A novel mechanism for the initiation of Tacaribe arenavirus genome replication

In vivo analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements

Requirements for capped leader sequences for use during transcription initiation by tomato spotted wilt virus (TSWV) were tested using mutant alfalfa mosaic virus (AMV) RNAs as specific cap donors in transgenic Nicotiana tabacum plants expressing the AMV replicase proteins. Using a series of AMV RNA3 mutants modified in either the 5'-non-translated region or in the subgenomic RNA4 leader, sequence analysis revealed that cleaved leader lengths could vary between 13 and 18 nucleotides. Cleavage occurred preferentially at an A residue, suggesting a requirement for a single base complementarity with the TSWV RNA template, which could be confirmed by analyses of host mRNAs used in vivo as cap donors.

Evidence that the genomic RNA of hepatitis E virus is capped

Hepatitis E virus (HEV) is an unclassified virus with a positive-sense RNA genome and an undefined replication strategy. In order to determine whether the HEV genome is capped or not, we developed a reverse transcription-PCR assay that is based on the ability of a monoclonal antibody to recognize 7-methylguanosine (m(7)G). Antibody to m(7)G bound RNA extracted from virions of two different HEV genotypes. The cap analog competitively inhibited the binding of virion RNAs, demonstrating that HEV has a capped RNA genome.

Transcript initiation and 5'-end modifications are separable events during vesicular stomatitis virus transcription

In this report we describe a novel, bipartite vesicular stomatitis virus (VSV) replication system which was used to study the effect of mutations in the transcription start sequence on transcript initiation and 5'-mRNA modifications. The bipartite replication system consisted of two genomic RNAs, one of which (VSVDeltaG) was a recombinant VSV genome with the G gene deleted and the other (GFC) contained the G gene and two non-VSV reporter genes (green fluorescent protein [GFP] and chloramphenicol acetyltransferase [CAT]). Coinfection of cells with these two components resulted in high-level virus production and gave titers similar to that from wild-type-VSV-infected cells. Mutations were introduced within the first 3 nucleotides of the transcription start sequence of the third gene (CAT) of GFC. The effects of these changes on the synthesis and accumulation of CAT transcripts during in vivo transcription (e.g., in infected cells), and during in vitro transcription were determined. As we had reported previously (E. A. Stillman and M. A. Whitt, J. Virol. 71:2127-2137, 1997), changing the first and third nucleotides (NT-1 and NT-3) reduced CAT transcript levels in vivo to near undetectable levels. Similarly, changing NT-2 to a purine also resulted in the detection of very small amounts of CAT mRNA from infected cells. In contrast to the results in vivo, the NT-1C mutant and all of the second-position mutants produced near-wild-type amounts of CAT mRNA in the in vitro system, indicating that the mutations did not prevent transcript initiation per se but, rather, generated transcripts that were unstable in vivo. Oligo (dT) selection and Northern blot analysis revealed that the transcripts produced from these mutants did not contain a poly(A)(+) tail and were truncated, ranging in size from 40 to 200 nucleotides. Immunoprecipitation analysis of cDNA-RNA hybrids with an antibody that recognizes trimethylguanosine revealed that the truncated mutant transcripts were not properly modified at the 5' end, indicating the transcripts either were not capped or were not methylated. This is the first demonstration that transcript initiation and capping/methylation are separable events during VSV transcription. A model is proposed in which polymerase processivity is linked to proper 5'-end modification. The model suggests that a proofreading mechanism exists for VSV and possibly other nonsegmented minus-strand RNA viruses, whereby if some transcripts do not become capped during transcription in a normal infection, a signal is transduced such that the polymerase undergoes abortive elongation and the defective transcript is terminated prematurely and subsequently degraded.

