The Picornaviridae family contains a number of pathogens which are economically important including Poliovirus, Coxsakievirus, Hepatitis A Virus, and Foot-and-Mouth-Disease-Virus. Recently the emergence of novel picornaviruses associated with gastrointestinal, neurological and respiratory diseases in humans has been reported. Although effective vaccines for viruses such as FMDV, PV and HAV have been developed there are currently no antivirals available for the treatment of picornavirus infections. Picornaviruses proteins are classified as: the structural proteins VP1, VP2, VP3 and VP4 which form the subunits of the viral capsid and the replication proteins which function as proteases, RNA-polymerases, primers and membrane binding proteins. Although the host specificity and viral pathogenicity varies across members of the family, the icosahedral capsid is highly conserved. The capsid consists of 60 protomers, each containing a single copy of VP1, VP2 and VP3. A fourth capsid protein, VP4, resides on the internal side of the capsid. Capsid assembly is integral to life-cycle of picornaviruses; however the process is complex and not fully-understood. The overall aim of the study was to broaden the understanding of the evolution and function of the structural proteins across the Picornaviridae family. Firstly a comprehensive analysis of the phylogenetic relationships amongst the individual structural proteins was performed. The functions of the structural proteins were further investigated by an exhaustive motif analysis. A subsequent structural analysis of highly conserved motifs was performed with respect to representative enteroviruses, Foot-and-Mouth-Disease-Virus and Theiler’s Virus. This was supplemented by the in silico prediction of interacting residues within the crystal structures of these protomers. Findings in this study suggest that the capsid proteins may be evolving independently from the replication proteins through possible inter-typic recombination of functional protein regions. Moreover the study predicts that protomer assembly may be facilitated through a network of multiple subunit-subunit interactions. Multiple conserved motifs and principle residues predicted to facilitate capsid subunit-subunit interactions were identified. It was also concluded that motif conservation may support the theory of inter-typic recombination between closely related virus sub-types. As capsid assembly is critical to the viral life-cycle, the principle interacting motifs may serve as novel drug targets for the antiviral treatment of picornavirus infections. Thus the findings in the study may be fundamental to the development of treatments which are more economically feasible or clinically effective than current vaccinations.

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Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from ​Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...

In the twenty-first century, advances in synthetic biology and molecular tools to implement programmable behavior into microbes have fueled significant efforts to develop microbial-based therapeutics. Bacteria and viruses have been explored independently for their ability to replicate and induce cytotoxic effects in cancer cells selectively. This dissertation aims to co-opt the anti-tumor capabilities of gram-negative Salmonella enterica subspecies enterica serotype Typhimurium (referred to as Salmonella typhimurium moving forward) and picornaviruses (small RNA viruses with positive sense genomes) to develop a potent, single bacterial-viral consortium- based system to treat solid tumors.I first describe our efforts to co-opt S. typhimurium’s natural internalization into hosts and intracellular space-sensing to deliver self-amplifying picornaviral RNA. Protein effectors that promote intracellular survival of S. typhimurium within the Salmonella-Containing-Vacuole (SCV) are transcribed by Salmonella Pathogenicity Island-2 (SPI-2) promoters, which turn on after sensing the intracellular pH, ion concentrations, and oxidative stressors. These effectors are then translocated into the host’s cytoplasm by a needle apparatus that connects the SCV and cytoplasm, which is also transcribed by SPI-2 promoters. By using the SPI-2 promoter PsseA to drive the expression of fluorescent reporters and membrane-disrupting proteins (eukaryotic and prokaryotic), efficient escape of Salmonella-produced proteins into tumor-host cells was established. RNA delivery into host cells was also made possible by a secondary SPI-2 promoter, PsseJ, which transcribes RNA polymerase T7 (T7), which then transcribes a T7-promoter-driven Poliovirus replicon or full-length Senecavirus A (SVA). Inoculation of this engineered S. typhimurium strain on a panel of cancer cell lines identified the system’s ability to deliver viral replicons and full-length viruses in a small cell cancer cell line, H446. In a murine model, S. typhimurium delivery of SVA was then shown to clear xenografted H446 tumors. Motivated by the possibility of delivering other picornaviral species with similar anti-tumor properties, but documented healthy tissue cytotoxicity, S. typhimurium was further engineered to control SVA viral spread. By driving Tobacco Etch Virus (TEV) protease expression via a second SseA promoter, and replacing a natural cleavage site on SVA with the TEV-cleavage domain, we demonstrate TEV-dependent SVA spread in H446 cells. I conclude with efforts on engineering TEV-dependent-SVA transgene expression to confer greater antitumor properties. Interferon-gamma and granulocyte-macrophage colony-stimulating factor (GM-CSF) have been reported to attenuate H446 growth in vitro. Expression of interferon-gamma off SVA would produce a direct selective pressure against viral replication and virion production. However, a fusion of human GM-CSF to Nano-Luciferase protein on the TEV-dependent SVA genome maintained luminescent signals, GM-CSF activity, and TEV-dependent spread, providing a framework to survey anti-tumor properties of SVA-transgenes. Furthermore, I address our development of syngeneic models for Salmonella-mediated delivery of SVA, an important step towards clinical applications of the system as immunocompetent models more closely correlate to immunocompetent patient populations. SVA’s efficient entry and replication in neuroendocrine-derived tissue identified murine neuroblastoma N1E-115 cells as a suitable cell line for SVA cytotoxicity studies. However, the ability of these cells to support bacterial-viral superinfections is unknown. Here, we show that Salmonella-mediated launch of SVA leads to viral spread that can attenuate heterologous hind flank tumor growth and improve their survival along with mice engrafted with orthotopic intracranial brain tumors.

Bibliography: leaves 129-137 / viii, 137 leaves, [27] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--Dept. of Entomology, Waite research Institute, University of Adelaide, 1986