Satellite panicum mosaic virus (SPMV) depends on its helper Panicum mosaic virus (PMV) for replication and movement in host plants. The positive-sense single-stranded genomic RNA of SPMV encodes a 17-kDa capsid protein (CP) to form 16-nm virions. Previous studies showed that SPMV CP has multiple functions during infection including encapsidation, symptom exacerbation, inhibiting the accumulation of SPMV DIs, and facilitating systemic movement. This dissertation confirms and extends the results of our previous reports with new biological and biochemical evidence. For example, the dosage effect of SPMV CP on symptom severity supports its function as a pathogenicity factor. Biological assays also demonstrate compensatory effects of SPMV CP on virus mutants defective in systemic movement. In addition, it is shown for the first time that SPMV CP is involved in cellto- cell movement of SPMV RNA and associated with the cell wall and membranes, a signature property of plant virus movement proteins. However, SPMV CP in the cytosol exists exclusively as virions and is dispensable for symptom exacerbation. SPMV CP contains a distinctive N-terminal arginine-rich motif (N-ARM), which is required for the in vitro binding of SPMV and PMV genomic RNAs by SPMV CP. Mutations of this region impair all known functions of SPMV CP. Interestingly, manipulation of the C-terminus of SPMV CP resulted in the same phenotypes as alterations in the N-ARM except that this does not affect the RNA binding activity of SPMV CP. Biological experiments demonstrate that virions are not required for the properties of SPMV CP to facilitate local and systemic movement and inhibit the accumulation of SPMV DIs, suggesting that SPMV CP and RNA form alternative complexes for these purposes. This dissertation study reveals the nucleolar localization of SPMV CP and its interaction with PMV CP in the form of virions. The identification of distinct functional domains of SPMV CP and its complex subcellular localization profile resulted in the proposal of a tentative model on how the functions of SPMV CP are coordinated for a robust infection. This dissertation provides a foundation for further understanding of the complex interactions among host plants, helper viruses, and satellites.

Abstract Taiwan marine fish suffers the epidemic infection of iridovirus. In this research, infected fish of Epinephelus. lanceolatus was diagnozed by polymerase chain reaction. Transmission electron microscopy showed the morphology of viral particles from tissue lysate. The nucleotide sequence of major capsid protein (MCP) was compared to OSGIV, thereafter the novel virus from Epinephelus lanceolatus is named OSGIV-like iridovirus. By cloning expression of the MCP of TGIV and OSGIV-like, the MCP of 51 kDa was insoluable although minor virus-like substance was observed in TEM. Triton X-100 of 2.5% improved the solubility of protein to 30.95 £gg/£gl. Chloroform treatment enhanced the antibody-detection for the MCP of virus in the tissue. We inference that iridovirus MCP is associated with the envelope because of its hydrophobicity.

Parvoviruses cause dreadful enteritis in waterfowls and lead to tremendous financial losses. This study aims at developing effective way to prevent waterfowl parvoviral infection. Duck parvoviruses (DPVs) and goose parvoviruses (GPVs) were isolated from organs of infected waterfowls. The presence of virus in the specimens was identified using polymerase chain reaction (PCR) and subsequent restriction fragment length polymorphism (RFLP) analysis. To reveal the genetic variation of viral capsid proteins (VPs), full length VPs gene were amplified and sequenced. The sequence data indicated the sequences diverge 4.1 to 4.4% among viral strains isolated during 1990 to 1999. The variant amino acids cluster in the common regions of VP3 at residues 203-266 and 482-534, which overlaps with the regions proposed to expose on the outer surfaces of parvoviral particles. These data implying that selective pressure from host immune system might play a part. The nucleotide sequences of VPs also reveal that DPV and GPV share 77 % similarity at the DNA, and 84.6% at the protein level. The most variable regions reside in the N-terminal of VP2 before the initiation codon of VP3 with 35% (19/54) amino acids divergence. This study also reveals the presence of conserved strain-specific residues in VPs and these residues seldom vary among different isolates of the same virus, suggesting that they might be important in maintaining viral structure or host specificity which worth further investigation. To investigate the antigenicity of VPs, the GPV genomic DNA encoding common region of VPs was fused in frame with glutathione S-transferase (GST) gene for the expression of GST-GPV (248-516) fusion protein in bacterial cells. Purified fusion protein was used as immunogen for the generation of rabbit anti-GPV (248-516) antiserum. The potential diagnostic usage was confirmed by the fact that this antiserum was able to differentiate between viral infected and uninfected primary embryonic fibroblast cells by immunocytochemical analysis. In addition, VPs in purified DPV and GPV virions were analyzed by Western blotting. This antiserum detected two prominent proteins bands with the molecule weight of 80 and 70 kilodaltons, which correspond to the sizes of VP1 and VP2 reported in the literature. The fact that VP1 of DPV reacts weakly with this antiserum suggests the existence of antigenic discrepancy between DPV and GPV. For the purpose of developing subunit vaccine for the control of Derzy's disease, recombinant full length VPs were expressed using both prokaryotic, GST and histidine-tagged fusion proteins, and eukaryotic, baculovirus and mammalian vero cell, expression systems. After large- scale production and purification, same amount of 4 recombinant VPs were individually used to immunize 1-week-old geese. The antibodies induced after immunization were then evaluated by enzyme-linked immunosorbent assay (ELISA). All four recombinant proteins stimulate approximately 7 to 8 folds increases of ELISA antibodies titers, and together with preliminary data of safety tests suggest a potential usage as subunit vaccine for the control of parvoviral infection.

