Conditional lethal mutants of vesicular stomatitis virus. I. Phenotypic characterization of single and double mutants exhibiting host restriction and temperature sensitivity

Putative domain-domain interactions in the vesicular stomatitis virus L polymerase protein appendage region

The multidomain polymerase protein (L) of nonsegmented negative-strand (NNS) RNA viruses catalyzes transcription and replication of the virus genome. The N-terminal half of the protein forms a ring-like polymerase structure, while the C-terminal half encoding viral mRNA transcript modifications consists of a flexible appendage with three distinct globular domains. To gain insight into putative transient interactions between L domains during viral RNA synthesis, we exchanged each of the four distinct regions encompassing the appendage region of vesicular stomatitis virus (VSV) Indiana serotype L protein with their counterparts from VSV New Jersey and analyzed effects on virus polymerase activity in a minigenome system. The methyltransferase domain exchange yielded a fully active polymerase protein, which functioned as well as wild-type L in the context of a recombinant virus. Exchange of the downstream C-terminal nonconserved region abolished activity, but coexchanging it with the methyltransferase domain generated a polymerase favoring replicase over transcriptase activity, providing strong evidence of interaction between these two regions. Exchange of the capping enzyme domain or the adjacent nonconserved region thought to function as an "unstructured" linker also abrogated polymerase activity even when either domain was coexchanged with other appendage domains. Further probing of the putative linker segment using in-frame enhanced green fluorescent protein (EGFP) insertions similarly abrogated activity. We discuss the implications of these findings with regard to L protein appendage domain structure and putative domain-domain interactions required for polymerase function.

IMPORTANCE

NNS viruses include many well-known human pathogens (e.g., rabies, measles, and Ebola viruses), as well as emerging viral threats (e.g., Nipah and Hendra viruses). These viruses all encode a large L polymerase protein similarly organized into multiple domains that work in concert to enable virus genome transcription and replication. But how the unique L protein carries out the multiplicity of individual steps in these two distinct processes is poorly understood. Using two different approaches, i.e., exchanging individual domains in the C-terminal appendage region of the protein between two closely related VSV serotypes and inserting unrelated protein domains, we shed light on requirements for domain-domain interactions and domain contiguity in polymerase function. These findings further our understanding of the conformational dynamics of NNS L polymerase proteins, which play an essential role in the pathogenic properties of these viruses and represent attractive targets for the development of antiviral measures.

Analysis of virion associated host proteins in vesicular stomatitis virus using a proteomics approach

BACKGROUND

Vesicular stomatitis virus (VSV) is the prototypic rhabdovirus and the best studied member of the order Mononegavirales. There is now compelling evidence that enveloped virions released from infected cells carry numerous host (cellular) proteins some of which may play an important role in viral replication. Although several cellular proteins have been previously shown to be incorporated into VSV virions, no systematic study has been done to reveal the host protein composition for virions of VSV or any other member of Mononegavirales.

RESULTS

Here we used a proteomics approach to identify cellular proteins within purified VSV virions, thereby creating a "snapshot" of one stage of virus/host interaction that can guide future experiments aimed at understanding molecular mechanisms of virus-cell interactions. Highly purified preparations of VSV virions from three different cell lines of human, mouse and hamster origin were analyzed for the presence of cellular proteins using mass spectrometry. We have successfully confirmed the presence of several previously-identified cellular proteins within VSV virions and identified a number of additional proteins likely to also be present within the virions. In total, sixty-four cellular proteins were identified, of which nine were found in multiple preparations. A combination of immunoblotting and proteinase K protection assay was used to verify the presence of several of these proteins (integrin beta1, heat shock protein 90 kDa, heat shock cognate 71 kDa protein, annexin 2, elongation factor 1a) within the virions.

CONCLUSION

This is, to our knowledge, the first systematic study of the host protein composition for virions of VSV or any other member of the order Mononegavirales. Future experiments are needed to determine which of the identified proteins have an interaction with VSV and whether these interactions are beneficial, neutral or antiviral with respect to VSV replication. Identification of host proteins-virus interactions beneficial for virus would be particularly exciting as they can provide new ways to combat viral infections via control of host components.

