Nucleic Acids Research, Vol 24, Issue 14 2660-2665, Copyright © 1996 by Oxford University Press
CB Reusken and JF Bol
The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV)
and ilarviruses contain a number of AUGC-motifs separated by hairpin
structures. Binding of coat protein (CP) to such elements in the RNAs is
required to initiate infection of these viruses. Determinants for CP
binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed
by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains
AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop
structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all
three AUGC-motifs were involved in CP binding. Mutation of the A- and
U-residues of motifs 1 or 3 had no effect on CP binding but similar
mutations in motif 2 abolished CP binding. A mutational analysis of the
stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP
binding. Randomization of the sequence of the stems and loops of STLP1 and
STLP2 had no effect on CP binding as long as the secondary structure was
maintained. This indicates that the two hairpins are not involved in
sequence-specific interactions with CP. They may function in a secondary
structure- specific interaction with CP and/or in the assembly of the
AUGC-motifs in a configuration required for CP binding.
ARTICLES
Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs
Institute of Molecular Plant Sciences, Goriaeus Laboratories, Leiden University, The Netherlands.
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