Aug 2026· Journal of Structural Biology· pp.
108359
· 0 citations· 27 references
Medicine
TL;DR
The solution structure of mature Saccharomyces cerevisiae Mba1 is determined using multidimensional nuclear magnetic resonance (NMR) spectroscopy and reveals a compact α + β fold with a central hydrophobic cavity and distinct charged surface regions, providing a structural framework for interpreting previous functional studies of Mba1.
Abstract
Co-translational membrane insertion is essential for the efficient integration of mitochondrially encoded proteins into the inner mitochondrial membrane (IMM) and is critical for respiratory chain biogenesis. Mba1 is a mitochondrial ribosome-associated protein implicated in coupling mitochondrial translation with inner-membrane protein biogenesis, but its structural basis of function remains poorly understood. Here, we determined the solution structure of mature Saccharomyces cerevisiae Mba1 (mMba1) using multidimensional nuclear magnetic resonance (NMR) spectroscopy. The structure reveals a compact α + β fold with a central hydrophobic cavity and distinct charged surface regions. Ribosome titration, paramagnetic relaxation enhancement, and Cox2-derived peptide titration identified several regions of mMba1 that are affected by these different interaction conditions. Mapping these regions onto the structure reveals spatially distinct surfaces that may contribute to ribosome association, membrane proximity, and interactions with hydrophobic peptide segments. These findings provide a structural framework for interpreting previous functional studies of Mba1 and support a working model in which Mba1 may function as a peripheral adaptor at the mitoribosome-inner membrane interface. Further structural and biochemical studies will be required to establish the molecular mechanisms underlying these interactions.
The metabolic and signaling function of mitochondria rely on a network of chaperones within the inner membrane space (IMS) that regulate the biogenesis of nascent mitochondrial proteins. Using a genome wide CRISPRi screen we found that in human cells FAM136A is required for biogenesis of all three voltage-dependent anion channel (VDAC) paralogs, an abundant and essential family of β-barrel metabolite transporters in the outer mitochondrial membrane (OM). FAM136A is a ubiquitously expressed essential gene, that is conserved in metazoa and plants. Using a combination of experiments in human cells and in vitro reconstitution, we determined that FAM136A associates with unfolded VDACs in the IMS; solubilizes nascent VDAC through a direct interaction; and facilitates insertion of VDAC into the OM. FAM136A also binds and chaperones a subset of α-helical subunits of the electron transport chain. We therefore conclude that FAM136A is an IMS-resident chaperone, necessary and sufficient to maintain nascent membrane proteins in a folding-competent state to mediate their integration into the bilayer.
M. Ernst, Jichen Zhang, Haoqi Xu et al.· bioRxiv· 0 citations
Mitochondrial biogenesis requires the coordinated synthesis, targeting, and import of nuclear-encoded mitochondrial precursor proteins. Although ribosome-associated chaperones support co-translational protein folding, their genetic contributions to mitochondrial protein import and cellular homeostasis remain incompletely defined. Here, we investigate the roles of the nascent polypeptide-associated complex (NAC) and the ribosome-associated Hsp70 system Ssb1/2 in Saccharomyces cerevisiae. We show that NAC and Ssb1/2 have distinct yet partially overlapping functions in the handling of mitochondrial precursor proteins. Loss of NAC activates the mitochondrial retrograde pathway and enhances growth on ethanol as a non-fermentable carbon source without compromising respiratory competence, indicating metabolic adaptation rather than overt mitochondrial dysfunction. In contrast, Ssb1/2 deficiency disrupts cytosolic proteostasis, sensitizes cells to TORC1 inhibition, and impairs autophagy and mitophagy. Using a TEV protease-based import reporter, we show that Ssb1/2 promotes efficient co-translational distribution of precursor proteins, whereas NAC limits the accumulation of misfolded proteins at the mitochondrial surface. Biochemical analyses further reveal that Ssb1/2 supports the association of translating cytosolic ribosomes with the mitochondrial outer membrane, while NAC loss partially restores this interaction in the absence of Ssb1/2. Together, these findings establish NAC and Ssb1/2 as key components of an integrated network linking co-translational targeting, mitochondrial signaling, and cellular homeostasis.
J. E. Bravo-Arévalo, Ariann E Mendoza-Martínez, T. Ballado et al.· Genetics· 0 citations
Mitochondrial protein import and local translation at the mitochondrial outer membrane (MOM) require coordinated interactions between protein translocases and RNA-associated factors, yet the molecular organisation of these interactions remains largely unresolved. Here, we used APEX2-mediated proximity labelling to define the proximal proteomes associated with the cytosolic face of the TOM and SAM complexes by fusing APEX2 to TOMM22 and MTX2, respectively. Quantitative mass spectrometry identified known TOM/SAM-associated proteins together with multiple RNA-binding proteins (RBPs), supporting the emerging role of the MOM in localised translation and other RNA-related processes. Among identified RBPs, the exonuclease EXD2 was consistently enriched in APEX2-TOMM22 and MTX2-APEX2 datasets and remained associated upon puromycin treatment, indicating a translation-independent interaction. Together, our findings provide insights into the molecular organisation of mitochondrial import sites and identify EXD2 as a TOM/SAM-associated factor at the MOM.
