HIV-1 Capsid-Cyclophilin Interactions Determine Nuclear Import Pathway, Integration Targeting and Replication Efficiency
Open accessAbstract
Lentiviruses such as HIV-1 traverse nuclear pore complexes (NPC) and infect terminally differentiated non-dividing cells, but how they do this is unclear. The cytoplasmic NPC protein Nup358/RanBP2 was identified as an HIV-1 co-factor in previous studies. Here we report that HIV-1 capsid (CA) binds directly to the cyclophilin domain of Nup358/RanBP2. Fusion of the Nup358/RanBP2 cyclophilin (Cyp) domain to the tripartite motif of TRIM5 created a novel inhibitor of HIV-1 replication, consistent with an interaction in vivo. In contrast to CypA binding to HIV-1 CA, Nup358 binding is insensitive to inhibition with cyclosporine, allowing contributions from CypA and Nup358 to be distinguished. Inhibition of CypA reduced dependence on Nup358 and the nuclear basket protein Nup153, suggesting that CypA regulates the choice of the nuclear import machinery that is engaged by the virus. HIV-1 cyclophilin-binding mutants CA G89V and P90A favored integration in genomic regions with a higher density of transcription units and associated features than wild type virus. Integration preference of wild type virus in the presence of cyclosporine was similarly altered to regions of higher transcription density. In contrast, HIV-1 CA alterations in another patch on the capsid surface that render the virus less sensitive to Nup358 or TRN-SR2 depletion (CA N74D, N57A) resulted in integration in genomic regions sparse in transcription units. Both groups of CA mutants are impaired in replication in HeLa cells and human monocyte derived macrophages. Our findings link HIV-1 engagement of cyclophilins with both integration targeting and replication efficiency and provide insight into the conservation of viral cyclophilin recruitment.
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Mutations in HIV-1 CA and its interactions with cyclophilin do not inhibit viral integration but favor integration into genomic regions that are not transcriptionally active, as opposed to wild-type virus typically integrating into transcriptionally active regions.
“Evidence toward this has been drawn from experiments that have shown that mutations in HIV-1 CA and its interactions with cyclophilin do not inhibit viral integration but favor integration into the genomic regions that are not transcriptionally active, as opposed to wild-type virus typically integrating into the transcriptionally active regions (Lewinski et al. 2006, Schaller et al. 2011, Engelman”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Schaller et al. 2011
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Experimental — accuracy not yet measuredHIV-1 nuclear import is mediated by the viral capsid, which directly interacts with several components of the cellular nuclear import machinery, including Nup153 and Nup358.
“HIV-1 nuclear import is mediated via the viral capsid, which interacts directly with several components of the cellular nuclear import machinery, including the nuclear pore complex components Nup153 and Nup358 (REF.76–78).”
From Structure and function of retroviral integrase (2022) · cites this paper as [77]
The Discussion reports direct binding between HIV-1 capsid and the cyclophilin domain of Nup358, supporting a capsid-mediated nuclear-entry pathway. The Nup153-dependent nuclear-entry section shows that Nup153 affects infection, but the Discussion describes interaction with Nup153 as a possibility, not a demonstrated direct capsid–Nup153 interaction. The claim overstates what this paper establishes for Nup153. (LLM, conf=0.88)
Experimental — accuracy not yet measuredGag-derived protein(s), especially CA, play an important role during retroviral integration.
“For example, it has been suggested that Gag-derived protein(s), especially CA, plays an important role during retroviral integration.”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Schaller et al. 2011
The Discussion states that HIV-1 capsid (CA) sequence influences where HIV-1 integrates, and the CA-mutant results show altered integration-site distributions. This supports a role for CA in integration targeting, but the paper does not establish the broader claim that Gag-derived proteins play an important role in retroviral integration generally. (LLM, conf=0.86)
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“…with cyclophilin do not inhibit viral integration but favor integration into the genomic regions that are not transcriptionally active, as opposed to wild-type virus typically integrating into the transcriptionally active regions (Lewinski et al. 2006 , Schaller et al. 2011 , Engelman 2021 ).”
- Authors
- Schaller, T., Ocwieja, K. E., Rasaiyaah, J., Price, A. J., Brady, T. L., Roth, S. L., Hué, S., Fletcher, A. J., Lee, K., KewalRamani, V. N., Noursadeghi, M., Jenner, R. G., James, L. C., Bushman, F. D., & Towers, G. J.
- Affiliations
- University College London (GB)
- University of Pennsylvania (US)
- MRC Laboratory of Molecular Biology (GB)
- National Cancer Institute (US)
- Corresponding author
- Towers, Greg J.
- ORCID
- Venue
- PLoS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-12-08
- Volume
- 7
- Issue
- 12
- Pages
- e1002439
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC3234246
- OpenAlex
- W2122523609
- Cited by
- 470
- References
- 59
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- FWCI
- 14.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
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- Locations
- PLoS Pathogens (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- Pennsylvania Department of Health
- University of Pennsylvania
- Wellcome Trust (090940, WT090940)
- University College London Hospitals NHS Foundation Trust
- National Institutes of Health
- Center for AIDS Research, University of Washington
- Medical Research Council
- National Institute of Allergy and Infectious Diseases (P01AI090935, AI52845, R01AI082020, R01AI052845, AI082020)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- HIV-1, capsid protein, cyclophilin A, nuclear import, nuclear pore complex, transcription units, TRIM5, Nup153, cyclosporine, HIV-1 replication
- MeSH terms
- Cell Line, Cell Nucleus, HeLa Cells, Humans, Macrophages, Virus Replication, Blotting, Western, HIV-1, HIV Infections, Molecular Chaperones, Reverse Transcriptase Polymerase Chain Reaction, Active Transport, Cell Nucleus, Cyclophilin A, Nuclear Pore Complex Proteins, Capsid Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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