Identification of the 5' terminal structure of influenza virus genome RNA by a newly developed enzymatic method

A combination of T4 polynucleotide kinase, Escherichia coli alkaline phosphatase, yeast Saccharomyces cerevisiae capping enzyme consisting of alpha (RNA guanylyltransferase) and beta (RNA 5'-triphosphatase) subunits. and its alpha subunit without RNA 5'-phosphatase activity was used to establish a simple enzymatic method for determination of RNA species with 5'-hydroxyl, 5'-monophosphate, 5'-diphosphate or 5'-triphosphate termini. Using this method, we found that viral genome RNA (vRNA) segments of both A-type and C-type influenza viruses carry tri- or diphosphates at their 5' termini. The conclusion was based on the observations that: (i) 5' phosphorylation of vRNAs by T4 polynucleotide kinase takes place only after phosphatase treatment; and (ii) capping of vRNAs can be observed with both the intact yeast capping enzyme and its alpha subunit alone devoid of RNA 5'-triphosphatase activity; but (iii) the level of capping is higher for the alphabeta holoenzyme than the alpha subunit though the relative level varies depending on RNA preparations. The results support the de novo initiation for the RNA replication although transcription of influenza vRNAs is initiated by host cell capped RNAs as primers.

A novel type of defective viral genome suggests a unique strategy to establish and maintain persistent lymphocytic choriomeningitis virus infections

Defective interfering RNAs have long been thought to be a causal factor of persistent RNA virus infections. Here we describe a novel type of defective genome of lymphocytic choriomeningitis virus and the unique mechanism by which these RNAs appear to contribute to the establishment and maintenance of persistent infection. The defective genomes have short deletions in the untranslated regions at their termini and additional nontemplated terminal nucleotides. This and previous work from our laboratory suggested that the RNAs were competent for replication but not for transcription. From experiments using a technique to unambiguously determine the sequences of individual RNA termini, it appears that some truncated RNAs can be repaired. The data suggest that the loss or gain of nucleotides from the RNA termini during the course of infection is the mechanism for establishing and maintaining persistence.

Normal cellular replication of Sendai virus without the trans-frame, nonstructural V protein

The Sendai virus V protein is a nonstructural trans-frame protein in which a highly conserved cys-rich Zn2+-binding domain is fused to the N-terminal half of the P protein via mRNA editing. Using a recently developed system in which infectious virus is recovered from cDNA, we have engineered a virus in which a translation stop codon was placed at the beginning of the V ORF. Translation of the V(stop) mRNA yields a W-like protein, i.e., a protein composed of the N-terminal half of the P protein alone which is naturally expressed at low levels from the P gene. This V-minus but W-augmented virus was found to replicate normally in cell culture and embryonated chicken eggs. The Sendai virus V protein is thus an accessory protein, and the cys-rich Zn2+-binding domain is likely to function in a specialized role during virus propagation.

The 5' ends of Thogoto virus (Orthomyxoviridae) mRNAs are homogeneous in both length and sequence

Thogoto (THO) virus is a tick-borne member of the Orthomyxoviridae whose genome consists of six segments of linear, negative sense, single-stranded RNA. To gain insight into the mechanism by which viral mRNA transcripts are initiated, poly(A)+ RNA isolated from THO virus-infected cells was characterized by (i) primer extension experiments, (ii) immunoprecipitation studies with an anticap monoclonal antibody, (iii) direct sequencing analysis of the isolated RNA, and (iv) cloning and sequencing of individual mRNA molecules. The results indicated that THO virus mRNAs are capped and homogeneous in both length and sequence at their 5' end. These findings contrast with the situation found in all other segmented, negative sense or ambisense, single-stranded RNA viruses so far analyzed in which the 5' ends of viral mRNAs are heterogeneous in length and sequence. These results are discussed in terms of the mechanism used by THO virus to initiate mRNA synthesis.

Nucleoprotein viral RNA and mRNA of Thogoto virus: a novel "cap-stealing" mechanism in tick-borne orthomyxoviruses?

Tick-borne Thogoto virus (THOV) represents the prototype virus of a new genus in the Orthomyxoviridae family. Its genome consists of six segments of negative-sense, single-stranded RNA. We have cloned and sequenced the fifth genomic segment, which codes for the viral nucleoprotein (NP). The deduced amino acid sequence shows 43% similarity to the NP of Dhori virus, a related tick-transmitted orthomyxovirus, and about 14% sequence similarity to those of the influenza viruses. To reveal the mechanism by which THOV initiates mRNA synthesis, we characterized the 5' ends of the NP mRNAs. Transcripts were recognized by a cap-specific monoclonal antibody, indicating that THOV mRNAs are capped. Surprisingly, no large heterogeneous extensions were found at the 5' end, as would have been expected if THOV were using a classical "cap-stealing" mechanism. We therefore propose that THOV is stealing only the cap structure with one or two additional nucleotides from cellular mRNAs to generate appropriate primers for initiation of viral mRNA transcription.

