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Étant donnée la séquence hautement conservée de la NC et son rôle crucial dans le cycle viral de VIH-1, les molécules inhibant la NC sont susceptibles d'agir comme complément aux thérapies anti-rétrovirales à haute activité (HAART) basées sur des médicaments ciblant les enzymes virales, Des médicaments anti-NC sont ainsi susceptibles d'entraîner un maintien de l'inhibition de la réplication d'un large panel d'isolats VIH-1 incluant des lignées virales résistantes aux médicaments ciblant les enzymes virales. Récemment, dans le cadre du consortium Européen TRIoH, de nouvelles stratégies visant à cibler spécifiquement les propriétés chaperonnes de la NC sur les acides nucléiques ont été développées. Selon une stratégie protégée par un brevet soumis, une série de peptides a été conçue afin d'agir comme compétiteurs de la NC et pouyant ainsi inhiber la réplication du virus. Au sein de cette série, plusieurs peptides ont montré une inhibition efficace des propriétés de déstabilisation des acides nucléiques par la NC. Quatre de ces peptides ont été testés en milieu cellulaire et trois d'entre eux ont montré qu'ils pouvaient inhiber efficacement la réplication du HIV-1 dans les lymphocytes. Dans ce contexte, un premier objectif de cette thèse fût de caractériser avec précision les propriétés de ces peptides. En outre, un objectif supplémentaire fût de caractériser le mécanisme moléculaire vis-à-vis de la NC de petites molécules anti-virales développées par les groupes de D. Daelemans (Leuven) et M. Botta (Sienne). / Due to the highly conserved §equence ofNC and its crucial function during HIV-I life cycle, molecules directedagainst NC are believed to be able to complement the highly active anti-retroviral therapies (HAART) based on drugstargeting the viral enzymes. Anti-NC drugs are thought to provide a sustained replication inhibition of a large panel ofHIV-I isolates including virus strains resistant to drugs targeting viral enąrmes. Recently, within the Europeanconsortium TRIoH, new strategies to specifically target the nucleic acid chaperone properties ofNC were developed.According to a strategy protected by a submitted patent, a series of peptides have been desigrred to act as competitorsforNC and thus, inhibit virus replication. Among this series, several peptides were found to efficiently ińibit therrrrcleic acid destabilization properties ofNC. Four of them have been tested in the cellular context and t}ree out ofthemwere found to efficientĘ ińibit the replication of HIV-I in lymphocytes. In this context, the objective of the thesis wasto characterize in depth the properties ofthese peptides. Moreover, an additional objective was to characterize themolecular mechanism in respect to NC of small antiviral drugs developed by the group of D. Daelemans (Leuven) andM. Botta (Siena).

Transgenic plants expressing a foreign gene are a suitable system for the production of relevant immunogens in high amounts that can be used for the development of a new generation of vaccines against a variety of infectious diseases. In the present study, the expression of the nucleocapsid (N) protein of hantavirus serotype Puumala in tobacco and potato plants was investigated. Transgenic tobacco and potato plants were generated and established. These transgenic plants expressed the N protein of Puumala virus strain CG-1820. No major differences were observed when the phenotype and growth rates of transgenic plants were compared to those of normal plants. However, it was found that the leaves of transgenic tobacco plants were more slender and the tubers of transgenic potato plants were smaller than those in normal plants. In order to investigate the distribution of the expression of the foreign gene in transgenic plants, the proteins of leaves and roots of the individual transgenic tobacco and potato plants were examined by Western blot analyses. It was found that all transgenic tobacco and potato plants expressed the N protein in the leaves, whereas transgenic potato plants are able to significantly express the viral proteins also in the tubers and roots. The antigens were expressed at a level of 1 ng of protein/5 μg of dried leaves. The hantaviral recombinant N proteins obtained from transgenic tobacco and potato plants were able to elicit specific humoral and mucosal immune responses when administered intraperitoneally or orally to rabbits and mice. The expression of viral proteins in plants has two major advantages compared to other expression systems: firstly, there is no risk of contamination with mammalian viruses or other pathogens, and secondly, the production of high amounts of antigens is cheap and therefore of great economic interest. