Submitted by Luciane Willcox (luwillcox@gmail.com) on 2016-09-01T16:51:25Z No. of bitstreams: 1 TESE AXEL.pdf: 13901759 bytes, checksum: 6f744b4d3c67d9fcc80db57c1c5944a7 (MD5) / Approved for entry into archive by Luciane Willcox (luwillcox@gmail.com) on 2016-09-01T17:02:42Z (GMT) No. of bitstreams: 1 TESE AXEL.pdf: 13901759 bytes, checksum: 6f744b4d3c67d9fcc80db57c1c5944a7 (MD5) / Made available in DSpace on 2016-09-01T17:02:42Z (GMT). No. of bitstreams: 1 TESE AXEL.pdf: 13901759 bytes, checksum: 6f744b4d3c67d9fcc80db57c1c5944a7 (MD5) / Messenger ribonucleoprotein particles (mRNPs) são complexos formados por RNA mensageiro (mRNA) e um pool de diferentes proteínas que se ligam diretamente ou indiretamente ao mRNA. Proteínas diferentes podem formar diferentes mRNPs com diferentes funções. Agregação de mRNPs formam grânulos que são visíveis ao microscópio. Dois desses grânulos comumente encontrados em células eucarióticas são os processing bodies (PB) e os grânulos de estresse (GE) possuem função fundamental na regulação pós-transcricional, mais especificamente, na degradação (PB) e na estocagem (PB e GE) do mRNA. Enquanto os PB são constitutivamente encontrados, GE são vistos somente em condições de estresse. TTP e RCK são componentes presentes em ambos os grânulos enquanto que TIA1 e TIAR são exclusivos de GE e DCP2 exclusivo de PB. Human Adipocyte Derived Stem Cells (ADSCs) são células-tronco adultas multipotentes com capacidade de autorrenovação e diferenciação em células de diversos tecidos. Desde que pouco se sabe sobre a função dos PB e dos GE durante a diferenciação das células-tronco, nosso objetivo é elucidar a dinâmica e função desses grânulos nestas celulas. Foram utilizadas ADSCs derivadas de cirurgia bariátrica e lipoaspiração. Diversos componentes de PB e de GE foram analisados por Imunofluorescência após 1, 4, 7 e 12 dias de diferenciação adipogênica. Oligos de RNA de interferência (siRNA) específicos para RCK, DCP2, TTP, TIAR e TIA1 foram transfectados concomitantemente com a indução à diferenciação adipogênica e as culturas mantidas por 1, 4, 7 e 14 dias de diferenciação. A diferenciação foi mensurada por intensidade de fluorescência após marcação com AdipoRed. GE são ausentes em ADSCs indiferenciadas e durante a diferenciação como determinado por imunomarcação com TIAR que se localiza predominantemente no núcleo. Interessantemente imunomarcação com TIA1/R mostrou que ADSCs possuem grande quantidade de grânulos contendo TIA1/R em células indiferenciadas e não estressadas. Sob estresse oxidativo há um aumento de PB em ADSCs e a formação de GE. Esses grânulos parecem variar de composição, uma vez que eIF4E é ausente e GE imunomarcados com eIF4B são mais perinucleares do que GE imunomarcados com TIAR. PB variam em número e tamanho em células diferenciadas. Notavelmente, em ADSCs possuem poucos PB e até mesmo ausente em algumas células, além disso, TIA1/R e PB significativamente aumentam após 24 horas de diferenciação e após 12 dias o número de PB é similar a células diferenciadas enquanto que os grânulos de TIA1/R praticamente desaparecem. siRNA de componentes essenciais de PB e GE em ADSCs indiferenciadas (tempo 0) mostrou que há um aumento significativo na diferenciação em adipócito após 4, 7 e 12 dias de diferenciação adipogênica. Interessantemente esse aumento se deu pela maturação do adipócito, i.e. tamanho da vesícula de lipídio e não pelo aumento da quantidade de células diferenciadas. Nossos dados mostram que PB estão em baixo número e que existem grânulos de TIA1/R citoplasmárico nunca antes mostrados em ADSCs indiferenciadas. Ainda, esses grânulos aumentam durante a diferenciação e parecem exercer um papel importante na maturação dos adipócitos uma vez que ensaios de siRNA de componentes de PB e GE levam a uma diferenciação mais acelerada. Também, os GE são formados após indução a estresse oxidativo e esses grânulos são praticamente ausentes de eIF4E mostrando que a composição desses grânulos varia em relação a células diferenciadas.

