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

The full-length cDNA corresponding to the mRNA of the fusion (F) protein of the Yamagata-1 strain of subacute sclerosing panencephalitis (SSPE) virus was cloned, and its complete nucleotide sequence was determined. The F gene was composed of 2369 nucleotides and contained a single large coding region, which is located between two noncoding regions. The 5'-terminal noncoding region consisted of 584 nucleotides comprising 44.9% cytosine, and had several inverted repetitious sequences. The 3'-terminal noncoding region had a relatively low homology of 91.7% with the MV. The coding region was expanded for nucleotides 585-2189, which encoded 534 amino acids with a molecular weight of 57,963. The homology of the amino acid sequence of the F protein between the MV and SSPE virus was 96.27%, and the positions of cysteine and proline were almost identical in the two viruses. The functional domains of SSPE-virus F protein closely resembled those of MV F protein, including the cleavage site, a signal sequence, the fusion-related stretch, the transmembrane region, and four potential glycosylation sites. Four antigenic epitopes on the MV F protein were also conserved on the SSPE-virus F protein. However, deletion of one nucleotide (position 2155) of the SSPE virus was found when compared with the MV, and shifted the coding frame, causing the substitutions of 27 C-terminal amino acids of the MV F protein with 11 different residues. The variations of the C-terminal region of the F protein were observed with two other SSPE viruses, suggesting that this may be a common property of SSPE virus that differs from MV.