The thesis is aimed at understanding of molecular mechanisms of autophagic degradation of peroxisomes (pexophagy) in the yeast Yarrowia lipolytica. This microorganism has been extensively used to explore peroxisome biogenesis (Titorenko and Rachubinski, 2000). Gunkel et al. (1999) intoduced Y. lypolitica into pexophagy studies. However, the field of pexophagic research on this yeast remains quite unexplored. This work involved following tasks: (1) the development and optimization of Y. lipolytica as a model system to study peroxisome degradation; (2) Y. lipolytica genes and proteins implicated in pexophagy should be found and characterized; (3) a proper easy-to-handle selection procedure to isolate novel peroxisome degradation-deficient(pdd) mutants of Y. lipolytica should be devised.

The retrotransposon Ylt1 was described previously from the genome of the dimorphic fungus Yarrowia lipolytica. Remarkably, Ylt1 is currently the largest LTR retrotransposon reported from fungal genomes. However, little was known about its biology and its interactions with host genome. So, the aim of this work was the characterization of properties of Ylt1.Analysis of proteins encoded by Ylt1 (Gag protein and integrase) was carried out during this work. To enable their detection, both proteins were tagged with HA epitopes. The sizes of Gag protein and putative precursors of Gag protein and integrase were estimated, and a model for the proteolytic processing of the polyprotein of Ylt1 was proposed. It was shown that Gag protein of Ylt1 is about 2-fold larger than Gag proteins of other studied yeast retrotransposons. An analysis of Ylt1 expression was also performed. Production of the Ylt1 Gag protein under different conditions was analyzed by Western blotting. Expression of Ylt1 occurred on all tested carbon sources. The amount of Ylt1 decreased rapidly upon transition to stationary growth phase, in the presence of copper sulfate and under heat shock conditions. It is suggested that Ylt1 is expressed in actively growing cells, whereas stress conditions have a negative impact on its expression. Such expression pattern was not previously reported for other yeast retrotransposons. Activity of Ylt1 in vivo was characterized using an Ylt1 elements tagged with SUC2 gene of Saccharomyces cerevisiae. Mobilization of the marked Ylt1 element and its transposition from autonomous plasmid into host genome was observed in performed experiments. Obtained results strongly support the idea that Ylt1 is transpositionally active. Formation of tandem repeats by newly inserted Ylt1 elements was observed in several cases. It is suggested that integrase function was affected in this case, and that the integration was mediated by homologous recombination instead. Analysis of the Ylt1 insertion specificity and of the Ylt1 distribution in the genome of Y. lipolytica E150 was done. The remarkable sequence specificity of Ylt1 insertions, which is unusual for LTR retrotransposons, was revealed during this analysis. Also, it was shown that Ylt1 insertions are found mainly in intergenic regions, often at a significant distance (>500 bp) from the next reading frame. No association of Ylt1 insertions with tRNA genes was observed. Searches for Ylt1-related elements in the Y. lipolytica genome database were performed. The novel Ty3/gypsy element Tyl6 was found in the genome of Y. lipolytica E150. The sequence analysis of this element was carried out. It was shown that structural properties of Tyl6 resemble the properties of the Ty3 element of S. cerevisiae. However, two reading frames of Tyl6 (gag and pol) are separated by -1 frame-shift, which was not previously reported for retrotransposons of hemiascomycetous yeasts. Phylogenetic analysis placed Tyl6 within chromoviruses, and the Tse3 element of S. exiguus was shown to be the closest relative of Tyl6. The distribution of Tyl6 among Y. lipolytica strains was analyzed. Interestingly, the novel element was found only in strains derived from the strain YB423-12. The strains of independent origin included in the analysis were shown to be Tyl6-free. The same distribution was previously reported for the retrotransposon Ylt1 and for the DNA transposon Mutyl. Two models of the evolution of transposable elements in Y. lipolytica genome were proposed based on these results.

No description available.