Cytoplasmic mRNA-containing granules in eukaryotic cells play key roles inthe storage, localisation and degradation of mRNA. In yeast, depletion of glucoseleads to the rapid inhibition of translation initiation and consequent appearance of Pbodiesand EGP-bodies. P-bodies contain factors of the mRNA decay pathway andtherefore, are likely to be sites in which mRNAs targeted for degradation arelocalised. In contrast, EGP-bodies lack decay components and contain onlytranslation initiation factors and RNA binding proteins. Thus EGP-bodies have beensuggested to be storage repositories for mRNAs that need to be rapidly translatedfollowing glucose readdition. In this study we utilised the m-TAG system to investigate the localisation ofendogenous MS2-tagged mRNAs with P-bodies and EGP-bodies. A triplefluorescent labelled system developed show that a class of unregulated mRNAslocalised into P-bodies following glucose starvation. It was also observed that thesespecific abundant classes of mRNAs can be found in aggregates prior to any cellularstress and upon glucose starvation these aggregates coalesce into larger granules thatcolocalise with P-body components. This coalescence of mRNA aggregatesfollowing glucose starvation does not rely upon the recruitment of mRNA decayfactors and appears to precede this event. Indeed mRNAs in mutants deficient in Pbodyformation still develop large aggregates following glucose stress. In unstressedcells it appears that the mRNA granules are implicated in high-level translation ofthese specific abundant mRNAs. Following the inhibition of translation initiation inresponse to stress, these granules nucleate P-body formation via aggregation and therecruitment of mRNA decay factors.

No description available.

No description available.

La dégradation des ARN est un mécanisme essentiel à la régulation de l’expression des génomes. L’importance de l’uridylation dans les mécanismes de dégradation des ARN commence juste à être appréciée. Cette thèse présente l’étudede l’UTP :RNA Uridylyltransferase 1 (URT1) et de son rôle dans la dégradation des ARN chez Arabidopsis thaliana. L’étude des propriétés catalytiques de URT1 montre que cette uridylyltransférase est intrinsèquement spécifique des UTP et distributive pour les premières uridines ajoutées. URT1 est responsable in vivo de l’uridylation des ARNm après une étape de déadénylation, protégeant leur extrémité 3’ et polarisant la dégradation de 5’ en 3’. URT1 est localisée dans le cytosol au niveau des granules de stress et des processing bodies. Le mécanisme d’adressage de URT1 dans les processing bodies implique une partie de la région N terminale prédite comme intrinsèquement désorganisée, alors que le domainenucléotidyltransférase C terminal semble suffisant pour permettre l’adressage de URT1 au niveau des processing bodies et granules de stress en réponse à un stress thermique. Ces travaux de thèse ont permis de mieux comprendre les mécanismes et les rôles de l’uridylation dans la dégradation des ARNm chez Arabidopsis. Ils ouvrent des perspectives dans l’étude d’autres fonctions de l’uridylation comme l’inhibition de la traduction. / RNA degradation is an essential mechanism for the regulation of genome expression. The importance of uridylation for RNA degradation is just emerging. This thesis presents the study of URT1 (UTP :RNA Uridylyltransferase 1) and its role in RNA degradation in Arabidopsis thaliana. URT1 is an uridylyltransferase intrinsically and strictly specific for UTP and is distributive for the first nucleotides added. URT1 uridylates mRNA in vivo after a deadenylation step. This uridylation protects mRNA’s3’ end from further attacks and polarise degradation in the 5’ to 3’ direction. This protection of 3’ ends by uridylation and its conferred polarity of 5’ to 3’ degradation are also detected in polysomes. Uridylation is therefore likely important in case of cotranslational degradation of mRNAs. A region in URT1’s N terminal region predicted to be intrinsically disorganised is required for addressing URT1 to processing bodies. However, following heat shock, the nucleotidyltransferase domain present in the C terminal region of URT1 is sufficient to address URT1 to both processing bodies and stress granules, This work contributes to a better understanding of the mechanisms and roles of uridylation in RNA degradation in Arabidopsis thaliana. These results also open perspectives for studying other functions of uridylation such as translation inhibition.

