Sequence analysis of P gene of human parainfluenza type 2 virus: P and cysteine-rich proteins are translated by two mRNAs that differ by two nontemplated G residues

Expression and properties of the V protein in acute measles virus and subacute sclerosing panencephalitis virus strains

Measles virus (MV) inserts one guanosine (G) residue at a specific site in a subpopulation of the mRNA transcribed from the phosphoprotein (P) gene to produce V mRNA. Using an antiserum against the unique carboxyl-terminal region of the predicted V protein, we found that a phosphorylated V protein was expressed in two acute MV strains (Edmonston and Nagahata) and three SSPE virus strains (Biken, Yamagata, and Niigata). The V protein of Biken strain SSPE virus was electrophoretically and antigenically indistinguishable from the V protein of Nagahata strain acute MV, the likely progenitor of the Biken strain. The V protein of these two viruses was not present in the intracellular viral nucleocapsids, but was found only in the cytosolic free protein pool. Pulse-chase experiments failed to show transport of the V protein to the plasma membrane. The V protein was also absent in the extracellular virions. The P protein synthesized from the cloned gene associated with the MV nucleocapsids in vitro, but the V protein had no affinity to the MV nucleocapsids. These results suggest that expression and properties of the V protein are conserved in chronic MV infection.

Molecular evolution of human paramyxoviruses. Nucleotide sequence analyses of the human parainfluenza type 1 virus NP and M protein genes and construction of phylogenetic trees for all the human paramyxoviruses

The nucleotide sequences of the NP and M genes of human parainfluenza type 1 virus (HPIV-1) were determined. The NP gene was 1677 nucleotides long excluding polyadenylic acid. The NP gene contained a single large open reading frame (ORF), which encoded a polypeptide of 524 amino acids with a calculated molecular weight of 57,736. The M gene 1173 nucleotides long excluding the poly(A) tract and the sequence also contained a single large ORF which encoded a polypeptide of 348 amino acid with a molecular weight of 38,445, which was inconsistent with 28 kDa previously determined by SDS-PAGE. We aligned the deduced HPIV-1 NP and M protein sequences with 12 and 13 other paramyxoviruses, respectively, suggesting that a common tertiary structure was found in the NPs or Ms of HPIV-1, Sendai virus (SV), HPIV-3 and BPIV-3 and that other common structure was also maintained in these proteins of HPIV-2, SV 41 and 5, MuV, HPIV-4. Phylogenetic trees were constructed for the NP and M proteins of all the paramyxoviruses of which nucleotide sequences had been previously reported. Paramyxoviruses could be subdivided into two groups, i.e., PIV-1 group and PIV-2 group; the former group is composed of HPIV-1, SV, HPIV-3 and BPIV-3, and the latter group consists of HPIV-2, SV 41, SV 5, MuV, HPIV-4 A and HPIV-4 B.

RNA editing in the phosphoprotein gene of the human parainfluenza virus type 3

RNA editing of the human parainfluenza virus type 3 (HPIV3) phosphoprotein (P) gene was found to occur for the accession of an alternate discontinuous cistron. Editing occurred within a purine-rich sequence (AAUUAAAAAAGGGGG) found at the mRNA nucleotides 791-805. This sequence resembles an HPIV3 consensus transcription termination sequence and is located at the 5'-end of the putative D protein coding sequences. Editing at an alternate site (AAUUGGAAAGGAAAGG), mRNA nucleotides 1121-1136, for accession of a conserved V cistron, which is present in a number of paramyxovirus P genes, was not found to occur in HPIV3. In contrast with many other paramyxoviruses, editing was indiscriminate with the insertion of 1-12 additional G residues not present in the gene template. RNA editing was found to occur in both in vivo (HPIV3 infected cells) and in vitro (purified nucleocapsid complexes) synthesized mRNAs. Further, the in vitro prepared mRNA was edited regardless of whether the nucleocapsid complexes were transcribed in the presence or absence of uninfected human lung carcinoma (HLC) cell lysates. These results support the notion that RNA editing appears to be exclusively a function of viral proteins.

Synthesis of leader RNA and editing of the P mRNA during transcription by purified measles virus

A transcription system with detergent-disrupted purified measles virus was developed. Synthesis of authentic, full-length measles virus N, P, M, and F mRNAs by purified virus occurred as identified by dot-blot hybridization analysis of individual measles virus clones and gel electrophoresis. The relative abundance of the first five viral mRNAs synthesized in vitro decreased significantly with their distance from the 3' end. The addition of the soluble protein fraction from uninfected A549 cells stimulated overall viral RNA synthesis but did not alter the relative abundance of each of the mRNAs. Measles virus synthesized in vitro a leader RNA of approximately 55 nucleotides in length, suggesting that like other negative-strand viruses, transcription initiated only at the 3' end of the genome RNA. Purified measles virus also catalyzed RNA editing during the synthesis of the P mRNA as shown by modified primer extension analysis of the mRNA products and by translation of the modified RNA into the V protein in rabbit reticulocyte lysates. These data suggested that the RNA editing activity was virus encoded.

