Mutated and hypermutated genes of persistent measles viruses which caused lethal human brain diseases

Constant and variable regions of measles virus proteins encoded by the nucleocapsid and phosphoprotein genes derived from lytic and persistent viruses

The nucleotide sequences of the N and P genes of two wild type measles virus strains JM and CM in two distinct lineages of the virus have been analyzed and compared with those of other MV strains in order to assess which parts of the internal proteins are variable. Most variations in the P protein appear to occur in the N-terminus, while the middle part of the protein (residues 201-350) and the C-terminus are conserved. The C protein varies primarily in its N-terminal amino acids. The C-terminal amino acid residues of the V protein, which are unique to this protein, do not vary significantly between measles virus strains. The data show that evolutionary trees determined on the basis of the N, P, or M genes are the same and that probably no recombination has taken place between these genes in the strains investigated so far. The M protein appears to be less variable than the other genes and thus changes observed in this gene in some SSPE and MIBE viruses may be of greater significance than were assumed earlier.

The Sendai virus nonstructural C proteins specifically inhibit viral mRNA synthesis

An in vitro transcription system for paramyxoviruses is described, in which polymerase-free templates are combined with cell extracts containing polymerase made in vivo via transfected plasmids. Both P and L are required for polymerase activity, and both must be coexpressed for optimum activity. mRNA synthesis here was found to be inversely proportional to the level of C expression, whereas defective interfering genome replication was largely unaffected by the level of C in the extract. The inhibition of transcription appeared to be due to the C' and C, but not the Y1 and Y2 proteins, and only occurred when C'/C was coexpressed with P and L. C'/C appears to intervene during polymerase formation, possibly by forming polymerase complexes which are inactive for transcription, but still competent for genome replication.

Subacute sclerosing panencephalitis is typically characterized by alterations in the fusion protein cytoplasmic domain of the persisting measles virus

Our recent extensive analysis of three cases of subacute sclerosing panencephalitis (SSPE) revealed intriguing genetic defects in the persisting measles virus (MV): the fusion (F) genes encoded truncated cytoplasmic F protein domains (Cattaneo et al., Virology 173, 415-425, 1989). Now this MV genomic region has been investigated in eight additional SSPE cases by PCR amplification, replacement cloning into a vector containing the F gene of a lytic MV, in vitro expression, and sequencing. In all cases at least part of the clones showed mutations leading to F protein truncations, elongation, or nonconservative amino acid replacements. It is proposed that alteration of the F protein cytoplasmic domain may play a critical role in the development of SSPE.

Genetic variability of the glycoprotein genes of current wild-type measles isolates

The glycoprotein coding sequences from three wild-type measles viruses isolated in the United States during 1988-1989 were examined by mRNA templated sequencing to determine whether contemporary strains have undergone genetic changes relative to the vaccine strain, Moraten. These studies revealed variation in the hemagglutinin (HA) gene and, to a far lesser degree, the fusion (F) gene. The F protein coding region was highly conserved with only three predicted amino acid changes. Among the predicted amino acid changes identified in the HA was a new potential glycosylation site at residue 416, located toward the carboxy-terminal end of the HA peptide. Eighty percent of the predicted amino acid changes in the HA shared by the three wild-type isolates were clustered near the five previously identified potential glycosylation sites. A linear pattern of evolutionary change was observed after comparing the predicted amino acid HA changes from the 1988-1989 viruses to those predicted in the HA protein from U.S. wild types isolated in 1977 and 1983.

Subacute sclerosing panencephalitis virus dominantly interferes with replication of wild-type measles virus in a mixed infection: implication for viral persistence

