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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Wain-Hobson, S., Sonigo, P., Danos, O., Cole, S., & Alizon, M. (1985) · Cell · doi:10.1016/0092-8674(85)90303-4 · Cited by 1,202
Nucleotide sequence of Moloney murine leukaemia virus
Shinnick, T. M., Lerner, R. A., & Sutcliffe, J. G. (1981) · Nature · doi:10.1038/293543a0 · Cited by 1,039
Characterization of ribosomal frameshifting in HIV-1 gag-pol expression
Jacks, T., Power, M. D., Masiarz, F. R., Luciw, P. A., Barr, P. J., & Varmus, H. E. (1988) · Nature · doi:10.1038/331280a0 · Cited by 966
Genome organization and transactivation of the human immunodeficiency virus type 2
Guyader, M., Emerman, M., Sonigo, P., Clavel, F., Montagnier, L., & Alizon, M. (1987) · Nature · doi:10.1038/326662a0 · Cited by 866
Nucleotide sequence of rous sarcoma virus
Schwartz, D. E., Tizard, R., & Gilbert, W. (1983) · Cell · doi:10.1016/0092-8674(83)90071-5 · Cited by 856
Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot
Brierley, I., Digard, P., & Inglis, S. C. (1989) · Cell · doi:10.1016/0092-8674(89)90124-4 · Cited by 675
RNA Structure Prediction
Turner, D. H., Sugimoto, N., & Freier, S. M. (1988) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.17.060188.001123 · Cited by 647
Signals for ribosomal frameshifting in the rous sarcoma virus gag-pol region
Jacks, T., Madhani, H. D., Masiarz, F. R., & Varmus, H. E. (1988) · Cell · doi:10.1016/0092-8674(88)90031-1 · Cited by 615
Nucleotide sequence of the visna lentivirus: relationship to the AIDS virus
SONIGO, P., ALIZON, M., STASKUS, K., KLATZMANN, D., COLE, S., DANOS, O., RETZEL, E., TIOLLAIS, P., HAASE, A., & WAINHOBSON, S. (1985) · Cell · doi:10.1016/s0092-8674(85)80132-x · Cited by 565
Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses
Chakrabarti, L. A., Guyader, M., Alizon, M., Daniel, M. D., Desrosiers, R. C., Tiollais, P., & Sonigo, P. (1987) · Nature · doi:10.1038/328543a0 · Cited by 542
Retroviruses
Varmus, H. (1988) · Science · doi:10.1126/science.3287617 · Cited by 523
Expression of the Rous Sarcoma Virus pol Gene by Ribosomal Frameshifting
Jacks, T., & Varmus, H. E. (1985) · Science · doi:10.1126/science.2416054 · Cited by 469
Complete nucleotide sequence of the genome of bovine leukemia virus: its evolutionary relationship to other retroviruses.
Sagata, N., Yasunaga, T., Tsuzuku‐Kawamura, J., Ohishi, K., Ogawa, Y., & Ikawa, Y. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.3.677 · Cited by 444
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Self-citation
Nucleotide sequence and genomic organization of feline immunodeficiency virus.
Talbott, R. L., Sparger, E. E., Lovelace, K., Fitch, W. M., Pedersen, N. C., Luciw, P. A., & Elder, J. H. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.15.5743 · Cited by 383
Complete nucleotide sequence of an infectious clone of human T-cell leukemia virus type II: an open reading frame for the protease gene.
Shimotohno, K., Takahashi, Y., Shimizu, N., Gojobori, T., Golde, D. W., Chen, I. S., Miwa, M., & Sugimura, T. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.10.3101 · Cited by 379
Nucleotide sequence of Mason-Pfizer monkey virus: An immunosuppressive D-type retrovirus
SONIGO, P., Barker, C., Hunter, E., & Wain-Hobson, S. (1986) · Cell · doi:10.1016/0092-8674(86)90323-5 · Cited by 337
Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon.
Yoshinaka, Y., Katoh, I., Copeland, T. D., & Oroszlan, S. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.6.1618 · Cited by 335
Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group
Fukasawa, M., Miura, T., Hasegawa, A., Morikawa, S., Tsujimoto, H., Miki, K., Kitamura, T., & Hayami, M. (1988) · Nature · doi:10.1038/333457a0 · Cited by 334
The Plant Viruses: Polyhedral Virions with Tripartite Genomes
(1985) · Springer eBooks · doi:10.1007/978-1-4684-4937-2 · Cited by 331
An efficient ribosomal frame‐shifting signal in the polymerase‐encoding region of the coronavirus IBV.
Brierley, I., Boursnell, M. E. G., Binns, M. M., Bilimoria, B., Blok, V. C., Brown, T., & Inglis, S. C. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb02713.x · Cited by 314
Complete nucleotide sequence of a milk-transmitted mouse mammary tumor virus: two frameshift suppression events are required for translation of gag and pol
Moore, R., Dixon, M., Smith, R., Peters, G., & Dickson, C. (1987) · Journal of Virology · doi:10.1128/jvi.61.2.480-490.1987 · Cited by 256
The Double-stranded RNA Genome of Yeast Virus L-A Encodes Its Own Putative RNA Polymerase by Fusing Two Open Reading Frames
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Equine Infectious Anemia Virus gag and pol Genes: Relatedness to Visna and AIDS Virus
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The Drosophila melanogaster Gypsy Transposable Element Encodes Putative Gene Products Homologous to Retroviral Proteins
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HIV expression strategies: Ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems
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Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster
Saigo, K., Kugimiya, W., Matsuo, Y., Inouye, S., Yoshioka, K., & Yuki, S. (1984) · Nature · doi:10.1038/312659a0 · Cited by 212
Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins.
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Nucleotide sequence of AKV murine leukemia virus
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Sequence and organization of barley yellow dwarf virus genomic RNA
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Analysis of the primary structure of the long terminal repeat and the gag and pol genes of the human spumaretrovirus
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Nucleotide sequence of a complete mouse intracisternal A-particle genome: relationship to known aspects of particle assembly and function
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Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA
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The gag and pol genes of bovine leukemia virus: Nucleotide sequence and analysis
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Sequence relationships of type D retroviruses which cause simian acquired immunodeficiency syndrome
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Translational readthrough of an amber termination codon during synthesis of feline leukemia virus protease
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Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis
Valle, R. P. C., & Devignes, M. (1988) · FEBS Letters · doi:10.1016/0014-5793(88)81225-0 · Cited by 75
Overlapping genes in a yeast double-stranded RNA virus
Diamond, M. E., Dowhanick, J. J., Nemeroff, M. E., Pietras, D. F., Tu, C. L., & Bruenn, J. A. (1989) · Journal of Virology · doi:10.1128/jvi.63.9.3983-3990.1989 · Cited by 73
Expression strategies of the yeast retrotransposon Ty: a short sequence directs ribosomal frameshifting
Wilson, W., Malim, M. H., Mellor, J., Kingsman, A. J., & Kingsman, S. M. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.17.7001 · Cited by 71
[21] RNA pseudoknot: Structure, detection, and prediction
Pleij, C. W. A., & Bosch, L. V. D. (1989) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(89)80107-7 · Cited by 64
Self-citation
Nucleotide sequence of the gag gene and gag-pol junction of feline leukemia virus
Laprevotte, I., Hampe, A., Sherr, C. J., & Galibert, F. (1984) · Journal of Virology · doi:10.1128/jvi.50.3.884-894.1984 · Cited by 50
Molecular cloning, complete nucleotide sequence, and gene structure of the provirus genome of a retrovirus produced in a human lymphoblastoid cell line
Oda, T., Ikeda, S., Watanabe, S., Hatsushika, M., Akiyama, K., & Mitsunobu, F. (1988) · Virology · doi:10.1016/0042-6822(88)90109-2 · Cited by 46
The effect of specific mutations at and around thegag-polgene junction of Moloney murine leukaemia virus
Jones, D. S., Nemoto, F., Kuchino, Y., Masuda, M., Yoshikura, H., & Nishimura, S. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.15.5933 · Cited by 45
Provirus of M7 baboon endogenous virus: nucleotide sequence of the gag-pol region
Tamura, T. A. (1983) · Journal of Virology · doi:10.1128/jvi.47.1.137-145.1983 · Cited by 40
Retroviral gag gene amber codon suppression is caused by an intrinsic cis-acting component of the viral mRNA
Panganiban, A. T. (1988) · Journal of Virology · doi:10.1128/jvi.62.10.3574-3580.1988 · Cited by 33
Nucleotide sequence of the protease-coding region in an infectious DNA of simian retrovirus (STLV) of the HTLV-I family
Inoue, J., Watanabe, T., Satô, M., Oda, A., Toyoshima, K., Yoshida, M., & Seiki, M. (1986) · Virology · doi:10.1016/0042-6822(86)90278-3 · Cited by 33
Molecular Cloning of the Closed Circular Provirus of Human T Cell Leukaemia Virus Type I: A New Open Reading Frame in the gag-pol Region
Hiramatsu, K., Nishida, J., Naito, A., & Yoshikura, H. (1987) · Journal of General Virology · doi:10.1099/0022-1317-68-1-213 · Cited by 28
Luteoviruses
Casper, R. (1988) · Springer eBooks · doi:10.1007/978-1-4613-0921-5_8 · Cited by 24

