Cited by 214RNA and protein synthesis mechanismsDNA and Nucleic Acid ChemistryRNA Research and Splicing

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RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs

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Ten Dam, Edwin B., Pleij, Cornelius W. A., Bosch, Leendert·1990·Virus Genes

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Abstract

Ribosomal frameshifting on retroviral RNAs has been proposed to be mediated by slippage of two adjacent tRNAs into the -1 direction at a specific heptanucleotide sequence. Here we report a computer-aided analysis of the structure around the established or putative frameshift sites in a number of retroviral, coronaviral, toroviral, and luteoviral RNAs and two dsRNA yeast viruses. In almost all cases a stable hairpin was predicted four to nine nucleotides downstream of the shifty heptanucleotide. More than half of the resulting hairpin loops give rise to potential pseudoknotting with sequences downstream of this hairpin. Especially in the case of the shifty heptanucleotides U UUA AAC and G GGA AAC, stable downstream pseudoknots are present. Indications were also found for the presence of pseudoknots downstream of amber stop condons at readthrough sites in some retroviral RNAs.

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Gene expression strategies of barley yellow dwarf virus
Dinesh-Kumar, S. P. (1993) · Iowa State University Digital Repository (Iowa State University) · doi:10.31274/rtd-180813-11064 · Cited by 5
V, 2.Ribosomal frameshifting in astroviruses
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Retracted
Elaborated pseudoknots that stimulate −1 programmed ribosomal frameshifting or stop codon readthrough in RNA viruses
Huang, X., & Du, Z. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2292296 · Cited by 4
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Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors
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Identification and Analysis of Frameshift Sites
Vimaladithan, A., & Farabaugh, P. J. (2003) · Humana Press eBooks · doi:10.1385/0-89603-397-x:399 · Cited by 4
Translational frameshifting by barley yellow dwarf virus RNA
Di, R. (1992) · Iowa State University Digital Repository (Iowa State University) · doi:10.31274/rtd-180813-11052 · Cited by 4
Gene expression and secondary mRNA structures in different Mycoplasma species
Соколов, В. С., Likhoshvai, V. A., & Matushkin, Y. G. (2014) · Russian Journal of Genetics Applied Research · doi:10.1134/s207905971403006x · Cited by 3
Single-Molecule FRET Studies on Frameshifting RNA Structures of Human Immunodeficiency Virus
Hong, H.-S., Kim, Y., & Hohng, S. (2010) · Bulletin of the Korean Chemical Society · doi:10.5012/bkcs.2010.31.04.1021 · Cited by 3
Function Annotation for Pseudoknot Using Structure Similarity
Chen, Q., & Chen, Y. P. (2011) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2011.50 · Cited by 3
Programmed −1 Frameshifting in Eukaryotes
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Mining Characteristic Relations Bind to RNA Secondary Structures
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Authors: Ten Dam, E. B., Pleij, C. W. A., & Bosch, L.
Affiliations: Leiden University (NL)
Venue: Virus Genes
Publisher: Springer Science and Business Media LLC
Published: 1990-07
Volume: 4
Issue: 2
Pages: 121-136
ISSN: 0920-8569 (ISSN-L)
1572-994X
DOI: 10.1007/bf00678404
PMC: PMC7089070
OpenAlex: W2067191137
Cited by: 214
References: 55
Citations by year: 2026: 1 · 2025: 2 · 2024: 3 · 2023: 2 · 2022: 3 · 2021: 3 · 2020: 1 · 2018: 1 · 2017: 2 · 2016: 4 · 2015: 5 · 2014: 9 · 2013: 5 · 2012: 4
FWCI: 5.49
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
www.springer.com/tdm (tdm)
Locations: Virus Genes (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords: RNA pseudoknots, ribosomal frameshifting, translational readthrough, retroviral RNA, amber stop codon, RNA secondary structure prediction
MeSH terms: Electronic Data Processing, Base Sequence, Codon, Molecular Sequence Data, Mutation, Nucleic Acid Conformation, Retroviridae, RNA, Viral, Suppression, Genetic, Protein Biosynthesis

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RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs

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