Eine der für die biotechnologische Nutzung interessanten Eigenschaften der Hefe Yarrowia (Y.) lipolytica ist ihr Vermögen, unter bestimmten Kultivierungsbedingungen große Mengen an organischen Säuren, darunter auch Citronensäure (CS), ins extrazelluläre Medium zu sekretieren. Aufgrund ihrer Apathogenität, ihres breiten Substratspektrums und ihrer guten molekulargenetischen und verfahrenstechnischen Handhabbarkeit, stellt sie einen idealen Mikroorganismus zur biotechnologischen Gewinnung von Citronensäure dar. Bei der durch eine Stickstofflimitation ausgelösten Überproduktion von CS mit Y. lipolytica kommt es parallel auch zur Ausscheidung von Isocitronensäure (ICS), deren Anteil am Gesamtsäureprodukt in Abhängigkeit von der C-Quelle in Wildtypstämmen zwischen 10 % (Glucose, Saccharose, Glycerol) und 40-55 % (Pflanzenöle, Alkan) liegt. In der Literatur beschriebene Mutantenstämme von Y. lipolytica besitzen ein von Wildtypstämmen abweichendes Produktmuster und können sowohl weniger (2-5 % auf Glucose, 5-10 % Alkan und Pflanzenöl) als auch mehr ICS (15-35 % Glu¬cose, 65-75 % Alkan, Ethanol bzw. Pflanzenöl) sekretieren. Die gezielte Überexpression des für die Isocitratlyase codierenden Gens ICL1 durch die Erhöhung der Kopiezahl führte zu einer drastischen Erhöhung der Enzymaktivität in den entsprechenden ICL1 multicopy Transformanden (10-15fach gegenüber Wildtyp) aufgrund des Gen-Dosis-Effektes. Auf den getesteten hydrophilen C-Quellen Glucose, Glycerol und Saccharose verringerte sich der ICS-Anteil von durchschnittlich 10-12 % auf 3-5 %, auf den hydrophoben C-Quellen Hexadecan und Sonnenblumenöl sogar von durchschnittlich 40-55 % auf Werte um 5-10 %. Im Ergebnis dieser Untersuchungen entstand ein Patent (DE10333144A1), welches ein Verfahren zur Gewinnung von CS mit einer genetisch veränderten Hefe Y. lipolytica beschreibt. Die Zerstörung des Leserahmens des ICL1 Gens in Mutantenstämmen bewirkte das Ausbleiben der Synthese einer funktionell aktiven Isocitratlyase, was den Verlust der Fähigkeit zur Verwertung gluconeogenetischer C-Quellen wie Ethanol, Alkan und Pflanzenölen zur Folge hatte. Auf Glucose bzw. Glycerol zeigten diese Mutantenstämme im Vergleich zum Wildtypstamm jedoch nur eine geringe Erhöhung des ICS-Anteils um durchschnittlich 2-5 Prozentpunkte. Die Zerstörung des Leserahmens des IDP2 Gens, codierend für die NADP-abhängigen Isocitratdehydrogenase, führte zur Glutamat-Auxotrophie des entsprechenden Mutantenstammes auf allen getesteten C-Quellen. In der Produktbildung zeigte diese Mutante im Vergleich zum Wildtypstamm eine Verringerung des ICS-Anteils um durchschnittlich 2-4 Prozentpunkte. Es konnte gezeigt werden, dass Saccharose ein geeignetes Substrat zur Gewinnung von CS mit rekombinanten Stämmen von Y. lipolytica darstellt, die das