bims-mitpro 2025-09-07 papers

Issue of 2025–09–07
four papers selected by
Andreas Kohler, Umeå University

Nat Struct Mol Biol. 2025 Aug 28.

Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting.

Yuqi Yang, Shanshan Wang, Guopeng Wang, Yuke Lian, Lingfeng Xue, Wenhong Jiang, Qiang Guo, Chen Song, Long Li.

The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM-TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM-TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17-Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM-TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins.

DOI: https://doi.org/10.1038/s41594-025-01662-x

EMBO Rep. 2025 Aug 29.

Peri-mitochondrial actin filaments inhibit Parkin assembly by disrupting ER-mitochondria contacts.

Tak Shun Fung, Amrapali Ghosh, Maite R Zavala, Zuzana Nichtova, Dhavalkumar Shukal, Marco Tigano, Gyorgy Csordas, Henry N Higgs, Rajarshi Chakrabarti.

Mitochondrial damage represents a dramatic change in cellular homeostasis, necessitating metabolic adaptation and clearance of the damaged organelle. One rapid response to mitochondrial damage is peri-mitochondrial actin polymerization within 2 min, which we term ADA (Acute Damage-induced Actin). ADA is vital for a metabolic shift from oxidative phosphorylation to glycolysis upon mitochondrial dysfunction. In the current study, we investigated the effect of ADA on Pink1/Parkin mediated mitochondrial quality control. We show that inhibition of proteins involved in the ADA pathway significantly accelerates Parkin recruitment onto depolarized mitochondria. Addressing the mechanism by which ADA resists Parkin recruitment onto depolarized mitochondria, we found that ADA disrupts ER-mitochondria contacts in an Arp2/3 complex-dependent manner. Interestingly, overexpression of ER-mitochondria tethers overrides the effect of ADA, allowing rapid recruitment of not only Parkin but also LC3 after mitochondrial depolarization. During chronic mitochondrial dysfunction, Parkin and LC3 recruitment are completely blocked, which is reversed rapidly by inhibiting ADA. Taken together we show that ADA acts as a protective mechanism, delaying mitophagy following acute damage, and blocking mitophagy during chronic mitochondrial damage.

Keywords: Actin; Arp2/3 Complex; ER; LC3; Parkin

DOI: https://doi.org/10.1038/s44319-025-00561-y

Trends Biochem Sci. 2025 Aug 27. pii: S0968-0004(25)00193-8. [Epub ahead of print]

MitoTraP: mitochondrial protection for cellular proteostasis.

Michaela Oborská-Oplová, Michael A Ruoss, Vikram G Panse.

Cells depend on the efficient import of thousands of nuclear-encoded mitochondrial proteins to maintain mitochondrial function. A new study by Flohr et al. reveals a quality control strategy that traps a subset of mitochondrial precursors in the intermembrane space during energy stress, preventing their toxic accumulation in the cytosol or nucleus.

Keywords: mitochondrial import; mitochondrial intermembrane space; mitochondrial quality control; mitochondrial ribosomal proteins (MRPs); mitochondrial stress; proteotoxic stress

DOI: https://doi.org/10.1016/j.tibs.2025.08.004

FEBS J. 2025 Sep 02.

Synthetic trap-peptides identify a TOM complex phosphatase - PP2A dephosphorylates Tom6.

Laura Scheinost, Christina Ludwig, Nico Höfflin, Asli Aras Taskin, Adinarayana Marada, F-Nora Vögtle, Chris Meisinger, Maja Köhn.

The identification of phosphatases that dephosphorylate specific sites in proteins remains a major challenge, particularly for the major class of serine/threonine-specific phosphatases, which function as holoenzymes. Here, we report the development of synthetic trap-peptides to identify phosphatases that bind to Tom6, a subunit of the mitochondrial translocase of the outer membrane (TOM) complex. The TOM complex is regulated by reversible phosphorylation, and although responsible kinases have been identified, the corresponding phosphatases so far remain unknown. Here, the trap-peptides enriched phosphoserine/threonine-specific protein phosphatases 2A (PP2A) and 4 (PP4) as full holoenzymes from yeast cytosolic fractions. We observed that their interaction with Tom6 was mediated through their regulatory subunits Cdc55reg and Psy2reg, respectively, and that PP2A was able to dephosphorylate Ser16 of Tom6 in vitro. In summary, synthetic trap-peptides facilitate the identification of complete holoenzymes that bind to the target sequence and reveal PP2A as the first TOM phosphatase.

Keywords: PP2A; PP4; TOM complex; Tom6 Phosphatase substrates

DOI: https://doi.org/10.1111/febs.70246