L’objectif de ce projet de thèse est d’étudier et caractériser les mécanismes impliqués dans la bascule respiro-fermentaire chez des cellules eucaryotes dotées d’un métabolisme mitochondrial. Les cellules eucaryotes ont des besoins différents en oxygène pour la production d’énergie et leur survie dans un environnement donnée. Elles sont qualifiées de type aérobie stricte lorsque la présence d’oxygène leur est nécessaire ou aéro-anaérobie facultatif dans le cas où l’oxygène n’est pas indispensable à la production d’énergie. La levure Yarrowia lipolytica a été choisie comme modèle d’étude de par sa particularité à être un micro-organisme aérobie strict avec une grande capacité d’accumuler de lipides et de production d’acides organiques. Les études expérimentales et analytiques, par l’emploi de méthodes mathématiques de modélisation du métabolisme, ont permis d’identifier des contraintes métaboliques impliquées dans la transition respiro-fermentaire chez cette levure au métabolisme énergétique oxydatif. La production de l’acide citrique par Y. lipolytica, déjà rapportée dans la littérature, a été choisi comme un marqueur de cette transition respiro-fermentaire. Nous avons découvert que l’inhibition de la protéine oxydase alternative (AOX), impliquée dans la respiration mitochondriale, par la molécule n-propyl gallate (nPG) permet d’améliorer le rendement de production d’acide citrique par fermentation du glucose dans une culture de Y. lipolytica. Ces résultats montrent que la nPG, déjà utilisée dans l’industrie agro-alimentaire et pharmaceutique en tant que conservateur joue sur la bascule respiro-fermentaire par inhibition de la consommation d’oxygène et stimule ainsi la production d’acide citrique. La modélisation du réseau métabolique de Y. lipolytica, décrit à l’échelle du genome, par dynamic Flux Balance Analysis (dFBA) a permis d’identifier l’accumulation des espèces oxydantes dites ROS (Reactive Oxygen Species) comme un levier majeur de la bascule respiro-fermentaire et donc de la production d’acide citrique chez la levure Y. lipolytica. De plus, nos résultats préliminaires montrent que l’oxydation des lipides accumulés par Y. lipolytica pourrait être à l’origine de la génération des ROS. Cette étude doit être approfondie expérimentalement et constitue un apport important pour l’industrie agro-alimentaire et pharmaceutique.Mots clés : Bascule respiro-fermentaire, Acide citrique, lipides, Yarrowia lipolytica, n-propyl gallate, Reactive Oxygen Species, modélisation, dynamic Flux Balance Analysis / The main goal of this thesis project is to study and characterize mechanisms involved in respiratory to fermentative shift in eukaryotic cells endowed with mitochondrial metabolism. Eukaryotic cells have different oxygen requirements for energy production and survival in a given environment. They are described as strict aerobic when the presence of oxygen is necessary or optional aero-anaerobic in when oxygen is not essential for energy production. The yeast Yarrowia lipolytica was chosen as our study model thanks to its particularity since it is a strict aerobic microorganism with a high capacity to accumulate lipids and to produce organic acids. Experimental and analytical studies, using mathematical methods for modeling cell metabolism, allowed us to identify metabolic constraints involved in respiratory to fermentative transition in this yeast showing oxidative energy metabolism. Production of citric acid by Y. lipolytica, already reported in the literature, has been chosen as a marker for this in respiratory to fermentative shift. We found that the inhibition of the alternative oxidase protein (AOX) involved in mitochondrial respiration, by adding n-Propyl gallate (nPG) molecule improves the yield of citric acid production by fermentation of glucose in a Y. lipolytica culture. These results show that nPG, already used in food and pharmaceutical industry as a preservative, plays on respiratory to fermentative balance by inhibition of oxygen consumption and thus stimulates the production of citric acid. Modeling of the metabolic network of Y. lipolytica, described at genome-scale, by dynamic Flux Balance Analysis (FBA) has identified the accumulation of intracellular ROS (Reactive Oxygen Species) species as major levers for respiratory to fermentative shift and therefore the production of citric acid by Y. lipolytica. Therefore, our preliminary results show that oxidation of lipids accumulated by Y. lipolytica could be involved in generation of ROS species. This study must be experimentally deepened and constitutes an important contribution for the agri-food and pharmaceutical industry.Key words: Respiratory to fermentative shift, Citric acid, lipids, Yarrowia lipolytica, n-Propyl gallate, Reactive Oxygen Species, modeling, dynamic Flux Balance Analysis

Thesis (MScEng (Process Engineering))--University of Stellenbosch, 2009. / The abundance of alkane by-products formed in South Africa presents a feedstock opportunity for the production of a wide range of commercially important products, such as long-chain dioic acids and alcohols. These compounds are formed as intermediates through the biological conversion of alkanes, a route which is particularly attractive when compared with chemical conversion due to its operation under milder process conditions. Furthermore, advances in genetic manipulation, which enable the accumulation of a range of metabolic intermediates, make the biological route remarkably flexible. From the literature review Yarrowia lipolytica was identified as a promising organism for use in studying alkane bioconversion because of its ability to produce large quantities of fatty acids when grown on n-paraffins as a sole carbon source. The bioconversion of alkanes will not only depend on the genetic modification but also on the process conditions