The Sendai paramyxovirus accessory C proteins inhibit viral genome amplification in a promoter-specific fashion

Many paramyxoviruses express small basic C proteins, from an alternate, overlapping open reading frame of the P gene mRNA, which were previously found to inhibit mRNA synthesis. During recent experiments in which infectious Sendai virus (SeV) was recovered from cDNA via the initial expression of the viral N, P, and L genes from plasmids, the abrogation of C protein expression from the plasmid P gene was found to be necessary for virus recovery. We have investigated the effect of C coexpression on the amplification of an internally deleted defective interfering (DI) genome directly in the transfected cell, for which, in contrast to virus recovery experiments, genome amplification is independent of mRNA synthesis carried out by the SeV polymerase. We find that C protein coexpression also strongly inhibits the amplification of this DI genome but has little or no effect on that of a copy-back DI genome (DI-H4). We have also characterized the C protein from a mutant SeV and found that (i) it had lost most of its inhibitory activity on internally deleted DI genome amplification and (ii) its coexpression no longer prevented the recovery of SeV from DNA. However, consistent with the insensitivity of copy-back DI genomes to C protein inhibition, C coexpression did not prevent the recovery of copy-back nondefective viruses from DNA. The inhibitory effects of C coexpression thus appear to be promoter specific.

Sequence analysis of the 5' ends of tomato spotted wilt virus N mRNAs

Messenger RNAs transcribed from the tomato spotted wilt virus (TSWV) RNA genome have characteristic extra non-templated heterogeneous sequences at their 5' ends which may be the result of a cap-snatching event involving cellular mRNAs. In order to investigate the genetic origin of these extra sequences and to gain more insight in the process of cap-snatching as performed by TSWV, nucleocapsid protein (N) mRNAs derived from the TSWV S RNA were cloned and sequenced. Twenty clones were obtained which contained 5'-proximal sequences of non-viral origin, ranging in length from 12 to 21 nucleotides. None of the sequences analyzed were identical and no base preference at the endonucleolytic site was observed.

The 5' ends of Hantaan virus (Bunyaviridae) RNAs suggest a prime-and-realign mechanism for the initiation of RNA synthesis

We examined the 5' ends of Hantaan virus (HTN) genomes and mRNAs to gain insight into the manner in which these chains were initiated. Like those of all members of the family Bunyaviridae described so far, the HTN mRNAs contained 5' terminal extensions that were heterogeneous in both length and sequence, presumably because HTN also "cap snatches" host mRNAs to initiate the viral mRNAs. Unexpectedly, however, almost all of the mRNAs contained a G residue at position -1, and a large fraction also lacked precisely one of the three UAG repeats at the termini. The genomes, on the other hand, commenced with a U residue at position +1, but only 5' monophosphates were found here, indicating that these chains may not have initiated with UTP at this position. Taken together, these unusual findings suggest a prime-and-realign mechanism of chain initiation in which mRNAs are initiated with a G-terminated host cell primer and genomes with GTP, not at the 3' end of the genome template but internally (opposite the template C at position +3), and after extension by one or a few nucleotides, the nascent chain realigns backwards by virtue of the terminal sequence repeats, before processive elongation takes place. For genome initiation, an endonuclease, perhaps that involved in cap snatching, is postulated to remove the 5' terminal extension of the genome, leaving the 5' pU at position +1.

5' termini of Pichinde arenavirus S RNAs and mRNAs contain nontemplated nucleotides

Primer extension of Pichinde arenavirus purified virion RNA suggests that genomes have at least a single nontemplated base at the 5' end which is a G in all cDNA clones having one such single base. On the other hand, the predominant products of primer extension on total virus-infected-cell RNA are at positions -1 and -2. The primer extension product at position -2 is not represented in virion RNA, and neither of these products is proportionally represented in mRNA. mRNA is predominantly 3 or 4 bases longer than genomes and antigenomes, but primer extension products as long as 7 bases were observed. The sequence of nontemplated bases reported here is unambiguous with respect to the 5'-terminal base and supports the view that there is a sequence preference for a G at the 5' termini of mRNAs. Assessment of our sequence data in the context of the sequences of Tacaribe and lymphocytic choriomeningitis viruses suggests that the mechanism of initiation of arenavirus transcription is fundamentally different from that of members of the families Orthomyxoviridae and Bunyaviridae.

