Biology subjects

Herrmann, E.

Publications and source records attributed to Herrmann, E..

7 recordsLinked to original sources

bioRxiv2026

Structure and function of the DFCP1 membrane barrier responsible for ER microdomain organization in lysosome repair

The endoplasmic reticulum (ER) forms specialized microdomains that organize autophagy, lipid droplet formation, and the repair of damaged lysosomes. The PI3P-binding protein DFCP1/ZFYVE1 marks these microdomains, raising the question as to whether and how one protein could define such a subcompartment. Here we determine the structure of full-length human DFCP1 bound to membranes by cryo-electron tomography and single-particle cryo-electron microscopy. DFCP1 assembles into a helical coat, built from tetramers that stack around a constricted membrane tube. Its ATPase domains form the organizing core of the helix, while its ER-targeting domains insert deeply into the outer leaflet, and its FYVE domains grip PI3P. Coarse-grained molecular dynamics simulations show that the coat does not simply follow the curvature of the membrane but acts as a barrier to lipid diffusion, almost completely blocking the movement of its cognate lipid PI3P past the filament and concentrating it beneath the coat. Point mutations that break the assembly, membrane-insertion or PI3P-binding interfaces each impair lysosomal repair in cells, and the assembly is also required for the focal recruitment of the lipid transporter VPS13C. We propose that DFCP1 collars fence off a specialized ER microdomain, so that locally made lipids can reach sites of repair rather than escaping into bulk ER.

cell biology↗

bioRxiv2026

Nanoscale remodeling of mitochondrial architecture duringmtRNA surveillance failure

Mitochondria within a cell exhibit heterogeneity in their composition and metabolic functions, and how this specialization shapes the responses of individual organelles to stress is unclear. We applied fluorescence microscopy and in situ cryo-electron tomography to examine the composition of mitochondrial stress bodies and their relationship to inner mitochondrial membrane architecture in the context of a mitochondrial genome expression defect. We discovered that defective mitochondrial RNA processing prompted a loss of inner membrane domain identity, leading to the mislocalization of ATP synthase from cristae edges to the boundary membrane, perturbed cristae morphometrics, and complete cristae loss in a subset of organelles. Mitochondrial stress bodies were enriched with nucleic acid and protein components linked to oxidative pathways, while separate and distinct mitochondrial domains became enriched with oligomerized P5CS, a marker of reductive proline synthesis. We found that consolidation of mitochondrial RNA into stress bodies, as well as ATP synthase remodeling, were regulated independently from P5CS concentration into a subset of the mitochondria. We propose that stress compartmentalization enables independent tuning of the quality control of oxidative pathway components via spatial sequestration from the rest of the mitochondrial network.

cell biology↗

bioRxiv2026

Structural Mechanism and Cellular Restriction of Tau Seeding from Endolysosomes

The prion-like spread of tau from cell to cell in the central nervous system involves escape from the endolysosomal network, which is counteracted by the lysosomal repair activity of the ESCRT system. Here, we investigate whether other components of the lysosomal damage sensing and repair system, namely the ESCRT-recruiting Ca2+ sensor ALG-2, conjugation of ATG8s to single membranes (CASM), the phosphoinositide-initiated tethering and lipid transport (PITT) pathway, and the Parkinsons disease-related lipid transporter VPS13C are involved in tau spread. We found that the PITT pathway and VPS13C are strongly implicated in tau seeding by pre-formed fibrils (PFFs) in both neurons and astrocytes, CASM has a major role in astrocytes but not neurons, and ALG-2 has a lesser role in both. We then investigated the mechanism of damage and seeding by tau PFFs using cryo-electron tomography. Unlike the classical lysosome damage agent LLOMe, tau PFFs were not seen to directly interact with the lysosomal membrane, nor do they distort local membrane curvature. Lysosomes in PFF-treated cells were structurally intact. Extensive protein aggregates of similar character were seen in both the lysosomal lumen and in the cytosol proximal to lysosomes. The observations are consistent with the PFF-induced co-aggregation of tau with other cellular materials within lysosomes, with leakage to the cytosol attributed to reversible holes in the lysosome membrane.