to maximise growth and bioconversion. The overall objective of this project was therefore to investigate the potential of Y. lipolytica for alkane bioconversion by defining the conditions that maximise both cell growth and bioconversion. The Y. lipolytica strains supplied (TVN348, TVN493 and WT), however, were not yet modified to the extent that accumulation of metabolic intermediates was possible. Use was therefore made of a model system in which the alkane substrate was substituted with an even chain alkylbenzene. Since Y. lipolytica is unable to metabolise the benzene ring, the alkylbenzene is converted to the metabolic intermediate, phenyl acetic acid (PAA), and the potential for bioconversion assessed through measuring the accumulation of PAA. The specific objectives of the project were therefore 1) to define and quantify the parameters for the establishment of an effective model system in shake flasks with respect to trace elements, buffering, added nitrogen, oxygen supply, glucose concentration, alkylbenzene substrate and inducer requirements 2) to use the defined model system to identify the most promising strain of Y. lipolytica TVN348, TVN493 and WT 3) to use the defined model system and selected strain for evaluation of the influence of time of substrate addition and glucose concentration on cell growth and bioconversion of Y. lipolytica under controlled conditions in an instrumented bioreactor Furthermore, since poor reproducibility in cell growth and bioconversion had been prevalent in previous studies, it was also aimed to identify and statistically quantify the reproducibility between duplicate or triplicate samples in each experiment and between sets of different experiments with respect to PAA formation and cell concentrations. Studies were conducted in shake flask cultures to define and quantify the parameters for the model system. The parameters assessed included trace elements, buffering, nitrogen concentration, oxygen supply, glucose concentration, alkylbenzene substrate type and possible inducer requirements. Trace elements, phosphate buffering and added nitrogen did not significantly affect the cell growth of Y. lipolytica TVN348. The cell concentration of Y. lipolytica TVN348 and TVN493 was increased by 65% and 43% respectively for an increase in oxygen supply by decreasing the working volume from 150ml to 50ml, while the cell concentration of Y. lipolytica WT was increased by 41% when oxygen supply was increased by switching from non-baffled to baffled flasks in 50ml cultures. Bioconversion was also increased for an increase in oxygen supply: 2.4mM to 29.0mM PAA (Y. lipolytica TVN348) and 1.2mM to 21.7mM PAA (Y. lipolytica TVN493) for a decrease in working volume; 10.5mM to 46.6mM PAA (Y. lipolytica WT) when switching from non-baffled to baffled flasks. These results indicated that adequate oxygen supply is crucial to both growth and bioconversion, and that further study should be conducted in 50ml working volumes. Cell concentrations obtained in 1.6% (wt/v) and 3.2% (wt/v) glucose cultures (3.95x108cells/ml and 4.03x108cells/ml respectively) indicated that cell growth was neither enhanced nor inhibited by 3.2% (wt/v) glucose. Of the range of substrates examined (propylbenzene, butylbenzene, sec-butylbenzene, hexylbenzene, ethyltoluene and tert-butyltoluene for Y. lipolytica TVN348 and TVN493; octylbenzene and decylbenzene for Y. lipolytica WT), hexylbenzene was regarded as the best substrate for bioconversion (14.7mM and 14.1mM PAA for TVN348 and TVN493 respectively; 42.6mM PAA for WT). Lastly, the absence of a requirement for an additional inducer such as ethanol or oleic acid was confirmed when PAA was formed from hexylbenzene in the culture containing additional glucose (25.0mM). This suggested that when using hexylbenzene as substrate, bioconversion was induced provided sufficient glucose was available for cell maintenance. Results from duplicate or triplicate flasks in each individual shake flask experiment were reproducible and conclusions were based solely on results which showed 95% confidence intervals. However, reproducibility problems were experienced with results between different sets of experiments carried out under the same conditions. The model system was therefore defined by: 1) no addition of trace elements, additional buffering or added nitrogen, 2) cultures grown in 50ml volumes to supply an adequate amount of oxygen crucial for growth and bioconversion, 3) 3.2% (wt/v) glucose and 4) addition of 1% (v/v) hexylbenzene at 24h with no inducer requirements. Use of the model system in shake flask cultures to identify the most promising of the three strains of Y. lipolytica supplied demonstrated that there was no significant difference in cell growth or bioconversion between these strains. Y. lipolytica WT (which has no genetic modifications) was therefore used for further investigation until an appropriate strain could be substituted when it became available. The growth and bioconversion of Y. lipolytica WT was further investigated under controlled conditions in a bioreactor. The influence of time of substrate addition (11h, 24h, 48h) and glucose concentration (3.2% and 6.4% (wt/v)) on growth and bioconversion was examined. When hexylbenzene was added at 48h, cell growth was increased (8.90x108cells/ml) when compared to two of the triplicate cultures with hexylbenzene addition at 24h (4.74x108cells/ml and 3.92x108cells/ml) and the culture with hexylbenzene addition at 11h (2.82x108cells/ml). The third of the triplicate cultures with hexylbenzene addition at 24h, on the other hand, exhibited the strongest growth (2.23x109cells/ml). The poor reproducibility between the triplicate cultures with hexylbenzene addition as 24h made it difficult to determine whether hexylbenzene addition at 24h or 48h maximised cell