Global landscape of HIV-human protein complexes

Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern, Starlynn C. Clarke, Michael Shales, Gaelle Mercenne, Lars Pache, Kathy Li, Hilda Hernandez, Gwendolyn M. Jang, Shoshannah L. Roth, Eyal Akiva, John Marlett, Melanie Stephens, Iván D'Orso, Jason Fernandes, Marie Fahey, Cathal Mahon & 17 others Anthony J. Oĝdonoghue, Aleksandar Todorovic, John H. Morris, David A. Maltby, Tom Alber, Gerard Cagney, Frederic D. Bushman, John A. Young, Sumit K. Chanda, Wesley I. Sundquist, Tanja Kortemme, Ryan D. Hernandez, Charles S. Craik, Alma Burlingame, Andrej Sali, Alan D. Frankel, Nevan J. Krogan

Research output: Contribution to journalArticle

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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 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.

Original languageEnglish (US)
Pages (from-to)365-370
Number of pages6
JournalNature
Volume481
Issue number7381
DOIs
StatePublished - Jan 19 2012

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Human Immunodeficiency Virus Proteins
HIV
Viral Proteins
Proteins
Prokaryotic Initiation Factor-3
Eukaryotic Initiation Factor-3
Eukaryotic Initiation Factors
Polyproteins
Virus Diseases
Virus Replication
Primates
HIV-1
Mass Spectrometry
Peptide Hydrolases
Genome
Cell Line
Infection

ASJC Scopus subject areas

  • General

Cite this

Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., ... Krogan, N. J. (2012). Global landscape of HIV-human protein complexes. Nature, 481(7381), 365-370. https://doi.org/10.1038/nature10719

Global landscape of HIV-human protein complexes. / Jäger, Stefanie; Cimermancic, Peter; Gulbahce, Natali; Johnson, Jeffrey R.; McGovern, Kathryn E.; Clarke, Starlynn C.; Shales, Michael; Mercenne, Gaelle; Pache, Lars; Li, Kathy; Hernandez, Hilda; Jang, Gwendolyn M.; Roth, Shoshannah L.; Akiva, Eyal; Marlett, John; Stephens, Melanie; D'Orso, Iván; Fernandes, Jason; Fahey, Marie; Mahon, Cathal; Oĝdonoghue, Anthony J.; Todorovic, Aleksandar; Morris, John H.; Maltby, David A.; Alber, Tom; Cagney, Gerard; Bushman, Frederic D.; Young, John A.; Chanda, Sumit K.; Sundquist, Wesley I.; Kortemme, Tanja; Hernandez, Ryan D.; Craik, Charles S.; Burlingame, Alma; Sali, Andrej; Frankel, Alan D.; Krogan, Nevan J.

In: Nature, Vol. 481, No. 7381, 19.01.2012, p. 365-370.

Research output: Contribution to journalArticle

Jäger, S, Cimermancic, P, Gulbahce, N, Johnson, JR, McGovern, KE, Clarke, SC, Shales, M, Mercenne, G, Pache, L, Li, K, Hernandez, H, Jang, GM, Roth, SL, Akiva, E, Marlett, J, Stephens, M, D'Orso, I, Fernandes, J, Fahey, M, Mahon, C, Oĝdonoghue, AJ, Todorovic, A, Morris, JH, Maltby, DA, Alber, T, Cagney, G, Bushman, FD, Young, JA, Chanda, SK, Sundquist, WI, Kortemme, T, Hernandez, RD, Craik, CS, Burlingame, A, Sali, A, Frankel, AD & Krogan, NJ 2012, 'Global landscape of HIV-human protein complexes', Nature, vol. 481, no. 7381, pp. 365-370. https://doi.org/10.1038/nature10719
Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC et al. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19;481(7381):365-370. https://doi.org/10.1038/nature10719
Jäger, Stefanie ; Cimermancic, Peter ; Gulbahce, Natali ; Johnson, Jeffrey R. ; McGovern, Kathryn E. ; Clarke, Starlynn C. ; Shales, Michael ; Mercenne, Gaelle ; Pache, Lars ; Li, Kathy ; Hernandez, Hilda ; Jang, Gwendolyn M. ; Roth, Shoshannah L. ; Akiva, Eyal ; Marlett, John ; Stephens, Melanie ; D'Orso, Iván ; Fernandes, Jason ; Fahey, Marie ; Mahon, Cathal ; Oĝdonoghue, Anthony J. ; Todorovic, Aleksandar ; Morris, John H. ; Maltby, David A. ; Alber, Tom ; Cagney, Gerard ; Bushman, Frederic D. ; Young, John A. ; Chanda, Sumit K. ; Sundquist, Wesley I. ; Kortemme, Tanja ; Hernandez, Ryan D. ; Craik, Charles S. ; Burlingame, Alma ; Sali, Andrej ; Frankel, Alan D. ; Krogan, Nevan J. / Global landscape of HIV-human protein complexes. In: Nature. 2012 ; Vol. 481, No. 7381. pp. 365-370.
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AU - Hernandez, Ryan D.

AU - Craik, Charles S.

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N2 - 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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