The mitochondrial fission receptor MiD51 requires ADP as a cofactor

Abstract

Mitochondrial fission requires recruitment of dynamin-related protein 1 (Drp1) to the mitochondrial surface and activation of its GTP-dependent scission function. The Drp1 receptors MiD49 and MiD51 recruit Drp1 to facilitate mitochondrial fission, but their mechanism of action is poorly understood. Using X-ray crystallography, we demonstrate that MiD51 contains a nucleotidyl transferase domain that binds ADP with high affinity. MiD51 recruits Drp1 via a surface loop that functions independently of ADP binding. However, in the absence of nucleotide binding, the recruited Drp1 cannot be activated for fission. Purified MiD51 strongly inhibits Drp1 assembly and GTP hydrolysis in the absence of ADP. Addition of ADP relieves this inhibition and promotes Drp1 assembly into spirals with enhanced GTP hydrolysis. Our results reveal ADP as an essential cofactor for MiD51 during mitochondrial fission.

Figure 1. The Cytosolic Region of MiD51 Has a Nucleotidyl Transferase Domain

(A) Schematic of MiD51. The region determined by X-ray crystallography is indicated and color-coded as in (B). The red squiggle indicates a region predicted to have low probability of regular secondary structure. Boxes highlight residues important for nucleotide binding and the dimer interface. TMD, transmembrane domain. Cylinders represent α-helical segments and triangles strand segments. α helices and β strands from the crystallized segment are numbered. (B) Ribbon representation of mouse MiD51Δ1–133. Orange, N-terminal domain; gray, interdomain linker; blue, C-terminal domain. α helices and strands are numbered according to (A). Dashed lines denote residues missing from the model. N and C denote the N and C termini. The circle indicates the predicted nucleotide-binding pocket. (C) Structural overlay of MiD51 (colored as in B)and cyclic GMP-AMP synthase (cGAS) (green).

Figure 2. MiD51 Binds ADP with High Affinity

(A) Ribbon representation of mouse MiD51Δ1–133 bound to ADP. (B) Details of the nucleotide-binding pocket. The 2 Fo-Fc map for ADP (red) is contoured at 1.2 σ. Key residues are depicted, and interactions with the ADP are denoted with black dashed lines. (C) Binding of MiD51 to ADP. Equilibrium titrations were performed with MANT-labeled nucleotides to determine the affinity of MiD51Δ1–133 for MANT-ATP (no binding), MANT-GTP (no binding), MANT-ADP (K_d = 0.5 µM ± 0.008 µM) and MANT-GDP (8.0 µM ± 0.9 µM). (D) Mutational analysis of residues structurally implicated in ADP binding. Note that MiD51 S189A, H201A, and MiD49 do not bind MANT-ADP. MiD51 K368A has a K_d of 2.6 µM ± 0.4 µM.

Figure 3. MiD51 Forms a Dimer through Electrostatic Interactions

(A) MiD51 crystallizes as a dimer through an interface found in the N-terminal domain. The two molecules are differentially colored gray (left) and as in Figure 1B (right). In the bottom figure, the dimer has been rotated to view the interface from the top. The right panels are a 2-fold axis rotation. Red arrows indicate the α helix and loop shown in (B). Drp1 binding residues are colored green. (B) Detailed view of residues important for the dimer interface. Interactions are indicated with dashed lines. The color scheme is the same as in (A). Electrostatic interactions were determined using the PDBePISA server. R169 self-associates by hydrogen bonding with a sulfate ion (not depicted). (C) Mutational analysis of dimer formation. MiD51-GFP mutants were cotransfected with either empty vector or Myc tagged MiD51 constructs. For each reaction, the same mutant was used for both the GFP and Myc tagged constructs. Cells were treated with a reversible crosslinker and solubilized before immunoprecipitation against the Myc epitope. Top: expression of MiD51-GFP and MiD51-Myc in cell lysates. Actin is a loading control. Bottom: anti-Myc immunoprecipitates analyzed for MiD51-GFP. Comp Mut, compound dimerization mutant.