growth. Furthermore, the cell growth was not significantly improved when the glucose concentration was increased from 3.2% (wt/v) to 6.4% (wt/v) (7.47x108cells/ml for 6.4% glucose culture), however it was also not inhibited. The highest amount of specific PAA formed by Y. lipolytica WT was found when hexylbenzene was added at 11h (7.4x10-11mmol PAA/cell), however the highest accumulated PAA was produced in the culture that exhibited the strongest growth with hexylbenzene addition at 24h (41.4mM). This suggested that the bioconversion of hexylbenzene was maximised when it was added during the active growth phase. It is therefore recommended to conduct fed-batch experiments in future to maintain the active growth phase. Accumulated PAA was increased in 6.4% (wt/v) glucose culture (15.2mM PAA) when compared with two of the 3.2% (wt/v) glucose cultures (5.4mM and 4.3mM PAA). These results indicated that the increased glucose concentration did not inhibit the bioconversion. Furthermore, PAA was formed when 5% (wt/v) residual glucose was observed in the culture, suggesting that the bioconversion of hexylbenzene was not inhibited at glucose concentrations as high as 5.0% (wt/v). If future work were to be conducted in bioreactor culture where glucose is added in fed-batch operation, glucose concentrations in cultures of up to 5% (wt/v) could be considered for initial studies. During bioconversion by Y. lipolytica, the PAA measured after hexylbenzene exhaustion did not, however, correspond to 100% conversion. Further, poor reproducibility was found in the bioreactor cultures. The disappearance of hexylbenzene without a corresponding accumulation of PAA and poor reproducibility was investigated by determining whether PAA was further degraded or alternatively, whether other metabolic intermediates were being formed and accumulated from the hexylbenzene. However, substitution of the hexylbenzene with PAA as substrate confirmed that PAA could not be metabolised. Further, NMR analyses of both the aqueous and organic phases of the culture did not identify any additional metabolic intermediates. It is recommended that additional analyses be conducted on the aqueous and organic phases to further assess the possible accumulation of intermediates. The development of the model system in shake flask cultures demonstrated the importance of adequate oxygen supply for both cell growth and bioconversion. It was also shown that no inducer was needed because hexylbenzene acted as its own substrate inducer. Furthermore, comparison of Y. lipolytica strains TVN348, TVN493 and WT under the defined conditions of the model system revealed that the genetically modified strains (TVN348, TVN493) did not exhibit enhanced bioconversion. Bioreactor cultures using the model system under controlled conditions further showed that bioconversion was not inhibited at a 5% (wt/v) residual glucose concentration and suggested that bioconversion was maximised when hexylbenzene was added during active growth phase. This informs on future work, suggesting fed-batch operation in order to extend the active growth phase, where glucose concentrations in the bioreactor of up to 5% (wt/v) can be considered.

Complex I (NADH:ubiquinone oxidoreductase) couples electron transfer to proton translocation across the inner mitochondrial membrane, to drive the synthesis of ATP. Its distinctive L-shaped structure comprises 45 subunits, encoded by both the mitochondrial and nuclear genomes, which are assembled by a complicated modular pathway. Complex I genetic defects are the most common cause of mitochondrial disorders and often present in early childhood, with high mortality rates. Recent high-resolution electron cryo-microscopy structures of mammalian complex I provide a foundation for both interpreting biochemical and biomedical data and understanding the catalytic mechanism. First, this thesis explores how the flavin cofactor is inserted into the NADH-binding (N-) domain of complex I. Genetic manipulation of cultured human cells, to starve them of flavin, revealed a hierarchal impact on the mitochondrial flavoproteome. High riboflavin content in the growth media ameliorated observed phenotypes, requiring cell conditioning in low riboflavin conditions. CRISPR knockout of the putative mitochondrial flavin transporter SLC25A32 demonstrated the severe impact of decreased flavin on complexes I and II, and mass spectrometry 'complexome' analyses suggest that the N-domain is still assembled onto complex I in the absence of the flavin. Second, the model organism Yarrowia lipolytica was used to assess the importance of residues in the quinone-binding site of complex I. Three residues with proposed roles in binding the quinone head-group were targeted. One variant was catalytically inactive, while two retained some activity. They showed decreased ability to reduce physiologically-relevant, long chain quinones, but their ability to reduce short-chain analogues was affected less severely. The results suggest a complicated picture in which interactions between the protein and both the hydrophilic quinone head-group and hydrophobic isoprenoid chain contribute to quinone-binding affinity and catalysis. Finally, a model for human complex I, generated from a recent high-resolution structure of mouse complex I, was used to investigate whether the pathogenicity of human variants could be predicted. Structural information on variant residues, including their secondary structure, proximity to key features and surface exposure, was collated and the power of each property to predict pathogenicity investigated. The analysis was then extended to the whole structure, to identify potential pathogenic hotspots in the enzyme, inform future studies of functionally important regions in complex I, and aid the diagnosis of clinically relevant pathogenic variants.

