In human infection, herpes simplex virus (HSV) navigates two distinct life cycles; lytic and latent. The latent cycle takes place in sensory neurons, and is characterized as a dormant period punctuated by stress-induced episodes of viral reactivation. Understanding the mechanisms by which HSV latency and reactivation occur has been hindered by the lack of a model that faithfully recapitulates the environment of a human sensory neuron. Systems ranging from rat neurons to human fibroblasts have been developed to host HSV latency, however few available models have been able to investigate the role of human neuron-specific factors. To address this need, human medulloblastoma tumour cell lines, which derive from neuronal precursor cells, were differentiated and examined for their ability to host the HSV latency-reactivation cycle—in a manner similar to the differentiated PC-12 cell model. ONS-76 and UW228 medulloblastoma cell lines were screened for differentiation capacity. The differentiated cells were demonstrated to possess neuronal character as several neuron-specific proteins were found to be expressed. Differentiated ONS-76 cells were not compatible with hosting HSV latency, however, infection with a viral mutant impaired for lytic cycle initiation exhibited a deviant pattern of gene expression that resembles what has been observed in reactivation. Differentiated UW228 cells were found to host a low frequency, stable infection with the HSV mutant, characterized by the absence of infectious virus and viral lytic gene expression in the presence of persisting viral DNA. This DNA could further be induced to re-enter the lytic cycle through heat shock treatment and removal of differentiating agents from cell cultures. These results depict differentiated medulloblastoma cells as a novel tool in the study of HSV latency and reactivation, as these cells derive from the central nervous system and provide a new cellular perspective through which HSV biology can be viewed.

No description available.

VP16 initiates the HSV replication cycle by activating immediate early (IE) gene expression. It recruits the RNA pol II through an acidic C-terminal domain. The defective VP16 encoded by the V422 mutant of HSV-1 possesses a truncated C-terminal domain. Therefore, V422 replication is suppressed in most cell-lines, except U2OS osteosarcoma cells. The permissive phenotype of U2OS cells stems from a failure to express one or more inhibitory factors that are produced in restrictive cells. The initial project was designed to identify these host inhibitory factors in restrictive cells of V422, using siRNA silencing technology. To facilitate the siRNA screen, a GFP reporter gene has been inserted into the thymindine kinase (TK) gene of the V422 genome and the wild-type KOS genome. This thesis provides information about characterizing the kinetics of GFP expression from recombinant viruses at both protein and mRNA levels, during different infection times in HeLa and Vero cells. / Virology

No description available.

Infection of most cell types with herpes simplex virus (HSV) mutants lacking the activation functions of VP16 and/or ICP0 results in repression of viral gene expression. However, the human osteosarcoma cell line U2OS supports the replication of VP16 and ICP0 mutants to nearly wild type levels. Prior to the studies presented in this thesis, the basis for the permissivity of U2OS cells to VP16 and ICP0 mutants had not been explored. Here, somatic cell fusion assays were used to determine that U2OS cells support the replication of VP16 and ICP0 mutants due to a defect in an innate gene silencing mechanism. The artificial induction of interferon stimulated genes that occurs during the somatic cell fusion assays is not the basis for the observed repression of viral gene expression. As one means of identifying components of the antiviral pathway defective in U2OS cells, restrictive cell types were treated with kinase inhibitors and infected with VP16 and/or ICP0 mutants. Although several compounds were identified which compensate for the defect in gene expression of VP16 mutants, these drugs also stimulate mutant virus gene expression in U2OS. Thus, U2OS are most likely not defective in the cellular signalling pathway(s) targeted by these compound(s). Finally, the importance of VP16 and ICP0 in modulating chromatin structure on the viral genome in both restrictive and permissive cells was examined, uncovering an essential role for both proteins in altering histone occupancy and acetylation levels. Importantly, U2OS cells have a defect in the chromatin-based pathway targeted by ICP0. However, evidence suggests that the ability of VP16 and ICP0 to affect histone occupancy and acetylation levels is not required for viral gene expression. Taken together, the results of this thesis demonstrate that U2OS cells support the replication of VP16 and ICP0 mutants due to a defect in an innate antiviral mechanism which does not involve the targets of several well characterized kinase inhibitors. The significance of the defect in a chromatin-based pathway targeted by ICP0 in U2OS cells remains to be elucidated. / Virology

