Sendai virus Y proteins are initiated by a ribosomal shunt.

The Sendai virus P/C mRNA expresses eight primary translation products by using a combination of ribosomal choice and cotranscriptional mRNA editing. The longest open reading frame (ORF) of the mRNA starts at AUG104 (the second initiation site) and encodes the 568-amino-acid P protein, an essential subunit of the viral polymerase. The first (ACG81), third (ATG114), fourth (ATG183), and fifth (ATG201) initiation sites are used to express a C-terminal nested set of polypeptides (collectively named the C proteins) in the +1 ORF relative to P, namely, C', C, Y1, and Y2, respectively. Leaky scanning accounts for translational initiation at the first three start sites (a non-ATG followed by ATGs in progressively stronger contexts). Consistent with this, changing ACG81/C' to ATG (GCCATG81G) abrogates expression from the downstream ATG104/P and ATG114/C initiation codons. However, expression of the Y1 and Y2 proteins remains normal in this background. We now have evidence that initiation from ATG183/Y1 and ATG201/Y2 takes place via a ribosomal shunt or discontinuous scanning. Scanning complexes appear to assemble at the 5' cap and then scan ca. 50 nucleotides (nt) of the 5' untranslated region before being translocated to an acceptor site at or close to the Y initiation codons. No specific donor site sequences are required, and translation of the Y proteins continues even when their start codons are changed to ACG. Curiously, ATG codons (in good contexts) in the P ORF, placed either 16 nt upstream of Y1, 29 nt downstream of Y2, or between the Y1 and Y2 codons, are not expressed even in the ACGY1/ACGY2 background. This indicates that ATG183/Y1 and ATG201/Y2 are privileged start sites within the acceptor site. Our observations suggest that the shunt delivers the scanning complex directly to the Y start codons.

Inhibitors of protein synthesis inhibit both La Crosse virus S-mRNA and S genome syntheses in vivo.

The effect of drugs such as puromycin and cycloheximide, which inhibit protein synthesis, on the accumulation of La Crosse virus S genome RNAs in vivo has been examined. We have found that if these drugs are added to the cultures before infection, minuscule amounts of S-mRNA can be detected late in infection. Genome replication, on the other hand, cannot be detected at any time. When these drugs are added later in infection when RNA synthesis is well established, S-mRNA accumulation decreases in a dose-dependent manner proportional to the effect of these drugs on protein synthesis. This decrease cannot be accounted for by increased turnover of the mRNA in the presence of the drug. S genome replication, curiously, was found to be hypersensitive to the effects of these drugs. Our results confirm those of Abraham and Pattnaik (1983) that ongoing protein synthesis is required for the accumulation of complete bunyavirus S-mRNA.

Loss of V protein expression in human parainfluenza virus type 1 is not a recent event.

The P gene of paramyxoviruses usually contains an alternate overlapping ORF coding for a short cysteine-rich domain called V. This domain was thought to be a common feature of these genes as it is present in ten paramyxoviruses. However, the V ORF region of the P gene of one strain of human parainfluenza-virus type 1 (isolated in 1957) was recently found to be closed by no less than 9 stop codons. To determine whether the absence of the V ORF here might be due to the long adaptation of this strain in culture, 3 other more recent isolates were examined. Small differences in the V region were found, but all had conserved the vast majority of the stop codons. Moreover, examination of most of the intercistronic regions of the PIV1 genome failed to uncover a cryptic V gene. The V ORF is then unlikely to be a common feature of paramyxovirus P genes.

Measles virus nucleic acid sequences in human brain.

We constructed a measles virus genomic recombinant DNA library, and used clones coding for portions of the viral P, M and H proteins to probe for measles virus nucleic acid sequences in post-mortem multiple sclerosis, SSPE and control brains. By dot blot hybridization, the probes detected measles virus nucleic acid sequences in as little as 3 nanograms of total RNA extracted from measles virus-infected cells and also in highly diluted RNA extracted from SSPE brain, but did not detect measles virus sequences in RNA extracted from 11 multiple sclerosis or 8 control brains, even at a 1 000-fold higher concentration of RNA. By in situ hybridization, these probes detected measles virus nucleic acid sequences in virtually every cell and the surrounding neuropile of SSPE brain, but again did not detect such sequences in multiple sclerosis or control brains. Our findings using these highly specific probes confirm that measles virus is found in SSPE brains and indicate that measles virus genome is unlikely to be present in multiple sclerosis or normal brains.