Interaction between the Edmonston or Nagahata strain of acute measles virus (MV) and the defective Biken strain of MV isolated from a patient with subacute sclerosing panencephalitis (SSPE) was examined by a cell fusion protocol. Biken-CV-1 cells nonproductively infected with Biken strain SSPE virus were fused with neomycin-resistant CV-1 cells. All the fused cells selected with the neomycin analog G418 expressed Biken viral proteins, as determined by an immunofluorescence assay. This procedure enabled the transfer of Biken viral genomes into cells previously infected with MV. In the fused cells coinfected by Biken strain SSPE virus and Edmonston or Nagahata strain MV, early MV gene expression was suppressed, as determined by immunoprecipitation with strain-specific antibodies. Maturation of Edmonston strain MV was also suppressed. When the coinfected fused cells were selected with G418, Biken viral proteins remained at a constant level for up to 7 weeks. Wild-type MV proteins gradually decreased to a barely detectable level after 4 weeks and became undetectable after 7 weeks. Immunofluorescence studies showed a steady decline in cells expressing wild-type MV proteins in the coinfected cultures. These results suggest that Biken strain SSPE virus dominantly interferes with the replication of wild-type MV. The possible mechanisms of dominant interference and the implication for evolution of a persistent MV infection are discussed.

Irreversible modification of measles virus RNA in vitro by nuclear RNA-unwinding activity in human neuroblastoma cells

The matrix (M) gene of a measles virus (MV) variant passaged in IMR-32 human neuroblastoma cells displays numerous uridine-to-cytosine transitions called biased hypermutation. Using an in vitro assay, we show that IMR-32 cells contain high levels of an activity which unwinds and irreversibly alters the base pairing of double-stranded RNA synthesized from the M gene of MV. This activity is found exclusively in the cellular nucleus and is present at a lower level in African green monkey kidney Vero cells. Experiments with mixed cell extracts suggest that the low activity in Vero cells is not due to inhibitory factors. These findings support the hypothesis that this RNA-modifying and -unwinding activity is responsible for biased hypermutation of MV strains that infect the central nervous system. Possible functions of this neural cell activity and implications for central nervous system disorders are discussed.

Complete nucleotide sequence of the phosphoprotein of the Yamagata-1 strain of a defective subacute sclerosing panencephalitis (SSPE) virus

The complete nucleotide sequence of the phosphoprotein (P) gene of the Yamagata-1 strain of a defective subacute sclerosing panencephalitis (SSPE) virus was determined. Comparison with the P gene of the Edmonston strain of measles virus (MV) revealed 44 differences of which 23 nucleotides substitutions were identical with those revealed between other SSPE viruses and MV (Cattaneo et al. (1989) Virology 173, 415-425). The consensus sequence of the G insertion site was completely conserved, whereas mRNAs with one or three non-templated G residue insertions were found in addition to the mRNA of the exact genome copy. As a result of the frameshift downstream of the site of G insertion, the cysteine-rich V protein was predicted from the one G-inserted mRNA besides the P and C proteins predicted from the genome-copied mRNA.

Measles virus phosphoprotein retains the nucleocapsid protein in the cytoplasm

Measles virus (MV) proteins were efficiently expressed in COS and Vero cells from vectors based on the strong cytomegalovirus enhancer-promoter and the simian virus 40 origin of replication. When expressed alone, nucleocapsid protein (N) migrates predominantly into the nucleus whereas phosphoprotein (P) is located in the cytoplasm. Coexpression of N and P proteins results in retention of the N protein in the cytoplasm, as seen also in infected cells. The retention of N protein is due to specific interactions with the P protein since coexpression of N with either the matrix or the hemagglutinin protein had no effect. Mapping of the regions of N-P interactions on P protein revealed that the carboxy-terminal 40% of P was sufficient for specific binding to N; however, the carboxy-terminal 60% of P was required for retention of N in the cytoplasm. Thus, the V and C proteins encoded within the first half of the P gene are not involved in the cytoplasmic retention of N protein. N protein might be fortuitously targeted to the nucleus as a result of its many basic amino acids, presumably destined to interact with the MV genome. However, this set of experiments has allowed to analyze in vivo the interactions between the N and P proteins.

New viruses and new disease: mutation, evolution and ecology

Given the extraordinarily high mutation rate of viruses, particularly those with RNA genomes, it is not surprising that new viruses are continually evolving. However, the symptomatology of old viral diseases has remained stable for centuries. The combination of genetic and ecological factors that constrain as well as facilitate the emergence of new viruses is analyzed.