Analysis of Pichinde arenavirus transcription and replication in human THP-1 monocytic cells

Human promonocytic THP-1 cells were previously shown to be nonpermissive for Pichinde virus (PV) replication unless the cells were induced to differentiate to macrophages by stimulation with phorbol ester (PMA) (J. Virol. 65, 3575, 1991). The restriction did not involve receptor modulation, virus binding, nor internalization of virus but a requirement for a host cell function in PV replication was observed in that the phorbol ester effect required protein kinase C activation and was inhibited by actinomycin D. In this report we demonstrate that PV S RNA genomes, antigenomes, GPC mRNA and NP mRNA are expressed at high levels in PMA treated THP-1 cells but at significantly lower levels or not at all in untreated cells. We have also determined that degradation of input viral S RNA does not account for decreased PV RNA synthesis in the undifferentiated cells. This suggests that the restriction of PV replication in THP-1 cells is a post-penetration event which precedes transcription of viral mRNAs and replication of viral genomes and supports a role for differentiation-specific host cell factors early in PV replication.

Capped nonviral sequences at the 5' end of the mRNAs of rice hoja blanca virus RNA4

Subgenomic RNAs of both polarities corresponding to rice hoja blanca virus (RHBV) ambisense RNA4 were detected in RHBV-infected rice tissues. Total RNA extracted from RHBV-infected and noninfected rice tissues and RNA4 purified from RHBV ribonucleoprotein particles were used as templates for primer extension studies. The RNAs extracted from RHBV-infected tissues contain a population of RNA molecules with 10 to 17 nonviral nucleotides at their 5' end. The RNA-cDNA hybrids resulting from primer extension of such RNA molecules were specifically immunoselected with anti-cap antibodies, indicating that the subgenomic RNAs are capped and probably serve as mRNAs and that the additional nucleotides at their 5' end possibly derive from host mRNAs via a cap-snatching mechanism.

Sequence heterogeneity in the termini of lymphocytic choriomeningitis virus genomic and antigenomic RNAs

Sequence analysis of lymphocytic choriomeningitis virus L and S RNAs has revealed evidence of heterogeneity within the termini of the genomic and antigenomic RNAs. The RNAs are missing from 0 to 38 bases, show characteristic patterns of deleted nucleotides at both 5' and 3' termini, and often have a nontemplated base at the terminus. The same deletions, at either the 5' or the 3' terminus of the genomic L and S RNAs, are frequently found in the complementary strand of antigenomic RNA, suggesting that RNAs with deleted termini may be recognized as functional templates for replication. RNAs extracted from virions, or viral nucleocapsids isolated from acutely infected cells, are similar in the nature and extent of terminal heterogeneity that have been observed. This finding brings into question the function of the conserved sequences located at the termini of arenavirus genomic RNAs. Our data suggest that, while replication and packaging of the genomic and antigenomic RNA molecules can occur with terminally deleted molecules, mature transcripts may be derived only from full-length templates containing the conserved terminal sequence.

Concurrent sequence analysis of 5' and 3' RNA termini by intramolecular circularization reveals 5' nontemplated bases and 3' terminal heterogeneity for lymphocytic choriomeningitis virus mRNAs

We have used a technique of RNA circularization coupled with polymerase chain reaction amplification for simultaneous analysis of the 5' and 3' termini of subgenomic mRNAs derived from the S RNA of lymphocytic choriomeningitis virus during an acute infection of BHK cells. These mRNAs possess 1 to 7 nontemplated nucleotides of apparently random sequence at their 5' ends. The predominant mRNA species have 4 or 5 nontemplated nucleotides. The 5' termini of the mRNAs also have properties consistent with the presence of a 5' cap structure. The 3' termini of the mRNAs lack poly(A) tails, and we have shown that transcription termination occurs at heterogeneous positions within the intergenic region of the S RNA. The identification of several distinct termini in the vicinity of a putative stem-loop structure in the RNA templates suggests that transcription termination may be mediated by a structural signal rather than a precise sequence signal.