Identification of a new region in the vesicular stomatitis virus L polymerase protein which is essential for mRNA cap methylation

The vesicular stomatitis virus (VSV) L polymerase protein possesses two methyltransferase (MTase) activities, which catalyze the methylation of viral mRNA cap structures at the guanine-N7 and 2'-O-adenosine positions. To identify L sequences required for the MTase activities, we analyzed a host range (hr) and temperature-sensitive (ts) mutant of VSV, hr8, which was defective in mRNA cap methylation. Sequencing hr8 identified five amino acid substitutions, all residing in the L protein. Recombinant VSV were generated with each of the identified L mutations, and the presence of a single G1481R substitution in L, located between conserved domains V and VI, was sufficient to produce a dramatic reduction (about 90%) in overall mRNA methylation. Cap analysis showed residual guanine-N7 methylation and reduced 2'-O-adenosine methylation, identical to that of the original hr8 virus. When recombinant viruses were tested for virus growth under conditions that were permissive and nonpermissive for the hr8 mutant, the same single L mutation, G1481R, was solely responsible for both the hr and ts phenotypes. A spontaneous suppressor mutant of the rG1481R virus that restored both growth on nonpermissive cells and cap methylation was identified and mapped to a single change, L1450I, in L. Site-directed mutagenesis of the region between domains V and VI, amino acids 1419-1672 of L, followed by the rescue of recombinant viruses identified five additional virus mutants, K1468A, R1478A/D1479A, G1481A, G1481N, and G1672A, that were all hr and defective in mRNA cap methylation. Thus, in addition to the previously characterized domain VI [Grdzelishvili, V.Z., Smallwood, S., Tower, D., Hall, R.L., Hunt, D.M., Moyer, S.A., 2005. A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation. J. Virol. 79, 7327-7337; Li, J., Fontaine-Rodriguez, E.C., Whelan, S.P., 2005. Amino acid residues within conserved domain VI of the vesicular stomatitis virus large polymerase protein essential for mRNA cap methyltransferase activity. J. Virol. 79, 13373-13384], a new region between L amino acids 1450-1481 was identified which is critical for mRNA cap methylation.

A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation

The vesicular stomatitis virus (VSV) RNA polymerase synthesizes viral mRNAs with 5'-cap structures methylated at the guanine-N7 and 2'-O-adenosine positions (7mGpppA(m)). Previously, our laboratory showed that a VSV host range (hr) and temperature-sensitive (ts) mutant, hr1, had a complete defect in mRNA cap methylation and that the wild-type L protein could complement the hr1 defect in vitro. Here, we sequenced the L, P, and N genes of mutant hr1 and found only two amino acid substitutions, both residing in the L-polymerase protein, which differentiate hr1 from its wild-type parent. These mutations (N505D and D1671V) were introduced separately and together into the L gene, and their effects on VSV in vitro transcription and in vivo chloramphenicol acetyltransferase minigenome replication were studied under conditions that are permissive and nonpermissive for hr1. Neither L mutation significantly affected viral RNA synthesis at 34 degrees C in permissive (BHK) and nonpermissive (HEp-2) cells, but D1671V reduced in vitro transcription and genome replication by about 50% at 40 degrees C in both cell lines. Recombinant VSV bearing each mutation were isolated, and the hr and ts phenotypes in infected cells were the result of a single D1671V substitution in the L protein. While the mutations did not significantly affect mRNA synthesis by purified viruses, 5'-cap analyses of product mRNAs clearly demonstrated that the D1671V mutation abrogated all methyltransferase activity. Sequence analysis suggests that an aspartic acid at amino acid 1671 is a critical residue within a putative conserved S-adenosyl-l-methionine-binding domain of the L protein.

Gene expression of nonsegmented negative strand RNA viruses

Nonsegmented negative strand RNA viruses comprise major human and animal pathogens in nature. This class of viruses is ubiquitous and infects vertebrates, invertebrates, and plants. Our laboratory has been working on the gene expression of two prototype nonsegmented negative strand RNA viruses, vesicular stomatitis virus (a rhabdovirus) and human parainfluenza virus 3 (a paramyxovirus). An RNA-dependent RNA polymerase (L and P protein) is packaged within the virion which faithfully copies the genome RNA in vitro and in vivo; this enzyme complex, in association with the nucleocapsid protein (N), is also involved in the replication process. In this review, we have presented up-to-date information of the structure and function of the RNA polymerases of these two viruses, the mechanisms of transcription and replication, and the role of host proteins in the life-cycle of the viruses. These detailed studies have led us to a better understanding of the roles of viral and cellular proteins in the viral gene expression.

