Sendai virus gene sequences identified by oligonucleotide mapping

Expression of Sendai virus defective-interfering genomes with internal deletions

Sendai virus strain 7 has been shown to contain four defective interfering (DI) RNA species in which both genome termini and various adjacent fragments of the 3'-terminal NP gene and 5'-terminal L gene are represented, but most or all internal genes and gene boundaries are deleted. Previous sequence analyses of these mutant RNAs suggested that all four possessed the transcription initiation signal of the NP gene and the transcription termination signal of the L gene. The supposition that these signals should specify transcripts has now been supported by oligo(dT) selection of four DI 7 specific RNA species that had apparent molecular weights slightly lower than each DI genome. DI RNA 7a, which contains the entire NP gene, except for two U residues at the end of the poly(A) initiation signal, appeared to be transcribed solely as a readthrough product. Since DI RNA 7a contains the entire NP protein-coding sequence and DI RNAs 7c and 7d contain fragments of it, whereas DI RNA 7b is devoid of it, only transcripts of RNAs 7c and 7d were expected to specify fusion proteins containing NP gene-specific sequences. A strain 7-induced protein that reacted with monoclonal antibodies against the NP protein had the 33,000 Mr size appropriate for the translation product predicted by the sequence of RNA 7d. Other proteins of lower molecular weight were seen only in cells infected by strain 7, but they did not react with NP-specific antibody and their translation in vitro was not blocked by hybridization to an NP gene-specific oligonucleotide. Therefore, at least some of these proteins may be cellular products induced by DI virus infection. These DI transcripts and translation products may influence interference with replication of the parental helper virus.

Translational modulation in vitro of a eukaryotic viral mRNA encoding overlapping genes: ribosome scanning and potential roles of conformational changes in the P/C mRNA of Sendai virus

Expression of proteins from three overlapping genes in a single mRNA species of Sendai virus was modulated in a cell-free rabbit reticulocyte translation system. Hybrid-arrested translation by oligodeoxynucleotides complementary to specific regions of the mRNA that specifies the viral P, C, and C' proteins demonstrated that ribosomes scan the RNA from its 5' end to find initiation codons, and suggested that the secondary structure of the mRNA influences the selection of alternative initiation codons. Translational modulation of P, C, and C' proteins by Mg++ and spermidine indicated that RNA folding is involved in this selection process.

In vitro replication of Sendai virus wild-type and defective interfering particle genome RNAs

A system for studying the in vitro replication of the genome RNAs of Sendai virus and its defective interfering particle DI-H has been developed. Cytoplasmic extracts of baby hamster kidney cells infected with wild-type Sendai virus or coinfected with wild-type Sendai virus plus DI-H were prepared after lysolecithin treatment at 12 h postinfection. The extracts supported the transcription of six viral mRNAs as well as the replication of the Sendai virus 50S (wild-type) and 14S DI-H genome RNAs and their encapsidation into nucleocapsids in the absence of de novo protein synthesis. RNA replication in vitro represented more than 50% of total RNA synthesis, a relative level higher than that found in the infected cell. The proteins required for Sendai virus RNA replication were present in a soluble protein pool at the time of extract preparation. Depletion of the protein pool by prior treatment of infected cells with cycloheximide inhibited subsequent in vitro genome replication without affecting transcription. The cytoplasmic extract may be separated by high-speed centrifugation into two components: the Sendai virus wild-type and DI-H nucleocapsid templates containing the RNA and associated NP, L, and P proteins and the soluble protein fraction containing primarily the P, NP, and M viral proteins with trace amounts of the L, HN, Fo, and nonstructural C proteins. The isolated intracellular DI-H nucleocapsid template alone cannot replicate its RNA, but when recombined with the Sendai virus soluble protein fraction it catalyzes the replication and encapsidation of viral RNAs. The initiation of RNA replication in vitro can be demonstrated because detergent-disrupted purified DI-H virions replicate both positive- and negative-strand RNAs in the presence, but not in the absence, of the soluble protein fraction from an extract of infected cells.

