Global landscape of HIV–human protein complexes
Open accessAbstract
Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on the host cellular machinery to replicate. Identifying which host proteins and complexes come into physical contact with the viral proteins is crucial for a comprehensive understanding of how HIV rewires the host's cellular machinery during the course of infection. Here we report the use of affinity tagging and purification mass spectrometry to determine systematically the physical interactions of all 18 HIV-1 proteins and polyproteins with host proteins in two different human cell lines (HEK293 and Jurkat). Using a quantitative scoring system that we call MiST, we identified with high confidence 497 HIV-human protein-protein interactions involving 435 individual human proteins, with ∼40% of the interactions being identified in both cell types. We found that the host proteins hijacked by HIV, especially those found interacting in both cell types, are highly conserved across primates. We uncovered a number of host complexes targeted by viral proteins, including the finding that HIV protease cleaves eIF3d, a subunit of eukaryotic translation initiation factor 3. This host protein is one of eleven identified in this analysis that act to inhibit HIV replication. This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection.
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Cellular factors interacting with HIV-1 proteins and RNAs have been identified using proteomic approaches.
“In recent years, cellular factors interacting with HIV-1 proteins and RNAs have been identified using proteomic approaches (122-124).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
The Abstract (page not provided) reports identifying human proteins that interact with HIV-1 proteins using affinity purification and mass spectrometry. It does not report identifying cellular factors that interact with HIV-1 RNAs, so the RNA portion of the claim is unsupported by this source. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe MA domain of Gag is a major interaction partner of the MSC, and MA has also been reported to interact with a few non-MSC ARSs.
“The MA domain of Gag is a major interaction partner of the MSC, and MA has also been reported to interact with a few non-MSC ARSs (Table 1) (122).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
The paper’s study description (section labeled Abstract; page unavailable) says MA was among the HIV proteins assayed for host interactions. Searches for aminoacyl-tRNA synthetases, the multisynthetase complex, and MSC found no passage in our copy reporting MA interactions with either MSC or non-MSC ARSs. (LLM, conf=0.72)
Experimental — accuracy not yet measuredArgRS and EPRS interact with HIV-1 5ЈUTR.
“| Interacts with HIV-1 5ЈUTR | ArgRS a , EPRS a | 122 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
The paper’s discussion of HIV–human interactions describes eIF3 and a possible interaction with viral RNA, but does not identify ArgRS or EPRS as binding the HIV-1 5′ UTR. Searches for both protein names, their expanded names, and the 5′ UTR found no passage addressing the claimed interaction. (LLM, conf=0.75)
Experimental — accuracy not yet measuredLysRS and SerRS2 interact with RSV 5ЈUTR.
“| Interacts with RSV 5ЈUTR | LysRS a , SerRS2 | 122 |”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [122]
The paper’s HIV-interaction discussion (indexed under Abstract; page unavailable) addresses HIV proteins and host factors, but does not report LysRS or SerRS2 interacting with an RSV 5′ UTR. Searches for both protein names and the RSV 5′ untranslated region found no passage addressing the claimed interaction. (LLM, conf=0.75)
Experimental — accuracy not yet measuredIn a large-scale interactome study, all HIV-encoded proteins were individually expressed in 293 and Jurkat cells and subjected to tandem affinity purification-mass spectrometry.
“For example, in a large-scale interactome study, all the viral proteins encoded by the HIV genome were individually expressed in 293 and Jurkat cells and subjected to TAP AP-MS analysis (61).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
In the HIV interactome study, 97 of 127 selected interactions were confirmed by reciprocal isolations.
“Moreover, 97 of 127 selected interactions were confirmed by reciprocal isolations, highlighting the confidence of this data set.”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
Almost 200 interactions were identified in both cell types in the HIV interactome study.
“Almost 200 interactions were identified in both cell types.”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
MiST distinguished high-confidence virus-host protein interactions of epitope-tagged HIV proteins individually expressed in human cells.
“Another interaction specificity predictor, MiST, distinguished high-confidence virus-host protein interactions of epitope-tagged HIV proteins individually expressed in human cells (61).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [61]
Using AP-MS, nearly 500 specific HIV-host protein interactions were identified.
