The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure
Open accessAbstract
The 5' and 3' ends of HIV-1 transcripts are identical in sequence. This repeat region (R) folds a stem-loop structure that is termed the poly(A) hairpin because it contains polyadenylation or poly(A) signals: the AAUAAA hexamer motif, the cleavage site and part of the GU-rich downstream element. Obviously, HIV-1 gene expression necessitates differential regulation of the two poly(A) sites. Previous transfection experiments indicated that the wild-type poly(A) hairpin is slightly inhibitory to the process of polyadenylation, and further stabilization of the hairpin inhibited polyadenylation completely. In this study, we tested wild-type and mutant transcripts with poly(A) hairpin structures of differing thermodynamic stabilities for the in vitro binding of polyadenylation factors. Mutant transcripts with a destabilized hairpin efficiently bound the polyadenylation factors, which were provided either as purified proteins or as nuclear extract. The RNA mutant with a stabilized hairpin did not form this 'poly(A) complex'. Additional mutations that repair the stability of this hairpin restored the binding capacity. Thus, an inverse correlation was measured between the stability of the poly(A) hairpin and its ability to interact with polyadenylation factors. The wild-type HIV-1 transcript bound the polyadenylation factors suboptimally, but full activity was obtained in the presence of the USE enhancer element that is uniquely present upstream of the 3' poly(A) site. We also found that sequences of the HIV-1 leader, which are uniquely present downstream of the 5' poly(A) site, inhibit formation of the poly(A) complex. This inhibition could not be ascribed to a specific leader sequence, as we measured a gradual loss of complex formation with increasing leader length. We will discuss the regulatory role of RNA structure and the repressive effect of leader sequences in the context of differential HIV-1 polyadenylation.
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In HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5′ end of the transcript.
“Structure prediction and biochemical approaches suggest that in HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5′ end of the transcript (Berkhout et al. 1995, Das et al. 1999, Klasens et al. 1999).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Klasens et al. 1999
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Ashe, M. P., Griffin, P., James, W., & Proudfoot, N. J. (1995) · Genes & Development · doi:10.1101/gad.9.23.3008 · Cited by 125 · see citing works
Brown, P. H., Tiley, L. S., & Cullen, B. R. (1991) · Journal of Virology · doi:10.1128/jvi.65.6.3340-3343.1991 · Cited by 85 · see citing works
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Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication
Jehad, M. A., Ali, L. M., Pillai, V. N., Prabhu, S. G., Mustafa, F., & Rizvi, T. A. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf066 · Cited by 5 · see citing works
“Structure prediction and biochemical approaches suggest that in HIV-1, the polyA signal forms a stem-loop motif that could facilitate suppression of the polyA signal at the 5 end of the transcript (Berkhout et al. 1995 , Das et al. 1999 , Klasens et al. 1999 ).”
- Authors
- Klasens, B. I. F., Thiesen, M., Virtanen, A., & Berkhout, B.
- Affiliations
- Amsterdam UMC Location University of Amsterdam (NL)
- Uppsala University (SE)
- Corresponding author
- Berkhout, B.
- ORCID
- Berkhout, B.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-01-01
- Volume
- 27
- Issue
- 2
- Pages
- 446-454
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC148199
- OpenAlex
- W2043961657
- Cited by
- 80
- References
- 2
- Citations by year
- 2025: 2 · 2024: 3 · 2023: 2 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 1 · 2018: 2 · 2017: 1 · 2015: 2 · 2014: 4 · 2013: 5 · 2012: 4
- FWCI
- 2.07
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- UvA-DARE (University of Amsterdam) (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- UvA-DARE (University of Amsterdam) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Aids Fonds
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- HIV-1, polyadenylation, RNA secondary structure, polyadenylation factors, thermodynamic stability, stem-loop structure
- MeSH terms
- Enhancer Elements, Genetic, Models, Genetic, Mutation, Nucleic Acid Conformation, Protein Binding, RNA Processing, Post-Transcriptional, RNA, Messenger, RNA, Viral, HIV-1, Gene Expression Regulation, Viral, RNA-Binding Proteins, mRNA Cleavage and Polyadenylation Factors
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