Nucleotide sequence of a Sendai virus genome region covering the entire M gene and the 3' proximal 1013 nucleotides of the F gene

Simultaneous mutation of G275A and P276A in the matrix protein of Newcastle disease virus decreases virus replication and budding

The matrix (M) protein of Newcastle disease virus (NDV) is a highly conserved hydrophobic viral protein. In some paramyxoviruses (measles virus and Sendai virus), the paired glycine (G) near the C terminus of the M protein may form a turn that mediates the specific interaction with the cell membrane. Similar amino acids (glycine-proline [GP], at position 275-276) exist in the M protein of NDV. However, the role of these residues in the replication and pathogenicity of NDV is unknown. In this study, recombinant NDV with the sequence GP/AA or LGP/GGL in the M protein was generated to investigate the role of this conserved sequence. Budding experiments on the mutant viruses revealed that the GP/AA mutation reduced virus budding and virus replication in DF-1 cells; biological characterization revealed attenuated virulence and pathogenicity in chickens, indicating that the GP sequence plays a critical role in the life cycle of the virus.

Sendai virus, the mouse parainfluenza type 1: a longstanding pathogen that remains up-to-date

Biologically speaking, Sendai virus (SeV), the murine parainfluenza virus type 1, is perceived as a common respiratory pathogen that is endemic in many rodent colonies throughout the world. Currently it is believed that SeV is the leading cause of pneumonia in mice and together with the mouse hepatitis viruses, is the most prevalent and important of the naturally occurring infections of mice. The scientific community also considers SeV as the archetype organism of the Paramyxoviridae family because most of the basic biochemical, molecular and biologic properties of the whole family were derived from its own characteristics. Recently, scientific interest for this old pathogen has re-emerged, this time because of its potential value as a vector for gene transfer. This review aimed at drawing an exhaustive picture of this multifaceted pathogen.

Structure-function analysis of the Sendai virus F and HN cytoplasmic domain: different role for the two proteins in the production of virus particle

The role of the cytoplasmic domain (cytd) of the Sendai virus HN and F glycoproteins in the process of virus assembly and budding are evaluated. Recombinant Sendai virus (rSeV) mutants are generated carrying modifications in the cytd of each of the glycoprotein separately. The modifications include increasing truncations and/or amino acid sequence substitutions. Following steady-state (35)[S]methionine/cysteine labeling of the infected cells, the virus particle production is estimated. The radioactive virions in the cell supernatants are measured relative to the extent of the infection, assessed by the intracellular N protein signal. For both the F and HN cytd truncation mutants, the largest cytd deletions lead to a 20- to 50-fold reduction in virion production. This reduction cannot be explained by a reduction of the cell surface expression of the glycoproteins. For the F protein mutants, the virions produced in reduced amount always exhibit a normal F protein composition. It is then concluded that a threshold level of F is required for SeV assembly and budding. The rate or the efficiency with which this threshold is reached up appears to depend on the nature of the F cytd. A minimal cytd length is required as well as a specific sequence. The analysis of HN protein mutants brings to light an apparent paradox. The larger cytd truncations result in significant reduction of virion production. On the other hand, a normal virion production can take place with an underrepresentation of or, even, an undetectable HN in the particles. The HN uptake in virion is confirmed to depend on the previously proposed cytd SYWST signal (T. Takimoto, T. Bousse, E. C. Coronel, R. A Scroggs, and A. Portner. 1998. J. Virol. 72, 9747-9754.).

Large quantity production with extreme convenience of human SDF-1alpha and SDF-1beta by a Sendai virus vector

We describe a robust expression of human stromal cell-derived factor-1alpha (SDF-1alpha) and SDF-1beta, the members of CXC-chemokine family, with a novel vector system based upon Sendai virus, a non-segmented negative strand RNA virus. Recombinant SDF-1alpha and SDF-1beta were detected as a major protein species in culture supernatants, reached as high as 10 microg/ ml. This remarkable enrichment of the products allowed us to use even the crude supernatants as the source for biological and antiviral assays without further concentration nor purification and will thus greatly facilitate to screen their genetically engineered derivatives.

