Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection

• Published in: Cell reports (Cambridge) Vol. 27; no. 5; pp. 1579 - 1596.e7
• Main Authors: Greenwood, Edward J.D., Williamson, James C., Sienkiewicz, Agata, Naamati, Adi, Matheson, Nicholas J., Lehner, Paul J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 30.04.2019; Cell Press; Elsevier
• Subjects: Cell Line, Tumor; Conserved Sequence; G2 Phase Cell Cycle Checkpoints; HEK293 Cells; HIV; HIV Infections - metabolism; HIV Infections - virology; HIV-1 - metabolism; HIV-1 - pathogenicity; Humans; IP-MS; mass spectrometry; Proteolysis; Proteome - chemistry; Proteome - metabolism; proteomics; pulsed SILAC; SIV; TMT; Ubiquitin-Protein Ligases - metabolism; Ubiquitination; Vpr; vpr Gene Products, Human Immunodeficiency Virus - genetics; vpr Gene Products, Human Immunodeficiency Virus - metabolism; Vpx; SIV; HIV; proteomics; IP-MS; Vpr; mass spectrometry; TMT; Vpx; pulsed SILAC
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.04.025

HIV-1 encodes four “accessory proteins” (Vif, Vpr, Vpu, and Nef), dispensable for viral replication in vitro but essential for viral pathogenesis in vivo. Well characterized cellular targets have been associated with Vif, Vpu, and Nef, which counteract host restriction and promote viral replication. Conversely, although several substrates of Vpr have been described, their biological significance remains unclear. Here, we use complementary unbiased mass spectrometry-based approaches to demonstrate that Vpr is both necessary and sufficient for the DCAF1/DDB1/CUL4 E3 ubiquitin ligase-mediated degradation of at least 38 cellular proteins, causing systems-level changes to the cellular proteome. We therefore propose that promiscuous targeting of multiple host factors underpins complex Vpr-dependent cellular phenotypes and validate this in the case of G2/M cell cycle arrest. Our model explains how Vpr modulates so many cell biological processes and why the functional consequences of previously described Vpr targets, identified and studied in isolation, have proved elusive. [Display omitted] •HIV-1 Vpr is responsible for almost all proteomic changes in HIV-1-infected cells•Vpr directly targets multiple nuclear proteins for degradation•Vpr cellular phenotypes (e.g., cell cycle arrest) stem from broad substrate targeting•Targeting of a few proteins is conserved across diverse primate lentiviral species HIV infection results in global changes to the cellular proteome. Greenwood et al. show that one HIV protein, Vpr, is directly or indirectly responsible for almost all of these changes by targeting multiple proteins for degradation. This broad substrate specificity explains the difficulties to date in understanding this enigmatic protein.