für die Invertase codierende SUC2 Gens aus Saccharomyces cerevisiae exprimieren. Natürlicherweise kann Y. lipolytica diesen Zucker aufgrund des Fehlens des Enzyms Invertase nicht verwerten. Im Schüttelkolben wurden aus 100 g/l Saccharose unter nicht optimierten Bedingungen bereits 56 g/l CS+ICS gewonnen. Nach der Optimierung durch die Reduktion des für die Invertaseexpression durch pXPR2 notwendigen Peptonanteils von 1,7 auf 0,4 g/l erhöhte sich die Produktkonzentration auf 77 g/l. Die Übertragung des Produktionsprozesses in den Bioreaktor hatte die Verdopplung der Produktbildungsraten (RZA von 0,4 auf 0,85 g/l*h, r von 46 auf 89 mg/g*h) zur Folge, bedingt durch die Aufhebung der Sauerstofflimitation. Die Steigerung der Invertaseaktivität, die sich unter Bioreaktorbedingungen als ein Limi¬tationsfaktor her¬ausstellte, konnte durch die Anhebung des pH-Wertes von 5,0 auf 6,0 bzw. 6,8 er¬reicht werden. Dadurch konnten die Produktbildungsrate RZA um bis zu 80 % von 0,42 auf 0,76 g/l*h, die biomassespezifische Produktbildungsge¬schwin¬digkeit r um bis zu 70 % von 0,06 auf 0,1 g/g*h und die Ausbeute um bis zu 64 % von 0,5 auf 0,82 g/g gesteigert werden. Einen weiteren Limitationsfaktor für den CS-Bildungsprozess aus Saccharose stellt bei ausreichender Invertaseexpression offenbar die Aufnahme von Glucose und Fructose dar. Die Hefe Y. lipolytica zeigte höchste Produktbildungsraten aus Pflanzenölen, wie Sonnenblumen- oder Rapsöl, als nachwachsende Rohstoffe. Um zu prüfen, ob die Produktivität der CS-Bildung aus Pflanzenölen mit Y. lipolytica gesteigert werden kann, sollte die Triglyceridverwertung durch die Erhöhung der extrazellulären Lipaseaktivität verbessert werden. Dazu wurden zum einen Insertionsmutantenstämme, die auf eine erhöhte extrazelluläre Lipaseaktivität im Plattentest hin selektiert wurden, charakterisiert. Zum anderen wurde das für die extrazelluläre Lipase codierende LIP2 Gen in Y. lipolytica überexprimiert. Die erhaltenen LIP2 multicopy Transformanden zeigten eine bis zu 400fach erhöhte Lipaseaktivität im Vergleich zum Wildtypstamm (von 400 U/l auf bis zu 150000 U/l). Eine Verbesserung der Triglyceridverwertung aufgrund der Erhöhung der extrazellulären Lipaseaktivität in den untersuchten Insertionsmutanten und LIP2 multicopy Transformanden wurde nicht festgestellt. Die erhaltenen Daten für die Produktbildungsrate RZA (0,9-1,1 g/l*h), die biomassespezifische Produktbildungsgeschwindigkeit r (0,08-0,14 g/g*h) und die Ausbeuten (1,3-1,5 g/g) waren innerhalb der untersuchten Stämme vergleichbar und ließen keine verbesserte Produktbildung erkennen. Der geschwindigkeitsbestimmende Schritt liegt offenbar nicht bei der Hydrolyse der Triglyceride durch Lipasen, sondern bei der Aufnahme und dem Transport der Fettsäuren und/oder deren Katabolismus.

