Thesis advisor: Junona Moroianu / During the papillomavirus replication cycle, the L2 minor capsid protein enters the nucleus in the initial phase after uncoating of the incoming virions and in the productive phase when L2 together with L1 major capsid protein mediate the encapsidation of the newly replicated viral genome. L2 proteins of both high risk HPV16 L2 and low risk HPV11 L2 have two nuclear localization signals (NLSs): one at the N-terminus (nNLS) and one at the C terminus (cNLS). The purpose of these experiments is to determine the minimal mutations necessary to inhibit the function of the NLSs. In this study, subcellular localization of enhanced green fluorescent protein (EGFP) fusions with full length L2 and L2 mutants lacking either the cNLS (EGFP-L2ΔC), nNLS (EGFP-L2ΔN), or both NLSs (EGFP-L2ΔNΔC) was analyzed in HeLa cell transfection assays. Full length HPV16 L2 and HPV11 L2 proteins localize to the nucleus. For both HPV16 and 11 L2, each NLS could independently mediate nuclear import in vivo. EGFP fusions were also made with mutated nNLS (EGFP-L2ΔCSbN) or mutated cNLS (EGFP-L2ΔNSbC). Transfected HeLa cells were examined by fluorescence microscopy and quantitative studies were done. In both HPV16 and 11 L2 proteins, mutation of basic residues in either NLS inhibited its nuclear import ability. / Thesis (BS) — Boston College, 2008. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Biology. / Discipline: College Honors Program.

Bone morphogenetic protein 4 (Bmp4) is a well known growth factor that regulates gene expression through the SMAD signaling pathway. Bmp4 is involved in many developmental processes and has been identified as an important factor in several cancers, including melanoma, ovarian cancer, and colon cancer. Madoz-Gurpide et al. recently observed Bmp4 in the nuclei of a minor percentage of cells in colon cancer tissues. In addition, our lab has recently discovered a nuclear variant of Bmp2 (nBmp2), the TGF-β family member most closely related to Bmp4. These observations led us to hypothesize that a nuclear variant of Bmp4 (nBmp4) also exists. The results of chapter one report the existence of a nuclear variant of Bmp4. nBmp4 is translated from an alternative start codon downstream of the signal peptide sequence which allows a bipartite nuclear localization signal to direct translocation of nBmp4 to the nucleus. Chapter 2 and 3 further report that nBmp4 interacts with several subunits in the SCF E3 ubiquitin ligase, namely two Regulator of Cullins (ROC) proteins, five Cullin proteins, and two F-box proteins. Due to the known role of the SCF E3 ubiquitin ligase in regulating the cell cycle, the effect of nBmp4 on cell cycle progression was analyzed and the results show that nBmp4 affects the cell cycle by causing cells to accumulate in G0/G1. The association of nBmp4 and the SCF E3 ubiquitin ligase components and the affect that nBmp4 has on the cell cycle suggest that nBmp4 functions in the nucleus by inhibiting the SCF E3 ubiquitin ligase from ubiquitinating target proteins that are involved in regulating cell cycle progression. Finally, the initial stages in the generation of an nBmp4 over-expression mouse are described. The results of this research clearly change the traditional paradigm that Bmp4 performs all of its functions via extracellular signaling and introduce the existence of a nuclear variant that is involved in cell cycle regulation.