High-risk human papillomaviruses (HPVs) cause 5% of all human cancers worldwide. The HPV capsid consists of 72 disulfide-linked pentamers of major capsid protein L1 and up to 72 molecules of minor capsid protein L2. The viral genome (vDNA) is 8KB circular dsDNA, condensed with histones and complexed with L2. HPV infection requires the virion particle to get access to basal layer keratinocytes, binding and entry of the cells, uncoating, and transport of the viral genomes to the host cell nucleus. During infection, L2 is important for transport of the viral genome from membrane bound vesicular compartments, through the cytosol and into the host cell nucleus. Previous work has identified a conserved disulfide bond between Cys22 and Cys28, which is necessary for HPV16 infection. We hypothesize that endosomal reduction of this disulfide might be important for L2 conformational changes that allow a hydrophobic transmembrane-like region in L2 to span across endosomal membranes, exposing sorting adaptor binding motifs within L2 to the cytosol. Prior research suggests that cytosolic glutathione (GSH) redox potential is important for reduction of disulfide-linked proteins within the lumen of endosomes. This is achieved by endosomal influx of cytosolic reduced cysteine, where it can reduce disulfide bonds in lumenal proteins. Cytosolic GSH regenerates the pool of reduced cysteine needed to maintain endosomal redox potential. Here we studied the relationship between cytosolic GSH and HPV16 infection. siRNA knockdown of critical enzymes of the GSH biosynthesis pathway or the endosomal cystine efflux pump cystinosin caused partial abrogation of HPV16 infection. Likewise, inhibition of the GSH biosynthesis pathway with L-buthionine sulfoximine (L-BSO) blocked HPV16 infection in multiple cell types, suggesting that cytosolic GSH redox may be important for HPV16 infection. Further studies have revealed that the decrease of HPV16 infection is not because of defects in binding, entry, L2 cleavage or capsid uncoating, but rather is due to inefficient cytosolic translocation of L2/viral genome from the trans-Golgi network (TGN). Contrary to our initial hypothesis, we show that L2 is able to span the endosomal membrane and direct TGN localization in the presence of BSO. Lack of cytosolic GSH causes L2/viral genome to become trapped in the TGN lumen. This suggests that there are redox-sensitive viral or cellular factors necessary for L2/viral genome translocation at the TGN. Future research will focus on the redox state of the Cys22-Cys28 disulfide bond during infection of normal and GSH-depleted cells.

In this study, a Monte Carlo simulation was designed to observe the self-assembly of the HIV-1 capsid protein. The simulation allowed a coarse grained model of the capsid protein with defined interaction sites to move freely in three dimensions using the Metropolis criterion. Observations were made as to which parameters affected the assembly the process. The ways in which the assembly were affected were also noted. It was found that proper dimerization of the capsid protein was necessary in order for the lattice to form properly. It was also found that a strong trimeric interface could be responsible for double-layered assemblies. Further studies may be conducted by further varying of parameters or reworking the dynamics of the simulation. The possible causes of curvature within the assembly still need to be researched further.