Phosphorylation of the Sendai virus M protein is not essential for virus replication either in vitro or in vivo

A large proportion of intracellular Sendai virus (SeV) M proteins is phosphorylated, but in mature virions the M protein is not phosphorylated or dephosphorylated. Phosphorylated M protein in cells is bound to the cytoskeletal components more firmly than unphosphorylated M protein. Thus it has been hypothesized that M protein phosphorylation plays an important role in the virus life cycle, especially in the step of maturation. Here, a transient expression-mutation experiment of the M gene demonstrated that a change of the Ser residue at the 70th position from the N-terminus to Ala (S70A) totally abolished M protein phosphorylation, strongly suggesting that this residue is phosphorylated. The mutated M gene was then placed in the corresponding region in the cDNA plasmid which generates a full-length antigenome SeV RNA, and a mutant SeV M-S70A was successfully recovered from the cDNA. This mutant virus was indeed defective in M protein phosphorylation but did not differ at all from the wild-type SeV recovered from the parental cDNA either in the replication kinetics and plaque morphology in cultured cells or in in vivo replication and pathogenicity for mice. We thus concluded that no phosphorylation of the M protein was required for SeV replication either in vitro or in vivo.

The influence of imperfectly paired helices I and III on the catalytic activity of hammerhead ribozymes

Several catalytic antisense RNAs directed against different regions of the genomic or antigenomic RNA of Sendai virus were constructed. All RNAs contained the same catalytic domain based on hammerhead ribozymes but some had deletions or mutations resulting in imperfect helices I and III. Pre-annealed substrate/ribozyme complexes were used to determine the rates of the cleavage process for the different ribozymes under single-turnover conditions. It was found that the sequence context surrounding the cleavable motif influenced the cleavage efficiencies. Deletions or mutations of nucleotides 2.1 or 15.1 and 15.2 according to the numbering system for hammerhead ribozymes of Hertel et al. destroyed catalytic activity. Deletions of nucleotide 2.2 or additional nucleotides in the helix I-forming region of the ribozyme did not destruct, but only reduced the cleavage efficiencies. Similar results were observed for a deletion of nucleotide 15.3. Simultaneous deletions within helices I and III resulted in alternative cleavage sites. The potential consequences for the specificity of the ribozyme reaction are discussed.

Long-term replication of Sendai virus defective interfering particle nucleocapsids in stable helper cell lines

An essential prerequisite for generating a stable helper cell line, which constitutively expresses functional Sendai virus RNA-dependent RNA polymerase, is the expression of all three Sendai virus nucleocapsid (NC) proteins, NP, P, and L, simulataneously. Generating a stable helper cell line was accomplished by cotransfecting cell line 293 with all three corresponding viral genes under the control of cytomegalovirus promoter-enhancer elements. Cotransfection with a dominant selectable marker enabled selection for stably transfected cells. The levels of the expressed P and NP proteins reached up to 1/10th and 1/20th of the protein levels in Sendai virus-infected cells, respectively. The Sendai virus polymerase activity of the coexpressed proteins was demonstrated by an in vivo polymerase assay. The cell clone H29 gave the strongest signal and produced DI genomes continuously for at least 3 months. This result demonstrates that it is possible to stably express adequate levels of all three viral NC proteins to form Sendai virus polymerase activity, thereby performing the replication and encapsidation of viral RNA, essential prerequisites for a helper cell line to be competent in producing recombinant viruses.

A field isolate of Sendai virus: its high virulence to mice and genetic divergence form prototype strains

A field isolate of Sendai virus, the Hamamatsu strain, was far more virulent in mice than the prototype Z strain. The Hamamatsu strain replicated more efficiently in the mouse lung than the Z strain, causing deteriorating lung lesions. Nucleotide sequence analysis of the HN, F and M genes revealed that the Hamamatsu strain was divergent from the prototype Z, Harris and Fushimi strains.

Host cell proteases controlling virus pathogenicity

The majority of viral glycoproteins that undergo post-translational proteolysis are cleaved by ubiquitous intracellular proteases; however, a minority are cleaved by secreted proteases available only in a few host systems. The interplay of viral glycoproteins and cellular proteases may have a pivotal role in the spread of infection, host range and pathogenicity.