Calpain 5 (CAPN5) is a non-classical member of the calpain family. It lacks the EF-hand motif characteristic of the classical calpains, calpain 1 and 2, but retains catalytic and Ca2+ binding non EF domains. Tra-3, an ortholog of CAPN5, is involved in necrotic cell death in C.elegans; although specific role of CAPN5 has not been investigated in the mammalian CNS. I compared relative mRNA levels of calpains in rat CNS, which revealed that CAPN5 is the second most highly expressed calpain. We examined relative levels of CAPN5 from late embryonic day 18 to postnatal day 90 and found lower mRNA but higher protein levels during CNS development. Using X –gal staining in Capn5 +/- mice, immunostaining of rat brain sections and SH-SY5Y cells, and subcellular fractionation of rat brain cortex, we found that CAPN5 is a non-cytoplasmic calpain localized in the nucleus and enriched in synaptic mitochondria. Proteinase K treatment of mitochondria and mitoplasts from B35 rat neuroblastoma cells and rat synaptic mitochondria revealed CAPN5 was localized on the inner mitochondrial membrane and released from mitochondria on membrane permeabilization with alamethicin. We used immunolabelling, confocal imaging, nuclear subfractionation and transient transfections to evaluate the subnuclear localization of CAPN5. CAPN5 was detected in punctate domains and associated with promyelocytic leukemia (PML) protein, a tumor suppressor protein. We further demonstrated that CAPN5 carries a nonconventional bipartite nuclear localization signal. Together, these findings demonstrate that CAPN5 is a non-cytosolic calpain, abundant in the CNS and localized to the mitochondria inner membrane and nuclear PML bodies.

Potato yellow dwarf virus (PYDV) is the type species of the genus Nucleorhabdovirus and, like all members of this genus, replication and morphogenesis occurs inside the nuclei of infected cells. Protein localization prediction algorithms failed to identify a nuclear localization signal (NLS) in PYDV nucleocapsid (N) protein, although PYDV-N has been shown to localize exclusively to the nucleus when expressed as a green fluorescent protein (GFP):N fusion in plant cells. Deletion analysis and alanine-scanning mutagenesis identified two amino acid motifs, 419QKR421 and 432KR433, that were shown to be essential for nuclear import and interaction with importin-α. Additional bimolecular fluorescence complementation showed that the PYDV-N-NLS mutants cannot be ferried into the nucleus via interaction with PYDV-P or-M. In contrast, interaction with N-NLS mutants appeared to retard the nuclear import of PYDV-P. Taken together, it was determined that PYDV-N contains the bipartite NLS 419QKRANEEAPPAAQKR433. Similarly, alanine-scanning mutagenesis was performed to determine the regions responsible for the nuclear import of PYDV-M and -P. A non-canonical NLS was identified in PYDV-P, consisting of three regions in the N-terminus of the protein required for nuclear import. PYDV-P does not interact with any Nicotiana benthamiana importins, but was found to interact with importin-α7 and -α9 of the non-host plant Arabidopsis thaliana. Two amino acids of PYDV-M, 225KR226, were found to be critical for nuclear import and interaction with importin-α. In addition, site-directed mutagenesis identified that amino acids 223LL224 of PYDV-M, which are adjacent to the two amino acids identified as responsible for nuclear import, are critical for inducing invaginations of the inner nuclear membrane. Bimolecular fluorescence complementation (BiFC) was then used to identify any differences in localization and interaction caused by the mutations introduced to PYDV-P and -M. The PYDV-P and -M proteins were still able to interact with other PYDV proteins, although the localization of the interaction differs between mutants.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2004. / Vita. Bibliography: 118-130.

