Mitochondrial complex I plays an essential role in human respirasome assembly

Abstract

The biogenesis and function of the mitochondrial respiratory chain (RC) involve the organization of RC enzyme complexes in supercomplexes or respirasomes through an unknown biosynthetic process. This leads to structural interdependences between RC complexes, which are highly relevant from biological and biomedical perspectives, because RC defects often lead to severe neuromuscular disorders. We show that in human cells, respirasome biogenesis involves a complex I assembly intermediate acting as a scaffold for the combined incorporation of complexes III and IV subunits, rather than originating from the association of preassembled individual holoenzymes. The process ends with the incorporation of complex I NADH dehydrogenase catalytic module, which leads to the respirasome activation. While complexes III and IV assemble either as free holoenzymes or by incorporation of free subunits into supercomplexes, the respirasomes constitute the structural units where complex I is assembled and activated, thus explaining the significance of the respirasomes for RC function.

Figure 1. Steady-state levels of mitochondrial supercomplexes in human cell lines

Sixty μg of isolated mitochondria were analyzed by 2D-BN/SDS-PAGE. Western-blot analysis was performed using antibodies against the indicated OXPHOS subunits. SC, supercomplexes containing CI, CIII and CIV. CI*, partially-assembled CI. CIII₂, complex III dimer. CIV*, putative CIV dimer. III₂+IV, supercomplex containing CIII and CIV.

Figure 2. Incorporation rates of individual complex I subunits in supercomplexes

(A) Example of 2D-BN/SDS-PAGE western blot analysis in doxycycline-treated 143B cells using antibodies against the indicated CI subunits. SC, supercomplexes containing CI, CIII and CIV. CI*, partially-assembled CI. (B) Mean incorporation rates of CI subunits in large supercomplexes (SC). The signals corresponding to CI subunits were quantified in duplicate gels per cell line, and normalized by the CII SDHA subunit. (a.d.u.), arbitrary densitometric units. Mean values are expressed as percentages relative to untreated cells (SS). Error bars represent standard deviations (SD).

Figure 3. Assembly kinetics of individual complex III subunits in supercomplexes

(A) Example of 2D-BN/SDS-PAGE western blot analysis in doxycycline-treated 143B cells using antibodies against the indicated CIII subunits. (B) Densitometric histogram representing the assembly progress of the CORE2 and RISP subunits in CIII-containing structures. (C) Mean incorporation rates of CORE2 and RISP subunits in CIII-containing structures. The signals were quantified in duplicate gels per cell line, and normalized by CII. CIII₂, complex III dimer (left panel); III₂+IV, supercomplex containing CIII and CIV (middle panel); SC, supercomplexes containing CI, CIII and CIV (right panel). (a.d.u.), arbitrary densitometric units. Mean values are expressed as percentages relative to untreated cells (SS). Error bars represent standard deviations (SD).

Figure 4. Assembly kinetics of individual complex IV subunits in supercomplexes

(A) Example of 2D-BN/SDS-PAGE western blot analysis in doxycycline-treated 143B cells using antibodies against the indicated CIV subunits. (B) Mean incorporation rates of CIV subunits in CIV-containing structures. The signals were quantified in duplicate gels per cell line, and normalized by CII. CIV, complex IV (left panel); III₂+IV, supercomplex containing CIII and CIV (middle panel); SC, supercomplexes containing CI, CIII and CIV (right panel). CIV*, putative complex IV dimer. (a.d.u.), arbitrary densitometric units. Mean values correspond to percentages relative to untreated cells (SS). Error bars represent standard deviations (SD).

Figure 5. Comparative analysis of the incorporation rates of RC subunits into large supercomplexes

(A) Mean incorporation rates of RC subunits into I+III₂+IV_n supercomplexes (SC). SC2 represents the mean incorporation rates of NDUFA9, NDUFS2, CORE2, COX4 and COX5A subunits into SC. (B) 60 μg of crude mitochondrial pellets from the doxycycline assays were analyzed by BN-PAGE in combination with in-gel activity (IGA) assays. The left panel shows a CI in-gel activity (IGA) assay, where * indicate unspecific bands with NADH dehydrogenase activity. The right panel shows a CIV IGA assay. ** indicate the putative CIV dimer (CIV*) and supercomplex III₂+IV that stained for CIV activity (CIV_a). SC_a indicates CI and CIV activities in large supercomplexes. (C) Densitometric analysis of the CI and CIV SC_a bands performed in three independent experiments. (D) Spectrophotometric CI activities in digitonin-treated 143B cells. Triplicate measurements were normalized by the citrate synthase activity. (a.d.u.), arbitrary densitometric units. Mean values represent percentages relative to untreated cells (SS). Error bars represent standard deviations (SD).

Figure 6. Analysis of mitochondrial supercomplexes in COX2 mutant cybrids

(A) BN-PAGE was performed in COX2 mutant cybrids carrying the homoplasmic m.7896G>A mutation (M) and its corresponding isogenic control (C), followed by CI and CIV IGA assays, or alternatively, blotted on nitrocellulose and incubated with the indicated antibodies. (B) 2D-BN/SDS-PAGE western-blot analysis in control (C) and the COX2 mutant (M) cybrids using antibodies against the indicated OXPHOS subunits. CI*, partially-assembled CI. CIII₂, complex III dimer. CIV*, putative complex IV dimer.

Figure 7. Model for the assembly of mitochondrial supercomplexes

In a first stage, the syntheses of fully-assembled and active CIII and CIV take place until reaching a threshold that probably triggers the accumulation of free subunits and assembly intermediates from these two complexes. At this early stage the assembly of CI also initiates (steps 1 to 6) to building up a CI subassembly of ~830 kDa that constitutes the first supercomplex assembly intermediate (SC1). This subcomplex remains in a stable assembly-competent state for the subsequent binding of CIII subunit CORE2 and CIV subunits COX4 and COX5A, to form a second supercomplex assembly intermediate (SC2). The incorporations of CI NDUFS4 and CIV COX2 subunits, and maybe other free RC subunits or subassemblies, take place in a third stage (SC3). The catalytic CIII RISP and CIV COX1 subunits and the structural CIV subunit COX6C incorporate to the supercomplexes in a fourth stage (SC4). The latest supercomplex assembly step involves the association of catalytic subunits from the CI NADH dehydrogenase module prior to the respirasome activation (SC5).