Sequence characterization and expression of the matrix protein gene of human parainfluenza virus type 1

The nucleotide sequence of the M gene of human parainfluenza virus type 1 (hPIV1) was determined from genomic RNA and cDNA copies of the entire gene. The M gene contained 1173 nucleotides. It had one large open reading frame capable of encoding a protein of 348 amino acids (M(r) = 38,404). The predicted amino acid sequence of the hPIV1 M protein is highly basic (+20 at neutral pH). A pGEM-1 expression vector containing the M gene was used for cell-free transcription and translation. The resultant protein was confirmed to be M by electrophoretic mobility and immunoprecipitation. Among other paramyxoviridae the hPIV1 M amino acid sequence was most closely related to the Sendai virus M sequence (87% identity). The pattern of M gene relatedness observed from the alignment of 16 paramyxoviridae M protein amino acid sequences was not predicted by the viruses' taxonomic classification.

Rapid sequencing of the Sendai virus 6.8 kb large (L) gene through primer walking with an automated DNA sequencer

The determination of the complete DNA sequence of the large (L) polymerase gene of Sendai virus strain Fushimi was used to explore the potential and feasibility of primer walking with fluorescent dye-labelled dideoxynucleotide terminators on an automated ABI DNA sequencer. The rapid identification of the complete sequence demonstrated that this approach is a time- and cost-saving alternative to classical sequencing techniques. Analysis of the data revealed that the L gene of Sendai virus strain Fushimi consists of exactly 6800 nucleotides and that the deduced amino acid sequence identifies a single open reading frame encoding a protein of 252.876 kDa. In contrast to Sendai virus strain Enders, the L mRNA of strain Fushimi is monocistronic. The comparison of the deduced amino acid sequences of the L genes of three different Sendai virus strains confirmed the existence of conserved as well as variable regions in the L protein and revealed a high grade of conservation in the carboxyterminal third. Furthermore, functional amino acid sequence motifs, like elements of RNA-dependent RNA polymerases and ATP-binding sites as postulated previously, were identified.

Sendai virus protein-protein interactions studied by a protein-blotting protein-overlay technique: mapping of domains on NP protein required for binding to P protein

Proteins from Sendai virus particles and from infected cells were analyzed in a protein-blotting protein-overlay assay for their interaction with in vitro-synthesized, [35S]methionine-labeled viral proteins NP, P, and M. After separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transfer onto polyvinylidene difluoride membranes, and renaturation, the immobilized proteins were found to interact specifically with radiolabeled proteins. NP proteins from virus particles and from infected cells retained 35S-P protein equally well. Conversely, P protein from virus particles and from infected cells retained 35S-NP protein. 35S-M protein was retained mainly by NP protein but also by several cellular proteins. To determine the domains on NP protein required for binding to immobilized P protein, a series of truncated and internally deleted 35S-NP proteins was constructed. The only deletion that did not affect binding resides between residues 426 and 497. The carboxyl-terminal 27 residues (positions 498 to 524) contribute significantly to the binding affinity. Removal of 20 residues (positions 225 to 244) in the hydrophobic middle part of NP protein completely abolished its binding to P protein.

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.

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.

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.

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.

Restriction of measles virus gene expression in acute and subacute encephalitis of Lewis rats

Measles virus (MV) replication in brain tissue of Lewis rats with acute (AE) and subacute (SAME) encephalitis was characterized by biochemical techniques. Messenger RNAs specific for measles virus nucleocapsid (N), phospho (P)-, matrix (M), fusion (F), and haemagglutinin (H) protein were detected in all brain extracts examined. The quantity of the individual MV mRNA species was quite different in comparison to lytically infected Vero cells. A steep gradient of MV transcripts was found in brain tissue which is most likely due to strongly attenuated transcription of mRNAs along the viral genome, representing particularly low transcription of the glycoprotein genes. In addition, in vitro translation assays only revealed synthesis of N and P protein in consistent fashion. The mRNAs for the glycoproteins did not direct the synthesis of detectable viral proteins whereas the M mRNA revealed some activity in animals with AE. The data indicate a strong restriction of the MV envelope gene expression in infected brain tissue, which is independent of the incubation time and type of the central nervous system (CNS) disease. This phenomenon which is similar to the findings observed in measles inclusion body encephalitis and subacute sclerosing panencephalitis suggest that host factors may initially be responsible for the initiation of transcriptional and translational alterations.