Indiana University-Purdue University Indianapolis (IUPUI) / Infection with the single-celled parasite Toxoplasma gondii (phylum Apicomplexa) is usually benign in normal healthy individuals, but can cause congenital birth defects, ocular disease, and also life-threatening infection in immunocompromised patients. Acute infection caused by tachyzoites is controlled by a healthy immune response, but the parasite differentiates into a latent cyst form (bradyzoite) leading to permanent infection and chronic disease. Current therapies are effective only against tachyzoites, are highly toxic to the patient, and do not eradicate the encysted bradyzoites, thus highlighting the need for novel therapeutics. Inhibitors of histone deacetylases have been shown to reduce parasite viability in vitro demonstrating that chromatin remodeling enzymes, key mediators in epigenetic regulation, might serve as potential drug targets. Furthermore, epigenetic regulation has been shown to contribute to gene expression and differentiation in Toxoplasma. This dissertation focused on investigating the physiological role of a Toxoplasma GCN5-family histone acetyltransferase (HAT), termed TgGCN5-B. It was hypothesized that TgGCN5-B is an essential HAT that resides within a unique, multi-subunit complex in the parasite nucleus. Studies of TgGCN5-B have revealed that this HAT possesses a unique nuclear localization signal (311RPAENKKRGR320) that is both necessary and sufficient to translocate the protein to the parasite nucleus. Although no other protein motifs have been identified in the N-terminal extension of TgGCN5-B, it is likely that this extension plays a role in protein-protein interactions. All GCN5 homologues function within large multi-subunit complexes, many being conserved among species, but bioinformatic analysis of the Toxoplasma genome revealed a lack of many of these conserved components. Biochemical studies identified several potential TgGCN5-B associating proteins, including several novel apicomplexan transcription factors. Preliminary evidence suggested that TgGCN5-B was essential for tachyzoites; therefore, a dominant-negative approach was utilized to examine the role of TgGCN5-B in the physiology of Toxoplasma. When catalytically inactive TgGCN5-B protein was over-expressed in the parasites, there was a significant decrease in tachyzoite growth and viability, with initial observations suggesting defects in nuclear division and daughter cell budding. These results demonstrate that TgGCN5-B is important for tachyzoite development and indicate that therapeutic targeting of this HAT could be a novel approach to treat toxoplasmosis.

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix protein (M), glycoprotein (G), and large polymerase protein (L). The features of each protein including a nuclear localization signal, isoelectric point, and transmembrane domain, were determined by predictive algorithms. The gene coding region was flanked by leader and trailer, and each ORF was separated by a conserved intergenic junction. In the intergenic junctions, the highly conserved cis-regulatory elements, polyadenylation signal, gene spacer, and transcription start site, were identified. The similarities of amino acid sequences between each cognate protein of SYDV and CYDV were higher than 80% except for X and P proteins. The protein localization and interaction assays of each CYDV protein identified strain-specific associations in comparison with those of SYDV and generated unique protein interaction and localization map compared to SYDV. Phylogenetic analysis using L protein identified that CYDV forms a clade with other leafhopper-transmitted rhabdoviruses. Protein sequence comparisons revealed that CYDV X has greater similarity to the cognate protein of Eggplant mottle disease virus than to SYDV X. The localization patterns of CYDV-N and -Y were different compared the cognate proteins of SYDV. The functional nuclear export domain of SYDV M was identified using c-terminal fragments of the Mwt(aa 211-243), MLL223AA(aa 211-243), and MKR225AA(aa 211-243). Based on the data, the functional domains M mediating membrane association, nuclear import and export were mapped for both strains and suggested a model whereby M mediates intra- and intercellular movement of PYDV nucleocapsid.