Characterization of the Sendai virus V protein with an anti-peptide antiserum

The Sendai virus V protein, which is a fusion of the P and V ORFs of the P gene, was characterized with antisera to a portion of the V ORF and compared to the P protein. The only property found in common with P is that V is also highly phosphorylated, and this is so even when these proteins are expressed independently of the other viral proteins. Otherwise, V was not found in virions, was not strongly associated with viral nucleocapsids like P, and anti-V had no effect on viral RNA synthesis in vitro under conditions where anti-P was highly inhibitory. The available evidence suggests that V may play a role in RNA synthesis, but it is not an essential one like that of the P protein.

Transcripts of simian virus 41 (SV41) matrix gene are exclusively dicistronic with the fusion gene which is also transcribed as a monocistron

The complete nucleotide sequences of the matrix (M) and fusion (F) genes of simian virus 41 (SV41) were determined. Deduced amino acid sequences confirmed the close relationship of SV41 with human parainfluenza type 2 virus (PIV2). Analyses of noncoding regions between the F and the hemagglutinin-neuraminidase (HN) genes suggested the absence of the small hydrophobic gene, which is present between the F and the HN genes of simian virus 5 and mumps virus. It was striking that there was no apparent consensus gene end sequence between the M and the F genes and that the M gene was transcribed exclusively as a dicistron with the F gene. The number of monocistronic transcripts of the F gene was approximately half that of the dicistronic transcripts. However, the F protein of SV41 seemed to be efficiently translated, since viral multiplication and fusion from within were as efficient as in PIV2. These results suggest that the lack of a consensus gene end sequence resulted in the readthrough of viral RNA polymerases between the M and the F genes and that the initiation of F gene transcription could occur by newly entered polymerases independently of the polymerases that started the upstream M gene transcription.

Characterization of V protein in measles virus-infected cells

An edited mRNA transcribed from the phosphoprotein (P) gene of measles virus (MV) has been predicted to encode a cysteine-rich protein designated V. This mRNA contains a single additional nontemplated G residue which permits access to an additional protein-coding reading frame. Such an edited P gene-specific mRNA has been detected in MV-infected cells, but no corresponding protein has yet been identified in vivo. We report the use of antisera directed against synthetic peptides corresponding to five different regions of the predicted MV V protein amino acid sequence to analyse MV-specific proteins synthesized in vivo and in vitro. The MV V protein (40 kDa) was detected in MV-infected cells in a diffuse cytoplasmic distribution, a predominant subcellular localization distinct from that of virus nucleocapsids. The protein was found to be phosphorylated and to be maximally synthesized at 16 h postinfection, when MV-specific structural protein synthesis was also maximal. Antiserum directed against a peptide (PV2) corresponding to amino acids 65 to 87 of the V protein amino acid recognized the P protein but not the V protein, indicating that the P and V proteins may be folded differently at or near this region so that the PV2 sequence is in an exposed position at the surface of the P protein but not at the surface of the V protein.

Human parainfluenza virus type 3 transcription in vitro: role of cellular actin in mRNA synthesis

Purified ribonucleoprotein complexes of human parainfluenza virus type 3 (HPIV-3) virions required, in addition to the viral proteins, soluble cytoplasmic proteins from uninfected cells for the synthesis of mRNAs in vitro. In contrast to Sendai virus transcription, in vitro RNA synthesis from HPIV-3 ribonucleoprotein complexes was not stimulated significantly by purified tubulin. Moreover, cytoplasmic extract depleted of tubulin by immunoprecipitation stimulated HPIV-3 transcription effectively, suggesting involvement of a host protein(s) other than tubulin in the HPIV-3 transcription process. The transcription stimulatory factor was purified from uninfected cell extract by conventional chromatography and was found to contain a major 43-kDa polypeptide. In Western blot (immunoblot) analysis, this protein reacted with antiactin antibody, suggesting that the 43-kDa polypeptide is actin. This possibility was further supported by its polymerization activity and properties of binding to blue-Sepharose and heparin-Sepharose columns. Furthermore, when the cell extract was depleted of actin by immunoprecipitation by antiactin antibody, the stimulatory activity was abolished, indicating an involvement of actin in the stimulation of HPIV-3 transcription. After purification from RNAses, similar stimulatory activity associated with the 43-kDa protein was detected in other cell lines as well, including CV-1, HeLa, and BHK.

