Richard W. Hardy

Characterization of purified Sindbis Virus nsP4 RNA-dependent RNA Polymerase activity in vitro

The Sindbis virus RNA-dependent RNA polymerase (nsP4) is responsible for the replication of the viral RNA genome. In infected cells, nsP4 is localized in a replication complex along with the other viral non-structural proteins. nsP4 has been difficult to homogenously purify from infected cells due to its interactions with the other replication proteins and the fact that its N-terminal residue, a tyrosine, causes the protein to be rapidly turned over in cells. We report the successful expression and purification of Sindbis nsP4 in a bacterial system, in which nsP4 is expressed as an N-terminal SUMO fusion protein. After purification the SUMO tag is removed, resulting in the isolation of full-length nsP4 possessing the authentic N-terminal tyrosine. This purified enzyme is able to produce minus-strand RNA de novo from plus-strand templates, as well as terminally add adenosine residues to the 3 end of an RNA substrate. In the presence of the partially processed viral replicase polyprotein, P123, purified nsP4 is able to synthesize discrete template length minus-strand RNA products. Mutations in the 3 CSE or poly(A) tail of viral template RNA prevent RNA synthesis by the replicase complex containing purified nsP4, consistent with previously reported template requirements for minus-strand RNA synthesis. Optimal reaction conditions were determined by investigating the effects of time, pH, and the concentrations of nsP4, P123 and magnesium on the synthesis of RNA.

Recombinant vaccinia viruses expressing the F, G or N, but not the M2, protein of bovine respiratory syncytial virus (BRSV) induce resistance to BRSV challenge in the calf and protect against the development of pneumonic lesions.

The immunogenicity and protective efficacy of recombinant vaccinia viruses (rVV) encoding the F, G, N or M2 (22K) proteins of bovine respiratory syncytial virus (BRSV) were evaluated in calves, the natural host for BRSV. Calves were vaccinated either by scarification or intratracheally with rVV and challenged 6 to 7 weeks later with BRSV. Although replication of rVV expressing the F protein in the respiratory tract was limited after intratracheal vaccination, the levels of serum and pulmonary antibody were similar to those induced following scarification. The serum antibody response induced by the F protein was biased in favour of IgG1 antibody, whereas the G and the N proteins induced similar levels of IgG1:IgG2, and antibody was undetectable in calves primed with the M2 protein. The F protein induced neutralizing antibodies, but only low levels of complement-dependent neutralizing antibodies were induced by the G protein, and antibody induced by the N protein was not neutralizing. The F and N proteins primed calves for BRSV-specific lymphocyte proliferative responses, whereas proliferative responses were detected in calves primed with the G protein only after BRSV challenge. The M2 protein primed lymphocytes in only one out of five calves. Although there were differences in the immune responses induced by the rVVs, the F, G and N, but not the M2, proteins induced significant protection against BRSV infection and, in contrast with the enhanced lung pathology seen in mice vaccinated with rVV expressing individual proteins of human (H)RSV, there was a reduction in lung pathology in calves.

Alphavirus RNA synthesis and non-structural protein functions.

The members of the genus Alphavirus are positive-sense RNA viruses, which are predominantly transmitted to vertebrates by a mosquito vector. Alphavirus disease in humans can be severely debilitating, and depending on the particular viral species, infection may result in encephalitis and possibly death. In recent years, alphaviruses have received significant attention from public health authorities as a consequence of the dramatic emergence of chikungunya virus in the Indian Ocean islands and the Caribbean. Currently, no safe, approved or effective vaccine or antiviral intervention exists for human alphavirus infection. The molecular biology of alphavirus RNA synthesis has been well studied in a few species of the genus and represents a general target for antiviral drug development. This review describes what is currently understood about the regulation of alphavirus RNA synthesis, the roles of the viral non-structural proteins in this process and the functions of cis-acting RNA elements in replication, and points to open questions within the field.