Les levures non conventionnelles, dont Yarrowia lipolytica, sont devenues desusines cellulaires attractives pour la production de protéines recombinantes. Lasélection de promoteurs régulés impliqués dans le métabolisme de substratshydrophobes est d'un grand intérêt pour une telle application. Dans ce cadre,l’objectif de ce projet est de mieux comprendre la régulation des promoteurs desgènes POX2 et LIP2 dans le but d’améliorer la production de protéinesrecombinantes chez Y. lipolytica.D’un point de vue biotechnologique, l'analyse à l’échelle cellulaire est devenueune approche répandue pour l’analyse et l’optimisation des bioprocédés. Ainsi,l'objectif de la première partie de ce projet vise le développement d’une méthoded’analyse en ligne des paramètres de culture Y. lipolytica dans un milieu contenantde l’acide oléique. Cette technique consiste au couplage d’un bioréacteur à uncytomètre en flux via une interface d’échantillonnage automatique. Cetteméthodologie a conduit principalement à une analyse rapide de la croissancecellulaire, de l'accumulation des lipides, du dimorphisme ainsi qu’à l'analyse duniveau d’induction des promoteurs chez Y. lipolytica.Les systèmes d’expression basés sur les promoteurs LIP2 et POX2 sont difficilesà manipuler, principalement en raison de l’utilisation de substrats insolubles dansl’eau (acide oléique) comme inducteur. Dans ce travail, il a été clairement démontréque pLIP2 est le promoteur de choix à utiliser pour développer un procédé deproduction de protéines recombinantes par culture de Y. lipolytica dans un milieucomplexe. De plus, l’utilisation d’un mélange acide oléique-glucose 60/40 (w/w) aconduit à une amélioration du niveau d’induction du promoteur LIP2 par un facteurde 10 par rapport à utilisation l'acide oléique. De plus, l’analyse à l’échelle cellulairemontre que ces deux substrats sont co-consommés par les cellules.Enfin, la dernière partie de cette thèse a eu pour but d'étudier la régulation dupromoteur LIP2 par rapport à la transition dimorphique. Nos résultats ont clairement montré que le changement morphologique chez Y. lipolytica n'a pas d'impact sur larégulation de pLIP2.L’ensemble de ces études a conduit à une meilleure compréhension de laphysiologie de Y. lipolytica, soulignant son potentiel avéré de production desprotéines recombinantes. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Les composés hydrophobes sont connus comme des sources de carbone qui peuvent être utilisées par les levures comme Yarrowia lipolytica pour de multiples applications. Ces composés causent parfois des perturbations aux levures mais sont aussi rapportés comme conférant aux cellules une certaine résistance contre les stress environnementaux. Dans le cadre de cette thèse, nous avons étudié le rôle de l'oléate de méthyle comme source de carbone sur la résistance de la levure Y. lipolytica en réponse au choc d'un composé amphiphile, la -dodécalactone, et au stress thermique. Les résultats obtenus montrent que les cellules ayant poussé sur oléate sont beaucoup plus résistantes au choc lactone ainsi qu'au stress thermique que les cellules ayant poussé sur glucose. L'action de la lactone se trouve au niveau de la membrane où elle cause une fluidification membranaire et une déplétion de stérols qui sont considérés comme la cause de la mort cellulaire. Ce travail met en évidence le rôle des corps lipidiques dans la réponse cellulaire qui se manifeste de différentes manières en réponse à ces stress. Une accumulation des corps lipidiques est importante pour la résistance de la cellule aux stress. Les cellules ayant poussé sur glucose transforment leur stérol libre en esters de stéryle pour former les corps lipidiques en réponse au choc lactone, ce qui augmente leur sensibilité. Tandis que les cellules ayant poussé sur oléate qui ont accumulé des corps lipidiques pendant leur croissance ont tendance à convertir leurs esters de stéryle en stérol libre pour compenser la déplétion de stérol membranaire causée par la lactone ce qui diminue leur sensibilité. L'homéostasie de l'ergostérol, liée à la présence de corps lipidiques, semble donc jouer un rôle clé dans la résistance cellulaire à ces stress. Ce travail relève aussi que la présence de lipides modifie le processus de mort cellulaire programmée de Y. lipolytica en réponse à un stress thermique.

University, Diss., 2004--Frankfurt (Main). / Zsfassung in engl. und dt. Sprache.

University, Diss., 2005--Frankfurt (Main). / Zsfassung in engl. und dt. Sprache.

No description available.

