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J. Biol. Chem., Vol. 275, Issue 47, 37118-37126, November 24, 2000

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Recognition of RNA Encapsidation Signal by the Yeast L-A Double-stranded RNA Virus^*

Tsutomu Fujimura and Rosa Esteban

From the Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca 37007, Spain

The encapsidation signal of the yeast L-A virus contains a 24-nucleotide stem-loop structure with a 5-nucleotide loop and an A bulged at the 5' side of the stem. The Pol part of the Gag-Pol fusion protein is responsible for encapsidation of viral RNA. Opened empty viral particles containing Gag-Pol specifically bind to this encapsidation signal in vitro. We found that binding to empty particles protected the bulged A and the flanking-two nucleotides from cleavage by Fe(II)-EDTA-generated hydroxyl radicals. The five nucleotides of the loop sequence (⁴¹⁹⁰GAUCC⁴¹⁹⁴) were not protected. However, T1 RNase protection and in vitro mutagenesis experiments indicated that G⁴¹⁹⁰ is essential for binding. Although the sequence of the other four nucleotides of the loop is not essential, data from RNase protection and chemical modification experiments suggested that C⁴¹⁹⁴ was also directly involved in binding to empty particles rather than indirectly through its potential base pairing with G⁴¹⁹⁰. These results suggest that the Pol domain of Gag-Pol contacts the encapsidation signal at two sites: one, the bulged A, and the other, G and C bases at the opening of the loop. These two sites are conserved in the encapsidation signal of M1, a satellite RNA of the L-A virus.

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