LUBAC-Recruited CYLD and A20 Regulate Gene Activation and Cell Death by Exerting Opposing Effects on Linear Ubiquitin in Signaling Complexes

Abstract

Ubiquitination and deubiquitination are crucial for assembly and disassembly of signaling complexes. LUBAC-generated linear (M1) ubiquitin is important for signaling via various immune receptors. We show here that the deubiquitinases CYLD and A20, but not OTULIN, are recruited to the TNFR1- and NOD2-associated signaling complexes (TNF-RSC and NOD2-SC), at which they cooperate to limit gene activation. Whereas CYLD recruitment depends on its interaction with LUBAC, but not on LUBAC's M1-chain-forming capacity, A20 recruitment requires this activity. Intriguingly, CYLD and A20 exert opposing effects on M1 chain stability in the TNF-RSC and NOD2-SC. While CYLD cleaves M1 chains, and thereby sensitizes cells to TNF-induced death, A20 binding to them prevents their removal and, consequently, inhibits cell death. Thus, CYLD and A20 cooperatively restrict gene activation and regulate cell death via their respective activities on M1 chains. Hence, the interplay between LUBAC, M1-ubiquitin, CYLD, and A20 is central for physiological signaling through innate immune receptors.

Graphical abstract

Figure 1

HOIP Is Required for Recruitment of CYLD to the TNF-RSC whereas OTULIN Is Not Recruited (A) U937 cells were stimulated with TAP-TNF (1 μg/ml) for the indicated times. The TNF-RSC was immunoprecipitated via α-Flag beads and analyzed by western blot. (B) WT and HOIP-deficient A549 cells were stimulated with TAP-TNF (500 ng/ml) and subjected to immunoprecipitation as in (A). (C) HOIP-deficient A549 cells were reconstituted with either HOIP-WT-TAP or HOIP-C885S-TAP or vector control. Cells were subsequently stimulated with TNF (500 ng/ml) for 15 min or left untreated prior to LUBAC immunoprecipitation via α-Flag beads and analysis by western blot. (D) The TNF-RSC isolated from HOIP-deficient A549 cells reconstituted with vector control, HOIP-WT, or catalytically dead HOIP-C885S was analyzed by western blot.

Figure 2

HOIP Recruits CYLD to the NOD2-SC (A) A549 cells pro- or deficient in HOIP expression were stably transfected with NOD2-TAP, stimulated with L18-MDP (200 ng/ml) for the indicated times, and analyzed by western blot. (B) A549 cells pro- or deficient in HOIP were virally transfected with NOD2-TAP and stimulated with L18-MDP (200 ng/ml) for the indicated times. The NOD2-SC was isolated by Flag-tag immunoprecipitation. (C) Bone-marrow-derived macrophages (BMDMs) isolated from mice pro- or deficient in CYLD were stimulated with L18-MDP (200 ng/ml) for the indicated times and analyzed by western blot.

Figure 3

Mutually Exclusive Binding of CYLD and OTULIN to HOIP Causes CYLD-Selective Recruitment to SCs (A) A549 cells were incubated with pervanadate prior to lysis or left untreated. Indicated lysates were subjected to phosphatase treatment prior to OTULIN immunoprecipitation. (B) K562 cells expressing either HOIP-TAP, OTULIN-TAP, or vector control were subjected to α-Flag immunoprecipitation and analyzed by western blot. (C) Lysate from A549 cells was subjected to immunoprecipitation for HOIP (IP: HOIP) or OTULIN (first IP: OTULIN). OTULIN-immuno-depleted lysate was subsequently subjected to CYLD immunoprecipitation (second IP: CYLD). (D) A549 cells deficient in HOIP and reconstituted with HOIP-WT, HOIP-N102A, or vector control were subjected to immunoprecipitation for HOIP or OTULIN and subsequently analyzed by western blot. (E) A549 cells deficient in HOIP and reconstituted with HOIP-WT, HOIP-N102A, or vector control were stimulated with TAP-TNF (500 ng/ml) for 15 min or left untreated. The TNF-RSC was immunoprecipitated via α-Flag beads and analyzed by western blot. (F) A549 cells deficient in HOIP and reconstituted with HOIP-WT, HOIP-N102A, or vector control were stimulated with TNF (500 ng/ml) for indicated times, and lysates were analyzed by western blot.

Figure 4

OTULIN Constitutively Removes M1-Ubiquitin from LUBAC in Non-stimulated Cells (A) The TNF-RSC was isolated from either WT or OTULIN-KO A549 cells stimulated with TAP-TNF (500 ng/ml) for the indicated times and subjected to western blot. (B) A549 cells pro- or deficient in OTULIN and virally transduced to express NOD2-TAP were stimulated with L18-MDP (200 ng/ml) for the indicated times. The NOD2-SC was isolated by α-Flag immunoprecipitation. (C and D) WT or OTULIN-deficient A549 cells were stimulated with TNF (200 ng/ml) for the indicated times. M1-ubiquitin-specific affinity purification (M1-AP) was performed and samples were examined by western blot.

