The 3′-non-coding regions of alpharivus RNAs contain repeating sequences

Jing Hsiung Ou, Dennis W. Trent, James H. Strauss

Research output: Contribution to journalArticle

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Abstract

We have compared the 3′-terminal non-coding sequences of the RNAs from 10 alphaviruses and found this region to be composed of distinct domains in terms of base composition, degree of sequence conservation, and sequence organization. The first 50 to 60 nucleotides adjacent to the 3′-terminal poly(A) tract are extremely A + U-rich (up to 90% A + U). Of these, the first 19 nucleotides are highly conserved, and we postulate that this conserved sequence serves as a replicase recognition signal. For strains of Venezuelan, Western, and Eastern equine encephalitis viruses, Highlands J virus and Sindbis virus, only the sixth nucleotide of this sequence shows any variation. This conserved region is slightly more variable for Semliki Forest virus and Middelburg virus. The remainder of the A + U-rich region shows only limited homology among viruses and may contain signals for polyadenylation. Upstream from the A + U-rich domain, between 60 and 300 nucleotides from the poly(A) tract, there are repeated sequences in each viral RNA. These repeats are up to 60 nucleotides in length and can be either tandemly or nontandemly arranged. The repeated sequences show considerable conservation among closely related viruses, in contrast to the non-repeated sequences in this region which contain little homology.

Original languageEnglish (US)
Pages (from-to)719-730
Number of pages12
JournalJournal of Molecular Biology
Volume156
Issue number4
DOIs
StatePublished - Apr 25 1982

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Nucleotides
RNA
Viruses
Poly A
Western Equine Encephalitis Viruses
Eastern equine encephalitis virus
Venezuelan Equine Encephalitis Viruses
Semliki forest virus
Sindbis Virus
Alphavirus
Untranslated RNA
Polyadenylation
Conserved Sequence
Base Composition
Viral RNA

ASJC Scopus subject areas

  • Virology

Cite this

The 3′-non-coding regions of alpharivus RNAs contain repeating sequences. / Ou, Jing Hsiung; Trent, Dennis W.; Strauss, James H.

In: Journal of Molecular Biology, Vol. 156, No. 4, 25.04.1982, p. 719-730.

Research output: Contribution to journalArticle

Ou, Jing Hsiung ; Trent, Dennis W. ; Strauss, James H. / The 3′-non-coding regions of alpharivus RNAs contain repeating sequences. In: Journal of Molecular Biology. 1982 ; Vol. 156, No. 4. pp. 719-730.
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