“Using AP-MS, nearly 500 specific HIV–host protein interactions were identified”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
When eIF3d was knocked down via RNA interference, an additional 10 host factors were found to hinder HIV replication by means of virus-host protein interactions.
“When eIF3d was knocked down via RNA interference, an additional 10 host factors were found to hinder HIV replication by means of virus–host protein interactions.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
Approximately 40% of these interactions were prevalent in both HEK293 and Jurkat cells.
“approximately 40% of which were prevalent in both cell types.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
The observed overlap in interactions between HEK293 and Jurkat cells was limited.
“the observed overlap in interactions between HEK293 and Jurkat cells was limited.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
A host subunit of eukaryotic translation initiation factor 3, eIF3d, was found to be targeted for cleavage by an HIV protease.
“A host subunit of eukaryotic translation initiation factor 3, eIF3d, was found to be targeted for cleavage by an HIV protease.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
The comparison of HEK293 cells with Jurkat cells helped to substantiate the potential biological relevance of the subset of protein associations identified in both human cell types.
“the comparison of HEK293 cells with Jurkat cells, which are immortalized CD4+ T cells commonly used in HIV-1 studies, helped to substantiate the potential biological relevance of the subset of protein associations identified in both human cell types.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [54]
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- Authors
- Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G. M., Roth, S. L., Akiva, E., Marlett, J., Stephens, M., D’Orso, I., Fernandes, J., Fahey, M., Mahon, C., O’Donoghue, A. J., Todorovic, A., Morris, J. H., Maltby, D. A., Alber, T., Cagney, G., Bushman, F. D., Young, J. A., Chanda, S. K., Sundquist, W. I., Kortemme, T., Hernandez, R. D., Craik, C. S., Burlingame, A., Sali, A., Frankel, A. D., & Krogan, N. J.
- Affiliations
- University of California, San Francisco (US)
- QB3 (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Pennsylvania (US)
- Salk Institute for Biological Studies (US)
- University of California, Berkeley (US)
- University College Dublin (IE)
- University of Utah (US)
- Corresponding author
- Krogan, Nevan J.
- ORCID
- Jäger, Stefanie
- Gulbahce, Natali
- Johnson, Jeffrey R.
- McGovern, Kathryn E.
- Clarke, Starlynn C.
- Pache, Lars
- Li, Kathy
- Akiva, Eyal
- D’Orso, Iván
- Fernandes, Jason
- Fahey, Marie
- Mahon, Cathal
- O’Donoghue, Anthony J.
- Morris, John H.
- Cagney, Gerard
- Bushman, Frederic D.
- Young, John A.
- Chanda, Sumit K.
- Sundquist, Wesley I.
- Kortemme, Tanja
- Hernandez, Ryan D.
- Craik, Charles S.
- Burlingame, Alma
- Frankel, Alan D.
- Krogan, Nevan J.
- Venue
- Nature
- Published
- 2011-12-21
- Volume
- 481
- Issue
- 7381
- Pages
- 365-370
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3310911
- OpenAlex
- W1996076856
- Cited by
- 731
- References
- 29
- Citations by year
- 2026: 22 · 2025: 25 · 2024: 37 · 2023: 41 · 2022: 46 · 2021: 59 · 2020: 44 · 2019: 51 · 2018: 50 · 2017: 47 · 2016: 59 · 2015: 62 · 2014: 67 · 2013: 58 · 2012: 62
- FWCI
- 23.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (P50GM082250, P50GM081879, P50GM082545, P41GM103481, P01GM073732)
- National Institute of Allergy and Infectious Diseases (P01AI090935)
- National Center for Research Resources (P41RR001614, P41RR001081, U54RR022220)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- HIV-1, host-virus protein interaction, protein-protein interaction, HIV replication, integrase, eIF3, primate conservation
- MeSH terms
- Affinity Labels, Amino Acid Sequence, Humans, Protein Binding, Mass Spectrometry, Virus Replication, Reproducibility of Results, HIV-1, HIV Infections, HIV Protease, Conserved Sequence, Jurkat Cells, Protein Interaction Mapping, Eukaryotic Initiation Factor-3, Immunoprecipitation, Human Immunodeficiency Virus Proteins, Host-Pathogen Interactions, HEK293 Cells, Protein Interaction Maps
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