Figure 4. MiD51 Uses a Surface Loop to Bind Drp1

(A) A yeast two-hybrid screen to identify MiD51 regions necessary for Drp1 binding. The top panel shows the diploid selection plate, and the bottom panel shows the interaction selection plate. Three mutational clusters (6, 7, and 8) perturb MiD51 binding to Drp1. (B) The three clusters localize to a loop at the top surface of MiD51. Mutated residues are colored green and depicted as sticks. (C) Analysis of MiD51-Drp1 binding in 293T cells. Wild-type or mutant MiD51-Myc was coexpressed with mouse Drp1 and Myc-immunoprecipitates were analyzed for Drp1. Top: expression of MiD51-Myc and Drp1 in cell lysates. Actin is a loading control. Bottom: anti-Myc immunoprecipitate analyzed for Drp1 levels. Loading of immunoprecipitates was normalized to Myc levels. (D) MiD51 cluster mutants 6 and 7 fail to rescue mitochondrial Drp1 recruitment in Fis1/Mff null cells. Drp1 was visualized with anti-Drp1 immunofluorescence, and transfected cells were Myc positive. Fis1/Mff null cells are used because they have severely reduced recruitment of Drp1 to mitochondria, allowing the recruitment activity of MiD51 to be readily assessed (Losón et al., 2013).

Figure 5. ADP Binding and Dimerization Are Required for the Fission Activity of MiD51

(A) ADP and dimerization mutants localize to mitochondria but are defective for mitochondrial fission. Wild-type MEFs were transfected with empty vector or MiD51-Myc constructs and treated with antimycin A. NM, nucleotide-binding site mutant (S189A); DM, compound dimer mutant. (B) Quantification of results in (A). Mitochondrial morphologies were scored as described previously (Losón et al., 2013). (C) Mitochondrial morphology in Fis1/Mff null MEFs transfected with empty vector or MiD51-Myc and treated with vehicle (DMSO) or antimycin A. Transfected cells were visualized with anti-Myc immunofluorescence, and mitochondria were highlighted with anti-Tom20 immunofluorescence. (D) Quantification of results in (C). In (B) and (D), data are averages from three independent experiments ±SD. Mitochondrial morphology scoring: S, short; L, long; N, net-like; C, collapsed. Scale bars, 10 µm. Regions within the white boxes are shown in greater magnification below.

Figure 6. ADP Promotes Drp1 Oligomerization by MiD51

(A) Effect of MiD51 and ADP on Drp1 sedimentation. Recombinant mouse MiD49Δ1–124 or MiD51Δ1–133 was incubated with recombinant mouse Drp1 in the presence of GTPγS with or without ADP. Reactions were incubated for 30 min, and Drp1 oligomers were sedimented at 100,000 × g. Equivalent volumes of the supernatant (S) and pellet (P) were loaded and resolved by SDS-PAGE. Dashed boxes indicate key comparison groups. (B) Analysis of MiD51 mutants on Drp1 sedimentation. The MiD51 nucleotide binding mutant (NM, S189A) and the compound dimer mutant (DM) were assessed for their ability to facilitate Drp1 sedimentation in the presence of GTPγS and ADP.

Figure 7. MiD51 and ADP Promote Drp1 Spiral Assembly and GTP Hydrolysis

(A and B) Negative stain transmission electron microscopy of Drp1 oligomers. Images are representative of three independent experiments. (A) Recombinant mouse Drp1 forms regular spiral-tubular structures in the presence of a nonhydrolyzable analog of GTP, GTPγS. White arrow highlights the thin edge of spiral-tubular structures. (B) Effects on Drp1 spiral-tubular formation upon addition of MiD51 proteins with and without ADP. GTPγS was present in all reactions. Dashed boxes indicate inset boundaries. Scale bar, 100 nm; inset scale bar, 50 nm. (C) Effect of MiD51 and ADP on GTP hydrolysis by Drp1. Initial GTP hydrolysis rates were measured with the indicated proteins, with or without ADP. Reactions were performed at saturating GTP (1 mM) with 150 mM NaCl. NM, nucleotide-binding site mutant (S189A); DM, compound dimer mutant. T59A is a Drp1 catalytic mutant. Results are the average of three independent experiments ±SD.