The 3'-Non-coding Regions of Alpharivus RNAs Contain Repeating Sequences

We have compared the 3'-terminal non-coding sequences of the RNAs from 10 alphaviruses and found this region to be composed of distinct domains in terms of base composition, degree of sequence conservation, and sequence organization. The first 50 to 60 nucleotides adjacent to the 3'-terminal poly(A) tract are extremely A + U-rich (up to 90% A + U). Of these, the first 19 nucleotides are highly conserved, and we postulate that this conserved sequence serves as a replicase recognition signal. For strains of Venezuelan, Western, and Eastern equine encephalitis viruses, Highlands J virus and Sindbis virus, only the sixth nucleotide of this sequence shows any variation. This conserved region is slightly more variable for Semliki Forest virus and Middelburg virus. The remainder of the A + U rich region shows only limited homology among viruses and may contain signals for polyadenylation. Upstream from the A + U-rich domain, between 60 and 300 nucleotides from the poly(A) tract, there are repeated sequences in each viral RNA. These repeats are up to 60 nucleotides in length and can be either tandemly or nontandemly arranged. The repeated sequences show considerable conservation among closely related viruses, in contrast to the non-repeated sequences in this region which contain little homology.