Regulation of a double-stranded RNA modification activity in human cells

A double-stranded RNA (dsRNA)-specific modification activity from Xenopus oocytes and human cells dsRNA modifier) converts adenosine residues present in dsRNA to inosines. The function of the dsRNA modifier is unknown, although it has been suggested that it may be part of the cellular antiviral response. We investigated the relationship between the activity of the dsRNA modifier, viral infection, and the antiviral response in human cells induced by poly(rI)-poly(rC) [poly(I.C)] treatment. We found, unexpectedly, that treatment of HeLa cells with poly(I.C) or other dsRNA molecules resulted in the dramatic inhibition of the dsRNA modifier. Mixing experiments, reconstruction experiments, and pretreatment of extracts with RNases indicated that inhibition of the dsRNA modifier did not result from the continued presence of a soluble inhibitor such as dsRNA) in the in vitro modification reactions. Treatment of cells with cyclohexamide or dactinomycin simultaneously with the poly(I.C) demonstrated that in vivo inhibition of the dsRNA modifier did not require new transcription or translation. The dsRNA modification activity was also substantially inhibited in cells infected with poliovirus and was slightly inhibited in cells infected with adenovirus. The inhibition of the dsRNA modifier during the antiviral state is thus not consistent with an antiviral function, and instead suggests another cellular function for dsRNA modification.

Regulation of a double-stranded RNA modification activity in human cells

A double-stranded RNA (dsRNA)-specific modification activity from Xenopus oocytes and human cells dsRNA modifier) converts adenosine residues present in dsRNA to inosines. The function of the dsRNA modifier is unknown, although it has been suggested that it may be part of the cellular antiviral response. We investigated the relationship between the activity of the dsRNA modifier, viral infection, and the antiviral response in human cells induced by poly(rI)-poly(rC) [poly(I.C)] treatment. We found, unexpectedly, that treatment of HeLa cells with poly(I.C) or other dsRNA molecules resulted in the dramatic inhibition of the dsRNA modifier. Mixing experiments, reconstruction experiments, and pretreatment of extracts with RNases indicated that inhibition of the dsRNA modifier did not result from the continued presence of a soluble inhibitor such as dsRNA) in the in vitro modification reactions. Treatment of cells with cyclohexamide or dactinomycin simultaneously with the poly(I.C) demonstrated that in vivo inhibition of the dsRNA modifier did not require new transcription or translation. The dsRNA modification activity was also substantially inhibited in cells infected with poliovirus and was slightly inhibited in cells infected with adenovirus. The inhibition of the dsRNA modifier during the antiviral state is thus not consistent with an antiviral function, and instead suggests another cellular function for dsRNA modification.

Functional and nonfunctional measles virus matrix genes from lethal human brain infections

Subacute sclerosing panencephalitis (SSPE) is a lethal disease induced by the persistence of measles virus in the human brain. In many SSPE cases, the viral matrix (M) protein cannot be detected; in others, M proteins of the expected size are found and sequence analysis of M cDNAs has confirmed that the reading frames are intact, showing only several missense mutations. To determine whether these alterations result in nonfunctional proteins, we have replaced the M gene of an infectious full-length genomic cDNA (from vaccine strain Edmonston) with different M genes derived from four patients with SSPE. One of the SSPE M genes tested proved to be functionally competent, giving rise to a virus yielding titers similar to those of viruses containing the M gene from control lytic strains. The other three SSPE M genes were not functionally competent in the same test. In all three cases, the inactivating changes resided in the carboxyl-terminal half of the M protein, as shown by the exchange of either of the two genes halves. In summary, mutational M gene alterations, which either prevent synthesis of M protein altogether or only allow synthesis of nonfunctional M protein, have been detected by us and by others in 9 of 10 SSPE cases. The one functional M gene appears to be an exception to the rule, indicating that M gene alteration might not be an absolute requirement for disease development.

