Global changes in the RNA binding specificity of HIV-1 Gag regulate virion genesis
Open accessAbstract
The HIV-1 Gag protein orchestrates all steps of virion genesis, including membrane targeting and RNA recruitment into virions. Using crosslinking-immunoprecipitation (CLIP) sequencing, we uncover several dramatic changes in the RNA-binding properties of Gag that occur during virion genesis, coincident with membrane binding, multimerization, and proteolytic maturation. Prior to assembly, and after virion assembly and maturation, the nucleocapsid domain of Gag preferentially binds to psi and Rev Response elements in the viral genome, and GU-rich mRNA sequences. However, during virion genesis, this specificity transiently changes in a manner that facilitates genome packaging; nucleocapsid binds to many sites on the HIV-1 genome and to mRNA sequences with a HIV-1-like, A-rich nucleotide composition. Additionally, we find that the matrix domain of Gag binds almost exclusively to specific tRNAs in the cytosol, and this association regulates Gag binding to cellular membranes.
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tRNAs were identified as interacting with HIV-1 MA, but whether the interaction is specific is not yet clear.
“For example, although tRNAs were identified as interacting with HIV-1 MA (76), whether the interaction is specific is not yet clear.”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [76]
The Results section, “MA binds specifically to particular tRNAs,” confirms that HIV-1 MA interacts with tRNAs but directly contradicts the claim that specificity remains unclear. It reports highly selective binding to particular tRNAs, some up to 100-fold more frequently than most others. The Introduction describes specificity as uncertain before these experiments, not as the paper’s conclusion. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredtRNAs comprise over 60% of Gag-bound RNAs.
“As identified in a cross-linking-immunoprecipitation sequencing (CLIP-seq)-based study, tRNAs comprise over 60% of Gagbound RNAs (76).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [76]
The Results section, “tRNAs are the most frequently Gag-bound RNA in cells, but not in virions,” reports that tRNAs account for about 60–70% of Gag-bound reads in cells. It also says the tRNA fraction is greatly reduced in virions, so the unqualified claim omits an important condition. (LLM, conf=0.88)
Experimental — accuracy not yet measuredViral assembly revolves around a gRNA dimer that then requires the Gag selectivity switch from specific to nonspecific RNA binding.
“Thus, viral assembly revolves around a gRNA dimer that then requires the Gag selectivity switch from specific to nonspecific RNA binding”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Kutluay et al. 2014
The Introduction (page unavailable) reports that a viral RNA dimer nucleates assembly and that Gag initially binds discrete sites on viral RNA. The Results and Discussion (pages unavailable) describe broader genome binding as Gag multimerizes during assembly, but do not establish that assembly requires a switch to nonspecific RNA binding; the Discussion says the change contributes to selective packaging. (LLM, conf=0.86)
Experimental — accuracy not yet measuredMA binds full-length tRNAs, and the binding sites are in the 5'-half, specifically in the D-loop.
“MA binds full-length tRNAs, and the binding sites are in the 5Ј-half, specifically in the D-loop (76).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [76]
The MA domain of HIV-1 Gag interacts with RNAs in vitro and in cells.
“In addition to NC, which is well known for its viral gRNA binding and chaperone activities, the MA domain of HIV-1 Gag also interacts with RNAs in vitro and in cells (74 -76).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [76]
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Cites
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“Thus, viral assembly revolves around a gRNA dimer that then requires the Gag selectivity switch from specific to nonspecific RNA binding (Kutluay et al. 2014 ).”
- Authors
- Kutluay, S. B., Zang, T., Blanco-Melo, D., Powell, C., Jannain, D., Errando, M., & Bieniasz, P. D.
- Affiliations
- Aaron Diamond AIDS Research Center (US)
- Howard Hughes Medical Institute (US)
- Columbia University (US)
- Corresponding author
- Bieniasz, Paul D.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2014-11
- Volume
- 159
- Issue
- 5
- Pages
- 1096-1109
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4247003
- OpenAlex
- W2141556708
- Cited by
- 257
- References
- 10
- Citations by year
- 2026: 11 · 2025: 13 · 2024: 20 · 2023: 13 · 2022: 22 · 2021: 25 · 2020: 26 · 2019: 19 · 2018: 27 · 2017: 20 · 2016: 32 · 2015: 27 · 2014: 2
- FWCI
- 12.04
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 384 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- amfAR, The Foundation for AIDS Research
- National Institutes of Health
- National Institute of General Medical Sciences (P50GM103297)
- National Institute of Allergy and Infectious Diseases (R01AI501111, R01AI050111, K22AI116258)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and Retrovirus Studies
- Keywords
- HIV-1 Gag, RNA binding specificity, viral assembly, nucleocapsid domain, matrix domain, tRNA binding, Rev response element, genome packaging, membrane binding, Gag multimerization, proteolytic maturation
- MeSH terms
- Base Sequence, Cell Line, Humans, Molecular Sequence Data, RNA, Transfer, RNA, Viral, HIV-1, Genes, env, Protein Structure, Tertiary, Virus Assembly, Chromatin Immunoprecipitation, gag Gene Products, Human Immunodeficiency Virus
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