Submitted by Mario BC (mario@bc.ufrpe.br) on 2018-03-14T13:22:12Z No. of bitstreams: 1 Danyelle Khadydja Felix dos Santos.pdf: 27852030 bytes, checksum: 9c7b67c95867750ad685525f6607b8d1 (MD5) / Made available in DSpace on 2018-03-14T13:22:12Z (GMT). No. of bitstreams: 1 Danyelle Khadydja Felix dos Santos.pdf: 27852030 bytes, checksum: 9c7b67c95867750ad685525f6607b8d1 (MD5) Previous issue date: 2017-02-20 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Financiadora de Estudos e Projetos - Finep / Surfactants are amphipathic powerful agents with application in various industries, especially in the oil industry. Many types of chemically synthesized surfactants are used today, although the development of alternative products, biodegradable and less toxic as the so-called biosurfactants agents obtained by microbiological route, becomes an important strategy to achieve products adequate for use in the environment, and with specific properties and applications. Many biosurfactants have been produced, although few are marketed due to the high production cost involved in obtaining these compounds, especially as regards the use of expensive substrates and purification processes. In this sense, this project proposed studies directed towards maximizing the production of a low cost biosurfactant for application in environments contaminated by petroleum derivates and heavy metals. Experiments were conducted to maximize the production of the biosurfactant from Candida lipolytica UCP0988 cultivated on 5% animal fat and 2.5%corn steep liquor using a 23 full factorial design. The effects and interactions of the agitation speed (200, 300 and 400rpm), the variables aeration (0, 1 and 2vvm) and time of cultivation (48, 96 and 144h) on the surface tension, yield and biomass were evaluated. The results showed that the variable time of cultivation had positive influence on the production of biosurfactant, while the increase of the variables aeration and agitation showed a negative effect. This study investigated the large-scale production, characterization, evaluation of toxicity and economic analysis of the biosurfactant produced by Candida lipolytica UCP 0988 grown in amedium containing 5% animal fat and 2.5% corn steep liquor. The kinetics of biosurfactant production was described. The biosurfactant producedin the stationary growth phaseunder agitation of 200rpm andin the absence of aeration reducedthe surface tension of the medium to 28mN/m after 96 h, yielding 10.0 g/L ofisolated biosurfactant in a 2 L bioreactor. The production was maximized in a 50 L bioreactor, reaching 40 g/L biosurfactant and 25 mN/m. The cell biomasswas quantifiedand characterizedfor usein animal nutrition. Chemical structures of the biosurfactant were identified using Fourier transform infrared spectroscopy (FTIR) and Nuclear magnetic resonance spectroscopy (NMR). The crude biosurfactant was not toxic to the bivalve Anomalocardia brasiliana, to the microcrustacean Artemia salina, or three species of vegetables seeds. The formulated biosurfactant was also not toxic to the fish Poecilia vivipara. The addition of the biosurfactant to seawater stimulated the degradation of motor oil via the activity of the indigenous microorganisms. In tests carried out with seawater, the crude biosurfactant demonstrated 80% oil spreading efficiency in the screening dispersion test. Regarding the swirling bottle test, the dispersion rate was 50% for the isolated biosurfactant at a concentration twice the critical micelle concentration. The biosurfactant proved to be efficient in detergency tests, as it removed 70% of motor oil from contaminated cotton cloth. Application for the removal of heavy metals demonstrated that the crude biosurfactant removed 30 to 40% of Cu and Pb from standard sand, while the isolated biosurfactant removed approximately 30% of the heavy metals. The HCl solution tested removed 60 to 50% of Cu, Pb and Zn and greatly increased the removal of metals when used together with the biosurfactant. The conductivity of the solutions containing Cd and Pb was sharply reduced by the biosurfactant. To provide a commercial surfactant, the biosurfactant was subjected to a preservation method based on the addition of 0.2% potassium sorbate over 120 days to estimate the validity of the product to be offered to the market. The formulated biosurfactant was analysed for emulsification and surface tension under different pH values, temperatures and the addition of NaCl. The results showed that the formulation did not cause significant changes in the tensoactive capacity of the biomolecule, indicating the possibility of its use in specific environmental conditions. The biosurfactant from C. lipolytica demonstrated versatility as a bioremediation agent