Conservation of the 3′ terminal nucleotide sequence in five carlaviruses

Abstract

Carnation latent virus (CLV) is the type member of the carlavirus group (1), a group with positive sense RNA genomes of Mr 2.3-3.0X 10 which are polyadenylated at the 3' terminus. The nucleotide sequence of the 3' proximal regions of four carlaviruses: potato virus M (PVM), potato virus S (PVS), lily symptomless virus (LSV) and Helenium virus S (HelVS) have recently been presented (2, 3, 4, 5). Using a similar procedure for cloning, employing oligo (dT) priming of first strand cDNA synthesis, we have generated a library of 3' terminal clones of CLV RNA which have been sequenced by the dideoxynucleotide termination procedure. An examination of the 3' sequence of PVM (2), PVS (3), LSV (4) and HelVS (5) RNAs and a comparison with the 3' nucleotide sequence of CLV RNA reveals some striking similarities. These similarities are conserved in all five viruses in the central region of a putative 3 ' terminal openreading frame (ORF) coding for polypeptides of 12.6, 10.8, 11.6, 10.7 and 16 KDa for respectively HelVS, PVM, CLV, PVS and LSV (Figure 1). Within this region of high conservation four Cys residues which conform to a consensus sequence for a putative 'zinc-finger' nucleic acid-binding domain (6) are also conserved. All five proteins contain a high proportion of positively charged residues with CLV containing 15 Arg and 9 Lys residues and 10 residues of Glu and Asp. This 3' terminal ORF appears to be unique to carlaviruses and sets them apart from other virus groups but no direct evidence for its expression in vivo or in vitro has been presented (2, 3, 4, 5). Analysis of the 3' terminal non-coding regions of the five RNAs using the UWGCG GAP program (7) revealed over 60% homology between the nucleotide sequences of CLV compared with the other four viruses (Figure 2). This 3' region of the viral RNAs has the capacity to be folded into a series of stem-loop structures. Such strict sequence conservation at the 3' terminus of carlaviruses may have implications with regard to RNA secondary structure and configuration and might be important in RNA replication. However the putative polyadenylation signal AATAAA present in the terminal sequence of HelVS (5) and PVM RNAs (2) is not conserved in all of the viruses.