The genetics of vesiculoviruses

Phenotypic Consequences In vivo and In vitro of Rearranging the P Gene of RABV HEP-Flury

Phosphoprotein (P) of the Rabies virus (RABV) is critically required for viral replication and pathogenicity. Here we manipulated infectious cDNA clones of the RABV HEP-Flury to translocate the P gene from its wild-type position 2 to 1, 3, or 4 in gene order, using an approach which left the viral nucleotide sequence unaltered. The recovered viruses were evaluated for the levels of gene expression, growth kinetics in cell culture, lethality in suckling mice and protection of mice. The results showed that viral replication was affected by the absolute value of N protein which was regulated by P protein. Viral lethality in suckling mice was consistent with the ratio of P mRNA in one complete transcription. The protection of mice induced by viruses was related to the antibody titer 5 weeks post-infection which might be regulated by G protein. However, the ability to induce cell apoptosis and viral spread were not only related to the viral replication but also to the ratio of related gene which affected by the gene position. These findings might not only improve the understanding of phenotype of RABV and P gene rearrangement, but also help rabies vaccine candidate construction.

Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector

Recombinant vesicular stomatitis virus (rVSV) is currently under evaluation as a human immunodeficiency virus (HIV)-1 vaccine vector. The most compelling reasons to develop rVSV as a vaccine vector include a very low seroprevalence in humans, the ability to infect and robustly express foreign antigens in a broad range of cells, and vigorous growth in continuous cell lines used for vaccine manufacture. Numerous preclinical studies with rVSV vectors expressing antigens from a variety of human pathogens have demonstrated the versatility, flexibility, and potential efficacy of the rVSV vaccine platform. When administered to nonhuman primates (NHPs), rVSV vectors expressing HIV-1 Gag and Env elicited robust HIV-1-specific cellular and humoral immune responses, and animals immunized with rVSV vectors expressing simian immunodeficiency virus (SIV) Gag and HIV Env were protected from AIDS after challenge with a pathogenic SIV/HIV recombinant. However, results from an exploratory neurovirulence study in NHPs indicated that these prototypic rVSV vectors might not be adequately attenuated for widespread use in human populations. To address this safety concern, a variety of different attenuation strategies, designed to produce a range of further attenuated rVSV vectors, are currently under investigation. Additional modifications of further attenuated rVSV vectors to upregulate expression of HIV-1 antigens and coexpress molecular adjuvants are also being developed in an effort to balance immunogenicity and attenuation.

Density-dependent selection in vesicular stomatitis virus

We used vesicular stomatitis virus to test the effect of complementation on the relative fitness of a deleterious mutant, monoclonal antibody-resistant mutant (MARM) N, in competition with its wild-type ancestor. We carried out competitions of MARM N and wild-type populations at different multiplicities of infection (MOIs) and initial ratios of the wild type to the mutant and found that the fitness of MARM N relative to that of the wild type is very sensitive to changes in the MOI (i.e., the degree of complementation) but depends little, if at all, on the initial frequencies of MARM N and the wild type. Further, we developed a mathematical model under the assumption that during coinfection both viruses contribute to a common pool of protein products in the infected cell and that they both exploit this common pool equally. Under such conditions, the fitness of all virions that coinfect a cell is the average fitness in the absence of coinfection of that group of virions. In the absence of coinfection, complementation cannot take place and the relative fitness of each competitor is only determined by the selective value of its own products. We found good agreement between our experimental results and the model predictions, which suggests that the wild type and MARM N freely share all of their gene products under coinfection.

Modulating the function of the measles virus RNA-dependent RNA polymerase by insertion of green fluorescent protein into the open reading frame

Measles virus (MV) is the type species of the Morbillivirus genus and its RNA-dependent RNA polymerase complex is comprised of two viral polypeptides, the large (L) and the phospho- (P) proteins. Sequence alignments of morbillivirus L polymerases have demonstrated the existence of three well-conserved domains (D1, D2, and D3) which are linked by two variable hinges (H1 and H2). Epitope tags (c-Myc) were introduced into H1 and H2 to investigate the tolerance of the variable regions to insertions and to probe the flexibility of the proposed domain structures to spatial reorientation. Insertion into H1 abolished polymerase activity whereas introduction into H2 had no effect. The open reading frame of enhanced green fluorescent protein was also inserted into the H2 region of the MV L gene to extend these observations. This resulted in a recombinant protein that was both functional and autofluorescent, although the overall polymerase activity was reduced by over 40%. Two recombinant viruses which contained the chimeric L genes EdtagL(MMc-mycM) and EdtagL(MMEGFPM) were generated. Tagged L proteins were detectable, by indirect immunofluorescence in the case of EdtagL(MMc-mycM) and by autofluorescence in the case of EdtagL(MMEGFPM). We suggest that D3 enjoys a limited conformational independence from the other domains, indicating that the L polymerases of the Mononegavirales may function as multidomain proteins.

