Defective interfering Tacaribe virus and persistently infected cells

Alternative translation contributes to the generation of a cytoplasmic subpopulation of the Junín virus nucleoprotein that inhibits caspase activation and innate immunity

The highly pathogenic arenavirus, Junín virus (JUNV), expresses three truncated alternative isoforms of its nucleoprotein (NP), i.e., NP53kD, NP47kD, and NP40kD. While both NP47kD and NP40kD have been previously shown to be products of caspase cleavage, here, we show that expression of the third isoform NP53kD is due to alternative in-frame translation from M80. Based on this information, we were able to generate recombinant JUNVs lacking each of these isoforms. Infection with these mutants revealed that, while all three isoforms contribute to the efficient control of caspase activation, NP40kD plays the predominant role. In contrast to full-length NP (i.e., NP65kD), which is localized to inclusion bodies, where viral RNA synthesis takes place, the loss of portions of the N-terminal coiled-coil region in these isoforms leads to a diffuse cytoplasmic distribution and a loss of function in viral RNA synthesis. Nonetheless, NP53kD, NP47kD, and NP40kD all retain robust interferon antagonistic and 3'-5' exonuclease activities. We suggest that the altered localization of these NP isoforms allows them to be more efficiently targeted by activated caspases for cleavage as decoy substrates, and to be better positioned to degrade viral double-stranded (ds)RNA species that accumulate in the cytoplasm during virus infection and/or interact with cytosolic RNA sensors, thereby limiting dsRNA-mediated innate immune responses. Taken together, this work provides insight into the mechanism by which JUNV leverages apoptosis during infection to generate biologically distinct pools of NP and contributes to our understanding of the expression and biological relevance of alternative protein isoforms during virus infection.IMPORTANCEA limited coding capacity means that RNA viruses need strategies to diversify their proteome. The nucleoprotein (NP) of the highly pathogenic arenavirus Junín virus (JUNV) produces three N-terminally truncated isoforms: two (NP47kD and NP40kD) are known to be produced by caspase cleavage, while, here, we show that NP53kD is produced by alternative translation initiation. Recombinant JUNVs lacking individual NP isoforms revealed that all three isoforms contribute to inhibiting caspase activation during infection, but cleavage to generate NP40kD makes the biggest contribution. Importantly, all three isoforms retain their ability to digest double-stranded (ds)RNA and inhibit interferon promoter activation but have a diffuse cytoplasmic distribution. Given the cytoplasmic localization of both aberrant viral dsRNAs, as well as dsRNA sensors and many other cellular components of innate immune activation pathways, we suggest that the generation of NP isoforms not only contributes to evasion of apoptosis but also robust control of the antiviral response.

Arenavirus diversity and evolution: quasispecies in vivo

Arenaviruses exist as viral quasispecies due to the high mutation rates of the low-fidelity viral RNA-dependent RNA polymerase (RdRp). This genomic heterogeneity is advantageous to the population, allowing for adaptation to rapidly changing environments that present varying types and degrees of selective pressure. The significant variation in biological properties observed among lymphocytic choriomeningitis virus (LCMV) strains, the prototypic arenavirus, indicates to what extent a quasispecies dynamics may play a role in arenavirus adaptability and pathogenesis. Several aspects of arenavirus variability and its contribution to pathogenesis will be discussed.

Characterization of the arenavirus RING finger Z protein regions required for Z-mediated inhibition of viral RNA synthesis

The prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is an enveloped virus with a bisegmented negative-strand RNA genome whose proteomic capability is limited to four polypeptides, namely, nucleoprotein; surface glycoprotein (GP), which is proteolytically processed into GP1 and GP2; polymerase (L); and a small (11-kDa) RING finger protein (Z). Using a reverse genetic system based on the ARM strain of LCMV, we have previously shown that Z has a strong inhibitory activity on LCMV minigenome transcription and RNA replication (T. I. Cornu and J. C. de la Torre, J. Virol. 75:9415-9426, 2001). In the present study, we have identified regions and specific amino acid residues within Z which contribute to its inhibitory activity on RNA synthesis mediated by the LCMV polymerase. Z proteins from different LCMV strains had similar inhibitory activities on the expression of the LCMV ARM minigenome, whereas the Z protein of the genetically more distantly related Tacaribe virus had an approximately 10-fold lower inhibitory activity on ARM minigenome expression. Results from the use of chimera proteins between Z and Xenopus Neuralized, a nonviral RING finger protein, indicated that the structural integrity of the Z RING domain (RD) was required but not sufficient for the inhibitory activity of Z. Serial deletion mutants of the N and C termini of Z showed that the N terminus (residues 1 through 16) and C terminus (residues 79 through 90) do not contribute to the Z inhibitory activity. A highly conserved tryptophan (W) residue located at position 36 in ARM-Z, next to the second conserved cysteine (C) residue of the Z RD, also contributed to the Z inhibitory activity.