Requirement for the Amino-Terminal Domain of Sindbis Virus nsP4 during Virus Infection

ABSTRACT The Sindbis virus RNA-dependent RNA polymerase nsP4 possesses an amino-terminal region that is unique to alphaviruses and is predicted to be disordered. To determine the importance of this region during alphavirus replication, 29 mutations were introduced, and resultant viruses were assessed for growth defects. Three small plaque mutants, D41A, G83L, and the triple mutant GPG(8-10)VAV, had defects in subgenome synthesis, minus-strand synthesis, and overall levels of viral RNA synthesis, respectively. Large plaque viruses were selected following passage in BHK-21 cells, and the genomes of these were sequenced. Suppressor mutations in nsP1, nsP2, and nsP3 that restored viral RNA synthesis were identified. An nsP2 change from M282 to L and an nsP3 change from H99 to N corrected the D41A-induced defect in subgenomic RNA synthesis. Three changes in nsP1, I351 to V, I388 to V, or the previously identified change, N374 to H (C. L. Fata, S. G. Sawicki, and D. L. Sawicki, J. Virol. 76:8641-8649, 2002), suppressed the minus-strand synthetic defect. A direct reversion back to G at position 8 reduced the RNA synthesis defect of the GPG(8-10)VAV virus. These results imply that nsP4s amino-terminal domain participates in distinct interactions with other nsPs in the context of differentially functioning RNA synthetic complexes, and flexibility in this domain is important for viral RNA synthesis. Additionally, the inability of the mutant viruses to efficiently inhibit host protein synthesis suggests a role for nsP4 in the regulation of host cell gene expression.

Role for subgenomic mRNA in host translation inhibition during Sindbis virus infection of mammalian cells

Sindbis virus subgenomic mRNA is efficiently translated in infected vertebrate cells whereas host translation is shut-off. Deletions in the 5UTR of the subgenomic mRNA were made to investigate its role in viral gene expression. Deletion of nucleotides 1-10 and 11-20 caused a small plaque phenotype, reduced levels of subgenomic mRNA and structural proteins, and increased expression of nonstructural proteins. Whereas deletion 1-10 virus inhibited cellular protein synthesis, deletion 11-20 did so inefficiently. A large plaque revertant of deletion 11-20, possessing a duplication of the subgenomic promoter region, produced subgenomic mRNA at WT levels and restored inhibition of host protein synthesis. Further analysis of the mutant and revertant 5UTR sequences showed the ability to shut-off host cell translation correlated with the efficiency of translation of subgenomic mRNA. We propose that the translational efficiency and quantity of the subgenomic mRNA play a role in inhibition of host cell translation.

Sindbis Virus Infectivity Improves During the Course of Infection in Both Mammalian and Mosquito Cells

Alphaviruses are enveloped, single-stranded positive sense RNA viruses that are transmitted by an arthropod vector to a wide host range, including avian and mammalian species. Arthropods and vertebrates have different cellular environments and this may cause the different cellular pathologies that are observed between the invertebrate vector and vertebrate hosts in both whole organisms and cultured cell lines. In this report, we used Sindbis virus and examined mosquito and mammalian cell lines for their ability to produce progeny virus particles. Total particles produced, viral titers, and overall infectivity (or the ratio of total particles-to-infectious particles) was investigated. Our results show (1) Sindbis infectivity is more a function of the host cell used in titering the virus rather than the cell line used to produce the virus, (2) the number of total and infectious particles produced is cell line dependent, and (3) the infectivity of released virus particles improves during the course of infection in both cells that have cytolytic infections and persistent infections.

Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra

Searching spectral libraries in MS/MS is an important new approach to improving the quality of peptide and protein identification. The idea relies on the observation that ion intensities in an MS/MS spectrum of a given peptide are generally reproducible across experiments, and thus, matching between spectra from an experiment and the spectra of previously identified peptides stored in a spectral library can lead to better peptide identification compared to the traditional database search. However, the use of libraries is greatly limited by their coverage of peptide sequences: even for well‐studied organisms a large fraction of peptides have not been previously identified. To address this issue, we propose to expand spectral libraries by predicting the MS/MS spectra of peptides based on the spectra of peptides with similar sequences. We first demonstrate that the intensity patterns of dominant fragment ions between similar peptides tend to be similar. In accordance with this observation, we develop a neighbor‐based approach that first selects peptides that are likely to have spectra similar to the target peptide and then combines their spectra using a weighted K‐nearest neighbor method to accurately predict fragment ion intensities corresponding to the target peptide. This approach has the potential to predict spectra for every peptide in the proteome. When rigorous quality criteria are applied, we estimate that the method increases the coverage of spectral libraries available from the National Institute of Standards and Technology by 20–60%, although the values vary with peptide length and charge state. We find that the overall best search performance is achieved when spectral libraries are supplemented by the high quality predicted spectra.