Plant Expression of Trans-Encapsidated Viral Nanoparticle Vaccines with Animal RNA Replicons

The use of functionally deficient viral vectors as visualization tools to reveal complementation patterns between plant viruses and the silencing suppressor p19

Plant virus transport complementation is classically observed as a helper virus allowing another virus to regain cell-to-cell or systemic movement through a restrictive host plant (Malyshenko et al., 1989). The complementation effect is usually studied by observing virus infection after co-infection or super-inoculation of the helper virus. We herein demonstrate the utility of functionally deficient viral vectors as tools to determine the contribution of individual viral genes to plant viral transport complementation. Two functionally deficient viral vectors were engineered that derive from foxtail mosaic potexvirus and sunn-hemp mosaic tobamovirus, namely FECT (FoMV Eliminate CP and TGB, (Liu and Kearney, 2010)) and SHEC (SHMV Eliminate CP gene, (Liu and Kearney, 2010)), respectively. FECT had all the ORFs removed except for the replicase and thus is defective for both long-distance and cell-to-cell movement. SHEC lacked only the coat protein ORF and retained the movement protein (MP) and is functional for cell-to-cell movement. When FECT and SHEC vectors were inoculated with the silencing suppressor p19 in different zones of the same leaf, FECT was enabled to express its reporter gene beyond the original inoculation zone. When FECT, SHEC, and p19 were individually inoculated in separate zones, both FECT and SHEC reporter gene expression was observed within the p19 zone, distant from the original virus inoculation points. These observations indicate that SHEC movement protein could create a trafficking network to allow viral RNAs of FECT and SHEC and p19/p19 transcript to move from cell to cell. This system provides a tool to visually monitor the movement of viruses and silencing suppressors as well as to identify the effects of individual viral components on virus movement.

Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing

To characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: viral Photo-Activatable Ribonucleoside CrossLinking (vPAR-CL). In vPAR-CL, 4-thiouridine is incorporated into the encapsidated genomes of virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that vPAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant vPAR-CL signals across virus RNA genome, indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites coincide with previously identified functional RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining vPAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid interaction sites favored double-stranded RNA regions. We disrupted secondary structures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.

The RNA Capping Enzyme Domain in Protein A is Essential for Flock House Virus Replication

The nodavirus flock house virus (FHV) and the alphavirus Semliki Forest virus (SFV) show evolutionarily intriguing similarities in their replication complexes and RNA capping enzymes. In this study, we first established an efficient FHV trans-replication system in mammalian cells, which disjoins protein expression from viral RNA synthesis. Following transfection, FHV replicase protein A was associated with mitochondria, whose outer surface displayed pouch-like invaginations with a ‘neck’ structure opening towards the cytoplasm. In mitochondrial pellets from transfected cells, high-level synthesis of both genomic and subgenomic RNA was detected in vitro and the newly synthesized RNA was of positive polarity. Secondly, we initiated the study of the putative RNA capping enzyme domain in protein A by mutating the conserved amino acids H93, R100, D141, and W215. RNA replication was abolished for all mutants inside cells and in vitro except for W215A, which showed reduced replication. Transfection of capped RNA template did not rescue the replication activity of the mutants. Comparing the efficiency of SFV and FHV trans-replication systems, the FHV system appeared to produce more RNA. Using fluorescent marker proteins, we demonstrated that both systems could replicate in the same cell. This work may facilitate the comparative analysis of FHV and SFV replication.

Chimeric Flock House virus protein A with endoplasmic reticulum-targeting domain enhances viral replication and virus-like particle trans-encapsidation in plants

Flock House virus (FHV) RNA can be trans-encapsidated, entirely in planta, by tobacco mosaic virus coat protein to form virus-like particles (VLPs). Vaccination with these VLPs leads to strong antigen expression in mice and immune-activation. We hypothesize that creating an additional cellular site for replication and/or trans-encapsidation might significantly improve the final output of trans-encapsidated product. FHV protein A was engineered to target the endoplasmic reticulum (ER) via a heterologous tobacco etch virus ER-targeting domain, and was expressed in cis or in trans relative to the replicating FHV RNA1. A strong increase in marker gene expression in plants was noted when ER-targeted protein A was supplied in trans. RNA fluorescence in situ hybridization revealed RNA1 replication in both the mitochondria and ER, and total RNA1 accumulation was increased. In support of our hypothesis, VLP yield was increased significantly by the addition of this single genetic component to the inoculum.