Structural similarities between the RNAs of two satellites of tobacco necrosis virus

Abstract

The complete nucleotide sequence of satellite tobacco necrosis virus 2 (STNV-2) RNA has been determined. It has the same organization as the previously studied STNV-1 RNA. The 5' untranslated regions (about 30 nt) are nearly identical, while the coat protein coding regions (about 600 nt) have 55% nucleotide sequence similarity. The 620-nt-long trailer sequences, with 64% nucleotide sequence conservation, can fold into a phylogenetically conserved secondary structure consisting of three pseudoknots followed by a long-range interaction-born hairpin structure. The significance of these elements is discussed in view of the particular properties (stability, translational competitiveness, and replication) that characterize these RNAs.