Conserved and non-conserved regions in the sendai virus genome: Evolution of a gene possessing overlapping reading frames

We have sequenced the entire genome of a virulent field isolate of Sendai v irus, the Hamamatsu strain, and compared the sequence with that of a distan t related strain, the Z strain. Calculation of synonymous and non-synonymou s (amino acid changing) nucleotide substitutions revealed regions where cha nges were permissive and non-permissive, and the experimentally determined functional region were found to be conserved, showing that important region s for function were conserved during evolution. In the cistron-overlapping regions in the P gene, one reading frame was conserved, whereas the other o verlapping frame was flexible. The priority of one frame could be a strateg y for evolution of an overlapping gene of RNA viruses. We found that the ca rboxyl two thirds of the C protein was conserved over the amino-terminal on e third, possessing priority to the overlapping P polypeptide. This suggest s that the carboxyl two thirds of the C protein have a functional importanc e. We also found a highly variable region between the L coding frame and th e 5' trailer sequence. The relevance of these findings to actual viral repl ication should be clarified in the future.