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Nucleic Acids Research, 1980, Vol. 8, No. 15 3307-3318
© 1980

MOLECULAR BIOLOGY

Nucleotide sequence of the putative recognition site for coat protein in the RN As of alfalfa mosaic virus and tobacco streak virus

Ellen C. Koper-Zwarthoff and John F. Bol

Department of Biochemistry, State University of Leiden P.O. Box 9505, 2300 RA Leiden, Netherlands

Received June 13, 1980. The sequence of the 3'-terminal 180 and 140 nucleotides of RNAs 2 and 3, respectively, of tobacco streak virus (TSV) was deduced by reverse transcription in the presence of a specific primer and chain terminators. Homology between the two RNAs was found to be restricted to a 3'-terminal region of about 45 nucleotides. The data were compared with the sequence of the homologous region of 145 nucleotides occurring at the 3'-termini of the alfalfa mosaic virus (ALMV) RNAs, which contains the specific binding site for coat protein (Koper-Zwarthoff et al., Nucleic Acids Ree. 7, 1887-1900 (1979); Houwing and Jaspars, Biochemistry 17, 2927-2933 (1978)). This was done because of the evidence that the RNAs of ALMV and TSV contain specific binding sites for their own as well as each others coat protein, and that binding of coat protein to these sites is required to initiate infection (Van Vloten-Doting, Virology 65, 215-225 (1975)). The 3'-terminal homologous regions of ALMV and TSV have two features in common: the presence of several stable hairpins and the multiple occurrence of the tetranucleotide sequence AUGC. The hairpins cause the linear array of tandemly repeated AUGC-boxes. It is postulated that the primary interaction of coat protein molecules with the RNAs of ALMV and TSV is a cooperative process involving several binding sites each being composed of a hairpin flanked at its 3'-side by an AUGC-sequence.


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