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Nucleic Acids Research, 1983, Vol. 11, No. 9 2815-2826
© 1983

MOLECULAR BIOLOGY

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

M. Ravelonandro, T. Godefroy-Colburn and L. Pinck

Laboratoire de Virologie, Institut de Biologic Moleculaire et Cellulaire du C.N.R.S. 15 rue Descartes, 67000 Strasbourg, France

Received March 18, 1983. Accepted April 14, 1983.

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.


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