Das Borna Disease Virus (BDV, Bornavirus) besitzt ein einzelsträngiges RNA-Genom negativer Polarität und ist innerhalb der Ordnung Mononegavirales der Prototyp einer eigenen Virusfamilie, die der Bornaviridae. Eine außergewöhnliche Eigenschaft des Virus ist seine nukleäre Transkription und Replikation, eine weitere besteht in seiner Fähigkeit, als neurotropes Virus sowohl in vivo als auch in vitro persistente Infektionen zu etablieren. Die zugrunde liegenden Mechanismen sowohl der Replikation als auch der Persistenz sind derzeit noch unzureichend verstanden, auch deshalb, weil das Virus noch relativ „jung“ ist: Erste komplette Sequenzen des RNA-Genoms wurden 1994 publiziert und erst vor einigen Monaten gelang die Generierung rekombinanter Viren auf der Basis klonierter cDNA. Im Mittelpunkt dieser Arbeit standen das p10 Protein und das Phosphoprotein (P), die von der gemeinsamen Transkriptionseinheit II in überlappenden Leserahmen kodiert werden. <br><br> Als im Kern der Wirtszelle replizierendes Virus ist das Bornavirus auf zelluläre Importmechanismen angewiesen, um den Kernimport aller an der Replikation beteiligten viralen Proteine zu gewährleisten. Das p10 Protein ist ein negativer Regulator der viralen RNA-abhängigen RNA-Polymerase (L). In vitro Importexperimente zeigten, dass p10 über den klassischen Importin alpha/beta abhängigen Kernimportweg in den Nukleus transportiert wird. Dies war unerwartet, da p10 kein vorhersagbares klassisches Kernlokalisierungssignal (NLS) besitzt und weist darauf hin, dass der zelluläre Importapparat offensichtlich flexibler ist als allgemein angenommen. Die ersten 20 N-terminalen AS vermitteln sowohl Kernimport als auch die Bindung an den Importrezeptor Importin alpha. Durch Di-Alanin-Austauschmutagenese wurden die für diesen Transportprozess essentiellen AS identifiziert und die Bedeutung hydrophober und polarer AS-Reste demonstriert. <br><br> Die Fähigkeit des Bornavirus, persistente Infektionen zu etablieren, wirft die Frage auf, wie das Virus die zellulären antiviralen Abwehrmechanismen, insbesondere das Typ I Interferon (IFN)-System, unterwandert. Das virale P Protein wurde in dieser Arbeit als potenter Antagonist der IFN-Induktion charakterisiert. Es verhindert die Phosphorylierung des zentralen Transkriptionsfaktors IRF3 durch die zelluläre Kinase TBK1 und somit dessen Aktivierung. Der Befund, dass P mit TBK1 Komplexe bildet und zudem auch als Substrat für die zelluläre Kinase fungiert, erlaubt es, erstmalig einen Mechanismus zu postulieren, in dem ein virales Protein (BDV-P) als putatives TBK1-Pseudosubstrat die IRF3-Aktivierung kompetitiv hemmt. / The Borna Disease Virus (BDV) harbors a single stranded RNA genome of negative polarity. Within the order of Mononegavirales it is the prototype of a new virus family named Bornaviridae. Unique features of this neurotrope virus are its nuclear transcription and replication as well as its ability to establish persistent infections both in vivo and in vitro. The underlying mechanisms of BDV replication and persistence are currently not well understood amongst others due to the fact that BDV is quite a young virus: First complete sequences of the RNA genome have been published in 1994. Only a few months ago the generation of a recombinant Bornavirus from cloned cDNA has been accomplished. <br><br> The work presented here focused on the viral p10 protein and the phosphoprotein P that are both encoded by two overlapping reading frames of the transcription unit II. <br><br> Nuclear replication of the Bornavirus relies on cellular import mechanisms to allow for nuclear import of viral proteins involved in viral replication. The p10 protein has been described as a negative regulator of the viral RNA dependent RNA polymerase (L). In vitro import experiments revealed that p10 translocates into the nucleus via the classical importin alpha/beta; dependent pathway. This was unexpected since p10 does not contain a predictable classical nuclear localization signal (NLS) suggesting that the cellular import machinery is more flexible than generally believed. The first 20 amino acids mediate nuclear import and binding to the import receptor importin alpha. Analysis of di-alanine-exchange mutants identified essential amino acids and furthermore revealed the impact of hydrophobic and polar side chains in receptor binding and nuclear import. <br><br> The ability of the Bornavirus to establish persistent infections rises the question of how the virus circumvents cellular antiviral defense mechanisms, in particular the type I interferon system. This work characterizes the viral P protein as a potent antagonist of IFN beta induction. It prevents the activation of the central transcription factor IRF3 by interfering with the cellular kinase TBK1. The finding that P forms complexes with TBK1 and moreover serves as a kinase substrate allows to postulate a mechanism for the first time, in which a viral protein (BDV-P) acts as a putative TBK1 pseudo-substrate and thereby competitively inhibits IRF3 activation.