Phenotypic consequences of rearranging the P, M, and G genes of vesicular stomatitis virus

The nonsegmented negative-strand RNA viruses (order Mononegavirales) include many important human pathogens. The order of their genes, which is highly conserved, is the major determinant of the relative levels of gene expression, since genes that are close to the single promoter site at the 3' end of the viral genome are transcribed at higher levels than those that occupy more distal positions. We manipulated an infectious cDNA clone of the prototypic vesicular stomatitis virus (VSV) to rearrange three of the five viral genes, using an approach which left the viral nucleotide sequence otherwise unaltered. The central three genes in the gene order, which encode the phosphoprotein P, the matrix protein M, and the glycoprotein G, were rearranged into all six possible orders. Viable viruses were recovered from each of the rearranged cDNAs. The recovered viruses were examined for their levels of gene expression, growth potential in cell culture, and virulence in mice. Gene rearrangement changed the expression levels of the encoded proteins in concordance with their distance from the 3' promoter. Some of the viruses with rearranged genomes replicated as well or slightly better than wild-type virus in cultured cells, while others showed decreased replication. All of the viruses were lethal for mice, although the time to symptoms and death following inoculation varied. These data show that despite the highly conserved gene order of the Mononegavirales, gene rearrangement is not lethal or necessarily even detrimental to the virus. These findings suggest that the conservation of the gene order observed among the Mononegavirales may result from immobilization of the ancestral gene order due to the lack of a mechanism for homologous recombination in this group of viruses. As a consequence, gene rearrangement should be irreversible and provide an approach for constructing viruses with novel phenotypes.

Increased synthesis of polycistronic mRNA associated with increased polyadenylation by vesicular stomatitis virus

Electron microscopy suggested that the mRNA produced in vitro by tsG16(I), a temperature-sensitive mutant of vesicular stomatitis virus, contained an increased proportion of polycistronic mRNAs. Using hybrid selection, we found that the poly(A)+ mRNA synthesized in vitro by tsG16(I) contained approximately two to three times more polycistronic mRNA than did poly(A)+ mRNA synthesized in vitro by the parental wild-type (wt) virus. The increase in polycistronic mRNA occurred at all intergenic junctions examined. In vitro, tsG16(I) has an increased polyadenylation phenotype and a temperature-sensitive transcriptase activity that appear to be due to different mutations. Partial revertants of tsG16(I), which have lost the aberrant polyadenylation phenotype but retain the in vitro thermosensitive transcriptase, produced wt amounts of polycistronic mRNA. This suggested that the increased production of polycistronic mRNA by tsG16(I) may be associated with the increased polyadenylation phenotype of this mutant. These data further support the hypothesis that an increase in size of poly(A) tracts is associated with increased production of polycistronic mRNA.

Temperature-sensitivity of the replication of rabies virus (HEP-flury strain) in BHK-21 cells. I. Alteration of viral RNA synthesis at the elevated temperature

We investigated the nature of temperature sensitivity of the HEP strain of rabies virus. After initial incubation for appropriate period (more than 12 hr) at the permissive temperature (36-37 degrees), incubation temperature of the rabies virus infected cultures was shifted to a nonpermissive temperature (39.5-40.5 degrees). Upon the upshift, virion production was ceased, but the rate of viral RNA synthesis was greatly increased and reached almost 10 times that of 36 degrees-infection within 8-10 hr, and then the activity quickly decreased together with the onset of accelerated CPE. Little or no 42S genome-sized RNA was produced at the elevated temperature, and almost all RNAs produced in large amounts seemed to be viral mRNAs and were shown to be functional in t he cell-free translation system. Consistent with these observations, the viral ribonucleoprotein complex isolated from the temperature-upshifted culture was associated with relatively large amounts of small sized RNAs, which might reflect their increased transcriptive activity. These observations suggest that the viral RNA polymerase itself is not temperature-sensitive and the temperature-induced defect may reside in the regulatory factor which plays a role in turning on the synthesis of viral genome-sized RNA.