Polytranscripts of Sendai virus do not contain intervening polyadenylate sequences

Discrete high-molecular-weight RNA species with the properties of polytranscripts were observed in poly(A)-rich RNA extracted from Sendai virus-infected cells. These RNA species were virus specific, being synthesized in the presence of actinomycin D, but not seen in uninfected cells. They were not genome or antigenome fragments, since they were not encapsidated, as shown by their destruction when ribonuclease was added to cell homogenates and by their absence from the RNA fractions that did not bind to oligo(dT)-cellulose. Two lines of evidence indicated that the gene-specific regions of these polytranscripts were not linked by poly(A) sequences, but were faithful copies of virus genomic RNA sequences at gene boundaries. First, a small cDNA clone obtained by reverse transcription of poly(A)-rich RNA species from infected cells contained 90 bases from the 5' terminus of the gene for the P protein and about 600 bases from the 3' end of the downstream gene, which specifies the M protein, the entire cloned sequence being an accurate complement of the genomic RNA. Second, dideoxynucleotide sequencing of poly(A)-rich RNA species primed by virus gene-specific oligodeoxynucleotides revealed read-through products of transcription containing no detectable poly(A). If Sendai virus polytranscripts are intermediates in the production of monocistronic viral mRNAs by a cleavage process, and poly(A) sequences do not link the mRNAs, polyadenylation would have to follow the cleavage step; it seems more likely that these polytranscipts are aberrant transcription products generated by occasional termination failure in a stop-start mechanism of transcription.

Complete sequence of the Sendai virus NP gene from a cloned insert

A DNA molecule representing all but the three terminal bases of the Sendai virus nucleoprotein (NP) gene, copied from viral mRNA, was inserted into pBR322. The NP insert comprised 1673 bases. The first AUG protein initiation codon, at position 65, began an open reading frame of 1551 bases, encoding a protein of 517 amino acids with an amino acid composition corresponding to previously published data. The NP gene sequence determined in the present work is similar to that described by Shioda et al. [ Nucl . Acids Res. 11, 7317 (1983)], but there are 14 amino acid differences that probably reflect differences in virus strains. The predicted secondary structure of the NP molecule and the locations within that structure of potential protease cleavage sites are in accord with structural domains previously defined by controlled protease digestion.

Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

This chapter focuses on applications of oligonucleotide fingerprinting to the identification of viruses. Fingerprinting is a technique by which oligonucleotides, produced by cleavage of RNA molecules with specific ribonucleases, are separated in two dimensions. It is a definitive method of identifying RNA viruses according to their genotypes. It is not subject to the problems of antigenic drift or antigenic convergence that complicate serological identification. Furthermore, it provides a semiquantitative means of following the evolution of viral genomes in nature. Because all regions of the genome are represented by the large diagnostic oligonucleotides, a survey of the total genomic changes can be monitored. Fingerprinting has two limitations as a diagnostic tool. First, although highly definitive, fingerprinting is not as rapid or inexpensive as serological techniques and cannot be as easily scaled up for routine identification of a large number of samples. Second, the evolutionary range of fingerprinting is short and relationships may not be evident for isolates of rapidly evolving viruses obtained over long intervals. However, these limitations are not large, compared to the full benefits offered to the virologist by the fingerprinting method.

Isolation and characterization of measles virus intracellular nucleocapsid RNA

Protocols have been established for the preparation of large amounts of pure measles virus intracellular nucleocapsids. As a result, it has been possible to routinely achieve nucleocapsid RNA yields of approximately 200 micrograms (from approximately 5 X 10(8) infected cells). Electrophoretic analysis of this RNA under denaturing conditions revealed a single species whose mass was estimated at approximately 4.8 X 10(6) daltons. Electron microscopic assessment of nucleocapsid RNA contour lengths corroborated the electrophoretic size determination. Total nucleocapsid RNA was shown to contain both negative- and positive-stranded species distributed in a ratio of 2 to 3 genome polarity molecules for each antigenome RNA. Hybridization studies established that all of the virus-specified polyadenylated RNAs were encoded by the negative-stranded nucleocapsid RNA and, therefore, that this nucleocapsid RNA was the measles genome. Examination of the measles virus-specified, polyadenylated transcription products by HCHO-agarose gel electrophoresis revealed at least nine distinct RNA species (rather than the six predicted measles mRNAs). The significance of these observations is discussed.

Sendai virus contains overlapping genes expressed from a single mRNA

The mRNA coding for the Sendai virus P and C proteins was located on the viral genome using cloned DNA and the relevant regions of the DNA were sequenced. The nucleotide sequence revealed two overlapping open reading frames that could code for proteins of 568 and 204 amino acids. Primer extension and S1 nuclease mapping studies detected only a single 1.894 kb mRNA from this region. Hybrid arrest of translation studies using restriction fragments verified the overlapping nature of these genes. Sequence homologies at the beginning of three Sendai virus cistrons suggest that these genes may have arisen by duplication from a common ancestor, possibly an influenza-like virus gene.

