Global landscape of HIV–human protein complexes

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Abstract
Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins. Nevan Krogan and colleagues report a global analysis of human proteins that interact with the 18 proteins expressed by HIV-1. Using affinity tagging and mass spectrometry combined with a new quantitative scoring system and a high level of validation by co-immunoprecipitation, they identify 497 HIV–human protein–protein interactions, providing new insights into host proteins that could play a part in HIV replication. Functional validation of a few of these hits revealed a number of new factors that inhibit HIV replication, including EIF3d, which is cleaved by HIV protease, and DESP and HEAT1, which interact with integrase and inhibit integration. 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.