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Published July 25, 1983 | public
Journal Article

The 5'-Terminal Sequences of the Genomic RNAs of Several Alphaviruses


The 5'-terminal sequences of the genomic RNAs of several alphaviruses have been determined. The nucleotide sequences at the extreme 5' termini are not highly conserved among the alphaviruses, but a similar stem and loop structure, which begins at the 5' end and utilizes about the first 40 nucleotides, can be formed in each case. Downstream from this structure, beginning about 150 nucleotides from the 5' end, a conserved sequence of 51 nucleotides is found which can form two stable hairpin structures. Examination of the 5'-terminal and 3'-terminal sequences suggests that part of this conserved nucleotide sequence may be involved in cyclization of the RNA. A model is proposed for the function of the 5'-terminal sequences in RNA replication. In addition, sequence homologies among these RNAs strongly support the hypothesis that an AUG codon, which occurs at 60 to 80 nucleotides from the 5' end, depending on the virus, and which may or may not be the first AUG codon, is used for initiation of translation of the non-structural proteins and allows a comparison of the deduced amino acid sequences in the NH_2-terminal regions.

Additional Information

© 1983 Academic Press Inc. (London) Ltd. Received 17 January 1983, and in revised form 28 February 1983. We are deeply grateful to D. W. Trent for supplying us with virion RNAs of Highlands J and of Eastern and Venezuelan equine encephalitis viruses, to S. Schlesinger and S. Monroe for supplying us with defective interfering RNA of Sindbis virus, to W. K. Joklik for supplying us with vaccinia virus, to T. Hunkapiller for the computer programs used in manipulating the sequence data and preparing the Figures, to L. Hood for access to his computer facilities, and to C. M. Rice for helpful discussions. We thank Mrs Edith Lenches for preparations of chick embryo cell cultures. This work was supported by grants PCM 8022830 from the National Science Foundation, GM06965 and AI10793 from the National Institutes of Health, and Biomedical Research Support Grant 507RR 07003 from the National Institutes of Health. J.-H. Ou was supported in part by training grant GM 00086 from the National Institutes of Health.

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