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.

Analysis of the relationship between cleavability of a paramyxovirus fusion protein and length of the connecting peptide

The relationship between the length of the connecting peptide in a paramyxovirus F0 protein and cleavage of F0 into the F1 and F2 subunits has been examined by constructing a series of mutant F proteins via site-directed mutagenesis of a cDNA clone encoding the simian virus 5 F protein. The mutant F proteins had one to five arginine residues deleted from the connecting peptide. The minimum number of arginine residues required for cleavage-activation of the simian virus 5 F0 protein by host cell proteases was found to be four. F proteins with two or three arginine residues in the connecting peptide were not cleaved by host cell proteases but could be cleaved by exogenously added trypsin. The mutant F protein possessing a connecting peptide consisting of one arginine residue was not cleaved by trypsin. The altered F proteins were all transported to the infected-cell plasma membrane as shown by cell surface immunofluorescence or cell surface trypsinization. However, the only mutant F protein found to be biologically active as detected by syncytium formation was the F protein which has four arginine residues at the cleavage site. The results presented here suggest that in the paramyxovirus F protein the number of basic amino acid residues in the connecting peptide is important for cleavage of the precursor protein by host cell proteases but is not the only structural feature involved. In addition, the data indicate that cleavage of F0 into F1 and F2 does not necessarily result in biological activity and that the connecting peptide may affect the local conformation of the F polypeptide.

Complete nucleotide sequence of the matrix protein mRNA of mumps virus

The complete nucleotide sequence of the mumps virus membrane protein or matrix protein (M) has been determined by sequencing cDNA clones and confirmed by partially sequencing the M mRNA and the genome. The mRNA is 1248 nucleotides long excluding the poly(A) and encodes a protein of 375 amino acids. The molecular weight (38,670), deduced from the amino acid sequence, is in agreement with the molecular weight of the viral M protein estimated by polyacrylamide gel electrophoresis (39-40 kDa). The mumps virus M protein shows 23-27% homology with M proteins of Newcastle disease virus (NDV), measles virus, canine distemper virus (CDV), parainfluenza virus type 3, and Sendai virus, respectively. A comparison of the M protein sequences of the above six paramyxoviruses did not reveal any conserved area of homology common among all paramyxovirus M proteins.

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.

Sequence of the 3386 3' nucleotides of the genome of the AVO1 strain rabies virus: structural similarities in the protein regions involved in transcription

DNA fragments complementary to the genome of an avirulent strain (AVO1) of the rabies virus were cloned and sequenced. The sequence of the 3386 nucleotides from the 3' end covers the genes encoding the leader RNA, the nucleoprotein N, the phosphoprotein M1 and the matrix protein M2, as well as the intergenic regions. Comparison of the AVO1 sequence with those of other rabies strains reveals a very high conservation at both the nucleotide and the amino acid levels. The non-protein coding regions of the genome (leader gene, untranslated regions flanking mRNAs, untranscribed intergenic regions) are discussed in terms of their possible involvement in the rabies virus biology. Comparison of the rabies genome with those of other unsegmented negative strand RNA viruses (rhabdoviruses and paramyxoviruses) indicates that the start and stop transcription signals, located at the border of each gene encoding a protein, and the regions of the phosphoprotein and matrix proteins that could be implicated in the transcription process, retain a similar overall structure. Thus, it appears that during evolution, these virus genomes have diverged while keeping the protein structures and regulatory sequence important in transcription. These results prompt us to propose that the major distinctive feature of the rabies transcription may arise from the highly variable intergenic regions where the attenuation of transcription is assumed to take place.

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.