Isolation of vesicular stomatitis virus defective interfering genomes with different amounts of 5'-terminal complementarity.

I isolated at least 30 different vesicular stomatitis virus defective interfering (DI) genomes, distinguished by chain length, by five independent undiluted passages of a repeatedly cloned virus plaque. Labeling of the 3' hydroxyl ends of these DI genomes and RNase digestion studies demonstrated that the ends of these DI genomes were terminally complementary to different extents (approximately 46 to 200 nucleotides). Mapping studies showed that the complementary ends of all of the DI genomes were derived from the 5' ends of the nondefective minus-strand genome. Regardless of the extent of terminal complementarity, all of the DI genomes synthesized the same 46-nucleotide minus-strand leader RNA.

Isolation and characterization of Sendai virus DI-RNAs.

When passaged at high multiplicity, four strains of Sendai virus all showed evidence that they contained defective interfering (DI) particles. RNA isolated from nucleocapsids of cells infected with the high multiplicity passage stocks was found to consist of only minor amounts of nondefective genome length RNA and major amounts of smaller RNAs, the DI-RNAs. These DI-RNAs were found to have unusual and variable sedimentation properties in sucrose gradients, but were found to represent unique segments of the viral genome by length measurements in the electron microscope and by hybridization. A striking feature of the DI-RNAs is their ability to form circular structures, indicating that the ends of the DI-RNA are complementary. The implications of this finding in terms of the mechanism of genome replication is discussed.

Transfer ribonucleic acid nucleotidyltransferase and transfer ribonucleic acid in Sendai virions.

Sendai virions contain both transfer ribonucleic acid (tRNA) nucleotidyltransferase and its substrate, tRNA missing its CCA-OH end.

Modified model for the switch from Sendai virus transcription to replication.

RNase mapping was used to estimate the levels of unencapsidated Sendai virus plus-strand RNAs which cross the leader-NP junction relative to NP mRNA. Significant amounts of leader readthrough RNAs were found in Z strain-infected cells, similar to that described for the polR mutant of vesicular stomatitis virus, even though this strain is considered wild type. The levels of the readthrough RNAs detected fell sharply when progressively longer probes were used, unlike that of NP mRNA. These studies suggest that polymerases which read through the first junction terminate shortly afterwards in the absence of concurrent assembly of the nascent chain, whereas those which reinitiate at NP continue efficiently to the next junction. Reinitiation appears to be necessary to convert the polymerase to a mode in which elongation is independent of concurrent assembly. Concurrent assembly appears to be required not only for the polymerase to read through the junction efficiently, but also for it to continue elongation between junctions.

Scanning independent ribosomal initiation of the Sendai virus Y proteins in vitro and in vivo.

The Sendai virus P/C mRNA contains five ribosomal initiation sites between positions 81 and 201 from the 5' end. One of these sites initiates in the P open reading frame (ORF) (ATG/104), whereas four initiate in the C ORF (ACG/81 and ATGs/114, 183, 201), to give a nested set of C proteins (C', C, Y1, Y2). Introduction of new ATGs or physically breaking the mRNA upstream of these natural sites was used in vitro to prevent ribosomal scanning downstream. The results suggest that a minority of the ribosomes which initiate C (ATG/114) and all of those which initiate Y1 and Y2 (ATGs/183 and 201) do so by a scanning independent mechanism. When the leaky ACG/81 site is changed to a non-leaky ATG site in in vivo experiments, ribosomal initiation at Y is again not diminished, whereas that at C as well as at P becomes undetectable. Ribosomal initiation at Y appears to be scanning independent in vitro and in vivo. That at C is partly independent in vitro, but completely dependent in vivo. These results are discussed in terms of a model of internal initiation at Y.

La Crosse virus infection of mammalian cells induces mRNA instability.

La Crosse virus infection of BHK cells leads to a dramatic shutoff of not only host protein synthesis but also viral protein synthesis later in infection. This shutoff can be accounted for by the loss of the cytoplasmic cellular and viral mRNAs. The induction of mRNA instability requires extensive virus replication, since when cycloheximide is added early in infection the preexisting viral and cellular mRNAs do not decrease upon incubation of the cultures. Pretreatment of the cultures with actinomycin D does not affect the ability of La Crosse virus infection to induce mRNA instability, and examination of the rRNAs shows no evidence of specific degradation due to activation of the interferon-associated latent RNase. The induction of mRNA instability therefore does not appear to operate through an interferon pathway. Viral mRNA synthesis, on the other hand, is not turned off during infection, and the cap-dependent endonuclease involved in viral mRNA initiation may be responsible for the mRNA instability.