Thesis advisor: Junona Moroianu / The L2 minor capsid protein of human papillomavirus is one of two structural proteins that comprise the icosahedral shell. Two potential, leucine-rich nuclear export signals (NESs) had been identified in the HPV16 L2 sequence, one in the n-terminus (51MGVFFGGLGI60) and one in the c-terminus (462LPYFFDSVSL471). DNA primers for mutant L2 proteins were designed to specifically target these two potential NES regions. Two primers had mutations in the n-terminal located NES (nNES), while the other two primers had mutations in the c-terminal NES (cNES). L2 nuclear retention mutants, RR297AA (“MS4”) and RTR313AAA (“MS5”), served as the templates for these NES mutations. Using mutagenesis, the desired secondary mutations were introduced into the mutant L2 genes in order to create four, distinct mutants: RR297AA + P463_ (“MS4 T1”), RR297AA + V469_ (“MS4 T2), RTR313AAA + P463_ (“MS5 T1”), and RTR313AAA + V469_ (“MS5 T2”). In contrast to the pancellular localization of the MS4 and MS5 L2 mutants, the “MS4 T1,” “MS4 T2,” “MS5 T1”, and “MS5 T2” mutants were all localized nuclearly. These results suggest that deletion of the cNES inhibits nuclear export of the HPV16 L2 minor capsid protein. / Thesis (BS) — Boston College, 2011. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: College Honors Program. / Discipline: Biology Honors Program. / Discipline: Biology.

Porcine <i>Circovirus</i> 2 (PCV2) associated diseases (PCVAD) cause economic loss to the global swine industry. Control measures for PCVAD largely depend on the use of PCV2 vaccines. The available commercial PCV2 vaccines contain either inactivated whole virus particles or recombinant PCV2 capsid protein. These preparations most likely contain varying amounts of immune-irrelevant proteins that can cause adverse injection site reactions, with compromised efficacy due to alteration of protective immune epitopes arising during the viral inactivation process. Other constraints include high production cost attributed to propagation of slow growing virus and expression and extraction of recombinant proteins, a requirement for adjuvants, and the induction of a Th2-biased immune response. Hence, development of new PCV2 vaccines is necessary.<p> There are two recommended PCV2 vaccination strategies. They are i. vaccinating sows, which relies on the passive transfer of maternal immunity to offspring, and ii. immunizing young piglets to induce an active immune response. The piglet vaccination has been shown to confer better protection from mortality. Maternal antibody interference to the induction of an active immune response is an obstacle when piglets are vaccinated at an early age. Can we sidestep this maternal antibody interference? To address this issue, I investigated whether a prototypical PCV2 vaccine, parenterally administered, could override maternally-derived PCV2 antibodies in seropositive piglets. The results of this study were not conclusive. However, they laid the foundation for future studies based upon using varying levels of vaccine antigen with different adjuvants, and administered to piglets with defined maternally derived PCV2 antibodies.<p> Subsequently, I examined if a new PCV2 vaccine candidate comprised of bacteriophage lambda particles displaying part of the PCV2 capsid protein could induce anti-PCV2 immunity. Initial experiments showed that pigs do not have pre-existing anti-lambda antibodies and thus will not neutralize display particles used as a vaccine at primary vaccination. I produced and characterized lambda phage particles displaying four immunodominant regions of porcine circovirus 2 (PCV2) capsid protein fused to the lambda capsid protein D i.e., D-CAP, phage display particles. Expression of D-CAP in <i>Escherichia coli</i> (<i>E. coli</i>) and its presence in the vaccine preparation was shown by ELISA and Western blots using anti-PCV2 polyclonal antiserum from a gnotobiotic pig. The vaccine, lambda particles displaying PCV2 capsid protein immunogenic epitopes fused to lambda D protein (LDP-D-CAP), administered without an adjuvant induced both humoral and cellular immunity to PCV2 in conventional pigs, as shown by ELISA, Western blots, virus neutralization assay and delayed type hypersensitivity (DTH) reactions. This work produced the first potential phage vaccine to PCV2. In order to further investigate the feasibility of using the lambda display technology. I produced and characterized two additional lambda display particle preparations, LDP-D-FLAG and LDP-D-GFP, displaying a FLAG tag and the green fluorescent proteins, respectively.

