Sequence of 3,687 nucleotides from the 3' end of Sendai virus genome RNA and the predicted amino acid sequences of viral NP, P and C proteins

Sendai virus NP gene codes for a 524 amino acid NP protein

The complete nucleoprotein (NP) gene sequences of the Sendai virus Fushimi and 6/94 strains were determined. For both viruses an open reading frame of 524 amino acids can be predicted for the NP proteins. By comparing the sequences with others reported in the literature, the 5' noncoding region and the middle third of the coding region were found to be highly conserved. The carboxyl terminal part carries nine amino acid changes and a completely different sequence of the carboxyl terminus with a seven amino acid extension. This carboxyl terminus of the Sendai virus NP protein was confirmed using tryptic peptide sequence analysis.

Gene expression of nonsegmented negative strand RNA viruses

Nonsegmented negative strand RNA viruses comprise major human and animal pathogens in nature. This class of viruses is ubiquitous and infects vertebrates, invertebrates, and plants. Our laboratory has been working on the gene expression of two prototype nonsegmented negative strand RNA viruses, vesicular stomatitis virus (a rhabdovirus) and human parainfluenza virus 3 (a paramyxovirus). An RNA-dependent RNA polymerase (L and P protein) is packaged within the virion which faithfully copies the genome RNA in vitro and in vivo; this enzyme complex, in association with the nucleocapsid protein (N), is also involved in the replication process. In this review, we have presented up-to-date information of the structure and function of the RNA polymerases of these two viruses, the mechanisms of transcription and replication, and the role of host proteins in the life-cycle of the viruses. These detailed studies have led us to a better understanding of the roles of viral and cellular proteins in the viral gene expression.

Sequence analyses of the 3' genome end and NP gene of human parainfluenza type 2 virus: sequence variation of the gene-starting signal and the conserved 3' end

We cloned and determined the nucleotide sequences of cDNAs against nucleocapsid protein (NP) mRNA and the genomic RNA of human parainfluenza type 2 virus (PIV-2). The 3' terminal region of genomic RNA was compared among PIV-2, mumps virus (MuV), Newcastle disease virus (NDV), measles virus (MV), PIV-3, bovine parainfluenza type 3 virus (BPIV-3), Sendai virus (SV), and vesicular stomatitis virus (VSV), and an extensive sequence homology was observed between PIV-2 and MuV. Although no significant sequence relatedness was observed between PIV-2 and other viruses, the terminal four nucleotides were identical in the viruses compared, implying a specific role of these nucleotides on the replication of paramyxoviruses. A primer extension analysis elucidated the major NP mRNA initiation site with the sequence UCUAAGCC, which showed a moderate homology with the gene-starting consensus sequences of other paramyxoviruses. On the other hand, the NP mRNA was terminated at the nucleotide stretch AAAUUCUUUUU, and this sequence was conserved in all the PIV-2 genes, indicating that the oligonucleotides will form a part of the gene attenuation signal of PIV-2. Comparisons of NP protein sequence indicated a possible subgrouping of the paramyxoviruses into two groups, one of which is a group including PIV-2, PIV-4, MuV, and NDV, and another is a group including PIV-3, BPIV-3, and SV. This result supports an idea from our previous studies using polyclonal and monoclonal antibodies. Furthermore, our data indicated that the PIV-2 NP protein sequence was more closely related to MV and CDV than to other parainfluenza viruses, PIV-3 and SV.

Role of mass spectrometry in mapping strain variation and post-translational modifications of viral proteins

Enzymatically derived fragments of the nucleocapsid protein from one strain (V4) of the paramyxovirus, New castle disease virus (NDV), have been aligned with the sequence deduced for a related strain (D26) by gene sequence analysis. This process involved extensive use of fast atom bombardment (FAB) mass spectrometry of unfractionated tryptic digests and fragments separated from tryptic or AspN protease digests by high-performance liquid chromatography (HPLC). Amino acid analysis and stepwise Edman degradation sequence analysis were used to complement FAB mass spectral data or as alternatives where no ions were produced by FAB. The nature of biosynthetic processing and blockage (acetylation) at the N-terminus of the protein were confirmed using collision-induced dissociation. Data obtained by direct analysis of the V4 nucleocapsid protein facilitated mapping of sequence variations within the nucleocapsid protein of the antigenically distinct WA2116 strain of NDV. Most of the WA2116 protein was mapped by FAB mass spectrometric analysis of HPLC fractions, thus amino acid analysis or stepwise sequence analysis were only required where FAB mass spectral data were inconclusive or indicated amino acid variations. This approach to comparison of NDV nucleocapsid proteins is proposed as a general strategy for mapping strain variation and post-translational modifications of viral proteins.

