MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases

Abstract

The melanoma antigen (MAGE) family consists of more than 60 genes, many of which are cancer-testis antigens that are highly expressed in cancer and play a critical role in tumorigenesis. However, the biochemical and cellular functions of this enigmatic family of proteins have remained elusive. Here, we identify really interesting new gene (RING) domain proteins as binding partners for MAGE family proteins. Multiple MAGE family proteins bind E3 RING ubiquitin ligases with specificity. The crystal structure of one of these MAGE-RING complexes, MAGE-G1-NSE1, reveals structural insights into MAGE family proteins and their interaction with E3 RING ubiquitin ligases. Biochemical and cellular assays demonstrate that MAGE proteins enhance the ubiquitin ligase activity of RING domain proteins. For example, MAGE-C2-TRIM28 is shown to target p53 for degradation in a proteasome-dependent manner, consistent with its tumorigenic functions. These findings define a biochemical and cellular function for the MAGE protein family.

Figure 1. Tandem Affinity Purification of MAGE Proteins

(A) Dendrogram tree of MAGE protein family. Type I MAGEs include MAGE-A, MAGE-B, and MAGE-C families. Type II MAGEs include MAGE-D, MAGE-E, MAGE-F, MAGE-G, MAGE-H, MAGE-L2, and Nec-din families. Tandem affinity purification (TAP) was performed on the MAGE proteins indicated in red. (B) TAP scheme to identify MAGE-interacting proteins. (C) Colloidal Coomassie-stained SDS-PAGE gels of the indicated TAP-MAGEs isolated from HEK293 stable cell lines. See Table S1 for LC-MS/MS identification of indicated Coomassie-stained bands. TAP-GFP was used as an irrelevant negative control protein.

Figure 2. MAGEs Bind E3 RING Ubiquitin Ligases

(A) Interactions between MAGE and RING domain proteins were validated by coimmunoprecipitation (IP). The indicated Myc- and HA-tagged proteins were expressed in HeLa cells, Myc-RING proteins were IPed with an anti-Myc antibody, and HA-MAGE proteins were detected by anti-HA western blot (WB). HA-MMS21 was included as an irrelevant HA-tagged negative control protein. (B) MAGEs and their cognate E3 RINGs colocalize in specific subcellular compartments. The indicated GFP-tagged MAGEs and mCherry-tagged RING domain proteins were coexpressed and imaged in U2OS cells. (C) Endogenous MAGE-RING ligase complexes. Cell lysates were subjected to immunoprecipitation and western blotting with the indicated antibodies. (D) Endogenous MAGE-C2 and TRIM28 localize in the nucleus. MAGE-C2-negative (HEK293 and HeLa) and MAGE-C2-positive (HTB126 and HCC1806) cells were immunostained with mouse monoclonal MAGE-C2 (green) or mouse monoclonal TRIM28 (green). Nuclei were defined by DAPI staining (blue). (E) The majority of MAGE-C2 associates with TRIM28 in cells. Cell lysates were subjected to immunoprecipitation with anti-HA (negative control) or anti-TRIM28 antibodies. The amount of MAGE-C2, TRIM28, and APC2 (negative control) in the cell lysate before immunoprecipitation (WCL), after immunoprecipitation (unbound fraction), and bound to the antibody beads (bound fraction) is shown.

Figure 3. MAGE Proteins Directly Bind E3 RING Ubiquitin Ligases with Specificity

(A) Representative examples of strong, intermediate, weak, and not detectable in vitro binding from Figure S3A. (B) The relative binding affinities of the indicated MAGE and E3 RING ubiquitin ligases. (C) Summary of in vitro binding assays from Figures S3B–S3M mapping the interacting regions of MAGE-B18-LNX1, MAGE-C2-TRIM28, and MAGE-G1-NSE1. MHD denotes the MAGE homology domain (MHD) comprising WH-A and WH-B motifs.