The P gene of human parainfluenza virus type 1 encodes P and C proteins but not a cysteine-rich V protein

The nucleotide sequence of the P gene of human parainfluenza virus type 1 (PIV1) was determined from cloned cDNA copies of the mRNA. By analogy with the gene organization of Sendai virus, two open reading frames in the mRNA sense of the gene were identified as coding sequences for the P protein (568 amino acids with an estimated molecular weight of 64,655) and the C protein (204 amino acids with an estimated molecular weight of 24,108). Comparison of the deduced amino acid sequences of the P and C proteins of PIV1 with those of Sendai virus showed a high degree of homology. However, a sequence for the cysteine-rich V protein, which was considered a common feature of other paramyxoviruses, was interrupted by the presence of multiple stop codons. The sequence analysis of three P-gene-specific cDNA clones generated from genomic RNA by polymerase chain reaction and one additional clone generated from mRNA confirmed that the coding sequence for the cysteine-rich region is silent in the PIV1 gene and thus is not translated into protein. Two potential editing sites with the consensus sequence 3'UUYUCCC were found in the PIV1 P gene at positions 564 to 570 and 1430 to 1436. However, examination of the PIV1 mRNA population by a primer extension method indicated that neither of these sites is utilized. These results indicate that the PIV1 P gene has a coding strategy different from those of other paramyxovirus P genes.

Characterizations of the human parainfluenza type 2 virus gene encoding the L protein and the intergenic sequences

We cloned and determined the nucleotide sequences of cDNAs against genomic RNA encoding the L protein of human parainfluenza type 2 virus (PIV-2). The L gene is 6904 nucleotides long including the intergenic region at the HN-L junction and putative negative strand leader RNA, almost all of which is complementary to the positive strand leader RNA of PIV-2. The deduced L protein contains 2262 amino acids with a calculated molecular weight of 256,366. The L protein of PIV-2 shows 39.9, 28.9, 27.8 and 28.3% homologies with Newcastle disease virus (NDV), Sendai virus (SV), parainfluenza type 3 virus (PIV-3) and measles virus (MV), respectively. Although sequence data on other components of transcriptive complex, NP and P, suggested a closer relationship between PIV-2 and MV, as concerns the L protein, MV is closely related to another group as SV and PIV-3. From analysis of the alignment of the five l proteins, six blocks composed of conserved amino acids were found in the L proteins. The L protein of PIV-2 was detected in purified virions and virus-infected cells using antiserum directed against an oligopeptide corresponding to the amino terminal region. Primer extension analyses showed that the intergenic regions at the NP-P, P-M, M-F, F-HN and HN-L junctions are 4, 45, 28, 8 and 42 nucleotides long, respectively, indicating that the intergenic regions exhibit no conservation of length and sequence. Furthermore, the starting and ending sequences of paramyxoviruses were summarized.

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

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

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.

Antigenic and structural properties of a paramyxovirus simian virus 41 (SV41) reveal a close relationship with human parainfluenza type 2 virus

Seven structural component proteins of a paramyxovirus simian virus 41 (SV41) were identified with the aid of monoclonal antibodies prepared against SV41 and human parainfluenza type 2 virus (PIV2). The nucleoprotein is antigenically very close to that of PIV2, while it is comparatively far from that of simian virus 5 (SV5). The hemagglutinin-neuraminidase (HN) protein showed no immunological relationship to either of the HN proteins of PIV2 or SV5. The amino acid sequence of the SV41 HN protein was deduced from the nucleotide sequence of its HN gene and revealed that the SV41 HN is unexpectedly close to the PIV2 HN (61.2% identity in amino acid sequence), while the SV5 HN showed only 48.3% identity with the PIV2 HN. The SV41 HN is also related to the SV5 HN (51.3% identity); thus, the SV41 HN is phylogenetically situated between the PIV2 and SV5 HNs. These results indicate that SV41 is the virus closest to PIV2 at present.

Messenger RNA editing and the genetic code

Messenger RNA editing is defined as a process leading to predetermined modifications of the coding region of a primary gene transcript. By this definition, splicing processes are special forms of editing; however, they are not dealt with in this review. Editing processes different from splicing have been defined in mammalian cells, in RNA viruses, and in mitochondria of trypanosomes, higher plants and vertebrates. These post- or co-transcriptional processes involve addition, deletion, or modification-substitution of nucleotides, and represent previously unrecognized mechanisms for altering the coding potential of a gene and for modulating gene expression.

Complete nucleotide sequence of the matrix gene of human parainfluenza type 2 virus and expression of the M protein in bacteria

The sequence of the M gene of human parainfluenza virus type 2 (PIV-2) has been determined. The sequence contained a large open reading frame with 1131 nucleotides encoding a protein with a calculated molecular weight of 42,312. Comparison of M protein sequence indicated that PIV-2 was more closely related to mumps virus and Newcastle disease virus than to other parainfluenza viruses, Sendai virus (SV), and parainfluenza virus type 3 (PIV-3), indicating a possible subdividing of the Paramyxovirus into two groups. This grouping is consistent with that obtained from analysis of the HN gene. Measles virus and canine distemper virus definitely belong to the subgroup composed of SV and PIV-3. No homology region was found in all the paramyxoviruses compared. However, a tertiary structure may be conserved in each subgroup of paramyxovirus. The M protein of PIV-2 was expressed in bacteria, and the product was recognized by a monoclonal antibody specific for the PIV-2 M protein. The bacterial-expressed protein, however, was heterogeneous and smaller in size.