The Tacaribe arenavirus small zinc finger protein is required for both mRNA synthesis and genome replication

An antiserum to a peptide of the Tacaribe virus Z protein was used to determine whether this small Zn(2+)-binding protein was required for viral RNA synthesis in infected cell extracts. Specific immunodepletion of the extracts invariably reduced genome synthesis to near background levels, but strong effects on mRNA synthesis occurred only early in the infection or when mRNA synthesis was relatively weak. Our results suggest that the Z protein is required for both mRNA and genome synthesis, but in somewhat different manners.

Tacaribe arenavirus RNA synthesis in vitro is primer dependent and suggests an unusual model for the initiation of genome replication

A Tacaribe virus in vitro system for RNA synthesis was established and found in large part to faithfully reproduce RNA synthesis in vivo. Similar to influenza virus and bunyavirus in vitro systems, this system was also highly dependent on added oligonucleotides. Of the eight tested, only three were active, in the order GpC greater than CpG greater than ApApC. Determination of the 5' ends of the transcripts suggested that the oligonucleotides were acting as primers. In particular, whereas stimulation with CpG (complementary to positions +1 and +2 of the template) led to RNAs whose 5' ends were at position +1 as expected, GpC stimulation led to transcripts whose 5' ends were at position -1 rather than at position +2, as GpC is complementary to positions +2 and +3 of the template. This finding suggests a model for the initiation of genome replication in which pppGpC is first made on the template at positions +2 and +3 but slips backwards on the template so that the 5' end is at position -1 before elongation can continue.

Germiston virus transcriptase requires active 40S ribosomal subunits and utilizes capped cellular RNAs

The transcriptase associated with Germiston virus was assayed in an in vitro reaction in which transcription was coupled to translation by adding reticulocyte lysate under the appropriate salt conditions. When analyzed in polyacrylamide gels, the major transcripts migrated like authentic S mRNAs and possessed 12- to 18-base-long nontemplated 5' extensions similar to the 5' end of viral mRNAs. These transcripts were functional for the synthesis of at least proteins N and NSS. When translation was inhibited by adding protein synthesis inhibitors such as puromycin, cycloheximide, and anisomycin, a drastic inhibitory effect was observed on the synthesis of the complete S mRNA transcripts. However, initiation and part of the elongation process were still active, since short and incomplete RNA molecules with RNA primers at their 5' ends were synthesized. On the other hand, we found that edeine, another inhibitor of protein synthesis, stimulated not only synthesis of S mRNAs but also that of the full-length S cRNAs. Taking into account the mode of action of this antibiotic, we discuss the results, which emphasize the crucial role of active ribosomes during bunyavirus transcription and confirm the observations reported on La Crosse virions. Moreover, we showed that the RNA transcripts synthesized in a transcription-translation reaction were capped and that most of them have acquired the 5' terminal sequences of the alpha- or beta-globin mRNA.

Host-derived 5' ends and overlapping complementary 3' ends of the two mRNAs transcribed from the ambisense S segment of Uukuniemi virus

Two mRNAs, coding for the N and NSS proteins, are transcribed from the small (S) Uukuniemi virus RNA segment by an ambisense strategy (J. F. Simons, U. Hellman, and R. F. Pettersson, J. Virol. 64:247-255, 1990). In this report, we describe the analysis of the 5' and 3' ends of the two mRNAs. Primer extension as well as cloning and sequencing of individual mRNAs showed that the 5' ends of both mRNAs contained nonviral sequences ranging from 7 to 25 residues in length (mean, 12 residues), indicating a cap-snatching mechanism similar to the one originally described for priming of influenza virus mRNA synthesis. In 35% of the cases, the first virion-specified nucleotide (an A residue) was substituted with a G residue. Between the translation termination codons of N and NSS, there is a 74-residue-long noncoding intergenic region (Simons et al., J. Virol. 64:247-255, 1990). Nuclease protection assays using both RNA and DNA hybridization probes showed that the 3' ends of the N and NSS mRNAs overlap each other by about 100 nucleotides. The 3' end of the NSS mRNA extends into the coding sequence of the N mRNA, whereas the N mRNA is terminated just prior to the stop codon of NSS. To our knowledge, this is the first example of overlapping complementary mRNAs in viruses with an ambisense coding strategy. No obvious transcription termination sequence was identified. However, because of a short palindromic sequence in the intergenic region, the 3' ends of both mRNAs (and consequently also the template RNAs) can be folded into an A/U-rich hairpin structure. It remains to be determined whether this structure plays any role in transcription termination.