<p>Intracellular membrane trafficking is regulated by a large number of protein complexes and lipids. Blocking of trafficking disrupts normal membrane dynamics and causes membrane stress. Two similar proteins from <i>Saccharomyces cerevisiae</i>, Myr1 and Smy2, each containing a polyproline-binding GYF domain, were discovered in separate screens for dosage suppressors of trafficking mutations. The functions of GYF domain proteins are poorly described despite its determined structure and a number of known polyproline peptide ligands. We predicted, using computational analysis, associations between mRNA decay factors and both Myr1 and Smy2, and further demonstrated that they localize to sites of mRNA degradation upon stress, in a GYF domain dependent manner.</p><p>Ypt6 is a small GTPase that regulates vesicle docking at the late Golgi in budding yeast. Myr1 was found as a novel suppressor during the screening of a genomic library in a null ypt6 mutant. Myr1 additionally was capable of rescuing the temperature sensitive growth of a Ric1 deficient strain. Importantly, Ric1 is an activator of Ypt6 and is synthetic lethal with Myr1. Biochemical characterization of the Myr1 protein revealed a limited solubility and an ability to bind cellular membranes, likely relevant to the rescue of trafficking mutants.</p><p>We further assayed the affinity of Myr1 domains to liposomes of distinct composition. Preference for negatively charged lipids suggested possible electrostatic interactions with polybasic clusters within C-terminal regions of Myr1. In contrast, the N-terminus with the GYF domain was found to be capable of self-association. Membrane stress caused by a lipid-bilayer perturbing drug resulted in induced formation of mRNA processing bodies. Cumulatively, these studies suggest that Myr1 functions in the regulation of mRNA stability via its GYF domain, and can sense membrane stress by binding to the lipid bilayer.</p>

Intracellular membrane trafficking is regulated by a large number of protein complexes and lipids. Blocking of trafficking disrupts normal membrane dynamics and causes membrane stress. Two similar proteins from Saccharomyces cerevisiae, Myr1 and Smy2, each containing a polyproline-binding GYF domain, were discovered in separate screens for dosage suppressors of trafficking mutations. The functions of GYF domain proteins are poorly described despite its determined structure and a number of known polyproline peptide ligands. We predicted, using computational analysis, associations between mRNA decay factors and both Myr1 and Smy2, and further demonstrated that they localize to sites of mRNA degradation upon stress, in a GYF domain dependent manner. Ypt6 is a small GTPase that regulates vesicle docking at the late Golgi in budding yeast. Myr1 was found as a novel suppressor during the screening of a genomic library in a null ypt6 mutant. Myr1 additionally was capable of rescuing the temperature sensitive growth of a Ric1 deficient strain. Importantly, Ric1 is an activator of Ypt6 and is synthetic lethal with Myr1. Biochemical characterization of the Myr1 protein revealed a limited solubility and an ability to bind cellular membranes, likely relevant to the rescue of trafficking mutants. We further assayed the affinity of Myr1 domains to liposomes of distinct composition. Preference for negatively charged lipids suggested possible electrostatic interactions with polybasic clusters within C-terminal regions of Myr1. In contrast, the N-terminus with the GYF domain was found to be capable of self-association. Membrane stress caused by a lipid-bilayer perturbing drug resulted in induced formation of mRNA processing bodies. Cumulatively, these studies suggest that Myr1 functions in the regulation of mRNA stability via its GYF domain, and can sense membrane stress by binding to the lipid bilayer.

No description available.