Fusion glycoprotein of human parainfluenza virus type 3: Nucleotide sequence of the gene, direct identification of the cleavage-activation site, and comparison with other paramyxoviruses

Abstract The complete sequences of the fusion (F) mRNA and protein of human parainfluenza virus type 3 (PF3) were determined from overlapping cDNA clones. To confirm the cDNA sequence, the complete sequence of the F gene was determined independently by dideoxynucleotide sequencing of genomic RNA using synthetic oligonucleotide primers. The mRNA contains 1845 nucleotides, exclusive of poly (A), has an unusually long (193-nucleotide) 5′ nontranslated region, and encodes an F 0 protein of 539 amino acids. The site within F 0 of the proteolytic cleavage that activates fusion activity was established by direct amino acid sequencing of the NH 2 terminus of the F 1 subunit. The PF3 F 0 protein shares major structural features with the previously sequenced F 0 proteins of Sendai virus (murine parainfluenza type 1) and simian virus 5 (SV5, canine parainfluenza type 2), including: similarity in overall length; similarity in location of the site of the activating proteolytic cleavage; the presence of an NH 2 -terminal signal peptide and COOH-proximal membrane anchor; strong conservation of the sequence at the NH 2 terminus of the F 1 subunit; and nearly exact conservation in the number and positions of cysteine residues. Alignment of the F 0 protein sequences of PF3 with those of Sendai, SV5, and respiratory syncytial virus (RSV) using a matrix that stores both amino acid matches and mismatches provided highly significant statistical evidence that all four proteins are related. The order of decreasing relatedness to PF3 was found to be: Sendai virus, SV5, and RSV.