Structure of the 5′-terminal untranslated region of the genomk RNAs from two strains of Alfalfa Mosaic Virus

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Abstract
We report the sequences of the 5′-terminal regions of the 3 Alfalfa Mosaic Virus genomic RNAs for the Strasbourg strain (A1MV-S) and for a new isolate, A1MV-B ; they are compared to similar data obtained by Koper-Zwarthoff et al. (Nucleic Acids Res. 1980, 8, 5635–5647) for strain 425. The structure of the leaders is highly conserved in RNAs 1 and 2. The length of the leader is 102, 100 and 101 nucleotides in RNA1 for strains S, B and 425 respectively ; 55 and 56 1n RNA2 for strains S and B respectively. In RNA3 however, there are important differences near the 5′-terminus between strain S and the other two.: The total leader length is 258 nucleotides for strain S and 242 for strain B. The secondary structure models show a conserved hairpin near the 5′-end of each genomic RNA of A1MV-S. This hairpin is inexistent in RNA3 of the B and 425 strains. The degree of base-pairing increases with leader length. The initiator codon is located in a single stranded region in RNA2 whereas it is found in a hairpin stem 1n RNA 3.