Xu Wang, Claudia Cavarischia Rega, Boris Maček et al.· bioRxiv· 0 citations
Inner mitochondrial membrane proteins must be sufficiently hydrophilic to withstand aqueous exposure during translation and transit to the mitochondria. Meanwhile, their transmembrane segments must be sufficiently hydrophobic to stably embed in the lipid membrane. We hypothesized that sequence-level adaptations evolved to balance these constraints. Here, we integrate structure-informed evolutionary analyses of mitochondrial proteins with atomistic simulations and cell-based experiments to identify aliphatic-to-threonine substitutions (ATS) as a potential solution to these constraints. With high statistical confidence, this transmembrane segment-specific adaptation is recurrently and convergently observed throughout mitochondrial evolution. Conformational analyses show that threonine interacts with both water and the transmembrane helix backbone, thereby lowering hydrophobicity without destabilizing secondary structure. In the extremely hydrophobic ATP6 protein, reverting threonines to aliphatic residues disrupts mitochondrial targeting, while introducing threonines into a poorly targeted variant improves its mitochondrial localization. These findings have implications for mitochondrial genome evolution, the rational design of membrane proteins, and potentially mitochondrial gene therapy.
Tarun Yadav, Jonathan Borowsky, Á. Narbona-Pérez et al.· bioRxiv· 0 citations
Mitochondria perform diverse metabolic and signaling functions, yet how these activities are spatially organized within the mitochondrial network of cells remains poorly understood. Organelle contact sites are spatially restricted hubs that regulate mitochondrial metabolism, signaling, and dynamics, and are therefore well positioned to influence mitochondrial specialization. Investigation of contact site-associated mitochondrial populations has been hindered by a lack of methods to isolate these subpopulations. Here, we develop Organelle Contact-dependent Affinity Purification (ORCA), a workflow for the isolation and analysis of subpopulations of intact mitochondria and associated proteins defined by their organelle contacts. ORCA revealed distinct proteomes for mitochondria associated with the endoplasmic reticulum, lysosomes, peroxisomes, and the Golgi apparatus, demonstrating that organelle contacts define biochemically specialized mitochondrial populations. Focused analysis of Golgi-associated mitochondria showed enrichment of mitochondrial ribosomes and increased mitochondrial translation, revealing an unexpected role for Golgi-mitochondria contacts in regulating mitochondrial protein homeostasis. ORCA also identified the previously uncharacterized Golgi protein KIAA0930/GMO1 as an evolutionarily conserved regulator of oxidative phosphorylation at Golgi-mitochondria contacts. Together, our findings establish ORCA as a broadly applicable approach for investigating the spatial organization of intracellular organelles and reveal organelle contacts as key determinants of mitochondrial specialization.
G. M. Otto, Akimi Green, Jennifer Cabarrús et al.· bioRxiv· 0 citations
Mitochondria are cellular energy hubs best known for ATP production via oxidative phosphorylation; however, they also serve as biosynthetic centers for phospholipids. Mitochondrial phospholipids are critical for various cellular processes, and their loss underlies myriad mitochondrial diseases. The critical enzymes underlying these biosynthetic cascades are encoded in the nucleus, translated in the cytosol, and imported into mitochondria. Understanding of mechanisms and factors that ensure precise targeting of proteins to mitochondria has been long overlooked but remains critical. Recently, the J-protein/Hsp40 cochaperone Djp1 has emerged as a key player in mitochondrial protein targeting by promoting the transfer of precursors from the endoplasmic reticulum (ER) surface to mitochondria in a pathway termed ER-SURF. Molecular details regarding how Djp1 recognizes clients and more broadly supports mitochondrial function remain unknown. Using biochemical approaches, proteomics, and thin layer chromatography, we demonstrate that Djp1 is a regulator of Phosphatidylserine decarboxylase 1 (Psd1), an inner mitochondrial membrane resident responsible for mitochondrial phosphatidylethanolamine (PE) production. This regulation of Psd1 biogenesis is dependent on its mitochondrial targeting signal and is specific to Djp1 compared to other members of the Hsp40 family or ER targeting factors. Intriguingly, the combined loss of Djp1 and Psd1 results in a synthetic sick phenotype that unexpectedly reflects a role(s) for Djp1 in proper mitochondrial phospholipid metabolism independent of Psd1. Taken together, these findings expand our understanding of Djp1-dependent mitochondrial protein regulation and unveil Djp1 as important for mitochondrial phospholipid metabolism by multiple mechanisms.
Rashima Prem, Alex Maya-Romero, C. Xie et al.· bioRxiv· 0 citations
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