Revertants of a mutant of vesicular stomatitis virus which has an aberrant polyadenylation activity and a temperature-sensitive transcriptase

tsG16(l), a temperature-sensitive mutant of vesicular stomatitis virus, in vitro has at least three phenotypic differences from its parental wild-type (wt) virus due to mutation of the L gene. It was not known whether (i) the temperature-sensitivity of the transcriptase, (ii) the aberrant polyadenylation phenotype, and (iii) the extent of increased polyadenylation in response to S-adenosylhomocysteine (SAH) were associated with a single mutation. Spontaneous partial revertants were selected from tsG16(I) on the basis of the ability to form plaques at 34.7 degrees (35G16 revertants) or from 35G16 revertants on the basis of the ability to form plaques at 37 degrees (37G16 revertants). All six 35G16 revertants had fully (five) or partially (one) recovered the wt polyadenylation phenotype and the former five had also fully recovered the wt polyadenylation response to SAH. This suggested that a single mutation in tsG16(I) was probably associated with both of these phenotypes and also probably conferred the inability to grow at 34.7 degrees. None of the 35G16 revertants regained the wt phenotype for thermosensitivity of the transcriptase, although both of the 37G16 revertants did. This suggested that in vitro temperature-sensitivity of transcription by tsG16(I) might be due to a mutation different than the one affecting polyadenylation in the absence or presence of SAH.

Selective inhibition of translation of the mRNA coding for measles virus membrane protein at elevated temperatures

The elevation of culture temperatures of C6 cells that were persistently infected with the Lec strain of the subacute sclerosing panencephalitis (SSPE) virus (C6/SSPE) resulted in immediate selective inhibition of membrane (M) protein synthesis. This phenomenon was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cytoplasmic lysates and immunoprecipitation with monoclonal antibody against the M protein in short-time labeling experiments. The synthesis of various viral mRNAs in the presence of actinomycin D decreased gradually at similar rates after a shift to 39 degrees C. No specific disappearance of the mRNA coding for the M protein was observed when viral RNAs isolated from the infected cells were compared before and after a shift up by Northern blot analysis. Results of pulse-chase experiments did not show any significant difference in M protein stability between 35 and 39 degrees C. This rapid block of M protein synthesis was observed not only in Vero cells that were lytically infected with plaque-purified clones from the Lec strain, clones isolated from C6/SSPE cells and the standard Edmonston strain of measles virus but also in CV1, MA160, and HeLa cells that were lytically infected with the Edmonston strain. Poly(A)+ RNAs that were extracted from C6/SSPE cells before and after a shift to 39 degrees C produced detectable phospho, nucleocapsid, and M proteins in cell-free translation systems at 32 degrees C. Even higher incubation temperatures did not demonstrate the selective depression of M protein synthesis described above in vitro. All these data indicate that M protein synthesis of measles virus is selectively suppressed at elevated temperatures because of an inability of the translation apparatus to interact with the M protein-encoded mRNA.

Stereo images of vesicular stomatitis virus assembly

Viral assembly was studied by viewing platinum replicas of cytoplasmic and outer plasma membrane surfaces of baby hamster kidney cells infected with vesicular stomatitis virus. Replicas of the cytoplasmic surface of the basilar plasma membrane revealed nucleocapsids forming bullet-shaped tight helical coils. The apex of each viral nose cone was anchored to the membrane and was free of uncoiled nucleocapsid, whereas tortuous nucleocapsid was attached to the base of tightly coiled structures. Using immunoelectron microscopy, we identified the nucleocapsid (N) viral protein as a component of both the tight-coil and tortuous nucleocapsids, whereas the matrix (M) protein was found only on tortuous nucleocapsids. The M protein was not found on the membrane. Using immunoreagents specific for the viral glycoprotein (G protein), we found that the amount of G protein per virion varied. The G protein was consistently localized at the apex of viral buds, whereas the density of G protein on the shaft was equivalent to that in the surrounding membrane. These observations suggest that G-protein interaction with the nucleocapsid via its cytoplasmic domain may be necessary for the initiation of viral assembly. Once contact is established, nucleocapsid coiling proceeds with nose cone formation followed by formation of the helical cylinder. M protein may function to induce a nucleocapsid conformation favorable for coiling or may cross-link adjacent turns in the tight coil or both.

Expression of a cDNA encoding a functional 241-kilodalton vesicular stomatitis virus RNA polymerase

The large gene, L, of vesicular stomatitis virus (VSV), which codes for the multifunctional RNA-dependent RNA polymerase, was assembled from five overlapping cDNA clones. The sequence of the 6.4-kilobase gene of the final construct was identical to the consensus sequence reported earlier. The gene was inserted into the simian virus 40 transient expression vector pJC119. Antibodies directed against synthetic peptides corresponding to the amino and carboxyl termini of the L protein were raised in rabbits. Both antibodies specifically immunostained the cytoplasm of COS cells that had been transfected with the vector DNA. The expressed L protein was immunoprecipitated from cell extracts and it was identical in size to the L protein of the virion (241 kilodaltons). Most importantly, COS cells that expressed the recombinant L protein transcribed, replicated, and consequently complemented and rescued temperature-sensitive RNA polymerase mutants of VSV at the nonpermissive temperature. The kinetics of virus release were similar to those of a wild-type VSV infection. We conclude that the recombinant RNA polymerase protein L is indistinguishable in its size and its functions from the VSV polymerase.