Association of the Sendai virus C protein with nucleocapsids

The subcellular localization of the nonstructural protein C of Sendai virus was investigated by means of indirect immunofluorescence microscopy of Sendai virus-infected cells, using an antiserum specific for C protein. In infected cells, C protein was detected exclusively in the cytoplasm as granular fluorescence, which coincided very well with the distribution of nucleocapsid protein NP and phosphoprotein P, which were also detected with specific antisera. This suggested that these proteins are present together in inclusions, probably forming nucleocapsids. In contrast, when the NP and C proteins were individually expressed in COS cells by transfection with expression plasmids containing cDNA for these proteins, their distribution patterns in the cytoplasm were found to be quite different from each other. Protein-blot analyses of purified virions revealed the presence of a significant amount of the C protein in virions, which indicated that C protein is integrated into virions. Under conditions in which most of the envelope-associated proteins, such as HN, F, and M, were removed from the virions by a detergent, the C protein remained tightly associated with the nucleocapsids--about 40 molecules per nucleocapsid.

RNA editing by G-nucleotide insertion in mumps virus P-gene mRNA transcripts

A guanine nucleotide insertion event has been shown to occur at a specific site within mumps virus P-gene mRNA transcripts. The region of the mRNA containing the site expected to be used for RNA editing and the complementary portion of the genomic RNA were cloned, and their nucleotide sequences were obtained. The genomic RNA was found to possess six C residues at the insertion site, whereas 63% of the P-gene-specific mRNA transcripts were found to have from two to five G residues inserted at this position in the RNA. An unedited mRNA was shown to encode the mumps virus cysteine-rich protein V, and mRNA transcripts containing two and four inserted G residues were translated to yield the mumps virus P and I proteins, respectively.

Sendai virus gene expression in lytically and persistently infected cells

Sendai virus RNA species were quantitated in lytically and persistently infected cultured cells by Northern blot hybridization to region- and strand-specific cloned cDNA probes. Levels of NP, P and M mRNA in lytically infected cells were equally high, but F and HN mRNA were present in about 3-fold, and L mRNA in 30-fold, lower amounts, reflecting transcriptional attenuation especially at the M-F and HN-L gene junction. Two persistently infected cell lines, which release only 1% of the virus particles of lytically infected cells, were shown to contain only 4- to 8-fold-less amounts of each viral mRNA and 2- to 3-fold-less genomic RNA than lytically infected cells. Additionally, transcription was neither defective nor more attenuated as compared to the lytical infection. Taken together the results suggest the existence of an additional regulatory mechanism for the virus release. A cell-associated state of infection therefore seems to be achievable by a relatively weak general reduction of the copy numbers of viral mRNA and genomic RNA.

Molecular analysis of structural protein genes of the Yamagata-1 strain of defective subacute sclerosing panencephalitis virus. I. Nucleotide sequence of the nucleoprotein gene

The complete nucleotide sequence of cloned cDNAs corresponding to the full-length mRNA encoding the NP protein of the Yamagata-1 strain of subacute sclerosing panencephalitis (SSPE) virus was determined. The gene is composed of 1683 nucleotides and contains a single large open reading frame, which is capable of encoding 525 amino acids with a molecular weight of 58,399. Comparison of the nucleotide and predicted amino acid sequences with those of the Edmonston strain of measles virus (MV) showed that the gene and the protein were highly conserved. However, the antigenic sites on the NP protein of the Yamagata-1 strain were found to be changed by an epitope analysis using monoclonal antibodies against the NP protein of MV. Only 1 of 4 monoclonal antibodies reacted with the NP protein of SSPE virus, and the other three antibodies did not. Almost identical changes in nucleotides and amino acids were found to occur in the NP gene of the Yamagata-1 strain when compared with the IP-3-Ca strain of another SSPE virus. In addition, the deduced secondary structure of the NP protein of the IP-3-Ca strain was similar to that of the Yamagata-1 strain, but differed from the MV. These results suggest that the NP proteins of SSPE viruses have a common property that is different from MV.

Nucleotide sequence analyses of the genes encoding the HN, M, NP, P, and L proteins of two host range mutants of Sendai virus

Comparative nucleotide sequence analyses of the genome of Sendai virus (strain Z) and two host range mutants, ts-f1 and F1-R, previously described revealed that the ts defect of ts-f1 can be attributed to two nucleotide exchanges in the NP gene. These exchanges lead to a single amino acid substitution. A single base pair change was found in both the P and L genes of F1-R, but not of ts-f1. Both host range mutants have the two same exchanges in the M gene. These additional mutations are discussed concerning their significance in the pantropic properties of the host range mutants.

