Protein ubiquitination and its reverse reaction, deubiquitination, regulate protein stability, protein binding activity, and their subcellular localization. These reactions are catalyzed by the enzymes E1, E2, and E3 ubiquitin (Ub) ligases and deubiquitinases (DUBs). The Ub-proteasome system (UPS) is targeted by viruses for the sake of their replication and to escape host immune response. To identify novel partners of human papillomavirus 16 (HPV16) E6 and E7 proteins, we assembled and screened a library of 590 cDNAs related to the UPS by using the Gaussia princeps luciferase protein complementation assay. HPV16 E6 was found to bind to the homology to E6AP C terminus-type Ub ligase (E6AP), three really interesting new gene (RING)-type Ub ligases (MGRN1, LNX3, LNX4), and the DUB Ub-specific protease 15 (USP15). Except for E6AP, the binding of UPS factors did not require the LxxLL-binding pocket of HPV16 E6. LNX3 bound preferentially to all high-risk mucosal HPV E6 tested, whereas LNX4 bound specifically to HPV16 E6. HPV16 E7 was found to bind to several broad-complex tramtrack and bric-a-brac domain-containing proteins (such as TNFAIP1/KCTD13) that are potential substrate adaptors of Cullin 3-RING Ub ligases, to RING-type Ub ligases implicated in innate immunity (RNF135, TRIM32, TRAF2, TRAF5), to the substrate adaptor DCAF15 of Cullin 4-RING Ub ligase and to some DUBs (USP29, USP33). The binding to UPS factors did not require the LxCxE motif but rather the C-terminal region of HPV16 E7 protein. The identified UPS factors interacted with most of E7 proteins across different HPV types. This study establishes a strategy for the rapid identification of interactions between host or pathogen proteins and the human ubiquitination system. Abbreviations APC/C, anaphase-promoting complex/cyclosome; BTB, broad-complex tramtrack and bric-a-brac; CRL, Cullin-ring ubiquitin ligase; DUB, deubiquitinase; DWD, DBD1-binding W40 protein; Gluc1, Gaussia luciferase fragment 1; Gluc2, Gaussia luciferase fragment 2; Gluc, Gaussia luciferase; GPCA, Gaussia protein complementation assay; HECT, homology to E6AP C terminus; HPV, human papillomavirus; IQR, interquartile range; JAMM, Jab1/mov34/Mpr1 Pad1 N-terminal+; MJD, Machado/Josephin domain; NLR, normalized luminescence ratio; OTU, ovarian tumor protease; PBM, PDZ-binding motif; PPI, protein-protein interaction; PRS, positive reference set; RING, really interesting new gene; RLU, relative luciferase unit; RRS, random reference set; SOCS, suppressor of cytokine signaling; SRF, substrate recognition factor; Ubl, ubiquitin-like; Ub, ubiquitin; UCH, ubiquitin C-terminal hydrolase; UPS, ubiquitin-proteasome system; USP, ubiquitin-specific protease.

Reef-building corals form symbiotic relationships with dinoflagellates of the genus Symbiodinium. Symbiodinium are genetically and physiologically diverse, and corals may be able to adapt to different environments by altering their dominant Symbiodinium phylotype. Notably, each coral species associates only with specific Symbiodinium phylotypes, and consequently the diversity of symbionts available to the host is limited by the species specificity. Currently, it is widely presumed that species specificity is determined by the combination of cell-surface molecules on the host and symbiont. Here we show experimental evidence supporting a new model to explain at least part of the specificity in coral–Symbiodinium symbiosis. Using the laboratory model Aiptasia–Symbiodinium system, we found that symbiont infectivity is related to cell size; larger Symbiodinium phylotypes are less likely to establish a symbiotic relationship with the host Aiptasia. This size dependency is further supported by experiments where symbionts were replaced by artificial fluorescent microspheres. Finally, experiments using two different coral species demonstrate that our size-dependent-infection model can be expanded to coral–Symbiodinium symbiosis, with the acceptability of large-sized Symbiodinium phylotypes differing between two coral species. Thus the selectivity of the host for symbiont cell size can affect the diversity of symbionts in corals.

Highlights d OTUB1 is induced during IAV infection in an IFN-I-dependent manner d OTUB1 regulates the RIG-I complex via its enzymatic and E2-repressive activities d Optimal K63 versus K48 polyubiquitin chain concentrations determine RIG-I activation d Influenza NS1 targets OTUB1 for proteasomal degradation

Serine/threonine phosphorylation of the T cell adaptor proteins SLP76 and GADS by HPK1 induces their release from signaling microclusters and subsequent termination of the T cell response.