bims-mitpro 2025-08-31 papers

Issue of 2025–08–31
five papers selected by
Andreas Kohler, Umeå University

J Biol Chem. 2025 Aug 19. pii: S0021-9258(25)02465-2. [Epub ahead of print] 110614

Lipid bilayer properties govern substrate engagement and extraction by the AAA+ ATPase Msp1.

Heidi L Fresenius, Brian Acquaviva, Deepika Gaur, Baylee A Smith, Matthew L Wohlever.

An essential aspect of protein quality control is enzymatic removal of membrane proteins from the lipid bilayer. Failures in this critical cellular process are associated with neurodegenerative diseases and cancer. Msp1 is a AAA+ (ATPases Associated with diverse cellular Activities) ATPase that removes mistargeted membrane proteins from the outer mitochondrial membrane (OMM). How Msp1 selectively recognizes and extracts substrates within the complex OMM ecosystem, and how the lipid bilayer impacts these processes is unknown. Here, we describe the development of a fully defined, rapid, and quantitative extraction assay that retains physiological substrate selectivity. Using this new assay, we systematically modified both the model substrate and the lipid environment to demonstrate that Msp1 can recognize substrates by a hydrophobic mismatch between the substrate TMD and the lipid bilayer. We further demonstrate that the rate-limiting step in Msp1 activity is extraction of the TMD from the lipid bilayer. Together, these results provide foundational insights into how the lipid bilayer influences AAA+ mediated membrane protein extraction.

Keywords: ATPase Associated with diverse cellular Activities (AAA+); lipid bilayer; membrane protein; mitochondria; proteostasis

DOI: https://doi.org/10.1016/j.jbc.2025.110614

Biochem Soc Trans. 2025 Aug 26. pii: BST20253044. [Epub ahead of print]

Quality control at the powerhouse: mitochondrial proteostasis dysfunction and disease.

Megan J Baker, Kai Qi Yek, Diana Stojanovski.

Intrinsic protein quality control (QC) mechanisms are essential in maintaining mitochondrial health and function. These sophisticated molecular machineries govern protein trafficking and import, processing, folding, maturation and degradation, ensuring the organelle's health. Disruption in mitochondrial protein QC can lead to severe, multisystem disorders with variable age of onset and progression. In this review, we provide a snapshot of the intrinsic molecular protein QC machineries in mitochondria detailing their function, localisation and substrate specificity. We also highlight how dysfunction of these molecular machines contributes to mitochondrial disease. Ultimately, elucidating the consequences of proteostatic failure offers critical insights into the pathogenesis of complex mitochondrial disorders.

Keywords: AAA+; chaperone; disaggregase; extractase; mitochondria; mitochondrial disease; protease; protein quality control

DOI: https://doi.org/10.1042/BST20253044

Bioorg Med Chem. 2025 Aug 11. pii: S0968-0896(25)00291-3. [Epub ahead of print]130 118350

ClpP-based MtPTAC technology enables targeted degradation of inner mitochondrial membrane proteins.

Yuxin Yao, Dachi Wang, Haoyu Gong, Ruibin Jiang, Yang Liu, Yijun Liu, Xin Lai, Zhaoyang Xu, Wei Zhou, Haorong Li, Xiaohong Fang.

Mitochondrial proteostasis is essential for tumorigenesis, and mitochondrial inner membrane proteins have emerged as meaningful targets due to their crucial functions in regulating apoptosis, maintaining oxidative phosphorylation, and influencing tumor initiation and progression. Targeted protein degradation (TPD) has garnered significant attention as a promising therapeutic approach. However, conventional TPD platforms relying on the ubiquitin-proteasome system or lysosomal pathways encounter inherent obstacles in targeting proteins sequestered within the mitochondrial compartment and cannot degrade mitochondrial inner membrane proteins. Utilizing our previously established MtPTAC system, we selected dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme in de novo pyrimidine biosynthesis, as a model substrate. We designed and synthesized a series of degraders, with 3D-2 achieving over 50 % degradation efficiency of DHODH via the ClpP protease. This degrader can form a stable ternary complex with DHODH and ClpP, and it exhibits significant inhibitory effects across various tumor cell lines. This technological innovation is the first to successfully degrade endogenous mitochondrial inner membrane proteins. It provides a diverse toolkit for investigating mitochondrial protein functions and paving the way for novel anticancer therapies.