From rabies to rabies-related viruses

Antigenic differences between rabies virus strains characterized with monoclonal antibodies presently define at least four serotypes within the Lyssavirus genus of the Rhabdoviridae family: classical rabies virus strains (serotype 1), Lagos bat virus (serotype 2), Mokola virus (serotype 3) and Duvenhage virus (serotype 4). The wide distribution of rabies-related virus strains (serotypes 2, 3 and 4) and above all, the weak protection conferred by rabies vaccines against some of them (principally Mokola virus) necessitates the development of new specific vaccines. We first determined the complete nucleotide sequence of a rabies virus strain of serotype 1 (Pasteur virus) and characterized the structure of the viral genes and their regulatory sequences. We then extended this study to the Mokola virus genome. Five non-overlapping open reading frames were found in both viruses and had similar sizes and positions in both. Similarities were also found in the mRNA start and stop sequences and at the genomic extremities. Comparison of both genomes helps to analyze the basis of the particular antigenicity of these two serotypes. The sequence homology in the region coding for the viral glycoprotein was only 58% between the two viruses, compared with 94% between different rabies virus strains within serotype 1. This comparison, extended to other unsegmented negative strand RNA viruses, gives new insight into the understanding of rhabdoviruses and paramyxoviruses. Furthermore, molecular cloning provides a rationale for the genetic engineering of a future vaccine.

Separate domains of Sendai virus P protein are required for binding to viral nucleocapsids

The role of Sendai virus P protein in viral RNA synthesis involves association with the nucleocapsid template. There is evidence that the carboxyl-terminal region of P protein is responsible for this association (K. W. Ryan and D. W. Kingsbury, 1988, Virology 167, 106-112). To define the P protein sequences involved more precisely, deletions were generated in a cDNA clone of the P gene. Proteins synthesized in vitro from these altered P genes were mixed with extracts from infected cells to determine if they could attach to nucleocapsids. Under conditions where full-size P protein was able to bind, a protein comprising the 95 carboxyl-terminal residues of P protein (Sendai virus X protein) did not bind. This indicated that other P protein residues were required, in addition to the 95 residues at the carboxyl-terminal end. To locate these other residues, P genes were constructed with overlapping deletions of sequences encoding the carboxyl-terminal 40% of the protein. Analysis of these deleted proteins revealed that the necessary residues were in two separate binding domains, amino acids 345 to 412 and 479 to 568 (the carboxyl-terminus). Deletion of the 66 residues between these regions did not affect attachment. Therefore, the formation of a functional binding site requires residues within two separate regions of P protein.

Sequencing analyses and comparison of parainfluenza virus type 4A and 4B NP protein genes

The nucleotide sequences of the cDNA copies of the mRNA coding for the nucleocapsid proteins (NPs) of human parainfluenza viruses type 4A (PIV-4A) and type 4B (PIV-4B) were determined. The copy of PIV-4A NP mRNA contained 1885 nucleotides encoding a protein with a calculated molecular weight of 62,561. The same number of amino acids with a similar molecular weight (62,425) were predicted for the PIV-4B NP protein. Comparisons on the nucleotide sequence and the amino acid sequence of NP protein between these two subtypes revealed extensive homologies in the nucleotide sequence (87%) and in the amino acid sequence (93%). Furthermore, a conserved region with about 100 amino acids was observed between PIV-4s and other paramyxoviruses, Newcastle disease virus (NDV), Sendai virus, mumps virus (MuV), PIV-3, BPIV-3, measles virus (MV), and canine distemper virus (CDV), indicating a common ancestor for these nine viruses. Our data also indicated that the PIV-4 NP proteins were more closely related to MuV and NDV than to other parainfluenza viruses, PIV-3, BPIV-3, and Sendai virus. Interestingly, the NP protein homology between PIV-4s and the morbillivirus group, MV and CDV, was slightly higher than that between PIV-4s and the parainfluenza viruses, PIV-3, BPIV-3, and Sendai virus.

Editing of the Sendai virus P/C mRNA by G insertion occurs during mRNA synthesis via a virus-encoded activity

Two forms of the Sendai virus P/C mRNA have been predicted: one an exact copy of the viral genome, and the other with a single G insertion within a run of three G's. We directly cloned the mRNA or portions of it containing the insertion site and screened the resulting colonies with oligonucleotides that could distinguish the presence of three or four G's at this position. We found that 31% of the mRNAs did in fact contain the predicted insertion, whereas the viral genomes contained no heterogeneity at this position. A smaller fraction (7%) of the mRNA contained two to eight G's inserted at this position. The insertions also took place during RNA synthesis in vitro with purified virions but were not detected when the mRNA was expressed in vivo via a vaccinia virus recombinant. When the Sendai virus- and vaccinia virus-derived P/C mRNAs were coexpressed in the same cells under conditions in which each could be distinguished, those from the Sendai genome were altered as before, but those from the vaccinia virus genome remained unaltered. The activity that alters the mRNA is therefore likely to be coded for by the virus and cannot function in trans.