VP16 is an integral element in the HSV-1 strategy to overturn normal cellular functions and use the host machinery for the production of new virus. VP16 enhances the expression of viral immediate-early genes in the nucleus of the infected cell. By binding to the virion host shutoff protein (vhs), VP16 is able to downregulate its activity and prevent destruction of the viral transcripts. Finally, VP16 has an essential but specifically undetermined role in virus assembly. While a null mutation in VP16 correlates to a lethal defect in virus assembly, recent work has revealed that the C-terminal acidic activation domain of VP16 is not essential to virus survival. Viral mutants containing 422 and 379 amino acid tail-deleted derivatives of VP16 are viable. We have constructed a viable viral mutant which encodes a 369 amino acid VP16, revealing that the N-terminal 369 amino acids of VP16 retain a function which is essential to virus survival. The viral mutants encoding truncated VP16 derivatives displayed a characteristic preference for growth on a cell line which supplied full length VP16 in 𝘵𝘳𝘢𝘯𝘴. Furthermore, the preference for growth on the complementing cell line became more apparent as VP16 was progressively truncated from the C-terminus. To determine if full length VP16 was aiding these virtues in attenuating vhs activity or in performing a structural role in the presence of vhs, we constructed double mutant viruses encoding the truncated VP16s and containing an inactivating mutation in the vhs locus (ΔSma). The elimination of vhs activity and/or vhs-VP16 binding alleviated the preference for growth on the complementing cell line in these viruses. Thus, while the acidic activation domain of VP16 is not essential for viral replication in tissue culture, it clearly confers a growth advantage to the virus. The viral mutants constructed here will prove useful in understanding the significance of the interaction between VP16 and vhs. / Thesis / Master of Science (MS)

Herpes simplex virus protein VP16 activates immediate-early (IE) viral gene expression upon infection. VP16-mediated transactivation depends on formation of a multi protein complex with cellular factors on a cis-acting TAATGARA T sequence present in the IE promoters. The potent acidic activation domain, contained within the carboxyl terminus of VP16, is dispensable for the complex formation. The amino terminal part of VP16, which is inert in transactivation in mammalian cells, is sufficient for selective interactions with cellular factors, one of which has been identified as the ubiquitous transcription factor Oct-1. The yeast two-hybrid system was utilized to isolate the cellular factor(s) necessary in addition to Oct-1 for VP16 induced complex formation. This system, designed to directly clone proteins interacting with a given protein of interest, employs the yeast transcriptional activator GAL4. An interaction between VP16 and the cellular factor(s), fused to GAL4 DNA binding and activation domain, respectively, reconstitutes a hybrid transactivator that stimulates expression of a reporter lacZ gene in yeast. Thus, (beta)-galactosidase activity serves as a positive signal for protein-protein interaction. As a prelude of using this method for isolation of VP16-interacting cellular proteins, the system was tested with HSV-1 protein vhs, known to bind to VP16 in vitro. The obtained data demonstrated an interaction between VP16 and vhs in the two-hybrid system and deletion analysis revealed that VP16 sequence contained within the first 369 amino acids is required for binding to vhs. Thus, VP16 residues necessary for interaction with vhs in vivo coincide with these identified previously for VP16-vhs complex formation in vitro. VP16 fused to the GAL4 DNA binding domain activated expression of the reporter lacZ gene in yeast, despite the absence of its acidic activation domain. Deletion analysis showed that the amino terminal 369 residues of VP16 were sufficient for transactivation in yeast. Similar GAL4-VP16 derivatives were inactive in mammalian cells as measured by transient transfection assays. Thus, unlike in yeast, VP16 lacking the acidic activation domain is deficient in transactivation in mammalian cells even if it is directly bound to a promoter. VP16 sequences required for complex formation with vhs overlaps with those implicated in interaction with the mammalian factors, indicating that this region is involved in protein-protein interactions with both cellular and viral factors. Consistent with this, VP16 interaction with a yeast factor supplying an activation domain in trans would explain VP16-dependent transactivation in the absence of its acidic activation domain. Alternatively, a yeast specific activation domain might be present in the amino terminal part of VP16. / Thesis / Master of Science (MS)