Figure 5

CYLD Removes M1- and K63-Ubiquitin from TNFR1, TRADD, and RIP1 (A) WT or CYLD-deficient A549 cells were treated with TNF (200 ng/ml). M1-affinity purification (AP) was performed, and the samples were subsequently analyzed by western blot. (B) U937 cells were stimulated with TNF (200 ng/ml). Samples were denatured and subjected to M1-AP with subsequent treatment with recombinant OTULIN, vOTU, or both. (C) Cells were treated as in (B), and samples were subjected to total ubiquitin-AP followed by treatment with recombinant CYLD (aa 583–956), vOTU, or both. (D–F) MEFs deficient in CYLD were reconstituted with CYLD-WT or vector control. Cells were stimulated with TNF (200 ng/ml) for 24 hr in the presence or absence of zVAD (20 μM), Nec-1 (10 μM), or both, and cell death was evaluated as percentage of propidium iodide positive cells (data are presented as mean ± SEM [n = 3], ^∗p < 0.05, ^∗∗p < 0.0005, statistics were performed using t test) (D). Cells were stimulated with TAP-TNF (500 ng/ml) for the indicated times, and the TNF-RSC was isolated by α-Flag immunoprecipitation (E). Cells were stimulated with TNF (200 ng/ml) for the indicated times, and activation of gene-activatory signaling pathways was analyzed by western blot (F).

Figure 6

Recruitment of A20 to the TNF-RSC Requires Linear Ubiquitination (A) HOIP-pro- or deficient A549 cells were stimulated with TAP-TNF (500 ng/ml) for the indicated times and subjected to TNF-RSC isolation and western blot analysis. (B) A549 cells pro- or deficient in HOIP were transfected with NOD2-TAP and subsequently stimulated with L18-MDP (200 ng/ml). The NOD2-SC was immunoprecipitated via α-Flag beads and then analyzed by western blot. (C–E) A549 cells deficient in HOIP were reconstituted with HOIP-WT, enzymatically inactive HOIP-C885S, or vector control. Cells were stimulated with TNF (200 ng/ml) for the indicated times before analysis by western blot (C and E). Additionally, production of CCL2 and IL-8 was measured by ELISA after stimulation with TNF (50 ng/ml) for 24 hr (data are presented as mean ± SEM [n = 3]) (D). (F) HOIP-deficient A549 cells were reconstituted with HOIP-WT or enzymatically inactive HOIP-C885S. Samples were analyzed as in (A).

Figure 7

A20 Stabilizes Linear Ubiquitination at the TNF-RSC and NOD2-SC (A) A549 control or A20-KO cells were stimulated with TAP-TNF (500 ng/ml) for the indicated times, subjected to TNF-RSC purification and analyzed by western blot. (B) A549 cells pro- or deficient in A20 were virally transfected with NOD2-TAP and stimulated with L18-MDP (200 ng/ml) for the indicated times. The NOD2-SC was isolated by α-Flag immunoprecipitation. (C) A549 control cells or A549 cells lacking zinc finger 7 of A20 (A20-ΔZnF7) were analyzed as in (A). (D–F) A20-deficient MEFs were reconstituted with A20-WT, A20-C103S, A20-ZnF7mut, or empty vector. Cells were stimulated with TAP-TNF (500 ng/ml) and subjected to TNF-RSC purification (D). Cells were stimulated with TNF (200 ng/ml) for the indicated times before analysis by western blot (E). Cells were stimulated with TNF (200 ng/ml) in presence or absence of zVAD (20 μM) as indicated for 24 hr, and cell death was evaluated as percentage of propidium iodide positive cells (data are presented as mean ± SEM [n = 3], ^∗p < 0.05, statistics were performed using t test) (F). (G) Model of LUBAC regulation: (1) LUBAC is associated with OTULIN or CYLD in a mutually exclusive manner; (2) loss of LUBAC interaction with CYLD and OTULIN leads to unregulated LUBAC activity, ultimately resulting in enhanced linear ubiquitination of LUBAC components themselves. (H) Model of CYLD and A20 recruitment to, and activity at, the TNF-RSC: (1) CYLD-associated LUBAC is recruited to the SC, thereby enabling CYLD recruitment in a HOIP-dependent manner. (2) At the SCs, CYLD antagonizes M1- and K63-linked ubiquitination, thereby limiting gene activation and rendering cells more prone to TNF-induced cell death. (3) A20 is recruited to the SC by its ZnF7 domain interacting with LUBAC-generated M1 linkages placed on SC components. (4) A20 binding to M1 chains prevents their removal and restricts gene-activatory signaling, likely by competing with factors required for gene activation and, in case of the TNF-RSC, renders cells more resistant to cell death induction from this SC.