Leader sequence distinguishes between translatable and encapsidated measles virus RNAs

The 3'-terminal 55 nucleotides of the negative-strand measles virus RNA genome called the leader sequence is not transcribed into a detectable distinct RNA product. Most of the monocistronic N and bicistronic N-P RNAs lack the leader sequence. However, a subpopulation of the N and N-P RNAs and all of the antigenomes possess this leader. Here, we show that leader-containing subgenomic RNAs are functionally distinct from their leaderless counterparts. In measles virus-infected cells, leaderless monocistronic N and bicistronic N-P RNAs were associated with polysomes. By contrast, leader-containing N and N-P RNAs were found exclusively in nonpolysomal ribonucleoprotein complexes that were resistant to RNase and had a buoyant density of 1.30 g/ml, the same as that of antigenomic ribonucleoprotein complexes. Both antigenomic and subgenomic ribonucleoprotein complexes were specifically immunoprecipitated by antiserum against the N protein, and leaderless RNAs were not found in these complexes. These findings suggest that measles virus distinguishes RNAs destined for encapsidation or translation by the presence or absence of a leader sequence.

Budding efficiency of Sendai virus nucleocapsids: influence of size and ends of the RNA

The budding efficiency of Sendai virus antigenomes, as well as of defective interfering (DI) nucleocapsids of the deletion and copy-back types, was compared to that of the viral genome during infections of baby hamster kidney (BHK) cells. The antigenomes were shown to bud into virus particles as efficiently as the genomes, arguing for the irrelevance of the nucleocapsid-RNA ends in regulating the efficiency of budding. The DI nucleocapsids, however, were restricted in their budding by factors inversely proportional to their size, arguing for an effect of nucleocapsid size in this process. This restriction in budding, however, appeared to be only expressed under conditions of very efficient DI-RNA replication.

Replication of the genome RNAs of defective interfering particles of vesicular stomatitis and Sendai viruses using heterologous viral proteins

We have tested the ability of heterologous viral proteins to support the in vivo and in vitro replication of the RNA of defective interfering (DI) particles of two serotypes of VSV and of Sendai virus. In all the combinations of heterologous coinfections in vivo, DI particle replication was observed only in the coinfection with the VSV-Indiana DI particle and wild-type VSV-New Jersey. By quantitating RNA synthesis in reconstitution experiments we showed that with DI nucleocapsids isolated from infected cells, however, the soluble protein fraction from heterologous wild-type virus-infected cells could substitute in vitro to varying degrees for the homologous proteins in the elongation reaction of RNA replication and encapsidation. In these cases successful replication was confirmed by demonstrating the specific association of the heterologous N protein with the product nucleocapsid RNA. The initiation step, that is, the initial binding of the nucleocapsid protein to the leader RNA, in contrast, requires the homologous protein, since heterologous viral proteins could not support RNA replication and encapsidation from purified DI particles.

Rescue of Sendai virus from viral ribonucleoprotein-transfected cells by infection with recombinant vaccinia viruses carrying Sendai virus L and P/C genes

The Sendai virus ribonucleoprotein (RNP) showed only very low plaque-forming titers upon transfection and the virus yields after one-step growth were quite limited. We tried to enhance the Sendai virus yield by supplying the viral L and P/C gene products through vaccinia vectors. A combination of the recombinant vaccinia viruses carrying the L gene (Vac-HL) and the P/C gene (Vac-HPC), both of which were driven by the promoter of the vaccinia virus 7.5K protein gene, enhanced the yield only a little whereas another combination of Vac-HLd7.5, the L gene insert of which was driven by the promoter of the vaccinia virus thymidine kinase gene in place of the 7.5K promoter, and Vac-HPC greatly enhanced the Sendai virus yield. This seemed to correlate with the fact that the Vac-HL interfered with Sendai virus growth markedly while the Vac-HLd7.5 did not. These results strongly suggest that the L and P/C gene products act in cooperation as the RNA polymerase, and overproduction of the L protein is inhibitory for Sendai virus growth. This system seems to be of value as a tool for analyzing the functions of L and P/C genes of Sendai virus.

Virus-specific polypeptides of human parainfluenza virus type 4 and their synthesis in infected cells

We have studied the structural components of human parainfluenza virus type 4A (PIV-4A) and identified some virus-specific polypeptides by immunoprecipitation with polyclonal and monoclonal antibodies followed by one- or two-dimensional SDS-PAGE. HN polypeptides existed as monomer, disulfide-linked dimer, and disulfide-linked larger oligomer in cells infected with PIV-4A. Interestingly, the nonreduced NP, the nonreduced fusion, and the reduced F1 proteins migrated as doublets. Two F1 polypeptides were derived from different F1 + 2 proteins which migrated separately under nonreducing condition. In Vero cells infected with two strains of PIV-4A, two lower-molecular-weight proteins related to NP were detected. Oligopeptide patterns of the lower-molecular-weight protein were similar to those of NP protein synthesized in primary monkey kidney cells. The NP-related low-molecular-weight protein(s) was immunoprecipitated by 1 of 11 monoclonal antibodies against mumps virus NP protein. The MAb also reacted with NP proteins of PIV-2 and SV5. Thus, the epitope recognized by the MAb was common among PIV-2, PIV-4, mumps virus, and SV5, suggesting that the epitope might have an important biological function. However, the MAb did not react with the intact NP protein from cells infected with PIV-4, indicating that the epitope of PIV-4A was presented only when NP was cleaved. Phosphorylation was demonstrated for NP and P proteins.

