Identification of Binding Sites of Turnip Yellow Mosaic Virus Protein and RNA by Crosslinks Induced in situ

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Abstract
Turnip yellow mosaic virus RNA and protein could be crosslinked in situ by UV irradiation at pH 4.8 but not at pH 7.3, and by bisulfite treatment at pH 7.3. Crosslinked peptides could be located in the primary structure of the viral coat protein. Three regions were bound covalently by UV irradiation, and 2 of these 3 regions were bound also by bisulfite treatment. The yield of the crosslinking reaction could be high, indicating that almost all protein subunits of each virion reacted with the viral RNA. The crosslinked peptides contain most of the acidic and basic amino acids of the protein, often associated into pairs of opposite charge. Implications for the folding of the RNA into the virion and for models of RNA-protein interactions are discussed.