The molecular biology of influenza virus pathogenicity

It is an accepted concept that the pathogenicity of a virus is of polygenic nature. Because of their segmented genome, influenza viruses provide a suitable system to prove this concept. The studies employing virus mutants and reassortants have indicated that the pathogenicity depends on the functional integrity of each gene and on a gene constellation optimal for the infection of a given host. As a consequence, virtually every gene product of influenza virus has been reported to contribute to pathogenicity, but evidence is steadily growing that a key role has to be assigned to hemagglutinin. As the initiator of infection, hemagglutinin has a double function: (1) promotion of adsorption of the virus to the cell surface, and (2) penetration of the viral genome through a fusion process among viral and cellular membranes. Adsorption is based on the binding to neuraminic acid-containing receptors, and different virus strains display a distinct preference for specific oligosaccharides. Fusion capacity depends on proteolytic cleavage by host proteases, and variations in amino acid sequence at the cleavage site determine whether hemagglutinin is activated in a given cell. Differences in cleavability and presumably also in receptor specificity are important determinants for host tropism, spread of infection, and pathogenicity. The concept that proteolytic activation is a determinant for pathogenicity was originally derived from studies on avian influenza viruses, but there is now evidence that it may also be relevant for the disease in humans because bacterial proteases have been found to promote the development of influenza pneumonia in mammals.

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.

Molecular cloning and sequence analysis of the human parainfluenza 3 virus gene encoding the matrix protein

The sequence of the matrix (M) protein gene and contiguous intergenic regions of the human parainfluenza 3 virus (PF3) was determined by molecular cloning. The encoded M protein contains 354 amino acids and has a predicted mol wt of 39,506. The M protein amino acid sequence was compared to the homologous proteins from other members of the Paramyxoviridae family. The PF3 protein shared 61% homology with the Sendai virus protein and approximately 35% homology with measles and canine distemper virus proteins. Little homology was observed with respiratory syncytial virus. The M protein appears to be the most highly conserved among the Paramyxoviridae proteins.

Protease activation mutants of Sendai virus: sequence analysis of the mRNA of the fusion protein (F) gene and direct identification of the cleavage-activation site

Trypsin cleaves the fusion protein (F) of wild-type Sendai virus into two disulfide-linked polypeptides, F1 and F2, and thereby activates the membrane fusion activity of the virus. A. Scheid and P.W. Choppin [1976). Virology, 265-277) selected mutant viruses of which the F protein could be activated by different proteases, either elastase, chymotrypsin, or plasmin. Herein, we have further characterized five of these mutants. Sequencing of each mutant mRNA encoding the 60-70 amino acids surrounding the cleavage site revealed one or two amino acid changes near or at the cleavage sites. Virions cleaved in vitro by the appropriate proteases were assayed of their fusion activity by hemolysis, and the cleavage sites were determined by amino acid sequencing. In three cases, the change of protease specificity can be accounted for by changed amino acids right at the cleavage site, whereas several other mutations that potentiate cleavage at new sites by new proteases are somewhat removed from the actual cleavage site. We surmise that such mutations might alter local polypeptide conformation, thereby allowing the proteases access to existing sites. Cleavage at new sites produced fusion proteins with novel F1 NH-termini. We found that a mutant with a charged residue at the third position of this normally hydrophobic NH-terminal sequence retains activity in the hemolysis assay, whereas a mutant with a charged residue at the first position does not.

Complete nucleotide sequence of the matrix protein mRNA and three intergenic junctions of human parainfluenza virus type 3

The complete sequence of the gene encoding the matrix protein (M) of human parainfluenza virus type 3 (PIV-3) was determined from cDNA clones and from primer extension dideoxy sequencing of the viral genome. The M mRNA is 1150 nucleotides in length, exclusive of polyadenylate, and codes for a protein of 353 amino acids, having a calculated molecular weight of 39,480. The M protein of PIV-3 was found to have a high degree of sequence homology with that of a closely related paramyxovirus, Sendai virus, and to a lesser extent it contained sequence homology with two more distant paramyxoviruses, measles virus and canine distemper virus. We also determined the sequences of the intergenic junctions for the first four genes of PIV-3: NP, P, M, and F. Comparison of these sequences yielded a consensus mRNA start sequence of 5'-AGGANNAAAGA-3', an mRNA end sequence of 5'-UAAGAAAAA-3', and an intergenic sequence of 5'-CUU-3'. The end sequence of the M gene is unusual in that it contains an eight base insertion prior to the A5 tract found in the consensus sequence. This disruption appears to cause a high frequency of readthrough by the viral transcriptase at this junction.

