Similarities among plant virus (+) and (−) RNA termini imply a common ancestry with promoters of eukaryotic tRNAs

Abstract

The 5′ ends of brome mosaic virus (BMV) RNAs contain sequences similar to the consensus internal control region (ICR) of pol III promoters in tRNA genes. Comparison of BMV (+)RNA 5′ termini with BMV (−)RNA termini revealed the presence of two (tandem) repeats of some 30 nucleotides, the more internal containing a region of 73% similarity to the tRNA consensus ICR2 (downstream) region of the ICR. Tandem repeats containing motifs similar to the ICR2 consensus were found at the 5′ termini of (−)RNAs of cucumo-, tobamo-, and tymoviruses whose 3′ (+)RNAs have aminoacylatable tRNA-like structures. Single regions of homology to the BMV(+)RNA 5′ terminus, containing an ICR2-like motif, were detected for several tobravirus RNAs, and for satellite tobacco necrosis virus RNA. The (+)-stranded genomes of these viruses have not been shown to be capable of amino acid esterification. The ICR2 consensus (GGUUCGANUCC) is nearly palindromic, and is contained with the T4 /C loop of tRNAs and viral analogs. Consequently, tRNA promoter-like motifs can be seen at both termini of (+) and (-) RNAs of bromoviruses and other viruses. The presence of ICRI and ICR2-like sequences in BMV genomic 5′ (+)RNAs and the tobamovirus 5′ (−)RNAs may reflect promoter arrangements of primordial genomic RNAs ancestral to both modern plant viruses and eukaryotic tRNAs. Several derivative concepts related to genome evolution are discussed, including the origin of asymmetric strand synthesis of RNAs.