Retrovírus endógenos (ERVs) são vírus altamente difundidos no genoma de vertebrados. ERVs surgem quando retrovírus exógenos infectam células germinativas e se disseminam no genoma de seus hospedeiros, transmitindo seu material genético através das gerações por meio de herança mendeliana. ERVs são fundamentais na evolução dos genomas, sendo eles responsáveis por uma parte da diversidade genética de seus hospedeiros. O conhecimento sobre ERVs na família Felidae (Mammalia, Carnivora) estava praticamente restrito ao gato doméstico, e não se conhecia diversidade e padrões de evolução desses retroelementos em outras espécies. Este estudo teve como objetivo investigar diversidade, distribuição e padrões evolutivos de ERVs em espécies de gatos silvestres. Utilizando ferramentas de biologia molecular e bioinformática, foram identificadas e caracterizadas 85 sequências similares a retrovírus endógenos nos representantes das oito espécies brasileiras: Leopardus pardalis, L. wiedii, L. colocolo, L. geoffroyi, L. tigrinus, Puma concolor, P. yagouaroundi e Panthera onca. Encontrou-se uma predominância de ERVs similares a Gammaretrovirus, um padrão característico em muitas espécies de mamíferos. As análises filogenéticas evidenciaram três grupos principais de Gammaretrovirus, cada um evoluindo de maneira peculiar. Em uma visão geral, os ERVs provenientes de diferentes hospedeiros apresentaram-se distribuídos de forma heterogênea nas filogenias, dificultando a constatação de um padrão coevolutivo. No entanto, análises mais detalhadas de algumas sequências demonstraram peculiaridades, como no caso de um grupo de sequências similares a de um ERV oriundo do morcego Myotis lucifugus. Através de análises filogenéticas em comparação com dados obtidos na literatura, sugere-se que a infecção desse retrovírus ocorreu em uma espécie ancestral de felídeo, na segunda metade do Mioceno. Os resultados obtidos permitiram demonstrar que os felídeos neotropicais apresentam ERVs que seguem padrões semelhantes aos descritos a respeito de outros mamíferos, sugerindo também alguns casos de infecções de retrovírus muito similares entre diferentes ordens de mamíferos. / Endogenous retroviruses (ERVs) are widespread viruses in vertebrate genome. ERVs arise when exogenous retrovirus infects germinal cells and spread in the genome of their hosts, transmitting its genetic material throughout the generations by means of Mendelian inheritance. ERVs are fundamental for the evolution of genomes, being responsible for some part of the genetic diversity of their hosts. The knowledge on ERVs in felids (Mammalia, Carnivora, Felidae) was basically restricted to domestic cats, and the diversity and patterns of evolution of these retroviral elements in other species were not known. This study aimed to investigate diversity, distribution and evolutionary patterns of ERVs in wildcat species. Hence, by utilizing molecular biology and bioinformatics tools, 85 endogenous retrovirus-like sequences were identified and characterized in eight representative Brazilian species: Leopardus pardalis, L. wiedii, L. colocolo, L. geoffroyi, L. tigrinus, Puma concolor, P. yagouaroundi and Panthera onca. The analyses of these novel felid ERVs showed the predominance of Gammaretroviruslike sequences, which is a characteristic pattern present in many mammal species. Phylogenetic analyses have evidenced three major groups of Gammaretrovirus, each one evolving in a peculiar manner. ERVs from different hosts were distributed in a mixed way in the phylogenies, differently of a coevolutionary pattern. However, more detailed analyses of some sequences demonstrated peculiarities, as in the case of a group of sequences similar to an ERV from the bat Myotis lucifugus. Notably, through phylogenetic analyses, and in comparison to data obtained in the literature, it may be suggested that some infection by a retrovirus occurred in a felid ancestral species in the second half of the Miocene. Therefore, the results obtained demonstrate that ERVs from Neotropical felids follow patterns which are very similar to the ones described for other mammals, also suggesting some cases of similar retrovirus lineage infecting different mammal orders.