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Das in Europa vorkommende Dobravavirus (DOBV) gehört zu den Hantaviren und wird durch die Gelbhalsmaus Apodemus flavicollis übertragen und kann im Menschen zu einem "Hämorrhagischen Fieber mit renalem Syndrom" (HFRS) führen. Das Nukleokapsidprotein (N) von Hantaviren ist stark immunogen in Menschen und eine Impfung mit rekombinanten N Derivativen wie chimaere Hepatitis B Virus (HBV) Corepartikel oder das komplette N schützt in Nagetiermodellen vor einer Hantavirusinfektion. In der vorliegenden Arbeit wurde die Immunogenität von zwei auf dem DOBV N basierende Protein Derivativen in Mäusen getestet. Es wurden in E. coli exprimierte chimaere HBV Corepartikel verwendet, die einen Teil des DOBV N trugen (HBcdDOB120), sowie in Hefen eprimiertes komplettes DOBV rN. Anschließend wurden BALB/c und C57BL/6 Mäuse mit den jeweiligen Proteinen immunisiert. Sowohl BALB/c, als auch C57BL/6 Mäuse entwickelten eine starke, langanhaltende N-spezifische Antikörperantwort, die eine starke Kreuzreaktivität gegenüber der rN anderer Hantaviren aufwiesen, nach Impfung mit HBcdDOB120 oder DOBV rN-Protein. Es wurden Antikörper aller IgG Subklassen, sowie N-spezifische IFN-( und IL-4 sekretierende Lymphozyten induziert, was auf eine gemischte Th1/Th2 Antwort schließen lies. Die Frequenz der durch die Immunisierungen induzierte N-spezifischen Lymphozyten war allerdings gering. Auch in Mäusen, die hohe HBc-spezifische Antikörpertiter aufwiesen konnte eine starke N-spezifische Antikörperantwort mittels Impfung mit HBcdDOB120 induziert werden. HBcdDOB120 und DOBV rN stellen vielversprechende Vakzinekandidaten dar, die auf ihre Protektivität hin getestet werden sollten. Da HBcdDOB120 sowie DOBV rN eine starke Antikörperantwort und nur eine schwache T-Zellantwort induzieren sollte zusätzlich die Rolle von N-spezifischen Antikörpern im Schutz gegen die Virusinfektion weiter charakterisiert werden. / In Europe, the hantavirus Dobrava (DOBV) is carried by the yellow-necked mouse Apodemus flavicollis and causes "haemorrhagic fever with renal syndrome" in humans. The nucleocapsid protein (N) is very immunogenic in infections of humans and rodents. Immunisation with N protein derivatives, like chimeric hepatitis B virus core (HBc) particles and entire recombinant N could protect rodents from a hantavirus infection. In this study, the immunogenicity of the two following derivatives based on the DOBV N protein was tested in mice. Chimeric HBV core particles, consisting of truncated HBc (HBcd) particles carrying part of the DOBV N (HBcdDOB120) were expressed in E. coli and the entire DOBV rN in yeast. Hence BALB/c and C57BL/6 mice were immunised subcoutanously with both antigens. Mice of both strains elicited strong and longlived N-specific antibody responses after HBcdDOB120 as well as after DOBV rN immunisation. Both derivatives induced antibodies that were highly cross-reactive to the rN of the hantaviruses Puumala, Hantaan, Andes and Sin Nombre. HBcdDOB120 and DOBV rN induced N-specific antibodies of all IgG subclasses, suggesting a mixed Th1/Th2 immune response. In the same line, IFN-( and IL-4 was secreted by N-specific lymphocytes from mice immunised with HBcdDOB120 or DOBV rN after in vitro restimulation which also indicated a mixed Th1/Th2 response. However, the frequency of N-specific lymphocytes was low. In mice that exhibited a high HBc-specific antibody titer HBcdDOB120 also induced a strong N-specific immune response. HBcdDOB120 and DOBV rN represent promising vaccine candidates that should be tested for their protective potential in a DOBV challenge model as soon as one gets available. Additionally, as protection might be partially based on N-specific antibodies, their role in protecting against a hantavirus infection should be characterised further.