The vesicular stomatitis virus L protein possesses the mRNA methyltransferase activities

We have previously shown that the vesicular stomatitis virus (VSV) host range mutant, hr 1, is completely defective for the mRNA methyltransferase activities, but can synthesize full-length, unmethylated mRNAs in vitro [S. M. Horikami and S. A. Moyer (1982). Proc. Natl. Acad. Sci. USA 79, 7694-7698] and in vivo [S. M. Horikami, F. De Ferra, and S. A. Moyer (1984). Virology 138, 1-15]. Here we have used the hr 1 mutant to identify the viral protein which possesses the methyltransferase activities. The wild-type VSV L and NS proteins, subunits of the viral RNA polymerase, were separately purified and added to high salt dissociated mutant hr 1 nucleocapsids for in vitro transcription reactions. The results show that the purified wild-type L protein, but not the NS protein, restores methylation and thus possesses the viral mRNA methyltransferase activities.

Stimulation of vesicular stomatitis virus in vitro RNA synthesis by microtubule-associated proteins

Microtubule-associated proteins purified from bovine brains stimulated the in vitro transcription and replication reactions of vesicular stomatitis virus. The products of these reactions were intact messenger or genome-sized RNA species. A preparation from HeLa cells containing tubulin and microtubule-associated proteins also stimulated vesicular stomatitis virus transcription in vitro. This observation is in accord with previous studies, which suggested that a host cell factor was involved with the function of the vesicular stomatitis virus RNA polymerase, and others that indicated that several animal viruses displayed an association with host cell cytoskeletal elements during their replication cycles. We show evidence in this report of a host cell protein that seems to have a functional role in interacting with the virion polymerase.

Characterization of the infections of permissive and nonpermissive cells by host range mutants of vesicular stomatitis virus defective in RNA methylation

Two host range mutants of VSV, hr 1 and hr 8, which, unlike the wild-type virus, have a mRNA methylation defect and direct the in vitro synthesis of full-length capped but unmethylated viral mRNAs have been described previously (S.M. Horikami and S.A. Moyer, 1982, Proc. Natl, Acad. Sci. USA 79, 7694-7698). It is shown that the in vivo nonpermissive infection of HEp-2 cells by either of these two mutants is characterized by the reduced synthesis of full-length mRNAs at levels characteristic of primary transcription and the total lack of synthesis of genome-length RNA. The VSV mRNAs synthesized by either mutant in HEp-2 cells are not translated either in vivo or in vitro in mRNA-dependent rabbit reticulocyte lysates. Subsequent isolation and analysis of the mRNAs from infected HEp-2 cells has shown that the 5' termini of the messages contain a cap structure which is guanylylated, but unmethylated (GpppA), a finding that might account for the lack of translatability. Hence these mutants are unable to properly methylate mRNAs whether they are synthesized in vitro or in vivo within nonpermissively infected cells. It is also shown that unlike hr 1, the undermethylation of mRNA synthesized by hr 8 is partially reversible by the addition of high levels of AdoMet in vitro. It is interesting to note, therefore, that permissive baby hamster kidney (BHK) cells have a 10-fold higher level of endogenous AdoMet than the nonpermissive HEp-2 cells. Unlike singly infected cells, the coinfection of HEp-2 cells with either hr mutant and a poxvirus yields a permissive infection for these two host range mutants. Analysis of the VSV mRNAs produced in vivo under the conditions of rescue reveals the presence of fully methylated caps (7mGppp(m)Am), suggesting that poxvirus may rescue the mutants by converting the VSV mRNAs to a translationally active form due to methylation by the cytoplasmic poxvirus mRNA methyltransferase enzymes. Both mutants are, however, able to grow normally in permissive BHK cells. An analysis of the translationally active mRNAs from infected permissive cells shows the presence primarily of a 5'-monomethylated cap, 7mGpppA. Finally, we have examined the nonpermissive infections of two other host range mutants of VSV (hr 5 and hr 7). Unlike mutants hr 1 and hr 8 described above, these two mutants synthesize mRNA in HEp-2 cells which is translated both in vivo and in vitro.

