A stuttering model for paramyxovirus P mRNA editing.

Paramyxovirus P genes are transcribed into two mRNAs which differ from each other by either one (measles and Sendai virus) or two (SV5 and mumps virus) G insertions, and which code for either the P or V proteins. The G insertions always occur within a short run of Gs, and a stuttering mechanism for the insertions has been suggested in which the viral polymerase reiteratively copies a template C residue during mRNA synthesis. Support for this mechanism was obtained by varying the reaction conditions during Sendai virus mRNA synthesis in vitro. A stuttering model is proposed which accounts for how the ratio of inserted to uninserted mRNAs is controlled, and why some paramyxoviruses insert one G and others two Gs when insertions occur.     

Influenza A virus RNA polymerase has the ability to stutter at the polyadenylation site of a viral RNA template during RNA replication

The viral polymerase of influenza virus, a negative-strand RNA virus, is believed to polyadenylate the mRNAs by stuttering at a stretch of five to seven uridine residues which are located close to the 5' ends of the viral RNA templates. However, a mechanism of polyadenylation based on a template-independent synthesis of the poly(A) tail has not been excluded. In this report, we present new evidence showing the inherent ability of the viral polymerase to stutter at the poly(U) stretch of a viral RNA template during RNA replication. Variants which possess 1- to 13-nucleotide-long insertions at the poly(U) stretch have been identified. These results support a stuttering mechanism for the polyadenylation of influenza virus mRNAs.     

The P gene of bovine parainfluenza virus 3 expresses all three reading frames from a single mRNA editing site.

The P gene of bovine parainfluenza virus 3 (bPIV3) contains two downstream overlapping ORFs, called V and D. By comparison with the mRNA editing sites of other paramyxoviruses, two editing sites were predicted for bPIV3; site a to express the D protein, and site b to express the V protein. Examination of the bPIV3 mRNAs, however, indicates that site b is non-functional whereas site a operates frequently. Insertions at site a give rise to both V and D protein mRNAs, because a very broad distribution of Gs is added when insertions occur. This broad distribution is very different from the editing sites of Sendai virus or SV5, where predominantly one form of edited mRNA containing either a one or two G insertion respectively is created, to access the single overlapping ORF of these viruses. A model is proposed to explain how paramyxoviruses control the range of G insertions on that fraction of the mRNAs where insertions occur. The bPIV3 P gene is unique as far as we know, in that a sizeable portion of the gene expresses all 3 reading frames as protein. bPIV3 apparently does this from a single editing site by removing the constraints which control the number of slippage rounds which take place.     

Characterization of the polyadenylation signal of influenza virus RNA.

It has been shown that a stretch of uridines (U's) near the 5' end of the virion RNA of influenza A virus is the polyadenylation site for viral mRNA synthesis. In addition, the RNA duplex made up the 3' and 5' terminal sequences adjacent to the U stretch is also involved in polyadenylation. We have further characterized the polyadenylation signal of influenza virus RNA with a ribonucleoprotein transfection system. We found that the optimal length of the U stretch is 5 to 7 uridine residues. We also showed that the upstream sequence at the 5' end is not involved in polyadenylation and that the optimal distance between the 5' end and the U stretch is 16 nucleotides. The combination of these features defines the polyadenylation site and differentiates this signal from other U stretches scattered throughout the genomes of influenza viruses.     

Nucleotide sequence of the gene encoding respiratory syncytial virus matrix protein.

The amino acid sequence of the matrix protein of the human respiratory syncytial virus (RS virus) was deduced from the sequence of a cDNA insert in a recombinant plasmid harboring an almost full-length copy of this gene. It specifically hybridized to a single 1,050-base mRNA from infected cells. The recombinant containing 944 base pairs of RS viral matrix protein gene sequence lacked five nucleotides corresponding to the 5' end of the mRNA. The nucleotide sequence of the 5' end of the mRNA was determined by the dideoxy sequencing method and found to be 5' NGGGC, wherein the C residue is one nucleotide upstream of the cloned viral sequence. The initiator ATG codon for the matrix protein is embedded in an AATATGG sequence similar to the canonical PXXATGG sequence present around functional eucaryotic translation initiation codons. There is no conserved sequence upstream of the polyadenylate tail, unlike vesicular stomatitis virus and Sendai virus, in which four nucleotides upstream of the polyadenylate tail are conserved in all genes. There is no equivalent of the eucaryotic polyadenylation signal AAUAAA upstream of the polyadenylate tail. The matrix protein of 28,717 daltons has 256 amino acids. It is relatively basic and moderately hydrophobic. There are two clusters of hydrophobic amino acid residues in the C-terminal third of the protein that could potentially interact with the membrane components of the infected cell. The matrix protein has no homology with the matrix proteins of other negative-strand RNA viruses, implying that RS virus has undergone extensive evolutionary divergence. A second open reading frame potentially encoding a protein of 75 amino acids and partially overlapping the C terminus of the matrix protein was also identified.     

Signal sequence for generation of mRNA 3'' end in the Saccharomyces cerevisiae GAL7 gene.

We have identified a signal sequence (designated core signal) necessary to specify formation of mRNA 3' end of the GAL7 gene in Saccharomyces cerevisiae within a DNA segment 26 bp long. The sequence was located 4-5 nucleotides upstream from the 3' end, i.e. the polyadenylation site, of the GAL7 mRNA. Replacement of a DNA segment encompassing the polyadenylation site with a pBR322 DNA, leaving the core signal intact, resulted in alteration of the mRNA 3' end by several nucleotides, suggesting the existence of an additional signal (designated end signal) at or near the polyadenylation site. The normal end formation was abolished when the core signal was placed in the reverse orientation. A considerable fraction of pre-mRNA synthesized in vitro with SP6 RNA polymerase on the template of a DNA fragment containing these signals was cleaved and polyadenylated presumably at the in vitro 3' end during incubation in a cell-free system of yeast. By contrast pre-mRNA synthesized on the template with the core signal alone was processed but much less efficiently. No such processing was seen when the pre-mRNA either lacked the core signal or contained it in the reverse orientation.