Chez les espèces végétales soumises à dessiccation, les réserves lipidiques des graines sont stockées sous forme de globules, les oléosomes. Ces oléosomes sont composés d'un cœur de triglycérides (TGs), entouré d'une monocouche de phospholipides (PLs) dans laquelle s'insèrent de petites protéines, majoritairement des oléosines. Ces protéines sont constituées de trois domaines : N- et C-terminaux amphiphiles et un segment central hydrophobe de 72 acides aminés très conservé. Les oléosines sont certainement des protéines de structure et par leur présence, les oléosomes ne coalescent pas, même lors de la re-imbibition de la graine au moment de la germination. Bien que les levures présentent des organites de stockage similaires à ceux des végétaux, leur pool protéique est très différent. Nous avons cloné et exprimé deux isoformes d'oléosines d'A. thaliana dans E. coli et dans Y. lipolytica. Les oléosines exprimées chez la levure sont bien dirigées vers le corps lipidique. Par ailleurs, les oléosines exprimées chez la bactérie ont été purifiées à l'homogénéité en conditions dénaturantes. Par des études in silico et in vitro d'oléosine, nous postulons que le segment hydrophobe est organisé en hélices α. Des études de tension de surface ont montré que les oléosines recombinantes purifiées pouvaient s'insérer à des interfaces eau / huile et qu'elles en abaissaient fortement la tension de surface (ceci mieux que des caséines β). Elles peuvent aussi s'insérer dans des monocouches de PLs situées à l'interface eau / air. Les oléosines des végétaux présentent donc bien des caractéristiques d'émulsifiant huile dans eau.

Chez les espèces végétales soumises à dessiccation, les réserves lipidiques des graines sont stockées sous forme de globules, les oléosomes. Ces oléosomes sont composés d'un cœur de triglycérides (TGs), entouré d'une monocouche de phospholipides (PLs) dans laquelle s'insèrent de petites protéines, majoritairement des oléosines. Ces protéines sont constituées de trois domaines: N- et C-terminaux amphiphiles et un segment central hydrophobe de 72 acides aminés très conservé. Les oléosines sont certainement des protéines de structure et par leur présence, les oléosomes ne coalescent pas, même lors de la re-imbibition de la graine au moment de la germination. Bien que les levures présentent des organites de stockage similaires à ceux des végétaux, leur pool protéique est très différent. Nous avons cloné et exprimé deux isoformes d'oléosines d'A. thaliana dans E. coli et dans Y. lipolytica. Les oléosines exprimées chez la levure sont bien dirigées vers le corps lipidique. Par ailleurs, les oléosines exprimées chez la bactérie ont été purifiées à l'homogénéité en conditions dénaturantes. Par des études in silico et in vitro d'oléosine, nous postulons que le segment hydrophobe est organisé en hélices α. Des études de tension de surface ont montré que les oléosines recombinantes purifiées pouvaient s'insérer à des interfaces eau / huile et qu'elles en abaissaient fortement la tension de surface (ceci mieux que des caséines β). Elles peuvent aussi s'insérer dans des monocouches de PLs situées à l'interface eau / air. Les oléosines des végétaux présentent donc bien des caractéristiques d'émulsifiant huile dans eau.

La compréhension des organismes vivant a été une quête pendant longtemps. Depuis les premiers progrès des derniers siècles, nous sommes arrivés jusqu'au point où des quantités massives de données et d'information sont constamment générées. Bien que, jusqu'au present la plupart du travail a été concentré sur la génération d'un catalogue d'éléments biologiques, ce n'est pas que récemment qu'un effort coordonné pour dé- couvrir les réseaux de relations entre ces parties a'été constaté. Nous sommes intereses à comprendre non pas seulement ces réseaux, mais aussi la façon dont, à partir de ses connexions, émergent des fonctions biologiques. Ce travail se concentre sur la découverte, la modélisation et l'exploitation d'un de ces réseaux : le métabolisme. Un réseau métabolique est un ensemble des réac- tions biochimiques interconnectées qui se produisent à l'intérieur, ou dans les limites d'une cellule vivante. Une nouvelle méthode de découverte, ou de reconstruction des réseaux métaboliques est proposée dans ce travail, avec une emphase particulière sur les organismes eucaryotes. Cette nouvelle méthode est divisée en deux parties : une nouvelle approche pour la modélisation de la reconstruction basée sur l'instanciation des éléments d'un modèle squelette existant, et une nouvelle méthode de réécriture d'association des gènes. Cette méthode en deux parties permet des reconstructions qui vont au-delà de la capacité des méthodes de l'état de l'art, permettant la reconstruction de modèles métaboliques des organismes eucaryotes, et fournissant une relation détaillée entre ses réactions et ses gènes, des connaissances cruciales pour des applications biotechnologies. Les méthodes de reconstruction développées dans ce travail, ont été complétées par un workflow itératif d'édition, de vérification et d'amélioration du modèle. Ce workflow a été implémenté dans un logiciel, appelé Pathtastic. Comme une étude de cas de la méthode développée et implémentée dans le pré- sent travail, le réseau métabolique de la levure oléagineuse Yarrowia lipolytica, connu comme contaminant alimentaire et utilisé pour la biorestauration et comme usine cellulaire, a été reconstruit. Une version préliminaire du modèle a été générée avec Pathtastic, laquelle a été améliorée par curation manuelle, à travers d'un travail avec des spécialistes dans le domaine de cette espèce. Les données expérimentales, obtenues à partir de la littérature, ont été utilisées pour évaluer la qualité du modèle produit. La méthode de reconstruction chez les eucaryotes, et le modèle reconstruit de Y. lipolytica peuvent être utiles pour les communautés scientifiques respectives, le premier comme un pas vers une meilleure reconstruction automatique des réseaux métaboliques, et le deuxième comme un soutien à la recherche, un outil pour des applications biotechnologiques et comme un étalon-or pour les reconstructions futures.