Porcine <i>Circovirus</i> 2 (PCV2) associated diseases (PCVAD) cause economic loss to the global swine industry. Control measures for PCVAD largely depend on the use of PCV2 vaccines. The available commercial PCV2 vaccines contain either inactivated whole virus particles or recombinant PCV2 capsid protein. These preparations most likely contain varying amounts of immune-irrelevant proteins that can cause adverse injection site reactions, with compromised efficacy due to alteration of protective immune epitopes arising during the viral inactivation process. Other constraints include high production cost attributed to propagation of slow growing virus and expression and extraction of recombinant proteins, a requirement for adjuvants, and the induction of a Th2-biased immune response. Hence, development of new PCV2 vaccines is necessary.<p> There are two recommended PCV2 vaccination strategies. They are i. vaccinating sows, which relies on the passive transfer of maternal immunity to offspring, and ii. immunizing young piglets to induce an active immune response. The piglet vaccination has been shown to confer better protection from mortality. Maternal antibody interference to the induction of an active immune response is an obstacle when piglets are vaccinated at an early age. Can we sidestep this maternal antibody interference? To address this issue, I investigated whether a prototypical PCV2 vaccine, parenterally administered, could override maternally-derived PCV2 antibodies in seropositive piglets. The results of this study were not conclusive. However, they laid the foundation for future studies based upon using varying levels of vaccine antigen with different adjuvants, and administered to piglets with defined maternally derived PCV2 antibodies.<p> Subsequently, I examined if a new PCV2 vaccine candidate comprised of bacteriophage lambda particles displaying part of the PCV2 capsid protein could induce anti-PCV2 immunity. Initial experiments showed that pigs do not have pre-existing anti-lambda antibodies and thus will not neutralize display particles used as a vaccine at primary vaccination. I produced and characterized lambda phage particles displaying four immunodominant regions of porcine circovirus 2 (PCV2) capsid protein fused to the lambda capsid protein D i.e., D-CAP, phage display particles. Expression of D-CAP in <i>Escherichia coli</i> (<i>E. coli</i>) and its presence in the vaccine preparation was shown by ELISA and Western blots using anti-PCV2 polyclonal antiserum from a gnotobiotic pig. The vaccine, lambda particles displaying PCV2 capsid protein immunogenic epitopes fused to lambda D protein (LDP-D-CAP), administered without an adjuvant induced both humoral and cellular immunity to PCV2 in conventional pigs, as shown by ELISA, Western blots, virus neutralization assay and delayed type hypersensitivity (DTH) reactions. This work produced the first potential phage vaccine to PCV2. In order to further investigate the feasibility of using the lambda display technology. I produced and characterized two additional lambda display particle preparations, LDP-D-FLAG and LDP-D-GFP, displaying a FLAG tag and the green fluorescent proteins, respectively.

