Comparative studies of the 3′-terminal sequences of several alphavirus RNAs

Abstract

The 3′-termini of 26 S RNA of Sindbis virus and of the virion 49 S RNAs of Sindbis virus, Semliki Forest virus, and Middelburg virus have been sequenced by using a chain-terminating sequencing method with reverse transcriptase. Both 49 S and 26 S RNAs of Sindbis virus have identical 3′-terminal sequence for at least 146 nucleotides from the poly(A) tracts. The 26 S RNA is known to be a subgenomic RNA located at or near the 3′-end of 49 S RNA; our present results indicate that 26 S and 49 S RNA are coterminal. The 49 S RNAs of all three viruses contain a region of 20 nucleotides adjacent to the poly(A) which is highly conserved. This conserved sequence could be the replicase recognition site and/or a recognition site for encapsidation. After this conserved region the sequences of Sindbis and of Semliki Forest virus diverge significantly but there does appear to be some residual sequence homology in these regions. The 3′-termini of Sindbis virus and Semliki Forest virus RNAs contain a high content of A and U; of the first 50 nucleotides adjacent to the poly(A) tail over half are U and over one quarter are A. In addition repeating sequences are present in the 3′-termini.