The majority of surfactants commercially available is synthesized from petroleum, thus representing an important source of pollution, causing adverse biological effects to the aquatics organisms. In the detergent industries, despite of many trades available in the market are called as biodegradable and under the legislation actual, it's known that in real the actives components are tensoactives obtained by chemical and not by biochemical route. In other words, what occurred was only a change of the main active component alkylbenzene sodium sulphonate branched chain for one of linear chain, what in fact facilitated the molecular degradation by microorganisms, but not as much as compared to the natural surfactants. Arming to salve those problems, in this work we will show a development process of two biodetergents from biosurfactants that follow environmental appeal and available new alternatives products in the market, using a new technology which may be inserted promise of sustainable industrial development that give attention, specially, to the use of clean technologies. The purpose of this invention is to combine the main soap and synthetic detergent’s features providing an alternative to using of the latter, therefore it adds from the soap its higher biodegradability’s features and from the synthetic detergent its advantage on acting in a still efficient way, even when utilized in hard waters. Initially, were produced two biosurfactants called as liposan and rhamnolipid obtained from aerobic fermentation, using a Yarrowia lipolytica IMUFRJ 50682 yeast strain and another Pseudomonas aeruginosa INCQS 0588092 bacterium straim, respectively. After the analysis of the different experimental conditions, it was concluded that the pH 7.0, at temperature of 35°C with rotation of 150 rpm, were the main factor that influenced on the production of both biosurfactants. The response variables used were surface tension, the index E24, the production of biomass, biosurfactant production and consumption of substrate. After the separation and extraction of the liposan and the rhamnolipid, it was held the modification of the two molecules by a chemical reaction and the biodetergents were formulated adding the adjuvant agents and completing the final volume with distilled water. The efficiency of the biodetergents was evaluated comparing the viscosities from a sample of crude oil with a produced water emulsion/oil containing the biodetergents, where it was verified a reduction on the viscosity, about 8% for the biodetergent 1 derived from the liposan and 36% for the biodetergent 2 derived from the rhamnolipid. It was observed from the analysis of the DSC that the developed biodetergents didn’t show any physico-chemical change when dissolved in samples of distilled water and compared to the produced water, concluding that both show good thermal stability and it wasn’t detected any chemical interaction, on the studied thermal range, between the biodetergents and the present salts in great quantity in the produced water, showing also a good tolerance to ionic strength. Regarding the capacity to produce foam and remove dirt in tissues and dishes both produced biodetergents showed foaming power and detergent action similar when compared to the synthetic detergent commercial. Therefore, it’s concluded that the produced biodetergents show good surfactant and emulsification capacity compared to the chemical synthetic surfactants, maybe being used in substitution themselves for the presented advantages. / A maioria dos surfactantes disponíveis comercialmente é sintetizada a partir de derivados do petróleo, representando assim uma importante fonte de poluição, causando efeitos biológicos adversos a organismos aquáticos. Na indústria de detergentes, apesar das várias marcas disponíveis no mercado serem consideradas biodegradáveis e amparadas pela legislação em vigor, sabe-se que na verdade os componentes ativos são tensoativos obtidos por via química e não bioquímica, ou seja, o que houve foi apenas a mudança do principal componente ativo alquilbenzeno sulfonato de sódio de cadeia ramificada pelo de cadeia linear, o que de fato facilitou a degradação da molécula por microrganismos, mas não tanto quanto ao comparado com os surfactantes naturais. Com intuito de solucionar tais inconvenientes, neste trabalho apresentaremos um processo de desenvolvimento de dois biodetergentes, a partir de biossurfactantes que atendam ao apelo ambiental e que disponibilize no mercado novos produtos alternativos aos já existentes, utilizando uma nova tecnologia que possa estar inserida na promessa de desenvolvimento industrial sustentável que prima, sobretudo, pelo uso de tecnologias limpas. A presente invenção conjuga as principais propriedades do sabão e do detergente sintético proporcionando uma alternativa ao uso destes últimos, pois, agrega do sabão as características de maior biodegradabilidade e do detergente sintético a vantagem de agir de forma ainda eficiente mesmo quando utilizado em águas duras. Inicialmente produziram-se dois biossurfactantes denominados de liposan e ramnolipídeo obtidos a partir da fermentação aeróbia, utilizando-se uma cepa da levedura Yarrowia