Au cours de ce travail de thèse expérimental, nous nous sommes intéressés à l’étude de la localisation nucléaire et nucléolaire de la protéine de la nucléocapside (NC) du VIH-1. Des études antérieures menées au laboratoire avaient mis en évidence une très forte accumulation de la NC dans les nucléoles. Ce compartiment nucléaire est connu pour être ciblé par de nombreux virus afin de promouvoir leur réplication. Des expériences de microscopie électronique avaient révélé la structure complexe du nucléole et montré qu’il est composé de trois sous-compartiments : les centres fibrillaires, le compartiment fibrillaire dense et le compartiment granulaire dans lesquels se déroule la synthèse des ribosomes. Afin de caractériser la localisation de la NC dans ces trois sous-compartiments, nous avons développé une approche de microscopie optique à haute résolution permettant d’obtenir des images à deux couleurs avec une résolution spatiale améliorée. Pour cela, nous avons mis au point un protocole qui permet d’utiliser simultanément une protéine fluorescente photocommutable et un fluorophore organique introduit par immunomarquage. Après avoir minimisé les aberrations optiques et corrigé les dérives mécaniques inhérentes au montage, nous avons visualisé simultanément la localisation de la NC surexprimée dans des cellules HeLa avec des marqueurs spécifiques des trois sous-compartiments nucléolaires (immunomarquage). La microscopie de fluorescence à haute résolution a permis de résoudre pour la première fois les différents compartiments et de montrer que la NC se localise préférentiellement dans le compartiment granulaire. Finalement, des expériences préliminaires avec des cellules vivantes ont permis de mettre en évidence que la NC est transportée de manière active dans le noyau et qu’elle pourrait interagir directement avec des protéines nucléolaires / During this experimental thesis work, we investigated the nuclear and nucleolar localization of the nucleocapsid protein (NC) of HIV-1. Previous studies performed in our laboratory evidenced a strong accumulation of NC in a subnuclear structure called nucleolus. Playing role in multiple cellular processes, nucleolus is often targeted by viruses to promote their replication. Electron microscopy revealed three nucleolar components (fibrillar centers, dense fibrillar component and granular component) associated to specific steps of the ribosome biogenesis. To characterize the distribution of the NC in these three sub-compartments and therefore shed light on the nucleolar localization of NC during the replication cycle, we developed a high-resolution optical microscopy approach. After having minimized the optical aberrations and corrected the mechanical drifts inherent to the imaging setup, the NC-mEos2 fusion protein overexpressed in HeLa cells was visualized simultaneously with immunolabeled nucleolar markers. The use of high-resolution fluorescence microscopy enabled us to resolve for the first time the three nucleolar compartments and to demonstrate the preferential localization of NC in the granular compartment of nucleolus. Finally, preliminary experiments performed with living cells showed that NC is actively transported in the nucleus and therefore may interact directly with nucleolar proteins.