Nonpermissive infection of lymphoblastoid cells by vesicular stomatitis virus. I. Synthesis and function of the viral transcripts

The human B-lymphoblastoid cell line Raji is nonpermissive for infection by vesicular stomatitis virus (VSV) (Nowakowski et al. (1973) J. Virol. 12, 1272-1278). Viral-specific transcription begins immediately after infection, but Raji cells synthesize only about one-twentieth as much viral RNA as is synthesized by a permissive host. The viral primary transcripts appear to be unstable in Raji cells when prevented from engaging in protein synthesis by the addition of cycloheximide. The messages are undermethylated in the 5'-terminal cap structure and have a relatively short 3'-polyadenylate tail. Nevertheless, the subcellular distribution of the messages indicates that many of these RNAs are present in large polyribosomes. Analyses of the effects of a temperature-sensitive mutation in the viral matrix protein indicate that mRNA synthesis in Raji cells is limited only by the amount of available nucleocapsid templates and not by a specific defect in transcription.

Temperature-sensitive mutants of influenza A/Udorn/72 (H3N2) virus. III. Genetic analysis of temperature-dependent host range mutants

One hundred thirty-three ts mutants of influenza A/Udorn/72 virus were arranged into eight complementation groups, A-H, on Madin-Darby canine kidney (MDCK) monolayer cultures at the restrictive temperature of 40 degrees. The eight complementation groups, A-H, on MDCK cells corresponded to the eight recombination groups, A-H, on rhesus monkey kidney (RMK) cells, respectively, and this suggested that each MDCK complementation group represented one of the eight influenza A RNA gene segments. These ts viruses were used to identify the locus of the ts mutation in temperature-dependent host range (td-hr) mutants of the A/Udorn/72 virus. Sixteen of the 133 ts mutants exhibited distinct host (MDCK)-dependent restriction of plaque formation at 40 degrees but not at 34 degrees and were referred to as td-hr mutants. These 16 td-hr mutants were ts+ (not ts) on RMK cells but ts on MDCK cells. The td-hr mutants did not share a common lesion and the ts lesions were distributed among the eight complementation groups, A-H, when tested on MDCK cells. An analysis of one of the td-hr mutants indicated that an extrageneic RMK-dependent suppressor mutation did not account for the td-hr phenotype. These data suggested that a host-dependent ts mutation was responsible for the td-hr restriction of this mutant. Representation of td-hr mutations in each of the eight complementation groups indicates that the influenza A virus genome can undergo mutation leading to an altered host range in any of its eight RNA segments.

Host range mutants of vesicular stomatitis virus defective in in vitro RNA methylation

The viral RNA polymerase of detergent-treated vesicular stomatitis virus normally synthesizes viral mRNAs in vitro that are both guanylylated and methylated to give 5'-terminal 7mGpppAm caps. We have characterized a virus host range mutant, hr 1, that is totally defective in vitro in the methylation of mRNA, although full-length polyadenylylated mRNAs with 5' termini of the form GpppA are synthesized in normal yields. A second mutant, hr 8, is partially defective in methylation and synthesizes mRNAs in vitro with primarily GpppA and some GpppAm 5' termini. When used for in vitro translation, the unmethylated hr 1 mutant mRNA shows, as expected, reduced synthesis of viral proteins. These data provide direct evidence that the vesicular stomatitis virus-associated methyltransferase activities are virus encoded.

Synthesis in vitro of full length genomic RNA and assembly of the nucleocapsid of vesicular stomatitis virus in a coupled transcription-translation system

Synthesis of a small amount of 42S RNA in addition to the VSV specific mRNA species was observed in a coupled transcription-translation system containing ribonucleoprotein particles from L cell infected with vesicular stomatitis virus and nuclease-treated ribosomal extract obtained from uninfected HeLa cells. Analysis on a CsCl density gradient showed that the synthesized 42S RNA was associated with newly synthesized by protein as a nucleoprotein of bouyant density of 1.3 g/ml. The 42S RNA and the N protein present in the nucleoprotein were resistant to nuclease and protease, respectively. About 35% of the remaining 65% had a complementary polarity. The evidence presented here demonstrates that both the full length genomic and the complementary RNA are associated with N protein in the in vitro replication process. A template role for the complementary 42S RNA for replication of the genomic RNA is also suggested.