Assignment of the temperature-sensitive lesion in the replication mutant A1 of vesicular stomatitis virus to the N gene

The replication defect in the temperature-sensitive mutant A1 of the New Jersey serotype (Hazelhurst subtype) of vesicular stomatitis virus was confirmed by the absence of intracellular nucleocapsids in infected cells incubated at the restrictive temperature. After preamplification, the relative yield of the A1 N protein accumulated intracellularly after 1 h of incubation at the restrictive temperature was decreased by 50% that of the wild-type or revertant A1 N protein. This difference was not as apparent in pulse-chase experiments. The functional lesion in A1 was correlated with a structural alteration in the N protein on the basis of the thermolability of the template activity of the A1 N protein-RNA complex in in vitro transcription reactions and the covariance of this phenotype with the temperature-sensitive phenotype in a spontaneous A1 revertant. This correlation was consistent with a direct role of the N protein in replication and allowed the assignment of the N gene to complementation group A.

ATP dependence of vesicular stomatitis virus transcription initiation and modulation by mutation in the nucleocapsid protein

We recently reported that vesicular stomatitis virus pol R mutants contain a template-associated N-protein alteration which allows for efficient readthrough of leader RNA termination sites in vitro (Perrault et al., Cell 35:175-185, 1983). We show here that in vitro RNA synthesis mediated by pol R virions is much more resistant to replacement of ATP by the analog beta,gamma-imido ATP than by wild-type virus (approximately 50% inhibition versus approximately 95%). Characterization of beta,gamma-imido ATP-resistant and control products by size, polyadenylic acid content, frequency of initiation at the 3' end of the template, and readthrough of the leader-N gene junction leads us to conclude the following: (i) most likely, the ATP dependence of the transcription process primarily reflects a requirement for initiation or entry of the polymerase at the 3' end of the template; (ii) this requirement is largely bypassed in the mutant pol R viruses; (iii) the synthesis of small, internally initiated transcripts by wild-type virus is less dependent on ATP than that of leader RNA; and (iv) termination at leader RNA sites is not directly affected when beta,gamma-imido ATP is added before initiation of synthesis. These results are discussed in terms of the possible roles of ATP and the nucleocapsid protein in initiation and termination of vesicular stomatitis virus RNA synthesis.

Vesicular stomatitis virus mutants resistant to defective-interfering particles accumulate stable 5'-terminal and fewer 3'-terminal mutations in a stepwise manner

We have studied the evolution of sequences which include the RNA polymerase binding sites at the 5' and 3' termini of vesicular stomatitis virus mutants (Sdi-) resistant to defective-interfering particles. We observed a striking stepwise accumulation of stable base substitutions within the area of replication initiation at the 5'-terminal 54 nucleotides of Sdi- mutants isolated at intervals from persistent infections and undiluted lytic passage series. Fewer mutations accumulated in the region of transcription initiation at the 3' end and in those portions of the N and L protein coding cistrons examined. The termini changes are not strictly required to obtain the Sdi- phenotype. However, it is possible that they represent stepwise compensatory changes to accommodate Sdi- mutations affecting viral replication or encapsidation gene products or both. These results have important implications for RNA virus genome evolution.

Vesicular stomatitis virus mutant with altered polyadenylic acid polymerase activity in vitro

In vitro RNA synthesis by purified virions of a stock of tsG16(I) was aberrant compared with that of wild-type (wt) vesicular stomatitis virus. RNA made in vitro by tsG16(I) contained a larger proportion of A residues in polyadenylic acid [poly(A)] tracts than did RNA synthesized by wt virus, tsG13(I), tsG21(II) or tsG41(IV). Experiments to determine whether the aberrant polyadenylation was correlated with the known thermolability of the tsG16(I) L protein were inconclusive. Total product RNA made by tsG16(I) was methylated to almost the same extent as wt RNA, contained the same major methylated 5' cap structure as wt RNA, and was translated as well in a reticulocyte cell-free system, yielding the same molecular weight proteins in similar ratios. Most polyadenylated [poly(A)+] RNA made by tsG16(I) was considerably larger than wt poly(A)+ RNA and richer in AMP:UMP residues; however, the protein-coding capacities of mutant and wt poly(A)+ RNAs were similar. This suggested that most mRNAs made in vitro by tsG16(I) might possess very long poly(A)+ tracts, and digestion of RNA by T1 RNase supported this. It appeared, therefore, that a virally coded component of vesicular stomatitis virus could affect polyadenylation. This could be the poly(A) polymerase itself, a protein involved in control of polyadenylation, or a protein which affects an event spatially and temporally connected with polyadenylation (such as initiation of the subsequent mRNA).