Submitted by Ubirajara Cruz (ubirajara.cruz@gmail.com) on 2017-03-28T13:31:49Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_Giseli_Ritterbusch.pdf: 1007939 bytes, checksum: 6829555e6aeec4b59e73c9a7f0f29087 (MD5) / Approved for entry into archive by Aline Batista (alinehb.ufpel@gmail.com) on 2017-03-28T20:59:38Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_Giseli_Ritterbusch.pdf: 1007939 bytes, checksum: 6829555e6aeec4b59e73c9a7f0f29087 (MD5) / Made available in DSpace on 2017-03-28T20:59:38Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_Giseli_Ritterbusch.pdf: 1007939 bytes, checksum: 6829555e6aeec4b59e73c9a7f0f29087 (MD5) Previous issue date: 2015-01-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / O vírus da bronquite infecciosa das galinhas (VBI) é o agente etiológico da Bronquite Infecciosa (BI), uma enfermidade altamente contagiosa que causa grandes perdas econômicas na avicultura. O VBI é um vírus envelopado, que possui genoma constituído de RNA fita simples, que codifica 4 proteínas estruturais, dentre elas a Nucleoproteína (N), que é produzida em grande quantidade na infecção viral e é reconhecidamente imunogênica. O controle da BI se faz com a imunização das aves através da aplicação de vacinas vivas atenuadas, seguidas de vacinação utilizando antígeno inativado, sendo o sorotipo Massachusetts o único liberado para uso no Brasil. Um dos objetivos do presente trabalho foi realizar um estudo exploratório, afim de conhecer a opinião de diferentes segmentos da avicultura sobre a situação atual da ocorrência de BI nos planteis brasileiros e os custos que ela representa. Diante disso, surge então a necessidade do desenvolvimento de vacinas alternativas e seguras para controle da BI, entre elas a utilização de vacinas vetoriais. Dessa forma, com o objetivo de desenvolver uma vacina efetiva no controle da BI, amostras variantes de VBI foram clonadas em adenovírus humano recombinante e utilizadas para transfectar células HEK293, originando adenovírus recombinantes carreadores do gene N do VBI. Estes vírus foram purificados e utilizados como vacinas recombinantes para imunização de aves SPF. Com base nos dados obtidos, observou-se que apesar das diferentes estratégias de vacinação, a BI ainda é considerada uma doença de alta prevalência que continua causando significativas perdas econômicas na produção avícola de corte e postura no Brasil. Os resultados obtidos demonstraram que a vacina recombinante não induziu uma resposta sorológica detectável pelo teste de Elisa comercial utilizado, bem como não reduziu os escores de lesões nos tecidos das aves vacinadas e desafiadas. Assim, a vacina recombinante carreada por adenovírus defectivo expressando o gene N do VBI foi construída e caracterizada, porém se mostrou ineficaz e não induziu suficiente proteção às aves experimentalmente imunizadas frente ao desafio com VBI. / The infectious bronchitis virus (IBV) is the etiologic agent of Infectious bronchitis (IB), a highly contagious disease that causes great economic losses in the poultry industry. The IBV is an enveloped virus that has RNA single strand genome, encoding four structural proteins, among them Nucleoprotein (N), which is produced abundantly in viral infection and is known immunogenic. The IB control is done by immunization of birds by applying live attenuated vaccine, followed by vaccination using inactivated antigen, wherein the Massachusetts serotype is the only released for use in Brazil. One of the goals of the present work was to conduct an exploratory study in order to know the opinion of different segments of the poultry industry on the current situation of the occurrence of BI in Brazilian squads and the costs that it represents. Therefore, the development of alternative and safe vaccines to BI control is necessary, including the use of vectors. In order to develop an effective vaccine to IB control, samples from IBV field variants were cloned into recombinant human adenovirus and used to transfect HEK293 cells, resulting in recombinant adenovirus carriers of the N gene of the IBV. These recombinant viruses were purified and used as vaccines to immunization of SPF chickens. Based on the obtained data, it was observed that despite the different vaccination strategies, IB is still considered highly prevalent disease that causes significant economic losses in Brazilian poultry industry. The results here obtained showed that the recombinant vaccine does not causes detectable positive serological responses by commercial Elisa test in vaccinated chickens and does not reduce the tissues damage in vaccinated and challenged chickens. Thus, the recombinant vaccine carried by defective adenovirus expressing N gene of IBV was constructed and characterized, but seemed to be ineffective and did not induce sufficient protection to experimentally immunized chickens against IBV challenge.