Grouper nervous necrosis viruses belong to the Betanodavirus genus in the Nodaviridae family that is a group of small, non-enveloped icosahedron viruses. More than 30 species of fish are infected by the betanodaviruses, which cause massive mortality in hatchery-reared larvae and juveniles. The infection causes great economic losses to aquaculture and sea-ranching. To study the effects of N-terminus and disulfide bonds of capsid protein on particle formation and thermal stability of grouper nervous necrosis virus, virus-like particles (VLPs) of dragon grouper nervous necrosis virus (DGNNV) were used. Deletion of 35 residues at the N-terminus completely ruined the VLP assembly. When deletions were restricted to 4, 16, or 25 N-terminal residues, the assembly of VLPs remained. Site-directed mutagenesis was used to investigate the effects of N-terminus of capsid protein on particle formation and thermal stability of grouper nervous necrosis virus. Althought all arginine mutants could produce VLPs, the relative amounts and thermal stabilities of arginine-mutated VLPs were decrease. The VLPs from £GN25-R29A and £GN25 mutants have similar structural properties on particle formation and thermal stability. Therefore, the effects of Arg29 mutations are negligible. The relative amounts and thermal stabilities of VLPs from £GN25-R30A and £GN25-R31A mutants are lower than £GN25-R29A VLP. When 25 amino acids at N-terminus of DGNNV capsid protein were removed, Arg30 and Arg31 are important for particle formation and particel stability. Although particle could form as 12 positively charged amino acids were lost (¡µN25-R293031A), the efficiency of particles assembly were decrease to 1.2 ¡Ó 0.9% as compare to wild-type VLPs (WT-VLPs). Site-directed mutagenesis and chemical reducing reagents were used to investigate the roles of disulfide bonds in particle formation and thermal stability of grouper nervous necrosis virus. The homogeneous particles from C187A, C331A and C187A/C331A mutants are indistinguishable from the native virus and WT-VLPs in their sizes and shapes. C115A and C201A mutants could not produce VLPs. The dissociated capsomers from arginine- or cysteine-mutant VLPs all can be reassembled to icosahedrons with efficiencies as high as 100%. When VLP particles are pre-fabricated, the reducing agent cannot disrupt the VLP icosahedron structure. The thiol reduction only caused effects on the disulfide linkages inside the icosahedrons. £]-mercaptoethanol-treated WT-VLPs could not tolerate the thermal effects at a temperature higher than 70¢XC. Once the disulfide linkages in dissociated capsomers were entirely disrupted by £]-mercaptoethanol treatment, the resulting capsomers could not reassemble back to icosahedron particles.These results indicated that Cys115 and Cys201 were essential for capsid formation of DGNNV icosahedron structure in de novo assembly and reassembly pathways, as well as for the thermal stability of pre-fabricated particles. In the observation of Cryo-EM, the shapes and sizes of the N-terminus truncated particle (£GN25-VLP) are indistinct from the full-length particle (WT-VLP). The maximum diameter of DGNNV is approximately 380 Å. Like that of the insect nodaviruses, the surface morphologies of £GN25-VLP and WT-VLP are consistent with a T = 3 quasi-equivalent lattice. The protrusions (~154 to 192 Å), the inner shell of the capsid (~112 to 154 Å), and the RNA (¡Õ112 Å) were observed in the DGNNV structure. The protrusion domain is consisting of three capsid subunits, and the interactions between these subunits are different. Deletion of 25 residues at the N-terminus did not affect VLPs formation and the structure of £GN25-VLP is similar to WT-VLPs. Resolutions was calculated by Fourier shell correlation, and the resolution of WT-VLPs and £GN25-VLPs is 6.5Å and 11.8Å, respectively.

The rubella virus (RUB) capsid protein (C) is a multifunctional phosphoprotein with roles beyond encapsidation. It is able to rescue a large lethal deletion of the Q domain in the P150 replicase gene at a step in replication before detectable viral RNA synthesis, indicating a common function shared by RUB C and the Q domain. The goal of this dissertation was to use constructs containing the N-terminal 88 amino acids of RUB C, the region previously defined as the minimal region required for the rescue of Q domain mutants, to elucidate the function of RUB C in Q domain rescue and viral RNA synthesis. In the first specific aim, the rescue function of 1-88 RUB C and the importance of an arginine-rich cluster, R2, within 1-88 RUB C for rescue were confirmed. Rescue was not correlated with intracellular localization or phosphorylation status of RUB C. In the second specific aim, the involvement of RUB C in early events post-transfection with RUB RNA was analyzed. RUB C specifically protected RUB transcripts early post-transfection and protection required R2. However, it was concluded the protection observed was due to the encapsidation function of RUB C and not related to Q domain rescue. No differences in the translation of the RUB nonstructural proteins in the presence or absence of RUB C were observed. Interactions of RUB C with host cell proteins were analyzed. Although the interaction of RUB C with cellular p32 required the R2 cluster, both wild type (does not require RUB C for replication) and RQQ (requires RUB C for replication) Q domain bound p32, indicating interaction with this binding partner is not the basis of rescue. Using a human protein array phosphatidylinositol transfer protein alpha isoform (PITPα) was found to interact with RUB C but not its R2 mutant. However, co-immunoprecipitation experiments revealed that this protein binds both forms of RUB C. Although the mechanism behind the rescue of the RUB P150 Q domain by RUB C remains unknown, we propose a model that RUB C plays a role in generation of the virus replication complex in infected cells.