Nontemplated bases at the 5' ends of Tacaribe virus mRNAs

Centrifugation of Tacaribe arenavirus-infected cell extracts on CsCl density gradients was used to separate genomes and antigenomes, which band at 1.31 g/ml as nucleocapsids, from mRNAs which pellet. Primer extensions on the banded RNAs showed that the 5' ends of the genomes and antigenomes were unique, whereas primer extensions on the mRNAs showed that their 5' ends were heterogenous in length, extending 0-4 bases beyond the 3' ends of the templates for their synthesis. This suggests that arenavirus mRNAs may initiate by a cap-snatching mechanism, somewhat similar to influenza viruses and bunyaviruses. We also found an extra G residue at the 5' end of the genome RNA, which was not predicted according to current models. This is now the third time that the unexpected G residue has been found at the 5' end of arenavirus genomes.

Molecular analysis of viral RNAs in mice persistently infected with lymphocytic choriomeningitis virus

Infection of newborn mice with lymphocytic choriomeningitis virus (LCMV) results in a lifelong persistent infection. Persistently infected animals continuously produce low levels of infectious virus and accumulate large amounts of intracellular viral nucleic acid (P. J. Southern, P. Blount, and M. B. A. Oldstone, Nature [London] 312:555-558, 1984). We have used gel electrophoresis and hybridization techniques to analyze viral RNAs that appear during the establishment and maintenance of a persistent LCMV infection in vivo to identify any role for defective and/or defective interfering RNAs. We have found a complex, heterogeneously sized population of viral RNAs in multiple independent tissues that is uniquely associated with persistent infections in vivo, but we have not yet established whether these RNAs have a causal or a consequential association with persistent infection by LCMV. Within the complex virus RNA population, full-length genomic L and S RNAs were readily detectable and represented the most abundant individual viral RNA species. RNAs apparently corresponding in size to the viral nucleoprotein and glycoprotein mRNAs could also be detected in these tissue RNA samples. The presence of glycoprotein mRNA indicates a potential mechanism of posttranscriptional regulation to account for the previously documented restriction in viral glycoprotein expression in persistently infected mice (M. B. A. Oldstone and M. J. Buchmeier, Nature (London) 300:360-362, 1982).

Vero cells persistently infected with Tacaribe virus: role of interfering particles in the establishment of the infection

Eight Vero cell sublines (Vero T) persistently infected with wild type Tacaribe virus replicated in different hosts were established. In order to unravel the mechanism involved in the initiation and maintenance of persistence, the properties of virus shed by the sublines and the presence of interfering particles (IP) were analyzed. During the course of infection, persistent virus (Tac-pi) underwent mutations although no consistent pattern of virus evolution was observed. ts mutants were isolated from two Vero T sublines, whereas a slow growth variant was shed by another. The remaining sublines released virus resembling wt parental virus. Except for Vero T1 sublines, Vero T cultures shed no detectable IP. These results emphasize the point that neither the emergence of virus mutants nor the synthesis of IP is essential for the maintenance of the persistent state. To define the role of IP in the initiation of persistence, coinfection experiments with a characterized inoculum were performed. For that purpose, attempts were made to obtain IP stocks free from pfu by serial transfers of undiluted virus. Neither enrichment nor amplification of IP occurred, and virus stocks were freed of infectious virus by UV irradiation. If normal Vero cells were infected with Tac-pi virus released by Vero T2, Vero T3, Vero T4, Vero T5, Vero T6, Vero T7 and Vero T10 sublines, a complete destruction of the monolayer without cell recovery was observed. In contrast, parental and Vero T1 viruses always originated persistently infected sublines. Similarly, the addition of IP to virus inocula constituted by Tac-pi viruses released by Vero T2, Vero T3, Vero T4, Vero T5, Vero T6, Vero T7 and Vero T10 sublines gave rise to persistently infected cultures. These results suggest that although IP are not important by themselves in the maintenance of persistence, they play a major role in initiation.

Sequencing studies of pichinde arenavirus S RNA indicate a novel coding strategy, an ambisense viral S RNA

Analyses of the complete sequence of the 1.1 X 10(6)-dalton, small (S) RNA of the arenavirus Pichinde and virus-induced cellular RNA species have revealed that the viral nucleoprotein, N, is coded in a subgenomic, non-polyadenylated, virus-complementary mRNA corresponding to the 3' half of the viral RNA (Auperin et al., Virology 134:208-219, 1984). By contrast, a second S-coded product, presumably the viral glycoprotein precursor (GPC), is coded in a subgenomic, virus-sense mRNA corresponding to the 5' half of the RNA. Between the two genes is a unique RNA sequence that can be arranged in a hairpin configuration and may function as a transcription terminator for both genes. The term ambisense RNA is coined to describe this novel coding strategy of a viral RNA. The unique feature of the strategy is that the presumptive GPC mRNA and its translation product cannot be made until viral RNA replication has commenced. In addition, it allows the two subgenomic mRNA species to be regulated independently from each other or from other viral mRNA species. The implications of this strategy on possible mechanisms for the induction and maintenance of viral persistence, an important attribute of arenavirus infections, are discussed.