Role of biased hypermutation in evolution of subacute sclerosing panencephalitis virus from progenitor acute measles virus

We identified an acute measles virus (Nagahata strain) closely related to a defective virus (Biken strain) isolated from a patient with subacute sclerosing panencephalitis (SSPE). The proteins of Nagahata strain measles virus are antigenically and electrophoretically similar to the proteins of Edmonston strain measles virus. However, the nucleotide sequence of the Nagahata matrix (M) gene is significantly different from the M genes of all the acute measles virus strains studied to date. The Nagahata M gene is strikingly similar to the M gene of Biken strain SSPE virus isolated several years later in the same locale. Eighty percent of the nucleotide differences between the Nagahata and Biken M genes are uridine-to-cytosine transitions known as biased hypermutation, which has been postulated to be caused by a cellular RNA-modifying activity. These biased mutations account for all but one of the numerous missense genetic changes predicted to cause amino acid substitutions. As a result, the Biken virus M protein loses conformation-specific epitopes that are conserved in the M proteins of Nagahata and Edmonston strain acute measles viruses. These conformation-specific epitopes are also absent in the cryptic M proteins encoded by the hypermutated M genes of two other defective SSPE viruses (Niigata and Yamagata strains). Nagahata-like sequences are found in the M genes of at least five other SSPE viruses isolated from three continents. These data indicate that Biken strain SSPE virus is derived from a progenitor closely resembling Nagahata strain acute measles virus and that biased hypermutation is largely responsible for the structural defects in the Biken virus M protein.

Measles virus nucleocapsid protein protects rats from encephalitis

Lewis rats immunized with recombinant vaccinia virus expressing the nucleocapsid (N) protein of measles virus were protected from encephalitis when subsequently challenged by intracerebral infection with neurotropic measles virus. Immunized rats revealed polyvalent antibodies to the N protein of measles virus in the absence of any neutralizing antibodies as well as an N protein-specific proliferative lymphocyte response. Depletion of CD8+ T lymphocytes did not abrogate the protective potential of the N protein-specific cell-mediated immune response in rats, while protection could be adoptively transferred with N protein-specific CD4+ T lymphocytes. These results indicate that a CD4+ cell-mediated immune response specific for the N protein of measles virus is sufficient to control measles virus infections of the central nervous system.

Numerous transitions in human parainfluenza virus 3 RNA recovered from persistently infected cells

The nucleotide sequences at the 3'-termini of human parainfluenza virus 3 (HPIV3) genomic RNAs recovered from two lines of persistently infected LLC-MK2 cells were determined following PCR amplification. After 29 months of persistence the 3'-end of the HPIV3 genome was found to be highly mutated. Interestingly, the only types of nucleotide changes observed were U to C and A to G transitions. Both U to C and A to G transitions were present on individual RNA molecules. The data indicate that biased hypermutational activity leading to U To C and A to G mutations operates in cultured cells during persistent HPIV3 infections.

Molecular characterization of the M genomic segment of the Seoul 80-39 virus; nucleotide and amino acid sequence comparisons with other hantaviruses reveal the evolutionary pathway

The genomic M segment of Seoul 80-39 virus was characterized by cloning and nucleotide sequence analysis. The virion M RNA segment is 3651 nucleotides long with the 3' and 5' terminal sequences inversely complementary for 20 bases. A single open reading frame was detected in the viral complementary-sense RNA which can encode a polypeptide of 1133 amino acids. The Seoul 80-39 virus M segment was compared with the M segments of related viruses, Hantaan 76-118, Hallnas B1 and Sapporo Rat (SR-11) virus. Our results demonstrate a significant similarity between M RNA segments of the Seoul 80-39, Hantaan 76-118, Hallnas B1 and SR-11 viruses. The degree of conservation of both nucleic acid and protein sequences between these viruses reveals a close evolutionary relationship. Furthermore, it is evident that the serotypic profile of hantaviruses is determined by the rodent host species from which the virus was isolated and not by the geographical area.