In vitro susceptibilities of normal human skin fibroblasts to oncoviruses, and the decreased susceptibility to HSV of fibroblasts from untreated Hodgkin's patients

Fibroblast cultures established from the skin of 56 healthy controls and 15 untreated Stages I and II Hodgkin's patients (HD) were studied in their 3rd, 4th and 5th in vitro passage with respect to transformation with Simian sarcoma virus (SSV) and SV40 and with respect to replication of herpes simplex virus (HSV) Types 1 and 2, pox virus and interferon release. Susceptibility to the 5 viruses varied independently, except for an inverse correlation between susceptibility to SSV and HSV. HD cultures showed a depressed replication of both types of HSV. There was a borderline (P = 0.02) correlation between magnitude of HSV replication and presence of HL-A type B-w44, but this does not explain the HD control difference. Furthermore, the level of serum antibodies to HSV common antigen was not related to magnitude of in vitro replication. The results thus speak against generally enhanced cellular susceptibility to HSV as a reason for the high titres of serum antibodies to HSV in HD patients.

Replicative RNA synthesis and nucleocapsid assembly in vesicular stomatitis virus-infected permeable cells

A permeable-cell system has been developed to study the replication of vesicular stomatitis virus. When vesicular stomatitis virus-infected BHK cells were permeabilized by lysolecithin treatment, they incorporated nucleoside triphosphates into RNA and amino acids into proteins at nearly normal rates. The viral mRNA's synthesized appeared normal in polarity, size distribution, and polyadenylation, and all five viral proteins were synthesized. Replication of the viral genome proceeded, and full-length RNA strands were synthesized in amounts and polarities resembling those found in intact cells. These full-length RNAs associated with viral N proteins to form RNase-resistant nucleocapsids of normal buoyant density. Permeable cells appear to represent ideal hosts for studying vesicular stomatitis virus replication since they closely mimic in vivo conditions while retaining much of the experimental flexibility of current in vitro systems.

Neurovirulence mutant of vesicular stomatitis virus with an altered target cell tropism in vivo

Intracerebral infection of weanling Swiss mice with a temperature-sensitive (ts) mutant of vesicular stomatitis virus (VSV), ts pi364, resulted in a unique neuropathological syndrome not previously described with other VSV mutants. Mice infected with wild-type VSV died from an acute encephalitis characterized by neuronal necrosis and efficient virus replication in both brain and spinal cord. In contrast, with VSV ts pi364, the most prominent histopathological feature was destruction of the ependyma of the lateral ventricles. Virus antigen was also limited to the leptomeninges and the lateral ventricles. Infected mice survived and developed hydrocephalus. Replication of ts pi364 in the brain was 10- to 100- fold less than that of wild-type VSV, and appearance of virus in the spinal cord was delayed. VSV ts pi364 was isolated from mouse cells persistently infected with VSV. Another VSV ts pi mutant, isolated from the same persistent infection, behaved in vivo like wild-type VSV, even though both mutants were very similar in plaque size, reversion frequency, cut-off temperature, and synthesis of virus-specific proteins at semipermissive temperature. These results strongly suggest that VSV ts pi364 has a second, non-ts mutation which results in a restricted target cell range in vivo; wild-type VSV can infect both neurons and ependymal cells, whereas ts pi364 does not replicate in neurons.

Host range mutants of an influenza A virus

Temperature-sensitive (ts) mutants of fowl plague virus with a ts-lesion in segment 1 (ts 3, polymerase 1 gene) or segment 2 (ts 90, transport gene) do not form plaques on MDCK cells at the permissive temperature, while the wild type and ts-mutants of other groups are able to do so. This property is correlated with the ts-lesion, since revertants for the ts-lesion of ts 3 and ts 90 again form plaques on MDCK cells. The block on MDCK cells--at least for ts3--may be located in a late function, since viral RNA polymerase and hemagglutinin are formed in almost normal yields. MDCK cells infected with ts 3 or ts 90 exhibit a retarded cytopathic effect at 33 degrees C, but no cytopathic effect at 39 degrees C, at which temperature the infected cells can be passaged and super-infected with the wild type strain. Cells surviving the infection with ts 90 at 33 degrees C sometimes grow out again to a normal monolayer. It is suggested that the spread of virus is inhibited under these conditions.