lipolytica IMUFRJ 50682 e outra cepa da bactéria Pseudomonas aeruginosa INCQS 0588092, respectivamente. Após a análise exploratória das diferentes condições experimentais, concluiu-se que o pH 7,0, a temperatura de 35°C e agitação de 150 rpm, foram os fatores que mais influenciaram na produção dos dois biossurfactantes. As condições experimentais foram analisadas quanto à tensão superficial, o índice E24, a produção de biomassa, a produção do biossurfactante e o consumo do substrato. Após a separação e extração do liposan e do ramnolipídeo, realizou-se a modificação das duas moléculas através de uma reação química e formulou-se os biodetergentes adicionando-se os agentes coadjuvantes e completando-se o volume final com água destilada. A eficiência dos biodetergentes foi avaliada comparando as viscosidades de uma amostra de óleo bruto com uma emulsão água produzida/óleo contendo os biodetergentes, onde se verificou uma redução da viscosidade em torno de 8% para o biodetergente 1 derivado do liposan e 36% para o biodetergente 2 derivado do ramnolipídeo. Observou-se através da análise de DSC que os biodetergentes desenvolvidos não apresentaram transformações físico-químicas quando dissolvidos em amostras de água destilada e comparadas com água produzida, concluindo-se que ambos apresentaram boa estabilidade térmica e que não foi detectada nenhuma interação química, na faixa de temperatura estudada, entre os biodetergentes e os sais presentes em grande quantidade na água produzida, mostrando assim também uma boa tolerância à força iônica. Em relação à capacidade de produzir espuma e de remover sujidades em tecidos e em louças, os dois biodetergentes produzidos apresentaram poder espumante e ação detergente semelhante quando comparado ao sintético comercial. Desta forma, pode-se concluir que os biodetergentes produzidos apresentaram boa capacidade tensoativa e de emulsificação comparado aos surfactantes químicos sintéticos, podendo ser utilizados em substituição aos mesmos pelas vantagens apresentadas.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / Devido aos incentivos governamentais, os quais impulsionam a produÃÃo de biodiesel, tal combustÃvel tem sido produzido em larga escala. Entretanto, o referido crescimento tem se revelado exacerbado, fazendo surgir um preocupante fator: o destino do glicerol excedente da produÃÃo de biodiesel. Tal inquietaÃÃo se mostra clara ao se revelar um importante dado: para cada tonelada de biodiesel obtido, sÃo gerados 100 Kg de glicerol, o que provoca efeitos adversos à economia do biodiesel. Neste contexto, teme-se que o excesso de glicerina produzida, a qual provoca um elevado nÃvel de poluiÃÃo, possa ser descartada de maneira irresponsÃvel no meio ambiente. Sendo assim, tÃm-se desenvolvido pesquisas destinadas à busca de alternativas para a utilizaÃÃo do volume excedente de glicerol. A bioconversÃo de glicerol por via fermentativa à uma alternativa que agrega um valor significativo para a produtividade da indÃstria de biodiesel. O glicerol pode ser utilizado por inÃmeros micro-organismos, em processos metabÃlicos, como fonte de carbono. Leveduras como as da espÃcie Yarrowia lipolytica, quando cultivadas em meio com limitaÃÃo de nitrogÃnio, sÃo capazes de produzir quantidades significantes de Ãcido cÃtrico a partir do glicerol. O Ãcido cÃtrico Ã, atualmente, um dos mais importantes Ãcidos orgÃnicos produzidos por via fermentativa. Devido Ãs suas caracterÃsticas, tem sido amplamente utilizado na indÃstria de alimentos e bebidas e tambÃm como aditivo em detergentes, produtos farmacÃuticos, cosmÃticos e de higiene pessoal. Desta forma, o presente trabalho teve por objetivo avaliar, atravÃs de fermentaÃÃo, rotas de bioconversÃo do glicerol residual da produÃÃo de biodiesel com elevados nÃveis de impurezas, para obtenÃÃo de Ãcido cÃtrico. Para isso, foram utilizadas, inicialmente, duas cepas de leveduras potencialmente produtoras do Ãcido: Yarrowia lipolytica NRRL YB 323 e Yarrowia lipolytica NRRL YB 423. Utilizando a Metodologia de Planejamento Experimental e AnÃlise da SuperfÃcie de Resposta, foram investigadas as concentraÃÃes iniciais de fonte de carbono e fontes de nitrogÃnio orgÃnico (extrato de levedura) e inorgÃnico (sulfato de amÃnio) em frascos agitados. Os resultados revelaram que a concentraÃÃo inicial ideal de glicerol residual do biodiesel como fonte de carbono, dentro da faixa estudada, foi de 20g/L. Quanto Ãs fontes de nitrogÃnio, pÃde-se constatar que estas nÃo apresentaram notÃvel influÃncia para a produÃÃo do Ãcido. TambÃm verificou-se que a adiÃÃo de Tiamina ao meio nÃo promoveu o aumento na quantidade de Ãcido cÃtrico acumulado. A levedura Yarrowia lipolytica NRRL YB 423 se revelou mais eficaz na produÃÃo do Ãcido. Foram realizados ensaios em fermentador de bancada para avaliar- se a melhor concentraÃÃo de oxigÃnio dissolvido no meio. Viu-se que as concentraÃÃes mais elevadas de oxigÃnio dissolvido no meio fermentativo favorecem a produÃÃo de Ãcido cÃtrico. Para nÃveis de oxigÃnio de 50%, observou-se um menor rendimento, enquanto que, para 70%, a produÃÃo de Ãcido cÃtrico foi favorecida. O rendimento percentual final para a produÃÃo de Ãcido cÃtrico obtido a partir de 20g/L de