Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs.
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.
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Institute of Molecular Plant Sciences, Goriaeus Laboratories, Leiden University, The Netherlands.
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D017794:Alfalfa mosaic virus / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002213:Capsid / Q000302:isolation & purification / Q000378:metabolism*; D036022:Capsid Proteins; D004279:DNA, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship
D036022:Capsid Proteins; D004279:DNA, Viral; D012367:RNA, Viral; C095691:coat protein, Alfalfa mosaic virus