L'intégrase (IN) du VIH-1 est une enzyme qui catalyse l'intégration du génome du virus dans celui de la cellule infectée. Cette étape d'intégration est cruciale pour le virus pour qu'il puisse se répliquer de manière efficace, l'intégration est donc une cible de choix dans les thérapies antivirales. Comprendre les mécanismes qui participent à l'intégration est donc nécessaire afin de développer des solutions efficaces pour contrecarrer le virus.L’intégration rétrovirale est catalysée par une structure oligomérique d’IN et d’ADN viral bien particulière appelée intasome. Les intasomes rétroviraux catalysent l’intégration préférentiellement sur des nucléosomes, composés d’ADN enroulé de protéines histones, plutôt que sur de l’ADN nu. Ceci est en parti du aux contraintes physiques imposés par la structure de l’intasome, mais également grâce à des facteurs de ciblage cellulaires qui vont interagir avec à la fois l’intasome et des composants du nucléosome.Dans ce projet de thèse, nous avons pu mettre en évidence une nouvelle interaction hôte-pathogène entre l’IN du VIH-1 et la queue d’histone H4 (une des protéines constituant le nucléosome). Ce projet s’est ainsi focalisé autour de cette interaction et a permis de :• Démontrer l’importance de l’interaction entre l’IN du VIH-1 et la queue d’histone H4 lors du cycle viral et plus précisément pour l’étape d’intégration, validant ainsi cette interaction comme une nouvelle interaction hôte-pathogène.• D’identifier que la queue d’histone H4 est un partenaire essentiel de l’intasome du VIH-1 pour qu’il puisse s’ancrer sur le nucléosome.• Développer une nouvelle stratégie antivirale visant à bloquer cette interaction dans les cellules infectées grâce à des composés chimiques. / HIV-1 integrase (IN) catalyzes the insertion of the viral genome into the host cell chromatin. This step is crucial for the virus for its efficient replication, integration is thus of interest to target for antiviral strategies. Understanding the mechanisms involved in integration is important in order to develop efficient tools to fight the virus.Retroviral integration is catalyzed by the intasome, an oligomer of IN and viral DNA. Intasomes integrate onto nucleosomes, composed of DNA wrapped around histone proteins, over naked DNA.In this thesis project, we have identified a new host-pathogen interaction between HIV-1 IN and the H4 histone tail. The topic of the project was then focus on this interaction and has highlighted:• The importance of the HIV-1 IN – H4 histone tail interaction for the viral cycle, especially onto the integration step, validating a new host-pathogen interaction.• The identification of the H4 histone tail as an essential partner for HIV-1 intasome for its anchoring onto nucleosomes.• The development of a novel antiviral strategy aiming to block this interaction in infected cells using chemical compounds

Retroviruses are capable of infecting diverse vertebrates, and successful infection requires intimate interaction between virus and the host cell. During an infection, retroviral particles must bind specifically to cell surface receptors on the target cell, cross the plasma membrane, reverse-transcribe their RNA genome into double stranded DNA, find their way to the nucleus, enter the nucleus and integrate its DNA into host chromosomes. Following integration, expression of viral mRNA ensues, followed by viral mRNA export into the cytoplasm, translation of viral mRNA into proteins, and assembly of new virions that will egress from the host cell. We now appreciate that at many steps of this complex process, the virus must hijack the cellular machinery to replicate. At the same time, the host cell mobilizes a variety of cellular defense mechanisms to suppress viral infection. This thesis investigates various aspects of virus-host interactions. I will first describe the involvement of cellular transcriptional repressor protein ErbB3 binding protein 1 (EBP1) in facilitating transcriptional shutdown of Moloney murine leukemia virus (MLV) gene expression in mouse embryonic cells. Next, I describe a novel means of regulating the activity of Yin Yang 1 (YY1), a cellular transcription factor regulating retroviral gene expression, through post-translational modifications. I show that YY1 is a target of tyrosine phosphorylation by Src family kinases. Phosphorylation of YY1 impairs its ability to bind DNA and RNA, thereby downregulating its activity as a transcription factor on retroviral and cellular promoters. Apart from studying retroviral gene expression, I have also investigated intrinsic cellular defenses against retroviral infection. This is exemplified by our finding that mouse cells are intrinsically resistant to infection by betaretroviruses such as Mason-Pfizer monkey virus (M-PMV). The block against M-PMV occurs after reverse transcription and prior to viral nuclear entry. Finally, I will present ongoing work examining the fate of viral DNAs following infection, focusing on the kinetics of its association with cellular core histones and viral structural proteins. Together, this work provides critical insights into numerous aspects of the virus-host interactions.