glicerol residual do biodiesel adicionado inicialmente ao meio foi de 24,80% em trÃs dias de fermentaÃÃo. / Due to government financial incentives, which boost the production of biodiesel, there has been a large scale production of this fuel. However, this growth has proved to be exaggerated, rising a worrying factor: the destination of the glycerol excess from biodiesel production. Such concern is clearly shown to prove an important fact: for every ton of biodiesel produced, 100 kg of glycerol are generated, which leads to adverse effects on the biodiesel economy. In this context, it is feared that the over-produced glycerine, which causes a high level of pollution, can be discarded irresponsibly into the environment. So, researches have been being developed, aiming to find other alternatives for the use of the extra volume of glycerol. The bioconversion of glycerol by fermentation is good option that adds significant value to the productivity of the biodiesel industry. Glycerol can be used by several microorganisms in metabolic processes, as a carbon source. Some yeasts species, such as Yarrowia lipolytica, when grown on a media with a limited source of nitrogen, are able to produce significant amounts of citric acid from glycerol. Citric acid is currently one of the most important organic acids produced by fermentation. Due to its characteristics, it has been widely used in food and beverage industry and also as an additive for detergents, pharmaceuticals, cosmetics and toiletries. Thus, this study aimed to evaluate, through fermentation, bioconversion routes of residual glycerol from biodiesel production with high levels of impurities, in order to obtain citric acid. For this, two potential acid-producing yeast strains (Yarrowia lipolytica NRRL YB 323 and Yarrowia lipolytica NRRL YB 423) were initially used. Using the Methodology of Experimental Design and Response Surface Analysis, it was investigated the initial concentrations of carbon sources as well as organic (yeast extract) and inorganic (ammonium sulfate) nitrogen sources in shake flasks. The results obtained showed that the optimal initial concentration of glycerol from waste biodiesel as carbon source, within the studied range, was 20 g/L. As to the nitrogen sources, they were proved having no remarkable influence on the acid production. It was also found that thiamine addition to the media did not promote the increase on the amount of the previously accumulated citric acid. Yarrowia lipolytica NRRL YB 423 was proved more effective on the acid production. The tests which were carried out in the fermenter aimed to evaluate the optimal concentration of dissolved oxygen in the media. It was observed that highest concentrations of dissolved oxygen in fermentation media, promotes the production of citric acid. For levels of 50% oxygen, there was a lower yield, while for 70%, citric acid production was favored. The final percentage yield for the production of citric acid obtained from 20 g/L of residual glycerol from the biodiesel initially added to the media was 24.80%, at the end of three days of fermentation.

The thesis deals with the study of the different yeast strains from the point of view of extracellular lipolytic enzyme production. First part of this work consisting of appropriate yeasts was developed within study interships in Slovak Academy of Sciences, department of Glycomics in Bratislava. From ten given strains three yeasts such as Pseudozyma fusiformata, Meyerozyma guilliermondii, Yarrowia lipolytica were chosen, these strains showed the highest lipolytic activity and cell growth on basal medium with Tween 80. These yeasts were used for optimization of cultivation conditions and characterization of lipolytic enzymes. The yeasts were cultivated on media with different carbon sources, which appeared to be a most suitable medium the basal medium with Tween. Tween acted as and inducer of lipase production. The substrate specificity was determined using three p-nitrophenylester substrates with varying sizes of the fatty acid site chains. The results showed that tested lipases are probably triacylglycerol-acyl-hydrolases which has the highest activity towards in the water insoluble substrates with medium long chains. The pH optimum and temperature optimum were measured. The results showed that the tested lipases had the highest activity in neutral and mild acid region around 30°C. By measuring of thermal stability has been demonstrated that extracellular lipases are relatively thermostable enzymes. Afterwards the storage stability was measured for 5 weeks when supernatant was kept in fridge at 4°C and in freezing box at -20°C. The results showed that in both cases tested lipases exhibited high storage stability which allows to store the samples without loss of activity for a longer time. Finally, the results of lipolytic and proteolytic activity, cell growth and pH of the medium of yeast Y. lipolytica were compared between the batch cultivation in L-tubes with the continual cultivation in the bioreactor. The highest lipases production was achieved in bioreactor due to the setting conditions of the continual proces to regulate the production and enzymatic stability.