Research works printed but not linked: 5

MarlorR.L., ParkhurstS.M. and CorcesV.G., Mol Cell Biol6, 1129–1134, 1986.
PleijC.W.A., AbrahamsJ.P., vanBelkumA., RietveldK. and BoschL. in BrintonM.A. and RueckertR.R. (eds.)Positive Strand Viruses. UCLA Symposia on Molecular and Cellular Biology, New Series. Alan R. Liss, New York, 1987, Vol. 54, pp. 299–316.
OdaT., IkedaS., WatanabeS., HatsushikaM., AkiyamaK. and MitsunobuF., Virology167, 468–476, 1988.
MadhaniH.D., JacksT. and VarmusH.E. in FranzaR., CullenB. and Wong-StaalF. (eds.)The Control of HIV Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1988, pp. 119–125.
Bredenbeek P.J.,Nucleic Acid Domains and Proteins Involved in the Replication of Coronaviruses. PhD Thesis, Utrecht, 1990.

Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme
Matsufuji, S., Matsufuji, T., Miyazaki, Y., Murakami, Y., Atkins, J. F., Gesteland, R. F., & Hayashi, S. (1995) · Cell · doi:10.1016/0092-8674(95)90450-6 · Cited by 512
Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily
den Boon, J. A., Snijder, E. J., Chirnside, E. D., de Vries, A. A., Horzinek, M. C., & Spaan, W. J. (1991) · Journal of Virology · doi:10.1128/jvi.65.6.2910-2920.1991 · Cited by 391
Pseudoknots: RNA Structures with Diverse Functions
Staple, D. W., & Butcher, S. E. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030213 · Cited by 375
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
Atkins, J. F., Loughran, G., Bhatt, P. R., Firth, A. E., & Baranov, P. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw530 · Cited by 348
Distinctive features of foot-and-mouth disease virus, a member of the picornavirus family; aspects of virus protein synthesis, protein processing and structure
Belsham, G. J. (1993) · Progress in Biophysics and Molecular Biology · doi:10.1016/0079-6107(93)90016-d · Cited by 344

See all 214

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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