Measles virus synthesizes both leaderless and leader-containing polyadenylated RNAs in vivo

The minus-sense RNA genome of measles virus serves as a template for synthesizing plus-sense RNAs of genomic length (antigenomes) and subgenomic length [poly(A)+ RNAs]. To elucidate how these different species are produced in vivo, RNA synthesized from the 3'-proximal N gene was characterized by Northern RNA blot and RNase protection analyses. The results showed that measles virus produced three size classes of plus-sense N-containing RNA species corresponding to monocistronic N RNA, bicistronic NP RNA, and antigenomes. Unlike vesicular stomatitis virus, measles virus does not produce a detectable free plus-sense leader RNA. Instead, although antigenomes invariably contain a leader sequence, monocistronic and bicistronic poly(A)+ N-containing RNAs are synthesized either without or with a leader sequence. We cloned and characterized a full-length cDNA representing a product of the latter type of synthesis. mRNAs and antigenomes appeared sequentially and in parallel with leaderless and leader-containing RNAs. These various RNA species accumulated concurrently throughout infection. However, cycloheximide preferentially inhibited accumulation of antigenomes and leader-containing RNA but not leaderless and subgenomic RNAs late in infection, suggesting that synthesis of the former RNA species requires a late protein function or a continuous supply of structural proteins or both. These results reveal a previously undescribed mechanism for RNA synthesis in measles virus.

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.

Sequence analysis of the mumps virus mRNA encoding the P protein

The nucleotide sequence of the mumps virus phospho- or polymerase-associated (P) protein mRNA has been determined by sequencing a full-length cDNA clone and confirmed by partially sequencing the mRNA and the genome. The mRNA contains 1311 nucleotides excluding the poly(A) and encodes a protein of 390 amino acids with a calculated molecular weight of 41,574. Three small polypeptides were seen in in vitro translation of viral mRNA and hybrid-selected P mRNA, possibly representing internal initiation in the same reading frame of the P protein. A second overlapping reading frame is predicted from the sequence which has a capacity to code for two polypeptides of 56 and 34 amino acids, respectively. Whether these two polypeptides are expressed in infected cells is not known. Comparison of the P protein sequence with that of Sendai virus, measles virus, parainfluenza virus type 3, and canine distemper virus (CDV) showed no distinct homology but comparison with the P protein of Newcastle disease virus (NDV) showed 25.6% homology.

Expression of five proteins from the Sendai virus P/C mRNA in infected cells

The polycistronic P/C mRNA of Sendai virus is translated under cell-free conditions into five proteins (P, C', C, Y1, and Y2) from overlapping reading frames. In this study, we showed that in addition to the P, C', and C proteins, Y1 and Y2 were expressed by six different Sendai virus strains in infected cells. The Y proteins exhibited strain-specific variation in their gel mobility which corresponds to the variation seen in the cognate C proteins. While the relative levels of the P, C', and C proteins were consistent among various cell lines, the levels of Y1 and Y2 proteins varied among the cell lines used for viral infection.

Carboxyl-terminal region of Sendai virus P protein is required for binding to viral nucleocapsids

The Sendai virus P protein is a component of the viral nucleocapsid, where it participates in RNA synthesis. To identify domains of the protein involved in nucleocapsid recognition, deleted P protein molecules were generated from a cDNA clone of its gene. In vitro transcription of the complete gene and translation of the transcript generated a protein with electrophoretic mobility and immunoreactivity indistinguishable from those of authentic P protein. The in vitro product bound specifically to nucleocapsids when mixed with extracts from infected cells. However, a product lacking only 30 carboxyl-terminal amino acid residues (5% of the molecule) did not bind. Residues within a 195 amino acid region, adjacent to and overlapping by one amino acid with the carboxyl-terminal 30 residues, were also required for binding. No other protein region was required. Therefore, the 224-residue region which includes the carboxyl terminus appears to contain the nucleocapsid attachment site, and the 30 terminal residues either form part of the site or are required to maintain an active conformation.

Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5

The "P" gene of the paramyxovirus SV5 encodes two known proteins, P (Mr approximately equal to 44,000) and V (Mr approximately equal to 24,000). The complete nucleotide sequence of the "P" gene has been obtained and is found to contain two open reading frames, neither of which is large enough to encode the P protein. We have shown that the P and V proteins are translated from two mRNAs that differ by the presence of two nontemplated G residues in the P mRNA. These two additional nucleotides convert the two open reading frames to one of 392 amino acids. The P and V proteins are amino coterminal and have 164 amino acids in common. The unique C terminus of V consists of a cysteine-rich region that resembles a cysteine-rich metal binding domain. An open reading frame that contains this cysteine-rich region exists in all other paramyxovirus "P" gene sequences examined, which suggests that it may have important biological significance.

Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses

We have now completed the rabies genome structure by the cloning and the sequencing of the entire L gene and the 5' untranscribed region. The L gene encodes a single open reading frame 2142 amino acids in length (244,206 Da) that corresponds to the viral RNA-dependent RNA polymerase. In contrast with other isofunctional proteins, the rabies polymerase exhibits a high degree of homology with the vesicular stomatitis virus polymerase, and a lesser degree, although significant, with those of Sendai virus and Newcastle disease virus, which suggests a differential evolution of the different cistrons. We have observed several strongly conserved stretches which may designate the independent functional domains of this multifunctional protein. In addition to the conservation of related transcription signals (N. Tordo et al. (1986) Proc. Natl. Acad. Sci. USA 83, 3914-3918.), this highlights the striking selective pressure on elements involved in transcription and replication mechanisms, and provides further evidence for a common ancestry of Rhabdoviridae and Paramyxoviridae families. The terminal complementarity observed in the rabies genome suggests the conservation of important genomic signals.

Molecular cloning and complete nucleotide sequence of the genome of Japanese encephalitis virus Beijing-1 strain

The genomic RNA of the Japanese encephalitis virus (JEV) Beijing-1 strain was reversely transcribed and the synthesized cDNA was molecularly cloned. Six continuous cDNA clones that cover the entire virus genome were established and sequenced to determine the complete nucleotide sequence of the JEV RNA. The precise genomic size was estimated as 10,965 bases long. With flanking 95 bases at the 5' and 583 bases at the 3' non-coding regions, one long open reading frame (ORF) was revealed encoding a virus polyprotein with 3,429 amino acid residues. Because of sequence homologies observed between JEV and other flaviviruses, the genome organization of JEV appears to be identical with other flaviviruses. Genetic variation detected among flavivirus genomes is consistent with the established serological relatedness between JEV and other members of flaviviruses. The secondary structure of the JEV genome is deduced and discussed concerning its involvement in genome replication.

Sequence variability and function of measles virus 3' and 5' ends and intercistronic regions

Sequences critical for the activity of the measles virus (MV) RNA polymerase in transcription and replication were analyzed using a MV genomic cDNA library containing overlapping clones encompassing the entire MV genome. Clones corresponding to the 3' and 5' ends of the MV genome were identified and sequenced, and these sequences were confirmed by primer extension experiments. Neither (+) nor (-) strand leader RNAs were detected in MV-infected cell extracts, using high specific activity riboprobes made form these clones. Clones representing each of the MV gene boundaries were also sequenced, and variations including point mutations, insertions, and deletions were noted. Together with the sequence of the MV L gene region, this report completes the sequence determination of the MV genome.

Structure, function, and intracellular processing of paramyxovirus membrane proteins

Paramyxoviruses are a fascinating group of viruses with diverse hosts and disease manifestations. They are valuable systems for studying viral pathogenesis, molecular mechanisms of negative strand viral replication, and glycoprotein structure and function. In the past few years this group of viruses has received increased attention and as a result there is a wealth of new information. For example, most of the genes of many paramyxoviruses have been cloned and sequenced. The recent availability of sequence information from a number of paramyxoviruses now allows the direct comparison of the amino acid sequence and determinants of secondary structure of analogous genes across the family of viruses. Such comparisons are revealing for two reasons. First, results provide clues to the evolution of these viruses. Second, and more importantly, comparisons of analogous genes may point to sequences and structural determinants that are central to the function of the individual proteins. Below is a comparison of five of the paramyxovirus genes with a discussion of the implications of common structural determinants for function, intracellular processing, and evolutionary origin. The focus is on the paramyxovirus membrane proteins, although other proteins are discussed briefly.

Purification of the Sendai virus nonstructural C protein expressed in E. coli, and preparation of antiserum against C protein

An expression plasmid, ptac-C, was constructed by inserting the cDNA of the coding region of the Sendai virus nonstructural C protein downstream of the tac promoter of E. coli expression plasmid ptac12-Bam. A new protein produced in E. coli after induction was purified to near homogeneity. The purified protein was found to be identical with the C protein predicted from the C gene cDNA in molecular weight, isoelectric point, amino acid composition, and the amino acid sequence at the N-terminal of the protein as well as those of several fragments obtained on V8 protease digestion. Antiserum raised against the purified protein specifically reacted with the C protein in infected cells. Using this antiserum, the localization of the C protein in infected cells was examined by immunofluorescence, which revealed that it appeared in the cytoplasm but not in nuclei.

Encapsidation of Sendai virus genome RNAs by purified NP protein during in vitro replication

The ability of the Sendai virus major nucleocapsid protein, NP, to support the in vitro synthesis and encapsidation of viral genome RNA during Sendai virus RNA replication was studied. NP protein was purified from viral nucleocapsids isolated from Sendai virus-infected BHK cells and shown to be a soluble monomer under the reaction conditions used for RNA synthesis. The purified NP protein alone was necessary and sufficient for in vitro genome RNA synthesis and encapsidation from preinitiated intracellular Sendai virus defective interfering particle (DI-H) nucleocapsid templates. The amount of DI-H RNA replication increased linearly with the addition of increasing amounts of NP protein. With purified detergent-disrupted DI-H virions as the template, however, there was no genome RNA synthesis in either the absence or presence of the NP protein. Furthermore, addition of the soluble protein fraction of uninfected cells alone or in the presence of purified NP protein also did not support DI-H genome RNA synthesis from purified DI-H. Another viral component in addition to the NP protein appears to be required for the initiation of encapsidation, since the soluble protein fraction of infected but not uninfected cells did support DI-H genome replication from purified DI-H.