Experiments show that MgSO4 salt has a non-monotonic effect as a function of MgSO4 concentration on the ejection of DNA from bacteriophage lambda. There is a concentration, N0, at which the minimum amount of DNA is ejected. At lower or higher concentrations, more DNA is ejected. We propose that this non-monotonic behavior is due to the overcharging of DNA at high concentration of Mg⁺² counterions. As the Mg⁺² concentration increases from zero, the net charge of ejected DNA changes its sign from negative to positive. N0 corresponds to the concentration at which DNA is neutral. Our theory fits experimental data well. The DNA-DNA electrostatic attraction is found to be -0.004 kBT/nucleotide. Simulations of DNA-DNA interaction of a hexagonal DNA bundle support our theory. They also show the non-monotonic DNA-DNA interaction and reentrant behavior of DNA condensation by divalent counterions. Three problems in understanding the capsid assembly for a retrovirus are studied: First, the way in which the viral membrane affects the structure of in vivo assembled HIV-1 capsid is studied. We show that conical and cylindrical capsids have similar energy at high surface tension of the viral membrane, which leads to the various shapes of HIV-1 capsids. Secondly, the problem of RNA genome packaging inside spherical viruses is studied using RNA condensation theory. For weak adsorption strength of capsid protein, most RNA genomes are located at the center of the capsid. For strong adsorption strength, RNA genomes peak near the capsid surface and the amount of RNA packaged is proportional to the capsid area instead its volume. Theory fits experimental data reasonably well. Thirdly, the condensation of RNA molecules by nucleocapsid (NC) protein is studied. The interaction between RNA molecules and NC proteins is important for the reverse transcription of viral RNA which relates to the viral infectivity. For strong adsorption strength of the NC protein, there is a screening effect by RNA molecules around a single NC protein.

Du fait de sa haute conservation et de ses fonctions clés dans le virus VIH-1, la protéine de la nucléocapside NC est une cible de choix pour développer de nouveaux anti-viraux. Bien que la compréhension mécanistique des propriétés chaperonnes de NC vis-à-vis des acides nucléiques ait connu d’importants progrès, les aspects dynamiques de ces propriétés restent mal comprises, faute notamment d’outils appropriés pour les suivre au niveau moléculaire. L’objectif de ce travail de thèse a été de caractériser au niveau moléculaire la dynamique des interactions de NC avec les acides nucléiques, à l’aide d’outils fluorescents développés au laboratoire ou en collaboration. En utilisant des peptides NC et des oligonucléotides marqués en différentes positions par des analogues fluorescents d’acides aminés et de nucléosides, respectivement, nous avons pu donner une image complète du processus dynamique sous-tendant le mécanisme chaperon de NC dans le second transfert de brins de la transcription inverse du cycle du VIH-1. Cette compréhension est fondamentale pour concevoir des stratégies rationnelles afin de cibler le rôle spécifique de NC dans ses interactions avec ses cibles nucléiques. / Due to its high conservation and key functions in the HIV-1 virus, the nucleocapsid protein NC is a potential target for the development of new anti-viral drugs. Although the mechanistic understanding of the NC nucleic acid chaperone properties has achieved a significant progress, the dynamic aspects of these properties remain poorly understood, mainly due to the lack of the appropriate tools to monitor them at the molecular level. The objective of this thesis was to characterize the dynamic interactions of NC with nucleic acids at the molecular level using new fluorescent tools developed in the laboratory or in collaboration. Using NC peptides and its target oligonucleotides labeled in different positions by fluorescent amino acid and nucleoside analogs, respectively, we were able to give a complete picture of the dynamic processes underlying the chaperone activity of NC in the second strand transfer of HIV-1 reverse transcription. This understanding is fundamental to design rational strategies in order to target the specific role of NC in interaction with its nucleic acid targets.

