Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4

The specific binding of alfalfa mosaic virus coat protein to viral RNA requires determinants in the 3' untranslated region (UTR). Coat protein and peptide binding sites in the 3' UTR of alfalfa mosaic virus RNA 4 have been analyzed by hydroxyl radical footprinting, deletion mapping, and si...

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Bibliographic Details
Published in:Journal of Virology 1994-04, Vol.68 (4), p.2194-2205
Main Authors: Houser-Scott, F, Baer, M.L, Liem, K.F. Jr, Cai, J.M, Gehrke, L
Format: Article
Language:English
Subjects:
Agronomy. Soil science and plant productions
alfalfa mosaic virus
Alfalfa mosaic virus - genetics
Amino Acid Sequence
ARN
Base Sequence
Biological and medical sciences
Capsid - metabolism
Conserved Sequence
DNA Mutational Analysis
Fundamental and applied biological sciences. Psychology
GENOMAS
GENOME
Molecular Sequence Data
Mosaic Viruses - genetics
MUTACION
MUTATION
Nucleic Acid Conformation
Peptide Fragments - metabolism
Phytopathology. Animal pests. Plant and forest protection
Plant viruses and viroids
Protein Binding
Protein Biosynthesis
PROTEINAS
PROTEINE
Regulatory Sequences, Nucleic Acid - genetics
RNA, Viral - genetics
RNA, Viral - metabolism
SECUENCIA NUCLEICA
Sequence Homology, Nucleic Acid
SEQUENCE NUCLEIQUE
Structure-Activity Relationship
Systematics. Structure, properties and multiplication. Genetics
VIRUS DE LAS PLANTAS
VIRUS DES VEGETAUX
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Summary:The specific binding of alfalfa mosaic virus coat protein to viral RNA requires determinants in the 3' untranslated region (UTR). Coat protein and peptide binding sites in the 3' UTR of alfalfa mosaic virus RNA 4 have been analyzed by hydroxyl radical footprinting, deletion mapping, and site-directed mutagenesis experiments. The 3' UTR has several stable hairpins that are flanked by single-stranded (A/U)UGC sequences. Hydroxyl radical footprinting data show that five sites in the 3' UTR of alfalfa mosaic virus RNA 4 are protected by coat protein, and four of the five protected regions contain AUGC or UUGC. Electrophoretic mobility band shift results suggest four coat protein binding sites in the 3' UTR. A 3'-terminal 39-nucleotide RNA fragment containing four AUGC repeats bound coat protein and coat protein peptides with high affinity; however, coat protein bound poorly to antisense 3' UTR transcripts and poly(AUGC)10. Site-directed mutagenesis of AUGC865-868 resulted in a loss of coat protein binding and peptide binding by the RNA fragment. Alignment of alfalfa mosaic RNA sequences with those from several closely related ilarviruses demonstrates that AUGC865-868 is perfectly conserved; moreover, the RNAs are predicted to form similar 3'-terminal secondary structures. The data strongly suggest that alfalfa mosaic virus coat protein and ilarvirus coat proteins recognize invariant AUGC sequences in the context of conserved structural elements
ISSN:0022-538X
1098-5514
DOI:10.1128/JVI.68.4.2194-2205.1994