Abstract

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 spectrometry1,2,3 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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Acknowledgements

We thank A. Choi, Z. Rizvi and E. Kwon for cloning of human genes and J. Cate for purified eIF3. We also thank J. Gross, R. Andino, R. Harris, M. Daugherty and members of the Krogan lab for discussion. This research was funded by grants from QB3@UCSF and the National Institutes of Health (P50 GM082250 to N.J.K., A.D.F., C.S.C. and T.A.; P01 AI090935 to N.J.K., S.K.C., J.A.Y. and F.D.B.; P50 GM081879 to N.J.K. and A.B.; P50 GM082545 to W.I.S.; P41RR001614 to A.B.; U54 RR022220 to A.S.; P01 GM073732-05 to A.T.; CHRP-ID08-TBI-063 to S.K.C.; P41 RR001081 to J.H.M.) and from the Nomis Foundation (to J.A.Y.). N.J.K. is a Searle Scholar and a Keck Young Investigator.

Author information

Author notes

    • Iván D’Orso

    Present address: Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA, 75390

Affiliations

  1. Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA

    • Stefanie Jäger
    • , Natali Gulbahce
    • , Jeffrey R. Johnson
    • , Kathryn E. McGovern
    • , Michael Shales
    • , Kathy Li
    • , Hilda Hernandez
    • , Gwendolyn M. Jang
    • , Marie Fahey
    • , Cathal Mahon
    •  & Nevan J. Krogan
  2. California Institute for Quantitative Biosciences, QB3, San Francisco, California 94158, USA

    • Stefanie Jäger
    • , Peter Cimermancic
    • , Natali Gulbahce
    • , Jeffrey R. Johnson
    • , Kathryn E. McGovern
    • , Michael Shales
    • , Kathy Li
    • , Hilda Hernandez
    • , Gwendolyn M. Jang
    • , Eyal Akiva
    • , Marie Fahey
    • , Cathal Mahon
    • , Tanja Kortemme
    • , Ryan D. Hernandez
    • , Charles S. Craik
    • , Alma Burlingame
    • , Andrej Sali
    • , Alan D. Frankel
    •  & Nevan J. Krogan
  3. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA

    • Peter Cimermancic
    • , Eyal Akiva
    • , Tanja Kortemme
    • , Ryan D. Hernandez
    •  & Andrej Sali
  4. J. David Gladstone Institutes, San Francisco, California 94158, USA

    • Jeffrey R. Johnson
    •  & Nevan J. Krogan
  5. Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA

    • Starlynn C. Clarke
    • , Kathy Li
    • , Hilda Hernandez
    • , Cathal Mahon
    • , Anthony J. O’Donoghue
    • , John H. Morris
    • , David A. Maltby
    • , Charles S. Craik
    • , Alma Burlingame
    •  & Andrej Sali
  6. Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA

    • Gaelle Mercenne
    •  & Wesley I. Sundquist
  7. Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA

    • Lars Pache
    •  & Sumit K. Chanda
  8. Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA

    • Gwendolyn M. Jang
    • , Iván D’Orso
    • , Jason Fernandes
    •  & Alan D. Frankel
  9. Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

    • Shoshannah L. Roth
    • , Melanie Stephens
    •  & Frederic D. Bushman
  10. The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • John Marlett
    •  & John A. Young
  11. Department of Chemistry, University of California, Berkeley, California 94720, USA

    • Aleksandar Todorovic
  12. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

    • Tom Alber
  13. Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

    • Gerard Cagney
  14. Host Pathogen Circuitry Group, University of California, San Francisco, California 94158, USA

    • Tanja Kortemme
    • , Ryan D. Hernandez
    • , Andrej Sali
    • , Alan D. Frankel
    •  & Nevan J. Krogan

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Contributions

S.J. generated the protein–protein interaction map; P.C. developed the MiST scoring system; N.G., M. Shales, E.A., M.F., J.H.M., J.R.J. and R.D.H. provided computational support; K.E.M., K.L., J.R.J., H.H., G.M.J., I.D., J.F. and D.A.M. provided experimental support; S.J., S.C.C., A.J.O. and A.T. characterized the PR–eIF3d interaction; S.J., G.M.J., C.M. and G.M. confirmed the interactions by immunoprecipitation/western blot; L.P., S.L.R., J.M. and M. Stephens used RNAi for functional verification; T.A., G.C., F.D.B., J.A.Y., S.K.C., W.I.S., T.K., R.D.H., C.S.C., A.B., A.S., A.D.F. and N.J.K. supervised the research; and S.J., P.C., A.S. and N.J.K. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nevan J. Krogan.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    The file contains Supplementary Figures 1-20 with legends, Supplementary Tables 1-14, Supplementary Methods, a Supplementary Discussion and Supplementary References.

Excel files

  1. 1.

    Supplementary Data 1

    The data shows raw MS data.

  2. 2.

    Supplementary Data 2

    The data shows three components used for MiST scoring.

  3. 3.

    Supplementary Data 3

    The data shows MiST scored MS data (>0.75 and full list).

  4. 4.

    Supplementary Data 4

    The data shows functional enrichment of host factors.

  5. 5.

    Supplementary Data 5

    The data shows VirusMint PPIs.

  6. 6.

    Supplementary Data 6

    The data shows overlap of VirusMint with all MiST scores.

  7. 7.

    Supplementary Data 7

    The data shows published RNAi screens.

  8. 8.

    Supplementary Data 8

    The data shows overlap of RNAi screens with all MiST scores.

  9. 9.

    Supplementary Data 9

    The data shows human-human PPIs used in HIV-human network representation.

About this article

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DOI

https://doi.org/10.1038/nature10719

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