La protéine de nucléocapside du VIH-1 (NCp7) joue un rôle important dans plusieurs étapes du cycle viral. Ses interactions dans l’environnement intracellulaire dans les conditions proches d’une vraie infection sont peu décrites. L’objectif de ce projet de thèse a été de développer des approches d’imagerie permettant de suivre la NCp7 au cours des étapes précoces du cycle viral directement dans les cellules infectées. En analysant l’intensité des pseudovirus fluorescents nous avons montré un effet de « dequenching » de fluorescence témoignant d’une diminution de la concentration en NCp7 au sein des particules virales, résultant très probablement du relargage des molécules de nucléocapside à partir des complexes viraux. Ces résultats montrent pour la première fois la libération de la NCp7 dans le cytoplasme lors de la transcription inverse. Les pseudovirus NCp7-TC ont ensuite été imagés en haute résolution par microscopie PALM. Les images de distribution de la NCp7 marquée ont révélé la présence de la NCp7-TC à l'intérieur du noyau. Nous avons mis en evidence par microscopie électronique la presence de la NCp7-TC à proximité de pores nucléaires. / The nucleocapsid protein of HIV-1 (NCp7) plays an important role in several stages of the viral cycle. Its interactions in the intracellular environment under conditions close to true infection are not well described. The objective of this thesis project was to develop imaging approaches to monitor NCp7 during the early stages of the viral cycle directly in infected cells. By analyzing the intensity of the fluorescent pseudoviruses, we showed a fluorescence "dequenching" effect indicating a decrease in the NCp7 concentration within the virus particles, most likely resulting from the release of the nucleocapsid molecules from the viral complexes. These results show for the first time the release of NCp7 into the cytoplasm during reverse transcription. The pseudoviruses NCp7-TC were then imaged in high resolution by PALM microscopy. The distribution images of labeled NCp7 revealed the presence of NCp7-TC within the nucleus. We have demonstrated the presence of NCp7-TC in the vicinity of nuclear pores by electron microscopy.

La protéine de la nucléocapside (NC) possède un rôle important dans le cycle de viral du VIH-1 grâce à sa propriété chaperone des acides nucléiques (NA) qui implique la reconnaissance de son résidu Trp37 avec un résidu Guanine de l'acide nucléique cible. Nous avons caractérisé cette reconnaissance dynamique Trp37-G en utilisant des séquences impliquées dans la transcription inverse et l'assemblage de l'ARN génomique. En utilisant les analogues nucléosidiques fluorescents thienoguanosine (thG) et 2-thiényl-3-hydroxychromone (3HCnt), nous avons déterminé l'ensemble des constantes de vitesse cinétiques du mécanisme d’hybridation de la séquence (-)PBS avec (+)PBS en absence et en présence de NC. Nous avons également étudié le rôle du NA sucre dans les complexes NC-ARN et NC-ADN, puisque la protéine NC se lie avec la polarité opposée aux séquences d'ADN et d'ARN. Nous avons confirmé que l'interaction du résidu Trp37 avec les amino-acides de type guanines était critique lors de la formation des complexes avec les deux mutants d’ARN et d’ADN de PBS et de SL3. Enfin, nous avons réalisé un criblage de potentiels inhibiteurs de la protéine NC et examiné les touches identifiées à partir d’un test basé sur la fluorescence de la sonde thG. / Nucleocapsid protein (NC) plays crucial roles in HIV-1 life cycle through its nucleic acid (NA) chaperoning property that involves recognition of it’s Trp37 residue with a Guanine residue of the target nucleic acid sequences. Herein, we characterized this dynamic Trp37-G recognition with sequences involved in reverse transcription and genomic RNA packaging. Using the fluorescent thienoguanosine (thG) and 2-thienyl-3-hydroxychromone (3HCnt) nucleoside analogues, we determined the whole set of kinetic rate constants for annealing of (-)PBS with (+)PBS in the absence and presence of NC. We also investigated the role of NA sugar in NC-RNA and NC-DNA complexes, as NC binds with opposite polarity to DNA and RNA sequences. We confirmed that the interaction of the Trp37 residue with guanines was critical for the formation of complexes with both RNA and DNA variants of PBS and SL3. Finally, we performed screening of NC inhibitors and tested the selected hits on a thG-based assay.