Sendai virus P gene produces multiple proteins from overlapping open reading frames.

The Sendai virus P gene contains overlapping open reading frames (ORFs), and several unusual mechanisms are used to produce multiple proteins from all three ORFs of this gene. These include the use of a non-AUG start codon, leaky ribosomal scanning, what appears to be scanning-independent ribosomal initiation and/or ribosomal jumping, and a form of mRNA editing.

A novel mechanism for the initiation of Tacaribe arenavirus genome replication.

The ends of arenavirus genome and antigenome RNAs are highly conserved and where determined directly, always contain a 3' G (referred to as position +1). However, primers extended to the 5' ends of Tacaribe virus genomes and antigenomes extend to position -1. When genomes and antigenomes are annealed either inter or intramolecularly and treated with RNase A or T1, there appears to be a single unpaired G at the 5' ends of the hybrids. A single extra G is also found by cloning the 5' ends of S antigenomes, and studies with capping enzyme detect (p)ppG at the 5' ends of genome and antigenome chains. A model is proposed in which genome replication initiates with pppGpC to create the nontemplated extra G. In contrast, the nontemplated bases at the 5' ends of the N mRNAs, which extend to positions -1 to -5, were found to be capped and also heterogeneous in sequence.

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.

Ribosomal initiation from an ACG codon in the Sendai virus P/C mRNA.

The Sendai virus P/C mRNA expresses the P and C proteins from alternate reading frames. The C reading frame of this mRNA, however, is responsible for three proteins, C', C and Y, none of which appear to be precursors to each other in vivo. Using site-directed and deletion mutagenesis of the P/C gene cloned in SP6 and in vitro translation of the mRNAs, we show that the 5' most proximal initiation codon of the mRNA is an ACG at position 81, responsible for C' synthesis. The succeeding initiation codons, all ATGs, are responsible for the P protein (position 104), the C protein (position 114) and the Y protein(s) (either positions 183 or 201). Examination of the relative molar amounts of the C', P and C proteins found in vivo suggests that an ACG in an otherwise favorable context is almost as efficient for ribosome initiation as an ATG in a less favored context, but only 10-20% as efficient as an ATG in a more favored context. The judicious choice of increasingly more favorable initiation codons in the P/C gene allows multiple proteins to be made from a single mRNA.

Scanning independent ribosomal initiation of the Sendai virus X protein.

Both peptide antisera and monoclonal antibodies detect a 10-kd protein (X) in Sendai virus infected cells, which represents approximately the last 95 residues of the 568-amino-acid-long P protein. The X protein does not appear to be derived from a precursor P in vivo, and in in vitro X can be made under conditions in which P synthesis has been arrested by hybridized DNA fragments or specific cleavage of the mRNA. X initiation is nevertheless cap dependent. Ribosomes which initiate X appear to pass directly from the cap to the initiation codon.

Translational requirement for La Crosse virus S-mRNA synthesis: a possible mechanism.

Ongoing protein synthesis is required for La Crosse S-mRNA synthesis in vivo, and complete S-mRNA can be made in vitro only in the presence of an active rabbit reticulocyte lysate. Using in vitro systems based on the polymerase activity of purified virions, we further support the notion that it is translation of the nascent mRNA that is required for complete transcription. Since replacement of guanosine with inosine in the nascent mRNA substitutes for the translational requirement, it appears that translation is required to prevent interactions of the nascent chain from taking place, which, if not prevented, lead to premature termination. These interactions appear to be between the nascent mRNA chain and its nucleocapsid template. A model for the translational requirement for complete S-mRNA synthesis is presented.

Unusual transcripts in La Crosse virus-infected cells and the site for nucleocapsid assembly.

The La Crosse virus S genome segment is known to code for two plus-strand transcripts, free S-mRNA (nucleotide [nt] -15 to 886) and encapsidated antigenome RNA (nt 1 to 983). Early in infection only these plus-strand transcripts could be detected, but at later times plus-strand RNAs representing nt 1 to 886 in an encapsidated form and nt -15 to 983 as a free RNA could also be seen, as well as S-mRNA in an encapsidated form. The encapsidated S-mRNA became relatively important at later times because the free S-mRNA turned over rapidly after 5 h postinfection. The existence of these unusual RNAs and their presence as either free or encapsidated species suggests that the site for nucleocapsid assembly is located at the 5' ends of the genome and antigenome chains.