Thesis (Ph.D.)--Murdoch University, 2006. / Thesis submitted to the Division of Health Sciences. Bibliography: leaves 138-177.

Thesis (Ph. D. in Microbiology and Immunology)--Vanderbilt University, May 2009. / Title from title screen. Includes bibliographical references.

Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: CTL; dengue. Includes bibliographical references (p. 57-64).

Thesis (M.A.)--Ball State University, 2009. / Title from PDF t.p. (viewed on June 07, 2010). Includes bibliographical references (p. [47]-51).

Thesis (doctoral)--Lund University, 1995.

Thesis (doctoral)--Lund University, 1995.

Thesis (MSc)--University of Stellenbosch, 2005. / Bibliography. Also available via the Internet.

Thesis (Ph. D.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 61-74). Also available on the World Wide Web.

Retroviruses are obligate intracellular parasites that carry the information necessary for replication within their genomes. The three polyproteins, Gag, Pol, and Env, encoded by all retroviruses, function to generate progeny virions inside the host cell. Formation of new viral particles requires detailed instructions contained within the Gag polyprotein. Herein we describe our investigation into assembly of the Mason-Pfizer monkey virus (M-PMV). During retrovirus assembly, the transition from immature to a fully infectious mature particle is associated with the operation of molecular switches that trigger dramatic conformational changes of the Gag proteins. A dominant maturation switch that stabilizes the immature capsid lattice is located in the C-terminus of the capsid (CA) protein in many retroviral Gags. The HIV-1 Gag contains a stretch of five amino acid residues termed the 'clasp motif', important for the organization of the hexameric subunits that provide stability to the overall immature HIV-1 shell. Sequence alignment of the CA C-terminal domains (CTDs) of the HIV-1 and M-PMV highlighted a spacer-like domain in M-PMV that may provide comparable function. In the present study we report an examination of the role of the clasp motif in the M-PMV life cycle. Our results demonstrate that claps motif mutants display major defects in virion assembly and release, and even larger defects in infectivity. Our data identifies the clasp motif as a fundamental contributor to CA-CTD interactions necessary for efficient viral infection. The retroviral life cycle, unlike that of any other viral family, leads to the obligate integration of a proviral DNA into the host genome of somatic cells and in some cases even into the germ line. This remarkable feature of the Retroviridae family of viruses accounts for their extraordinary persistence through time and widespread abundance among vertebrate hosts. Because retroviral infection can have serious consequences to the host, there is great selective pressure to evolve strong networks that act to control incoming viruses. In the second study presented here, we report a novel cofactor of an antiviral system, Riplet, which operates to augment HIV-1 restriction by ZAP. The zinc-finger antiviral protein (ZAP) is an interferon-stimulated gene (ISG) with potent intrinsic antiviral activity. ZAP inhibits replication of retroviruses including MLV and HIV-1, as well as alphaviruses, filoviruses, hepatitis B virus, etc. ZAP operates at the post-transcriptional stage, reducing the number of viral transcripts available for translation in the cytoplasm, although additional pathways might be at play. The exact mechanisms by which ZAP restricts viral replication are not fully understood. ZAP lacks enzymatic activity and utilizes other cellular proteins to suppress viral replication. TRIM25 and the nuclease KHNYN have been identified as ZAP cofactors, but its activity may well involve other cellular proteins. Here we identify Riplet, a protein known to play a central role in the activation of the retinoic acid-inducible gene I (RIG-I), as a novel ZAP cofactor that acts to augment ZAP’s antiviral activity. Our data demonstrates that Riplet significantly augments ZAP-mediated restriction of HIV-1. Additionally, we show that Riplet interacts with ZAP via its PRY/SPRY domain and that the ubiquitin ligase activity of Riplet is not required to stimulate ZAP-mediated inhibition. Moreover, we show that Riplet interacts with TRIM25 suggesting that both Riplet and TRIM25 may operate synergistically to augment ZAP-mediated inhibition of HIV-1. The intracellular tropism of viruses is determined by a diverse combination of host proteins that allow infection to proceed efficiently. To achieve successful infection the virus needs the contribution of numerous cellular factors that assist at various steps of the life cycle. Conversely, replication requires resistance to species-specific restriction factors that act to suppress virus infection. The replication of M-PMV has been found to be highly restricted in mouse cell lines. The mechanism underlying the restriction of M-PMV replication in mouse cells has not been characterized. In the third study presented here, we examined this potent post-entry block and performed an unbiased genome-wide CRISPR-Cas9 screen, selecting for knock-out of host factors that relieved the block. Our data identified several candidate genes that encode proteins involved in virus trafficking and innate immune activation.

Viruses require a host cell to replicate and proliferate; upon infection they appropriate host resources and molecular machines. Specifically, viruses use ribosomes of the host to translate the information in their genome. Some viruses with single-stranded RNA genomes contain highly structured non-coding regions of RNA called internal ribosome entry sites (IRESs) which are used to hijack the host’s ribosomes through a non-canonical cap-independent initiation pathway. Canonical translation initiation is a highly complex and regulated process: at least a dozen translation factors are necessary, and it is the rate-limiting step in eukaryotic translation. Viruses containing an IRES forgo canonical eukaryotic translation initiation factors and bypass some steps of canonical translation initiation by mimicking part of the host’s initiation machinery. The simplest among these IRESs are found in the intergenic region (IGR) of viruses in the family Dicistroviridae. These type IV IRESs from dicistroviruses have been structurally characterized in great detail in using the cricket paralysis virus (CrPV) and Israeli Acute Paralysis Virus (IAPV). To better understand how structure affects the function of these type IV IRESs, using single-particle cryo-electron microscopy (cryo-EM), we have characterized a recently discovered IRES found in the IGR of the genome of Nedicistrovirus (NediV). Four complexes that represent each step in the alternative translation initiation mechanism were prepared and analyzed to solve the 3D structure and characterize the mechanism by which the NediV-IRES captures host ribosomes. With this, we were able to understand how the shorter stem-loop V (SL-V) of NediV-IRES impacts the well-characterized interaction of SL-V with eukaryotic small subunit ribosomal protein 25 (eS25) (Landry et al., 2009), which is important for the IRES:40S complex formation. This shortened stem-loop has been shown to fold in a way that does not support stable binding to the small ribosomal subunit (40S) and subsequent recruitment of the large ribosomal subunit (60S). NediV-IRES, rather, relies on direct recruitment of the 80S ribosome, which has been seen more commonly at low concentrations of Mg²⁺ for CrPV-IRES (Petrov et al., 2016). Solved structures also suggest that upon loading, NediV-IRES skips the first eEF2-dependent pseudo-translocation step necessary to bind to the ribosomal P site without the need of eEF2. Because of their simplicity, these type IV IRESs represent a robust potential tool for cell-free and vector-driven translation. Due to these structural and mechanistic differences observed, we propose that NediV-IRES, along with the NediV-like Antarctic picorna-like virus 1 (APLV-1)-IRES (Lu, 2019), represents a novel type IV IRES subclass.