Sequence of the 5' end of the Sendai virus genome and its variable representation in complementary form at the 3' ends of copy-back defective interfering RNA species: identification of the L gene terminus

Direct sequencing showed that the 5' termini of several defective interfering RNA species, both fusion and copy-back types, were homologous to the 5' terminus of the Sendai virus genome. Size analyses of spontaneously formed terminal duplexes (stems) of three copy-back defective interfering RNA species revealed variable extents of terminal complementarity, ranging from about 155 to 210 nucleotides. Direct sequencing of the 3' terminus of one of these copy-back RNA species demonstrated its complementarity to the 5'-terminal sequence of the virus genome. This copy-back sequence contained, in complementary form, the 5' terminus of the L gene, comprising the same sequence, 3'-AUUCUUUUU-5', that was previously identified at the 5' ends of the five other major Sendai virus genes.

Molecular cloning of the 3'-proximal third of Sendai virus genome

Portions of the Sendai virus genome were randomly cloned by using virion 50S RNA and calf thymus DNA pentanucleotides as primers. The recombinant clones were probed first with radiolabeled products of an in vitro virion RNA polymerase reaction to locate early message clones and then with a probe from the viral genome 3' end to locate the most 3'-proximal clones. Clones were then ordered from the 3' end of the genome and used to construct a genetic map of the 3'-proximal third of the genome by hybrid-selection of mRNAs. We report that the gene order for this region is 3'-NP - P + C - M-5' and that the genetic loci of the viral P and C proteins cannot be separated by these techniques.

Sequence relationships between Kirsten retrovirus genomes and the genomes of other murine retroviruses

RNA sequence relationships between the genomes of the Kirsten murine sarcoma virus (MSV-K) complex, the Kirsten murine leukemia virus (MuLV-K) complex, the Gross murine leukemia virus (MuLV-G), and the Moloney murine leukemia virus (MuLV-M) were investigated. Sedimentation analyses revealed the expected 30 and 34 S RNA subunits in the MSV-K complex and a previously undetected 30 S RNA subunit accompanying the 34 S RNA subunit in the MuLV-K complex. Nucleic acid hybridization data indicated that each Kirsten virus 30 S RNA subunit had about 40% sequence homology with the RNA genome of MuLV-G, although these sequences were only partially homologous between the two 30 S subunits. In contrast, the MuLV-K 34 S RNA subunit had 96% sequence homology with the MuLV-G genome, whereas the MSV-K 34 S RNA subunit displayed only 71% sequence homology with the MuLV-G genome. Similar relationships were indicated by oligonucleotide fingerprinting. The oligonucleotide data, taken with published sequence data on the MuLV-G and MuLV-M genomes, enabled us to construct partial sequence maps of the MuLV-K 34 S RNA subunit and the MSV-K 34 and 30 S RNA subunits. The sequence arrangements indicated that (1) the MuLV-K 34 S RNA subunit is a variant of the MuLV-G genome; (2) the MSV-K 34 S RNA subunit is a recombinant molecule, which maintains the length of its leukemia virus parent; and (3) the MSV-K 30 S RNA subunit may have been generated from the MuLV-K 34 S genome by a two-stage process, culminating in the retention of parental sequences only within the U5 and U3 noncoding segments and within several amino-terminal coding segments. Further examination of published retrovirus genome sequences revealed several strategically situated sets of potential recognition signals for transcription and translation and suggested a model for genetic recombination based on mRNA splicing signals and areas of limited sequence homology. This model may explain how foreign gene elements can be inserted into retrovirus genomes to generate either functional or defective recombinant retroviruses.

In vitro synthesis of the nonstructural C protein of Sendai virus

In vitro translation was used to study the mRNA for the Sendai virus nonstructural C protein. The C protein mRNA was found to be coordinately expressed with the mRNAs for the structural proteins. However, the C protein mRNA appeared to be translated more efficiently in vitro than the other mRNAs. In addition, the 22,000-dalton C protein mRNA cosedimented on sucrose gradients with the 79,000-dalton P protein mRNA. The C protein mRNA thus appears to be much larger than expected.