Sequence of the Sendai virus L gene: open reading frames upstream of the main coding region suggest that the gene may be polycistronic

The sequence of the L gene of Sendai virus, encompassing 6799 nucleotides, has been determined, completing the primary sequence of the entire virus genome. An open reading frame beginning at position 569 codes for a basic protein of 2048 amino acids with an estimated Mr of 231,608. No nucleotide sequence similarities with the analogous L gene of vesicular stomatitis virus were observed. However, comparison of the deduced amino acid sequences of both proteins revealed a conserved 18 amino acid sequence that may have functional significance. Two additional overlapping reading frames which precede the L protein sequence could encode proteins with MrS of 6474 and 14,026, suggesting that the gene is polycistronic.

Sequence of 2,617 nucleotides from the 3' end of Newcastle disease virus genome RNA and the predicted amino acid sequence of viral NP protein

DNA fragments complementary to the Newcastle disease virus genome (strain D26) were cloned and sequenced. The sequence of 2,617 nucleotides from the 3' end of the genome was determined and an open reading frame (OP-1) consisting of 1,467 nucleotides, most likely encoding NP protein, was found in this region. This was followed by a second unfinished open reading frame (OP-2) of at least 729 nucleotides which continued beyond the 2,617th nucleotide. Another relatively short (312 nucleotides long) open reading frame (OP-2') was found overlapping with OP-2, but its significance is still unclear. The amino acid sequence deduced from the nucleotide sequence of OP-1 showed a moderate homology to that of the NP protein of Sendai virus in the central portion of the peptide. The leader sequence of 53 nucleotides was also identified. The 5' end of mRNAs synthesized in the infected cells was analyzed and found to be m7GpppA, suggesting that the transcription of viral mRNAs starts with A, but not with G residue.

The fusion-related hydrophobic domain of Sendai F protein can be moved through the cytoplasmic membrane of Escherichia coli

Recent work on a prokaryotic membrane protein, gene III protein (pIII) of coliphage f1, showed that polypeptide segments of sufficient hydrophobicity functioned to stop transfer of the polypeptide across the cell membrane: strings of 16 or more hydrophobic amino acids sufficed. A fusion-related hydrophobic domain (FRHD) of Sendai F protein, a sequence of 26 consecutive uncharged residues, has been implicated in the fusion of the viral membrane envelope and the target-cell membrane through a hydrophobic interaction. As it is located on the exterior of the viral membrane, this sequence must be transferred across the host-cell membrane during synthesis. We have inserted either the FRHD or the F protein membrane anchor (the COOH-terminal region of the F protein) into an internal site of a secreted pIII, which lacks its natural membrane anchor. These two hydrophobic sequences behave in the bacteria just as they do in their natural eukaryotic cell host. The F protein membrane anchor functions to stop transfer, conferring a membrane-spanning topology to the F-pIII hybrid protein; however, the FRHD is moved through the cytoplasmic membrane and derivatives carrying this sequence are secreted to the periplasm. We discuss how the FRHD is compatible with passage through the membrane and yet is still able to mediate membrane fusion through a presumed hydrophobic interaction.

Matrix genes of measles virus and canine distemper virus: cloning, nucleotide sequences, and deduced amino acid sequences

The nucleotide sequences encoding the matrix (M) proteins of measles virus (MV) and canine distemper virus (CDV) were determined from cDNA clones containing these genes in their entirety. In both cases, single open reading frames specifying basic proteins of 335 amino acid residues were predicted from the nucleotide sequences. Both viral messages were composed of approximately 1,450 nucleotides and contained 400 nucleotides of presumptive noncoding sequences at their respective 3' ends. MV and CDV M-protein-coding regions were 67% homologous at the nucleotide level and 76% homologous at the amino acid level. Only chance homology was observed in the 400-nucleotide trailer sequences. Comparisons of the M protein sequences of MV and CDV with the sequence reported for Sendai virus (B. M. Blumberg, K. Rose, M. G. Simona, L. Roux, C. Giorgi, and D. Kolakofsky, J. Virol. 52:656-663; Y. Hidaka, T. Kanda, K. Iwasaki, A. Nomoto, T. Shioda, and H. Shibuta, Nucleic Acids Res. 12:7965-7973) indicated the greatest homology among these M proteins in the carboxyterminal third of the molecule. Secondary-structure analyses of this shared region indicated a structurally conserved, hydrophobic sequence which possibly interacted with the lipid bilayer.

