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Nucleic Acids Research, 1988, Vol. 16, No. 13 6205-6221
© 1988

Articles

Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP

Yoshio Inokuchi*, Ann B. Jacobson2, Tadaaki Hirose1, Seiichi Inayama1 and Akikazu Hirashima+

1Department of Molecular Biology and Institute, School of Medicine, Keio University Shinjuku-ku, Tokyo 160, Japan 2Department of Molecular Biology and of Microbiology, SUNY at Stony Brook, Stony Stony Brook, NY 11794-8621, USA

*To whom correspondence should be addressed

Received December 7, 1987. Revised May 11, 1988. Accepted May 11, 1988.

We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Qß The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through protein contains 330 amino acids and the replicase ß-subunit contains 575 amino acids. SP is 59 nucleotides longer than Qß We have analyzed both sequence and structural conservation between SP and Qß and shown that the sequences for the coat and central region of the replicase are strongly conserved between the two genomes. We also show that the S and M replicase binding sites of Qß are strongly conserved in SP. Interestingly, the base composition of SP and Qß differ significantly from one another , and most of the differences can be accounted for by a strong preponderance of U in the third position of each codon of Qß relative to SP. We also compare conserved hairpins associated with potential coat protein and replicase binding sites.

+present address: Genetic Engineering Laboratory, Yakult Central Institute for Microbiological Research, Kunitachi-shi, Tokyo 186, Japan


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