Durant les cultures cellulaires en bioréacteur, la physiologie des micro-organismes et les paramètres physico-chimiques (alimentations en gaz et en substrat, agitation, température, pH, pression) interagissent très fortement. La spécificité des bioréactions microbiennes, en relation avec les couplages irréductibles entre les transferts de chaleur, de matière et de quantité de mouvement, réside dans la complexité (milieu triphasique) et la dynamique (bioréaction autocatalysé) de ces systèmes. L’objectif de ce travail est de progresser dans la compréhension et le contrôle dynamique des intéractions entre les aspects biologiques et les aspects physiques à différentes échelles (macro, micro et moléculaire) pour conduire la réaction biologique vers l’objectif défini (production de biomasse, de métabolites intra ou extra cellulaires, …) et l’optimiser. Les cellules (concentration, forme, dimension, physiologie, …) affectent fortement les propriétés physico-chimiques des moûts et par conséquent, les performances des bioprocédés (vitesses spécifiques, rendements, productivité). Le comportement rhéologique particulier du moût est souvent utilisé pour comprendre l’impact de la biomasse microbienne sur le rendement et les performances du bioprocédé.Dans ce travail, des cultures axéniques, définies comme des cultures pures de microorganismes unicellulaires procaryote et eucaryote, sont considérées. Notre approche s’appuie sur des mesures physiques et physico-chimiques en ligne et hors ligne réalisées sur un bioréacteur instrumenté, mesures qui sont mises en place de façon à respecter les conditions imposées par les contraintes biologiques propres aux microorganismes et à la stratégie de culture choisie. Des cultures d’Escherichia coli et d’Yarrowia. lipolytica, à taux de croissance controlé par l’apport de substrat, ont été réalisées dans une gamme de concentration allant de 0.1 à 100 g l-1. Le bilan qui peut être dressé pour ce travail, tant sur les aspects scientifiques que technologiques, est le suivant :- conception et réalisation d’un outil d’investigation original construit sur la base d’un bioréacteur (20 l) et pourvu d’une boucle de recirculation instrumentée pour la mesure,- identification hydrodynamique (courbes de frottement) de conduites calibrées permettant la viscosimétrie en ligne durant une culture cellulaire, - conception, développement et validation d’un code, LoCoPREL, permettant simultanément le contrôle de la culture cellulaire suivant une stratégie définie, la gestion de séquences de débit dans la boucle de dérivation et l’acquisition des données issues de l’instrumentation spécifique employée,- comparaison des mesures réalisées en ligne à débit constant ou selon des séquences de débit,- mise en évidence du comportement non newtonien des moûts et d’écarts entre les mesures en ligne et hors ligne,- analyse des mesures physiques réalisées en ligne et hors ligne, en lien avec les performances de la culture / During cell cultures in bioreactors, micro-organism physiology closely interacts with physico-chemical parameters such as gas and feed flowrates, mixing, temperature, pH, pressure. The specificity of microbial bioreactions in relation with irreductible couplings between heat and mass transfers and fluid mechanics, led into complex (three-phase medium) and dynamic (auto-biocatalytics reaction) systems. Our scientific approach aims to investigate, understand and control dynamic interactions between physical and biological systems at different scales (macro, micro and molecular) for molecules, strains and/or bioprocess innovation. Cells (concentration, shape, dimension, physiology…) strongly affect physico-chemical properties of broth. Then the modification of these characteristics interacts with bioprocess performances (specific rates, yields…) with an improvement or, more frequently, a decrease of yields. Among these properties, rheological behaviour is a strategy widely used to understand the impact of cells and the derivation of bioprocess performances.In this manuscript, axenic cultures, defined as cultures of a pure and unicellular Prokaryote and Eukaryote microorganisms in bioreactors, are considered. Our approach is based on physical and physico-chemical on-line and off-line measurements in respect with accurate and stringent conditions imposed by cell culture strategy. Escherichia coli and Yarrowia lipolytica cultures were investigated with a control of growth rate by carbon feed in the range from 0.1 up to 100 g l-1. Our scientific and technical actions and results led:- to design and realize an original pilot based on a bioreactor (20 l) with a derivation loop including a specific on-line rheometric device as well as additional physical and biological measurements,- to identify, from a hydrodynamic standpoint, the generalized friction curves of calibrated ducts enabling on-line viscosimetry during cell cultures,- to conceive and validate a homemade software, named LoCoPREL, enabling simultaneously to control cell cultures under defined strategy and to manage flow sequences within the derivation loop,- to discuss and compare on-line physical measurements under constant flow rate and various sequence strategy related to investigated shear-rates,- to highlight about the non-newtonian rheological behaviour of broths and the gap between on-line and off-line measurements,- to analyse on-line and off-line physical measurements in the light of biological performances during fed-batch cultures (mass balance, specific rate, yield).