Figure 4. MAGE-G1-NSE1 Crystal Structure

(A) Crystal structure of MAGE-G1-NSE1 complex. MAGE-G1 MHD forms a tandem winged helix (WH-A, purple; WH-B, cyan). The two zinc ions coordinated by the NSE1 RING domain are shown as gray spheres. (B) Crystal structure of the MAGE-A4 MAGE homology domain (PDB: 2WA0) consisting of two winged helix motifs (WH-A, yellow-green; WH-B, cream). (C) Orientation of MAGE WH-A to WH-B differs between MAGE-G1 and MAGE-A4. (Left) MAGE-A4 aligned to MAGE-G1-NSE1 based on WH-A motif. (Right) MAGE-A4 WH-B aligns with MAGE-G1 WH-B after rotation, as indicated by the arrow.

Figure 5. MAGEs Enhance the Ubiquitin Ligase Activity of E3 RING Proteins

(A) MAGE-G1 enhances NSE1 ubiquitin ligase activity in vitro. Biotin-ubiquitin, ubiquitin E1, UbcH13/MMS2 E2, Mg-ATP, and the indicated MAGE-RING proteins were incubated for 60 min at 37°C. Biotin-ubiquitin was detected by Streptavidin-HRP. (B) Mutation of the dileucine motif within MAGE-G1 WH-A disrupts binding to the NSE1 RING protein, but not NSE4a. The indicated GST-tagged MAGE-G1 proteins were incubated with in vitro translated Myc-NSE1 or Myc-NSE4a. Proteins were detected by anti-Myc and anti-GST immunoblotting. (C) MAGE-C2 enhances TRIM28 ubiquitin ligase activity in vitro. FLAG-ubiquitin, ubiquitin E1, UbcH2 E2, Mg-ATP, and the indicated MAGE-RING proteins were incubated for 60 min at 37°C. FLAG-ubiquitin was detected by anti-FLAG immunoblotting. (D) MAGE-C2 enhances TRIM28 autoubiquitylation in vitro. Reactions were performed as in (C) except TRIM28 was detected by anti-TRIM28 immunoblotting. (E) MAGE-A2 and -C2 enhance p53 ubiquitylation by TRIM28 in vitro. Reactions were performed as in (A) except substrate (GST-p53 or negative controls GST-MMS21 AA1-165 or free GST) was added and detected by anti-GST immunoblotting. MAGE-G1-NSE1 complex was included as an irrelevant MAGE-RING ligase that does not target p53. (F) MAGE-C2-induced p53 ubiquitylation requires a functional TRIM28 RING domain and the ability to bind TRIM28. Reactions were performed as described in (E).

Figure 6. MAGE-TRIM28 Ligases Promote p53 Degradation in Cells

(A) RT-QPCR analysis of MAGE-A3 and MAGE-C2 expression in HCC1143, HCC1806, HTB126, and SK-BR-3 cells. Results were normalized to GAPDH expression. Data are represented as the mean ± standard deviation. # denotes no signal above background detected by QPCR. MAGE-A3 expression is representative of MAGE-A2 and MAGE-A6 (See Figure S1B). (B) Expression of MAGE-A2 or -C2 in HCC1143 MAGE-negative breast cancer cells results in decreased p53 protein levels in a proteasome-dependent manner. Twenty-four hours after transfection, HCC1143 cells were treated with 10 μM MG132 for 16 hr. Cell lysates were immunoblotted with the indicated antibodies. (C) MAGE-C2-induced p53 degradation requires TRIM28 binding. HCC1143 cells were transfected with wild-type or L152A L153A Myc-MAGE-C2 followed by immunoblotting with the indicated antibodies 48 hr later. (D) MAGE-C2-RNAi increases p53 protein levels in HCC1806 and HTB126 breast cancer cells. MAGE-C2-RNAi was rescued by a siRNA-resistant HA-MAGE-C2 construct in HTB126 cells. Cell lysates were collected 72 hr after transfection and immunoblotted with the indicated antibodies. (E) MAGE-A- and TRIM28-RNAi increase p53 protein levels in MAGE-positive HCC1806 and SK-BR-3 cells, but not in MAGE-negative HCC1143 cells. p53 levels were determined as described in (D). (F) MAGE-A2 and MAGE-C2 share similar activities in regulating p53. SK-BR-3 MAGE-A-positive, MAGE-C2-negative cells were treated with the indicated siRNAs for 24 hr before transfection with the indicated expression constructs. Cell lysates were collected 48 hr later and immunoblotted with the indicated antibodies.