Differences in bovine parainfluenza 3 virus variants studied by sequencing of the genes of viral envelope proteins

By determining gene nucleotide sequences we compared the primary structures of the membrane (M), fusion (F), and hemagglutinin-neuraminidase (HN) proteins of bovine parainfluenza 3 virus strains, M, SC, and MR which are substrains derived from a wild strain YN. The M and SC viruses are indistinguishable in having very weak hemagglutination (HA) and neuraminidase (NA) activities, but M virus' syncytium-inducing (SI) activity is considerably higher than that of the SC virus. However, the results showed that the amino acid sequence of the F protein was identical in M and SC viruses, demonstrating that M virus' high SI activity was not due to alteration of its F protein. Two differences in M and SC viruses' other proteins then seemed to be important, although their significance in the SI activity is not clear at present; the first being the 70th amino acid residue of the M protein, which was Asp in the M virus and Gly in the SC virus, and the other being the 539th residue of the HN protein, which was Tyr in the M virus and His in the SC virus. The nucleocapsid proteins of both M and SC viruses were identical. The MR virus, which is a variant derived from the M virus and has high HA and NA activities but very weak SI activity, was different from the M virus at only one site throughout the M, F, and HN proteins; the 193rd amino acid residue of the HN protein was Leu in the MR virus and Phe in the M virus. This result strongly suggested that the substitution of Leu with Phe at this particular site was closely linked to the drastic reduction in both HA and NA activities.

Viral RNA polymerases

Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.

Nucleotide sequence of the hemagglutinin-neuraminidase gene of Newcastle disease virus avirulent strain D26: evidence for a longer coding region with a carboxyl terminal extension as compared to virulent strains

The nucleotide sequence of DNA clones complementary to the genomic RNA of an extremely avirulent strain D26 of Newcastle disease virus was analyzed, and the sequence of 2102 nucleotides directly following F gene reported previously (Sato et al., 1987, Virus Res. 7, 241-255), and corresponding to HN0 gene was determined. A long open reading frame coding for the HN0 peptide of 616 amino acid residues was found in this sequence. It was flanked by the consensus sequences N1 and N2 (Ishida et al., 1986, Nucleic Acids Res. 14, 6551-6564), and the former was shown by the primer extension method to serve as the transcriptional initiation site. The deduced amino acid sequence of the HN0 peptide was highly homologous to that of the HN peptides of strains Beaudette C and B1, but had a carboxyl terminal extension of 39 amino acid residues with a potential glycosylation site in it. The terminal extension is likely to be excised during the processing, and this is consistent with the observation that unglycosylated HN0 is larger in size than unglycosylated HN. A microheterogeneity among the cDNA clones in the nucleotide sequence was also noted which may be relevant to the synthesis of a small amount of an HN-sized peptide in strain D26-infected cells.

Nucleotide sequence analysis of the L gene of Newcastle disease virus: homologies with Sendai and vesicular stomatitis viruses

The nucleotide sequence of the L gene of the Beaudette C strain of Newcastle disease virus (NDV) has been determined. The L gene is 6704 nucleotides long and encodes a protein of 2204 amino acids with a calculated molecular weight of 248822. Mung bean nuclease mapping of the 5' terminus of the L gene mRNA indicates that the transcription of the L gene is initiated 11 nucleotides upstream of the translational start site. Comparison with the amino acid sequences of the L genes of Sendai virus and vesicular stomatitis virus (VSV) suggests that there are several regions of homology between the sequences. These data provide further evidence for an evolutionary relationship between the Paramyxoviridae and the Rhabdoviridae. A non-coding sequence of 46 nucleotides downstream of the presumed polyadenylation site of the L gene may be part of a negative strand leader RNA.

Molecular cloning and nucleotide sequence of P, M and F genes of Newcastle disease virus avirulent strain D26

Molecular cloning of most if not all of the genome of an avirulent strain D26 of Newcastle disease virus (NDV) was carried out. cDNA clones were aligned by mutual hybridization and restriction map analysis. The nucleotide sequence of 3672 bases which completed the partial sequence of P gene reported in our previous paper (Ishida, N. et al., 1986, Nucleic Acids Res. 14, 6551-6564), and also covered M and F genes, was determined. Each gene contained one long open reading frame which could code for polypeptides of 395, 364, and 553 amino acid residues, respectively. The deduced amino acid sequences of P and M gene products showed little homology to those of other paramyxoviruses. In contrast, comparison of the amino acid sequence of the F gene product revealed highly conserved regions including the amino terminal sequence of the F1 portion following the putative processing site. There was only one basic amino acid residue at the putative processing site, which would explain the low virulence of this strain.