Response of cells persistently infected with arenaviruses to superinfection with homotypic and heterotypic viruses

Vero cell cultures persistently infected with the arenaviruses Junin, Pichinde, Tacaribe, and Tamiami were established and designated Vero-Jun, Vero-Pic, Vero-Tac, and Vero-Tam, respectively. Two types of carrier cultures could be easily distinguished: Vero-Jun and Vero-Tac systems were characterized by a lack of infectious virus production after a few cell transfers, whereas a more productive state with continuous release of virus was observed in Vero-Pic and Vero-Tam cultures. These differences appeared to be related to resistance of the culture to viral superinfection. In fact, Vero-Jun and Vero-Tac cultures totally excluded only the replication of the serologically more closely related arenaviruses Amapari, Junin, or Tacaribe, while the refractoriness of Vero-Pic and Vero-Tam cultures was extended to most of the virus group members. The resistance of Vero-Jun cells to superinfection by Junin or Tacaribe virus could be ascribed to the production of specific uv-resistant Junin interfering particles, which showed a specific range of interference against Junin and Tacaribe viruses. Interfering particles against homotypic and heterotypic arenaviruses were isolated from Vero-Pic cultures. However, the degree of interference developed by these Pic-interfering particles was not enough to fully explain reinfecting virus exclusion from Vero-Pic cultures. Viral susceptibility of persistent cultures is proposed as a useful tool to examine relationships of members of the arenavirus group.

Analysis of polypeptides in Tacaribe virus-infected cells

Two virus-induced polypeptides designated p79 (mol wt, 79,000) and p105 (mol wt, 105,000) in BHK21 or Vero cells infected with Tacaribe (Tac) virus have been identified. Both polypeptides were found in immune precipitates with antiserum to Tac virus, suggesting that they are virus specific. Two-dimensional gel analysis of Tac virus-infected Vero cell extracts indicated that p79 and p105 were acidic proteins which did not comigrate with any polypeptides from uninfected cells. Neither of the polypeptides was found to be phosphorylated under conditions in which phosphorylation of the N (nucleocapsid) protein was detected. Comparison of one-dimensional peptide maps of the p79 polypeptide and the nucleoprotein indicated that they are unrelated in primary sequences.

A protein kinase activity in lymphocytic choriomeningitis virus and identification of the phosphorylated product using monoclonal antibody

A cyclic AMP-independent protein kinase activity was found in purified preparations of the Armstrong CA 1371 strain of lymphocytic choriomeningitis virus (LCMV). Using the exquisite sensitivity of monoclonal antibodies to LCMV polypeptides, the internal nucleocapsid N protein was identified as the major virus-specific phosphorylated product of the endogenous protein kinase activity. This was accompanied by an increase in the electrophoretic mobility of N protein as detected by SDS-PAGE. After solubilization of the virus with 1% Nonidet P40 approximately 81% of the endogenous protein kinase activity remained associated with LCMV nucleocapsids recovered by equilibrium centrifugation at a density of 1.25 g/cm-3 in a linear renograffin gradient. Specific phosphorylation of N protein was reconfirmed in the purified nucleocapsid fraction and both phosphoserine and phosphothreonine found to be the phosphorylated products of the kinase reaction. Although the significance of this enzyme remains unclear, the presence of a protein kinase within LCMV may allow the regulation of LCMV replication and maturation by phosphorylation of virus-specific polypeptides. These events may in turn play a key role in determining the nature and outcome of LCMV infection.

Synthesis of virus-specific polypeptides and genomic RNA during the replicative cycle of Pichinde virus

A stock of plaque-purified Pichinde virus, prepared under conditions designed to limit the amounts of defective interfering virus, was used to infect BHK cells. At daily intervals after infection, cells were examined for infectious and radiolabeled virus particle production and for the synthesis of virus-specific polypeptides. Quantitative comparisons were also made of the concentrations of genomic Pichinde virus L and S RNAs in the cytoplasm of infected cells on different days after infection. Our results showed that virus particle production, rates of protein synthesis, and the intracellular levels of viral genomic RNAs all increased and decreased with similar kinetics, and that this regulation was independent of the cell growth cycle. We were unable to relate these changes in viral macromolecule and virus production to the appearance of readily identifiable defective interfering particles. Our findings suggest that regulation of virus replication early during the replicative cycle of Pichinde virus may not be dependent upon the generation of defective interfering virus.