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PMID: 1663382 Published · ppublish English Journal Article

RNA pseudoknots downstream of the frameshift sites of retroviruses.

Genetic analysis, techniques and applications ·Vol. 8 ·No. 7 ·1991-11-00 ·Pages 191-205

Le SY, Shapiro BA, Chen JH, Nussinov R, Maizel JV

Abstract

RNA pseudoknot structural motifs could have implications for a wide range of biological processes of RNAs. In this study, the potential RNA pseudoknots just downstream from the known and suspected retroviral frame-shift sites were predicted in the Rous sarcoma virus, primate immunodeficiency viruses (HIV-1, HIV-2, and SIV), equine infectious anemia virus, visna virus, bovine leukemia virus, human T-cell leukemia virus (types I and II), mouse mammary tumor virus, Mason-Pfizer monkey virus, and simian SRV-1 type-D retrovirus. Also, the putative RNA pseudoknots were detected in the gag-pol overlaps of two retrotransposons of Drosophila, 17.6 and gypsy, and the mouse intracisternal A particle. For each sequence, the thermodynamic stability and statistical significance of the secondary structure involved in the predicted tertiary structure were assessed and compared. Our results show that the stem-loop structures in the pseudoknots are both thermodynamically highly stable and statistically significant relative to other such configurations that potentially occur in the gag-pol or gag-pro and pro-pol junction domains of these viruses (300 nucleotides upstream and downstream from the possible frameshift sites are included). Moreover, the structural features of the predicted pseudoknots following the frameshift site of pro-pol overlaps of the HTLV-1 and HTLV-2 retroviruses are structurally well conserved. The occurrence of eight compensatory base changes in the tertiary interaction of the two related sequences allow the conservation of their tertiary structures in spite of the sequence divergence. The results support the possible control mechanism for frameshifting proposed by Brierley et al. and Jacks et al.

MeSH Terms
Base Sequence DNA Transposable Elements Molecular Sequence Data Nucleic Acid Conformation Protein Biosynthesis RNA, Viral/chemistry,genetics Retroviridae/genetics Sequence Homology, Nucleic Acid Thermodynamics
Chemicals
DNA Transposable Elements RNA, Viral
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Le S Y
Institute of Biological Sciences, National Research Council of Canada, Ottawa.
Shapiro B A
Chen J H
Nussinov R
Maizel J V
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Article Info
Journal
Genetic analysis, techniques and applications
Abbr.
Genet Anal Tech Appl
ISSN
1050-3862
DOI
10.1016/1050-3862(91)90013-h
Published
1991-11-00
Pages
191-205
Language
English
Region
Netherlands
NLM ID
9004550
PMCID
PMC7128882
Subset
IM
External Links
PubMed source DOI: 10.1016/1050-3862(91)90013-h PMC Full Text
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