ABSTRACT Chromatin insulators are required for proper temporal and spatial expression of genes in metazoans. Insulators are thought to play an important role in the regulation of gene expression through the formation of higher-order chromatin structures. One of the best characterized insulators is the Drosophila gypsy insulator, which is located in the gypsy retrovirus. Several proteins are required for gypsy insulator function, including Su(Hw), Mod(mdg4), and CP190. In addition to the gypsy insulator, these proteins are located throughout the genome at sites which are thought to correspond to endogenous insulators. Analysis of the distribution of insulator proteins across a region of chromosome 2R in Drosophila polytene chromosomes shows that Su(Hw) is found in three structures differentially associated with insulator proteins: bands, interbands and domains of coexpressed genes. Bands are formed by condensation of chromatin within genes containing one or more Su(Hw) binding sites, while Su(Hw) sites in interbands appear to form structures normally associated with open chromatin. Bands characterized by the lack of CP190 and BEAF-32 insulator proteins are formed by clusters of coexpressed genes, and these bands correlate with the distribution of specific chromatin marks. Conservation of the band interband pattern, as well as the distribution of insulator proteins in nurse cells, suggests that this organization may represent the basic organization of interphasic chromosomes. We also show that, in addition to the gypsy insulator, sequence analysis predicts the presence of Su(Hw) binding sites within a number of transposable elements. Su(Hw) binds to predicted sites within gtwin and jockey, which possesses enhancer-blocking activity. Su(Hw) affects the tissue-specific expression of transposable elements, although this effect is unrelated to the presence of Su(Hw) binding sites within the element or control of the elements via the piRNA pathway. Additionally, the effect of Su(Hw) on transposable element expression often differs from that of Mod(mdg4). Taken together, these results suggest that insulator proteins associate specifically with, and may help to define, various levels of chromatin organization on polytene chromosomes. Also, gypsy insulator proteins may influence the expression of transposable elements in a way that does not depend on Su(Hw) binding sites within the elements themselves.

Of the thousands of dividing progenitor cells (PCs) generated daily in the adult brain only a very small proportion survive to become mature neurons through the process of neurogenesis. Identification of the mechanisms that regulate cell death associated with neurogenesis would aid in harnessing the potential therapeutic value of PCs. Apoptosis, or programmed cell death, is suggested to regulate death of PCs in the adult brain as overexpression of B-cell lymphoma 2 (Bcl-2), an anti-apoptotic protein, enhances the survival of new neurons. To directly assess if Bcl-2 is a regulator of apoptosis in PCs, this study examined the outcome of removal of Bcl-2 from the developing PCs in the adult mouse brain. Retroviral mediated gene transfer of Cre into adult floxed Bcl-2 mice eliminated Bcl-2 from developing PCs and resulted in the complete absence of new neurons at 30 days post viral injection. Similarly, Bcl-2 removal through the use of nestin-induced conditional knockout mice resulted in reduced number of mature neurons. The function of Bcl-2 in the PCs was also dependent on Bcl-2-associated X (BAX) protein, as demonstrated by an increase in new neurons formed following viral-mediated removal of Bcl-2 in BAX knockout mice. Together these findings demonstrate that Bcl-2 is an essential regulator of neurogenesis in the adult hippocampus.

Die Familie der Retrovirinae wird in zwei Unterfamilien untergliedert, die Orthoretrovirinae und die Spumaretrovirinae. Foamyviren stellen aufgrund einiger besonderer Eigenschaften die einzigen Vertreter dieser Unterfamilie, die sie als Bindeglied zwischen den Retroviren und den Hepadnaviren erscheinen lassen. So erfolgt beispielsweise die reverse Transkription des viralen Genoms nicht erst nach Eintritt in die Zielzelle, sondern, anders als bei Orthoretroviren, bereits in der Produzentenzelle noch während oder kurz nach der Morphogenese. Diese Eigenschaft teilen Foamyviren mit den Hepadnaviren ebenso wie die obligate Koexpression der Kapsidproteine mit den viralen Hüllproteinen für die Freisetzung von Viruspartikeln. Im Gegensatz zu Orthoretroviren sind Foamyviren folglich nicht in der Lage virusähnliche Partikel (VLP) zu sekretieren und die spezifische Funktion des PFV Env Proteins kann nicht durch heterologe Hüllproteine übernommen werden. Die Synthese des PFV Env Vorläuferproteins erfolgt am rER, wobei es eine Typ III Membrantopologie erhält, mit sowohl dem N- als auch dem C-Terminus im Zytoplasma. Während des Transports des Proteins zum Ort der Partikelknospung, wird es posttranslational im Golgi-Apparat, oder dem trans-Golgi Netzwerk, durch Furin oder eine Furin-ähnliche Protease in drei partikelassoziierte Untereinheiten prozessiert. Eine Partikelassoziation retroviraler Signalpeptide ist bislang nur für Foamyviren nachgewiesen worden, genauso wie eine essentielle Rolle dieses Proteins bei der Interaktion zwischen dem