Keywords: DHODH degrader; Inner mitochondrial membrane; MtPTAC; Targeting protein degradation

DOI: https://doi.org/10.1016/j.bmc.2025.118350

Sci Adv. 2025 Aug 29. 11(35): eady0240

Putative PINK1/Parkin activators lower the threshold for mitophagy by sensitizing cells to mitochondrial stress.

William M Rosencrans, Ryan W Lee, Logan McGraw, Ian Horsburgh, Ting-Yu Wang, Baiyi Quan, Diana Huynh, Jennifer A Johnston, David C Chan, Tsui-Fen Chou.

The PINK1/Parkin pathway targets damaged mitochondria for degradation via mitophagy. Genetic evidence implicates impaired mitophagy in Parkinson's disease, making its pharmacological enhancement a promising therapeutic strategy. Here, we characterize two mitophagy activators: a novel Parkin activator, FB231, and the reported PINK1 activator MTK458. Both compounds lower the threshold for mitochondrial toxins to induce PINK1/Parkin-mediated mitophagy. However, global proteomics revealed that FB231 and MTK458 independently induce mild mitochondrial stress, resulting in impaired mitochondrial function and activation of the integrated stress response, effects that result from PINK1/Parkin-independent off-target activities. We find that these compounds impair mitochondria by distinct mechanisms and synergistically decrease mitochondrial function and cell viability in combination with classical mitochondrial toxins. Our findings support a model whereby weak or "silent" mitochondrial toxins potentiate other mitochondrial stressors, enhancing PINK1/Parkin-mediated mitophagy. These insights highlight important considerations for therapeutic strategies targeting mitophagy activation in Parkinson's disease.

DOI: https://doi.org/10.1126/sciadv.ady0240

EMBO J. 2025 Aug 26.

RTN4IP1 is required for the final stages of mitochondrial complex I assembly and CoQ biosynthesis.

Monika Oláhová, Rachel M Guerra, Jack J Collier, Juliana Heidler, Kyle Thompson, Chelsea R White, Paulina Castañeda-Tamez, Alfredo Cabrera-Orefice, Robert N Lightowlers, Zofia M A Chrzanowska-Lightowlers, Alexander Galkin, Ilka Wittig, David J Pagliarini, Robert W Taylor.

A biochemical deficiency of mitochondrial complex I (CI) underlies approximately 30% of cases of primary mitochondrial disease, yet the inventory of molecular machinery required for CI assembly remains incomplete. We previously characterised patients with isolated CI deficiency caused by segregating variants in RTN4IP1, a gene that encodes a mitochondrial NAD(P)H oxidoreductase. Here, we demonstrate that RTN4IP1 deficiency causes a CI assembly defect in both patient fibroblasts and knockout cells, and report that RTN4IP1 is a bona fide CI assembly factor. Complexome profiling revealed accumulation of unincorporated ND5-module and impaired N-module production. RTN4IP1 patient fibroblasts also exhibited defective coenzyme Q biosynthesis, substantiating a second function of RTN4IP1. Thus, our data reveal RTN4IP1 plays necessary and independent roles in both the terminal stages of CI assembly and in coenzyme Q metabolism, and that pathogenic RTN4IP1 variants impair both functions in patients with mitochondrial disease.

Keywords: Coenzyme Q; Complex I Assembly; Complexome Profiling; Mitochondria; RTN4IP1

DOI: https://doi.org/10.1038/s44318-025-00533-x