Nucleotide sequence of the bovine parainfluenza 3 virus genome: its 3' end and the genes of NP, P, C and M proteins

We present the nucleotide sequence of bovine parainfluenza 3 virus (BPIV3) genome from its 3' end to the opening region of the F gene, through the NP, P plus C, and M genes. Comparison of the sequence with those reported for other paramyxoviruses indicated that BPIV3 was most similar to human parainfluenza 3 virus (HPIV3), and also very similar to Sendai virus in the structural make-up of its genome and the amino acid sequences of its gene products, suggesting that these three viruses constitute a paramyxovirus subgroup from which Newcastle disease and measles viruses are separable. In BPIV3 and Sendai virus, the NP and M proteins, the main structural elements, were more highly conserved than the functionally important P and C proteins. This tendency was also observed even in BPIV3 and HPIV3. Virus-specific amino acid sequences of the NP and M proteins were found at the carboxyl and amino terminal regions, respectively. BPIV3 M mRNA was found to have aberrations in its poly A attachment site.

Interferon induction by transfection of Sendai virus C gene cDNA

To elucidate the mechanism of interferon (IFN) induction on virus infection, we constructed two types of plasmids by inserting a part of the cDNA of the Sendai virus into a simian virus 40-derived expression vector (pSV2-0). One, pSV2-PC, contained the P + C gene, which codes for the P and C proteins in overlapping reading frames, and the other, pSV2-C, contained only the C gene. After transfecting the plasmids into mammalian cells, we determined the IFN activity in the culture medium. We found that the level obtained with pSV2-PC was significantly positive but very low, whereas that obtained with pSV2-C was as high as or even higher than that observed in the culture medium after Sendai virus infection. By cleaving pSV2-C between the simian virus 40 promotor and the C gene or by inserting a stop codon within the C gene [pSV2-C(stop)], induction of IFN was greatly diminished. In Northern blot analyses of the transcripts obtained from the cells transfected with the plasmids with cDNA to the P + C gene as a probe, the transcript having the expected size was detected with both pSV2-C and pSV2-C(stop), whereas none was detected with cleaved pSV2-C or pSV2-0. The results indicate that both transcription and translation of the C gene seem to be required for IFN induction after Sendai virus infection.

Molecular cloning and sequence analysis of the human parainfluenza 3 virus mRNA encoding the P and C proteins

The sequence of the mRNA encoding the phosphoprotein (P protein) of the human parainfluenza virus 3 (PF3) was determined by molecular cloning. In other Parmyxoviridae the P protein mRNA is functionally bicistronic and encodes an additional smaller nonstructural protein termed C. In this report three open reading frames (ORF) are described. These consist of a single long ORF encoding the P protein, and two shorter ORFs encoding the structural Vp18 protein (analogous to the Sendai C protein) and a putative polypeptide termed D protein. The encoded phosphoprotein consists of 603 amino acids and has a predicted molecular weight of 67,683. The C protein consists of 199 amino acids and has a predicted molecular weight of 23,288. The D protein consists of 140 amino acids and has a predicted molecular weight of 16,270. Although the D protein has not yet been demonstrated in vivo its synthesis could be demonstrated in vitro using a rabbit reticulocyte lysate system. Thus it appears that unlike the other paramyxoviruses, the PF3 P protein mRNA may be functionally tricistronic.

Localization and characterization of Sendai virus nonstructural C and C' proteins by antibodies against synthetic peptides

Antibodies were raised in rabbits against two synthetic peptides, each 30 residues in length, one corresponding to the predicted common carboxyl termini of the nonstructural C and C' proteins of Sendai virus and the other to the unique amino terminus of the larger C protein. Each peptide was inoculated as a covalent complex with tetanus toxoid or in uncomplexed form. Only antibodies to the free carboxyl-terminal peptide precipitated both C and C' proteins made by in vitro translation of viral mRNA and reacted with the C protein from infected cells. These results confirm that the C and C' proteins are carboxyl-coterminal. Contrasting with the reported colocalization of intracellular measles virus C proteins with nucleocapsid inclusions, immunofluorescence studies revealed that Sendai virus C proteins were uniformly distributed in the cytoplasm whereas the viral P protein was present in inclusions that were mainly perinuclear. Since almost all P protein molecules are associated with viral nucleocapsids, these observations suggested that Sendai virus C protein molecules may be both nucleocapsid-associated and free in the cytoplasm. This interpretation was supported when the C and C' proteins were found in both nucleocapsid and free protein fractions of cell lysates. Anti-C antibodies did not inhibit viral RNA synthesis when added to an extract of infected cells. This result was consistent with the conclusion that the C proteins have no direct role in viral transcription, since virions lack C proteins but are transcriptionally active. Therefore, the functions of the C proteins remain undefined.