Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome

Abstract

So-called q0 cells lack mitochondrial DNA and are therefore incapable of aerobic ATP synthesis. How cells adapt to survive ablation of oxidative phosphorylation remains poorly understood. Complexome profiling analysis of q0 cells covered 1,002 mitochondrial proteins and revealed changes in abundance and organization of numerous multiprotein complexes including previously not described assemblies. Beyond multiple subassemblies of complexes that would normally contain components encoded by mitochondrial DNA, we observed widespread reorganization of the complexome. This included distinct changes in the expression pattern of adenine nucleotide carrier isoforms, other mitochondrial transporters, and components of the protein import machinery. Remarkably, ablation of mitochondrial DNA hardly affected the complexes organizing cristae junctions indicating that the altered cristae morphology in q0 mitochondria predominantly resulted from the loss of complex V dimers required to impose narrow curvatures to the inner membrane. Our data provide a comprehensive resource for in-depth analysis of remodeling of the mitochondrial complexome in response to respiratory deficiency.

Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module

“…S5 A ), we were able to identify a low-abundance population of SFXN4 migrating alongside MCIA complex subunits in the complexome data from the published complexome profiling of WT and rho-0 cells, which lack mtDNA ( SI Appendix , Fig. S5 B ) ( 21 ). Of note, these high-molecular-weight forms of SFXN4 collapsed to lower molecular weight forms in rho-0 cells ( SI Appendix , Fig.…”

The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase

“…1a , Supplementary Fig. 1a and Supplementary Data 1 ) 56 . Western blot analysis confirmed that mitochondrially encoded subunits of complex IV were absent, but the steady-state levels of nuclear-encoded subunits of complex IV and of the ATP synthase were affected differentially.…”

Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease

“…These cells represent an optimal system to study mtDNA-related defects and OXPHOS deficiencies. Beyond the impaired assembly of OXPHOS complexes I, III, IV and V, which did retain partially assembled intermediates formed by nuclear-encoded subunits, complexomes of ρ 0 cells displayed unexpected modifications in migration patterns of a wide range of membrane-embedded and water-soluble protein complexes ( Guerrero-Castillo et al, 2021b ). Changes in expression of, for example, mitochondrial inner membrane carrier proteins, TCA cycle enzymes, mtDNA maintenance proteins and protein translocases localized to both mitochondrial membranes were described.…”

“…Resultant data are clustered to visualize the inventory, abundance and arrangement of multi-protein complexes in a biological sample. Since its formal introduction a decade ago, CP has been primarily used in mitochondrial research ( Kiirika et al, 2013 ; Senkler et al, 2017 ; Giese et al, 2021 ; Guerrero-Castillo et al, 2021b ; Wittig and Malacarne, 2021 ); albeit CP can be applied to any kind of cellular fraction.…”