Orientador: Michel Georges Albert Vincentz / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-09T01:42:08Z (GMT). No. of bitstreams: 1 Silveira_AmandaBortolini_M.pdf: 20873886 bytes, checksum: 0c34c8a141f7bb11f8f3176ba7a976e0 (MD5) Previous issue date: 2007 / Resumo: O crescimento e o desenvolvimento dos organismos são baseados na capacidade celular de expressão gênica diferencial que resulta, principalmente, do controle da taxa de iniciação da transcrição por fatores reguladores de transcrição (FTs). FTs do tipo Basic Leucine QQjJer(bZIP) fQram descritos em todos os eucariotos. Seu domínio conservado é constituído de uma região de ligação ao DNA rica em aminoácidos básicos, flanqueada a um zíper de leucinas responsável pela dimerização. Em angiospermas, os bZIPs são reguladores importantes de processos específicos como fotomorfogênese, desenvolvimento de órgãos, elongação celular, controle do balanço de carbono/nitrogênio, mecanismos de defesa, via de sinalização de hormônios e sacarose, controle osmótico e florescimento. Mostramos que os genomas de Arabidopsis thaliana e Orysa sativa codificam para um conjunto completo e não redundante de 76 e 113 fatores bZIP respectivamente, que foram organizados em 11 grupos de proteínas evolutivamente relacionadas e 33 Possíveis Grupos de Genes Ortólogos (PoGO) de mono e eudicotiledôneas, o que deve permitir racionalizar o processo de caracterização funcional destes fatores em angiospermas. O Grupo C, que inclui genes homólogos ao lócus de regulação Opaco-2 (02) de milho, está organizado em três PoGOS, que possivelmente desempenham três funções ancestrais de angiospermas. Em Arabidopsis estas três possíveis funções ancestrais estão representadas por quatro genes (bZIP' 02 !1omologous, Bzo2h), Bzo2h3/AtbZIP63 (PoGO C1), Bzo2h1/AtbZIP10 e Bzo2h4/ AtbZIP25 (PoGO C2) e Bzo2h2/AtbZIP9 (PoGO C3). Visando um melhor conhecimento sobre a evolução das funções dos fatores bZIP de angiospermas do Grupo C, iniciamos a caracterização funcional de~tes quatro reguladores, focando principalmente em AtbZIP9, um gene único representativo de uma função ancestral de angiospermas e cujo papel ainda é desconhecido. Notamos que a expressão de AtbZIP9 é restrita as células do floema e regulada por glicose, ácido abscísico e citocinina, sugerindo que este gene integra as vias de sinalização destes sinais metabólicos e hormonais no floema. Abordagens de genética reversa como RNAi, knockout e superexpressão não permitiram elucidar de maneira clara a atuação de AtbZIP9 no ciclo de vida de Arabidopsis, indicando que mecanismos de regulação pós-transcricional e/ou redundância genética atuam sobre este gene. Visando dar continuidade e ampliar o estudo funcional de AtbZIP9, foram obtidas linhagens transgênicas de Arabidopsis expressando versões modificadas deste gene que codificam para proteínas ativadoras constitutivas fortes da transcrição. Estas novas versões de AtbZIP9 são teoricamente capazes de ativar de maneira constitutiva a expressão dos genes alvos de AtbZIP9, contornando assim, as dificuldades decorrentes da análise de famílias gênicas que apresentam redundância funcional. Quando comparados a plantas selvagens, transformantes primários para ativadores constitutivos fortes apresentaram diversas alterações de morfologia foliar, além de mudanças metabólicas e fisiológicas como acúmulo de compostos fenólicos em folhas, sintomas de morte celular e senescência. A análise destes transformantes ainda sugere uma possível participação de AtbZIP9 no controle do desenvolvimento do sistema vascular de raízes e folhas. Suspeitamos que as alterações de morfologia foliar e fisiologia observadas possivelmente representem conseqüências de mudanças nas propriedades funcionais de transporte do floema, decorrentes de defeitos no processo de diferenciação e organização das células do cilindro vascular / Abstract: Transcriptional regulatory factors (TFs) play an important role in controlling growth and development of ali organisms. bZIPs TFs have been described in ali eukaryotes and are characterized by a basic aminoacid rich DNA binding domain and a leucine zipper, responsible for dimerization. bZIPs have been reported to act in several different plantspecific processes such as organ development, cell elongation, defense mechanism, hormones and sucrose signalization, light response, control of nitrogen/carbon balance, osmotic control and flowering. We showed that Arabidopsis thaliana and Orysa sativa genomes encode a complete and non-redundant set of 76 and 113 bZIP transcription factors, respectively, which were divided into 11 unique groups of homologous genes. More detailed phylogenetic analysis led to the identification of 33 Possible Groups of Monocot and Eudicot Orthologous Genes (PoGO), which allows rationalizing functional studies in angiosperms. Group C, which includes genes homologous to the maize Opaque-2 locus, is formed by three PoGOs, suggesting that this group represents three ancestral functions among angiosperms. In Arabidopsis these three possible ancestral functions may be represented by the bZIP Qpaque-2. homologous genes (Bzo2h), Bzo2h3/AtbZIP63 (PoGO C1), Bzo2h1/AtbZIP10 and Bzo2h4/AtbZIP25 (PoGO C2) and Bzo2h2/AtbZIP9 (PoGO C3). To get insight into the evolution pattern and function of Group C members, we have iniciated the functional characterization of the Bzo2h genes concentrating initially on AtbZIP9, a unique gene that represents an ancestral function and for which no functional informational is available. We showed that AtbZIP9 expression is restricted to phloem cells and regulated by glucose, abscisic acid and cytokinin, suggesting that this gene is an element of the signalization pathways of these metabolic and hormonal signals in the phloem. Reverse genetic approaches such as RNAi, knockout and superexpression failed to reveal the biological function of AtbZIP9 in Arabidopsis life cycle and suggested that post-transcriptional regulation and/or functional redundancy may act on AtbZIP9. In order to improve our Rnowledge on AtbZIP9 function, Arabidopsis transgenic lines expressing constitutive transcriptional activator versions of AtbZIP9 were obtained. Since such modified versions of AtbZIP9 are theoretically able to promote the superexpression of AtbZIP9 target genes, this strategy should be independent of functional redundancy. When compared to wild type plants, primary transformants for constitutive transcriptional activator versions of AtbZIP9 showed alterations of leaf morphology, as well as metabolic and physiologic modifications, such as phenolic compound accumulation in leaves, cell death and senescence symptoms. Analyses of this transformants also suggest that AtbZIP9 is possibly involved in the control of leaf and root vascular system development. We suspect that the alteration of leaf morphology and physiology observed in primary transformants possibly reflects consequences of changes in phloem transport functional properties, due to defects in vascular cylinder cell differentiation and organization / Mestrado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis. Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements. The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%). The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25. The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

No description available.