of organic and inorganic pollutants as well as potential for industrial application as a stable, safe commercial agent. / Os surfactantes são poderosos agentes anfipáticos com aplicação em vários segmentos industriais, especialmente nas indústrias petrolíferas. Muitos tipos de surfactantes quimicamente sintetizados são hoje utilizados; entretanto o desenvolvimento de produtos alternativos, biodegradáveis e menos tóxicos, como os chamados biossurfactantes, agentes obtidos por via microbiológica, torna-se uma estratégia importante na obtenção de produtos mais compatíveis com o meio ambiente e na ampliação das propriedades específicas e aplicações desses compostos. Muitos biossurfactantes têm sido produzidos, embora poucos sejam comercializados em virtude do alto custo de produção envolvido na obtenção desses compostos, principalmente no que se refere à utilização de substratos custosos e aos processos de purificação. Neste sentido, este trabalho propôs estudos para a produção de um biossurfactante de baixo custo para aplicação na despoluição de ambientes contaminados por derivados de petróleo e metais pesados. A maximização da produção do biossurfactante de Candida lipolytica UCP0988 cultivada em 5% de gordura animal e 2,5% de milhocina, foi inicialmente realizada em biorreator de 2L a partir de um planejamento fatorial 23 com ponto central. Os efeitos e interações da velocidade de agitação (200, 300 e 400rpm), aeração (0, 1 e 2vvm) e tempo de cultivo (48,96 e 144h) sobre a tensão superficial, o rendimento e a biomassa foram avaliados. Os resultados mostraram que o tempo de cultivo teve uma influência positiva na produção do biossurfactante, enquanto que o aumento da aeração e da agitação provocou um efeito negativo. A produção do biossurfactante em condições de cultivo maximizadas de 200 rpm e na ausência de aeração, alcançou valores em torno de 10,0 g/L em biossurfactante, com redução da tensão superficial para 28 mN/m após 96 horas. A curva de produção do biossurfactante demonstrou que a biomolécula foi produzida na fase estacionária de crescimento como metabólito secundário. Com o scale-up de produção do biossurfactante em reator de 50L, 40 g/L de biossurfactante foram produzidos, com tensão superficial de 25 mN/m. A biomassa celular foi quantificada e caracterizada para utilização como complemento nutricional em ração animal. A estrutura química do biossurfactante foi identificada utilizando Espectroscopia de infravermelho de Fourier (FTIR) e Espectroscopia de ressonância magnética nuclear (RMN). O biossurfactante bruto não apresentou toxicidade frente ao bivalve Anomalocardia brasiliana e ao microcrustáceo Artemia salina e nem frente a três espécies de sementes de hortaliças testadas. O biossurfactante formulado também não apresentou toxicidade frente ao peixe Poecilia vivipara. A adição de biossurfactante à água do mar estimulou a degradação do óleo de motor através da ação dos micro-organismos autóctones. Testes de dispersão demonstraram 80% de dispersão do óleo na água do mar, enquanto que os experimentos conduzidos em garrafas cilíndricas demonstraram valores em torno de 50% de dispersão para o biossurfactante isolado no dobro de sua concentração micelar crítica (1,6%). O biossurfactante mostrou-se eficiente em testes de detergência, com remoção de 70% de óleo de motor em tecido de algodão. A aplicação do biossurfactante bruto na remoção de metais pesados em amostras de areia padrão demonstrou 30 e 40% de remoção de Cu e Pb, respectivamente, enquanto que o biossurfactante isolado removeu cerca de 30% dos metais pesados. A solução de HCl removeu 60-50% de Cu, Pb e Zn e aumentou consideravelmente a remoção dos metais quando utilizada juntamente com o biossurfactante. A condutividade de soluções aquosas de efluente de mina preparado em laboratório contendo Cd e Pb foi drasticamente reduzida pelo biossurfactante. Com a finalidade de fornecer um produto comercial com vida de prateleira prolongada, o biossurfactante foi submetido ao método de conservação baseado na adição de sorbato de potássio a 0,2% e testado ao longo de 120 dias a fim estimar a eficácia do produto a ser oferecido no mercado. O biossurfactante formulado foi então analisado quanto à emulsificação à tensão superficial, sob diferentes valores de pH, temperatura e a adição de NaCl. Os resultados mostraram que a formulação não causou alterações significativas na capacidade tensoativa da biomolécula, indicando a possibilidade da sua utilização em condições ambientais específicas. Os resultados obtidos nesse trabalho demonstraram a versatilidade do surfactante de C. lipolytica como agente de biorremediação de poluentes orgânicos e inorgânicos, bem como potencial para aplicação industrial como um agente comercial estável e seguro.