Orientador: Maria Helena Andrade Santana / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-08T14:24:33Z (GMT). No. of bitstreams: 1 Torre_LucimaraGazioladela_D.pdf: 28769884 bytes, checksum: 485f026c87d2f5b4fb99e642474200d0 (MD5) Previous issue date: 2006 / Resumo: Este trabalho visa o desenvolvimento tecnológico de uma vacina gênica, destinada ao combate à tuberculose, na qual o DNA encontra-se veiculado em lipossomas. Foram enfocados três aspectos principais: 1.A preparação e caracterização de estruturas lipídicas funcionais veiculando o DNA, projetadas para atenderem aos requisitos de imunização contra a tuberculose; 2. Complexação do DNA com peptídio sintético promotor de transporte nuclear e veiculação na estrutura lipossomal que se mostrou mais promissora nos ensaios in vitro e in vivo realizados no CPT-RP. 3. Análise do escalonamento da produção da estrutura lipossomal mais promissora para subsequente veiculação do DNA. Duas estruturas lipossomais foram compostas por lipídios com as seguintes funcionalidades: estrutural, de incorporação do DNA e atração eletrostática com a superfície das células, de intensificação da liberação do DNA no citoplasma celular. Foram preparadas pelo método da desidratação-rehidratação, gerando DRVs (¿dehydrated-hydrated vesicles¿). O DNA foi associado à essas estruturas, localizando-se no interior, [DRV(DNA)] ou prefencialmente na sua superfície [DRV-DNA]. A terceira estrutura, um agregado lipídico não lipossomal designado por lipoplexo, foi preparado na ausência do lipídio estrutural, contendo o DNA associado em toda a sua superfície. As estruturas foram caracterizadas através do seu diâmetro hidrodinâmico e distribuição de tamanhos, razão de cargas para completa incorporação do DNA, carga superficial, transição de fases, acessibilidade de sonda de fluorescência ao DNA e morfologia. O peptídio sintético com seqüência não convencional foi associado à estrutura DRV-DNA. O escalonamento da produção de lipossomas foi analisado através de dados experimentais e simulação matemática da cinética de produção de lipossomas em sistema multitubular. Dos resultados conclui-se que a estrutura DRV-DNA é promissora para a produção de vacina contra a tuberculose tanto pela sua efetividade biológica quanto do ponto de vista tecnológico / Abstract: This work contributes to the technological development of a gene vaccine against tuberculosis, where DNA is transported within liposomes. The three main aspects focused on were: 1. Functional lipid structures for DNA delivery were prepared and characterized in the attempt to obtain immunization standards against tuberculosis; 2. The best lipid structure was chosen from in vitro and in vivo assays performed in the ¿Centro de Pesquisas em Tuberculose de Ribeirão Preto¿ ¿ CPT-RP. A synthetic peptide that promotes nuclear transport was complexed to DNA and included into the best lipid structure. 3. Scale up analysis for the production of the best lipid structure that was used for DNA delivery. Two types of liposomes were composed by lipids with the following properties: (i) structure, (ii) DNA incorporation and electrostatic attraction with cell surface, and (iii) helper, that facilitates the DNA release to the citosol. These structures were prepared by the dehydrated-hydrated method, generating DRVs (dehydrated-hydrated vesicles). The DNA was associated in the inner compartment, [DRV(DNA)], or mostly at the surface [DRV-DNA] of these structures. The third structure, a lipid aggregate that does not form liposomes and was named lipoplex, was prepared in the absence of the structural lipid, used in previous preparations, which contained DNA associated with all of the aggregate¿s surface. The physico-chemical characterization of the structures were based on the hydrodynamic diameter and size distribution of the lipid particles, charge ratio for DNA incorporation into the lipid structure, surface charge, phase transition temperatures, the fluorescent probe accessibility to DNA and morphology of the particles. A synthetic peptide, with non-conventional sequence was associated to the DRV-DNA structure. The scale up for the liposome production was analyzed through the acquisition of experimental data and mathematical simulation of the liposomes production in a multitubular system. The results demonstrate that the incorporation of DNA into a lipid structure is very promising as a tuberculosis vaccine, especially in regards to the complexation of DNA with empty DRVs. The technological aspects of scaling up also confirm the viability of preformed liposomes production / Doutorado / Desenvolvimento de Processos Biotecnologicos / Doutor em Engenharia Química

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