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The nucleoside phosphonates cidofovir (CDV) and (S)-9-[3-hydroxy-(2-phosphonomethoxy)propyl]adenine [(S)-HPMPA] are analogs of dCMP and dAMP, respectively. Collectively these drugs are effective inhibitors of a wide range of DNA viruses, RNA viruses, and retroviruses. Because they are nucleotide analogs, the drugs are thought to target viral polymerases and inhibit viral genome replication. However, the precise mechanism by which these drugs block viral growth remains unclear. We have studied the mechanism of action of these antivirals against three viral polymerases, vaccinia virus DNA polymerase and the reverse transcriptases from human immunodeficiency virus type 1 (HIV-1) and Moloney murine leukemia virus (MMLV). In vitro experiments using the active intracellular metabolites of CDV and (S)-HPMPA, CDV diphosphate (CDVpp) and (S)-HPMPA diphosphate [(S)-HPMPApp], respectively, showed that the drugs are substrates for each enzyme and can be incorporated into DNA without causing chain termination, although the rate of DNA elongation catalyzed by the vaccinia virus and MMLV polymerases is slowed. We have also found that incorporation of CDV or (S)-HPMPA blocked the 3′-to-5′ proofreading exonuclease activity of the vaccinia virus DNA polymerase. In addition, we determined that when these drugs are incorporated into a template DNA strand, they inhibited replication across the drug lesion. These results indicate that although CDV and (S)-HPMPA can inhibit some enzymes when incorporated into the primer strand, the main effects of drug action occur when they are incorporated into the template strand. Our findings point to a new avenue of targeted drug design, one in which nucleoside or nucleotide analogues are efficient substrates for the viral nucleic acid polymerase, do not inhibit primer strand elongation, but exert their effects in subsequent rounds of nucleic acid synthesis. / Virology

Gene therapy is the delivery of genetic material to cells for a therapeutic effect. Retroviruses are one of the most common viral vectors used for gene therapy, especially lung gene therapy. However the lung has many physical and immunological barriers to gene transfer vectors, and currently, too few cells are genetically modified for the effective treatment of lung diseases such as cystic fibrosis. One of the main reasons for low cell transduction is the lack of commonly-used receptors for gene therapy vectors on the apical surface of polarized epithelial cells. The objective of this project was to determine how to incorporate proteins into the lentiviral lipid bilayer in order to develop a recombinant retrovirus that can efficiently deliver genes to polarized epithelial cells via their apical membranes. We analyzed the process of incorporating heterologous viral and non-viral proteins into lentiviruses and determined key factors that allowed for successful protein incorporation into the lentiviral lipid bilayer. We found that lipid rafts segregated raft proteins, and for a protein to be incorporated into virus particles, it must be colocalized with lentivirus-associated rafts. When cells were treated with the cholesterol-extracting compound, methyl-beta-cyclodextrin, previously sequestered viral and non-viral raft proteins were then colocalized and non-viral proteins were incorporated into lentiviruses. We also created a lentivirus pseudotyped with envelope proteins from human parainfluenza type 3 (HPIV3), which naturally targets polarized epithelial cells of the lung. Lentiviruses were able to incorporate HPIV3 glycoproteins, hemagglutinin-neuraminidase (HN) and fusion (F), and were able to transduce polarized cells in a manner consistent with lentiviral-mediated transduction via sialated receptors for HPIV3, however titers were too low for clinical use. We increased protein expression of HN and found that while expression, envelope incorporation, and titer increased, lentiviruses still incorporated too few envelope proteins for efficient transduction. We determined low envelope incorporation rates were due to lack of interactions with Gag, and increasing active and passive interactions with Gag enhanced HN and F incorporation into lentiviruses. Overall, this research is significant because it provides insight into viral assembly and protein incorporation for the generation of pseudotyped lentiviruses for human gene transfer.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2007. / Härtill 6 uppsatser.