Determination of the complete nucleotide sequence of the Sendai virus genome RNA and the predicted amino acid sequences of the F, HN and L proteins

We previously determined the 3' proximal 5,824 nucleotides of the Sendai virus genome RNA (Nucleic Acids Res. 11, 7317-7330, 1983; Nucleic Acids Res. 12, 7965-7973, 1984), and present here the sequence of the remaining 5' proximal 9,559 nucleotides. Thus, this is the first paramyxovirus to have its genome organization elucidated. The set of complementary DNA clones used was prepared by the method of Okayama and Berg from polyadenylylated viral genome RNA. We sequenced the region containing the 5' proximal half of the F gene, and the subsequent HN and L genes, and predicted the complete amino acid sequence of the products of these genes. Sequence analyses confirmed that all the genes are flanked by consensus sequences and suggest that the viral mRNAs are capable of forming stem-and-loop structures. Comparison of the F and HN glycoproteins of Sendai virus with those of simian virus 5 strongly suggests that the cysteine residues are highly important for maintenance of the molecular structures of these glycoproteins.

Inhibition of the assembly of Newcastle disease virus by monensin

Monensin inhibits the intracellular transport of the glycoproteins of Newcastle disease virus between cis and trans Golgi stacks of infected BHK cells, as evidenced by its effect upon their post-translational modifications such as fatty acid acylation, glycosylation and proteolytic cleavage. Thus the drug has markedly altered the subcellular distribution of the glycoproteins so that they accumulate in the internal smooth membranes but are virtually absent in the plasma membrane. These glycoproteins that accumulated in intracellular membranes have a cytoplasmic domain susceptible to protease digestion and thus are transmembranous. Under such conditions, the behavior of M protein, which plays a crucial role in virus assembly (Y. Nagai et al., 1976, Virology 69, 523-538), has been analyzed. It has been found that the M protein can neither associate with the internal membranes nor bind to the plasma membrane. Thus no virus budding has been observed, either at the plasma membranes or at internal membranes. These results substantiate the view that the interaction between M and glycoproteins is of great importance for virus assembly and suggest further that this interaction is possibly only when the glycoproteins have been incorporated into the plasma membrane.

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.

Nucleotide sequences responsible for generation of internally deleted Sendai virus defective interfering genomes

The deletion points of four internally deleted defective interfering (DI) RNA species (7a, 7b, 7c, and 7d) that reside in a single Sendai virus strain were defined by nucleotide sequencing. DI RNA 7a (Mr 1.24 x 10(6)) retained the entire NP gene with the complete NP protein-coding sequence, except for the last two U residues of the polyadenylation signal, fused to an 1800-nucleotide sequence comprising 5'-terminal genome and adjacent L gene sequences. DI RNA 7b (Mr, 0.70 x 10(6)) consisted of 100 3'-terminal nucleotides fused to 1900 5'-terminal bases; the deletion point in the NP gene precedes the NP protein initiation codon. DI RNA 7c (Mr 0.55 x 10(6)) retained 420 3'-terminal and 1150 5'-terminal nucleotides. The sequence just downstream of the sequenced deletion site is M gene specific, indicating that 7c arose from at least two deletion events and that it comprises NP, M, and L gene fragments. Transcription of RNA 7c could yield an MRNA encoding a fusion protein with a 14,000 Mr (N-terminal NP sequence fused to out of frame M-specific amino acids). DI RNA 7d (Mr 0.92 x 10(6)) retained 1027 3'-terminal nucleotides fused to 1600 bases from the 5'-terminus. It has an open reading frame for a 33,000 Mr N-terminal NP protein fragment. Nucleotide sequences flanking each deletion and just downstream of the NP gene deletion site suggested that these DI genomes were generated by a copy-choice mechanism, involving polymerase jumping during replication of negative polarity virus genome templates. In this process, the termination and reinitiation of RNA synthesis would involve recognition of sequences that regulate virus genome transcription and replication.