Altered translation of the matrix genes in Niigata and Yamagata neurovirulent measles virus strains

Niigata and Yamagata strains measles virus were isolated from subacute sclerosing panencephalitis patients. These viruses were defective in virion production and expression of matrix (M) protein. The Niigata M protein-coding frame was interrupted by an in-frame termination codon, whereas the Yamagata M gene lacked the normal translational initiation codon. These mutations prevented translation of a normal M protein. However, RNA derived from the cloned Niigata and Yamagata M genes was translatable in vitro into low levels of aberrant proteins that reacted with M-specific antiserum. These proteins were also translated from poly(A)+ RNA from cells infected by Niigata and Yamagata virus strains. The aberrant M protein of Niigata virus was initiated at a downstream AUG codon created by a second mutation. The Yamagata M gene produced two aberrant proteins: one initiated mainly in vitro at an ACG codon, and a second species initiated at a downstream site both in vitro and in vivo. These results define the abnormal translational functions of the Niigata and Yamagata M genes, and further implicate the involvement of M protein defects in chronic central nervous system infections by measles virus.

Structural homology between hemagglutinin (HA) of measles virus and the active site of long neurotoxins

The amino acid sequence of a carboxy terminal domain corresponding to the end of the outer envelope projection of the hemagglutinin glycoprotein (HA) of measles and subacute sclerosing panencephalitis viruses has a high degree of homology with the active domain of long neurotoxins, which specifically binds to the nicotinic acetylcholine receptor. The homology in amino acid sequence of HA to this domain of neurotoxin, as well as native alpha-bungarotoxin (BTx), was confirmed by the following evidence: a) rabbit anti-HA monospecific sera reacted with BTx in ELISA, b) HA dose-dependently blocked the binding of radio-labeled BTx in competitive radioimmunoassay, and c) antibody to a synthetic peptide of the active domain of BTx precipitated HA in radioimmunoprecipitation. In addition, SSPE patients had significantly high titers of antibody to BTx than healthy children who had been previously infected with measles. This epitope of HA may play an important role in the transsynaptic spreading of the virus in the brain.

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.

Double-stranded RNA unwinding and modifying activity is detected ubiquitously in primary tissues and cell lines

A double-stranded RNA unwinding and modifying activity was found to be present in a wide range of tissues and cell types. The level of activity did not vary significantly with respect to the state of cell differentiation, cell cycle, or transformation. Thus, the unwinding and modifying activity, localized in the nucleus in somatic cells and capable of converting many adenosine residues to inosine, appears to be one of the housekeeping genes.

Double-stranded RNA unwinding and modifying activity is detected ubiquitously in primary tissues and cell lines

A double-stranded RNA unwinding and modifying activity was found to be present in a wide range of tissues and cell types. The level of activity did not vary significantly with respect to the state of cell differentiation, cell cycle, or transformation. Thus, the unwinding and modifying activity, localized in the nucleus in somatic cells and capable of converting many adenosine residues to inosine, appears to be one of the housekeeping genes.

Sequence analysis of the phosphoprotein (P) genes of human parainfluenza type 4A and 4B viruses and RNA editing at transcript of the P genes: the number of G residues added is imprecise

We cloned and sequenced the cDNAs against genomic RNAs and mRNAs for phosphoproteins (Ps) of human parainfluenza virus types 4A (PIV-4A) and 4B (PIV-4B). The PIV-4A and -4B P genes were 1535 nucleotides including poly(A) tract and were found to have two small open reading frames, neither of which was apparently large enough to encode the P protein. A cluster of G residues was found in genomic RNA and the number of G residues was 6 in both PIV-4A and -4B. However, the number of G residues at the corresponding site in the mRNAs to the genomic RNA was not constant. Three different mRNA cDNA clones were obtained; the first type of mRNA encodes a larger (P) protein of 399 amino acids, the second type encodes V protein of 229 or 230 amino acids, and the third type encodes the smallest protein (156 amino acids). Comparisons on the nucleotide and the amino acid sequences P and V proteins between these two subtypes revealed extensive homologies. However, these homology degrees are lower than that of NP protein. The C-terminal regions of the P and V proteins of PIV-4s could be aligned with all other Paramyxoviruses, PIV-2, mumps virus (MuV), simian virus 5 (SV 5), Newcastle disease virus (NDV), measles virus (MV), canine distemper virus (CDV), Sendai virus (SV), and PIV-3. On the other hand, the P-V common (N-terminal) regions showed no homology with MV, CDV, SV, and PIV-3. Seven phylogenetic trees of Paramyxoviruses were constructed from the entire and partial regions of P and V proteins.