virulence genes and represents an important factor of pathogenicity. The structures involved in virulence in Nm are mainly present at the surface of the bacterium, including the pili and the capsule. The genes coding for these structures are controlled by the CrgA protein, a transcriptional regulator of the LysR family, which is induced during the adhesion of Nm to human cells. CrgA negatively regulates its own expression as well as the expression of those genes implicated in the synthesis of the capsule (sia) and pili (pilE and pilC1).Moreover, the PTS is a signal transduction system, which is involved, via phosphorylation or protein/protein interactions, in the transport of sugars and the regulation of the carbon metabolism. In Nm, the PTS is incomplete (only composed of the proteins EI, HPr and two EIIA), thus not functioning in the transport of sugars but it may have conserved regulatory functions.In this work, we demonstrate that the PTS proteins in Nm are active in vitro and in vivo and that the phosphorylation cascade of the PTS is functional. We further show that the inactivation of the ptsH gene, coding for the HPr protein, significantly reduces the synthesis of the capsule, enhances the adhesion of the mutants to human epithelial cells and increases the expression of crgA. Thus, the absence of HPr seems to inhibit the repression of crgA and as a consequence also the repression of the sia genes. Furthermore, from co-immunoprecipitation experiments we provide evidence that HPr directly interacts with the CrgA protein in vitro and in vivo. These results suggest that the HPr protein in Nm regulates the expression of the virulence genes via the regulation of crgA expression. Thus, we provide evidence of a link between carbon metabolism and virulence in Nm.

The aim of this thesis was to develop stable-isotope steady-state metabolic flux analysis (MFA) based on ¹³C labeling to quantify intracellular fluxes of central carbon metabolism in plants. The experiments focus on the analysis of a heterotrophic cell suspension culture of Arabidopsis thaliana (L) Heynh. (ecotype Landsberg erecta). The first objective was to develop a robust methodology based on combining high quality steady-state stable labeling data, metabolic modeling and computational analysis. A comprehensive analysis of the factors that influence the outcome of MFA was undertaken and best practice established. This allowed a critical analysis of the subcellular compartmentation of carbohydrate oxidation in the cell culture. The second objective was to apply the methodology to nutritional perturbations of the cell suspension. A comparison of growth on different nitrogen sources revealed that transfer to an ammonium-free medium: (i) increased flux through the oxidative pentose phosphate pathway (oxPPP) by 10% relative to glucose utilisation; (ii) caused a substantial decrease in entry of carbon into the tricarboxylic acid cycle (TCA); and (iii) increased the carbon conversion efficiency from 55% to 69%. Although growth on nitrate alone might be expected to increase the demand for reductant, the cells responded by decreasing the assimilation of inorganic N. Cells were also grown in media containing different levels of inorganic phosphate (Pi). Comparison of the flux maps showed that decreasing Pi availability: (i) decreased flux through the oxPPP; (ii) increased the proportion of substrate fully oxidised by the TCA cycle; and (iii) decreased carbon conversion efficiency. These changes are consistent with redirection of metabolism away from biosynthesis towards cell maintenance as Pi is depleted. Although published genome-wide transcriptomic and metabolomic studies suggest that Pi starvation leads to the restructuring of carbon and nitrogen metabolism, the current analysis suggests that the impact on metabolic organisation is much less extreme.

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