cell biology↗

bioRxiv2025

Tracheal tuft cell-released leukotrienes promote antibacterial immune responses

Tuft cells act as crucial sentinels in the airways that detect bacterial metabolites. In response, tuft cells release signaling molecules that trigger immune responses essential for clearing the infection. The molecular mechanisms driving immune cell activation following tuft cell stimulation in pneumonia are still not fully understood. Here, we identify tuft cells as the primary source of proinflammatory leukotrienes (LTs), which are released in the presence of pathogenic bacteria in the airways. We show that tracheal tuft cells discriminate pathogenic from non-pathogenic bacteria by sensing adenosine triphosphate (ATP) released from pathogens such as Pseudomonas aeruginosa and Rodentibacter pneumotropicus within the first 4 h of invasion, and recruit neutrophils and macrophages to the trachea and alveolar spaces. Taste signaling through the chemosensory transient receptor potential cation channel subfamily M member 5 (Trpm5) channel was essential for tuft cell activation and LT release. Mice lacking Trpm5 were not capable of detecting bacteria-released ATP and became colonized upon R. pneumotropicus infection. In contrast, Trpm5+/+ mice cleared the pathogen. We uncover a critical tuft cell-dependent sensing mechanism in pneumonia and establish tracheal tuft cells as both detectors of bacterial extracellular ATP and triggers of acute innate immune responses.

immunology↗

bioRxiv2025

Matters arising: Forced Symmetry Artifacts in a Prohibitin Complex Structure

In a recent publication, Lange et al.1 proposed an 11-spoked wheel model for the mitochondrial prohibitin complex consisting of six PHB1 and five PHB2 subunits built into low resolution density obtained from 11-fold symmetry averaging. The proposed unequal stoichiometry is inherently incompatible with symmetry. The building of an asymmetric molecular model into density obtained by 11-fold symmetry averaging is inherently self-contradictory. This contradiction alone calls the validity of the derived structure into question. Our own data revealed that the complex primarily adopts an asymmetric open conformation in situ. We show that it was the incorrect symmetry imposition on the open conformation that led to the spoked wheel density reported by Lange et al.. Further validation by re-analysis of crosslinking-mass spectrometry data, and a test of in situ template matching all support a larger prohibitin complex architecture. These findings underscore the need for great care in the imposition of symmetry cryo-ET at less than atomistic resolution.

cell biology↗

bioRxiv2025

In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment

Defective mitochondrial quality control in response to loss of mitochondrial membrane polarization is implicated in Parkinsons disease by mutations in PINK1 and PRKN. Application of in situ cryo-electron tomography (cryo-ET) made it possible to visualize the consequences of mitochondrial depolarization at higher resolution than heretofore attainable. Parkin-expressing U2OS cells were treated with the depolarizing agents oligomycin and antimycin A (OA), subjected to cryo-FIB milling, and mitochondrial structure was characterized by in situ cryo-ET. Phagophores were visualized in association with mitochondrial fragments. Bridge-like lipid transporter (BLTP) densities potentially corresponding to ATG2A were seen connected to mitophagic phagophores. Mitochondria in OA-treated cells were fragmented and devoid of matrix calcium phosphate crystals. The intermembrane gap of cristae was narrowed and the intermembrane volume reduced, and some fragments were devoid of cristae. A subpopulation of ATP synthases re-localized from cristae to the inner boundary membrane (IBM) apposed to the outer membrane (OMM). The structure of the dome-shaped prohibitin complex, a dodecamer of PHB1-PHB2 dimers, was determined in situ by sub-tomogram averaging in untreated and treated cells and found to exist in open and closed conformations, with the closed conformation is enriched by OA treatment. These findings provide a set of native snapshots of the manifold nano-structural consequences of mitochondrial depolarization and provide a baseline for future in situ dissection of Parkin-dependent mitophagy.

cell biology↗

bioRxiv2022

Targeting of the Mon1-Ccz1 Rab guanine nucleotide exchange factor to distinct organelles by a synergistic protein and lipid code

Activation of the small GTPase Rab7 by its cognate guanine nucleotide exchange factor (GEF) Mon1-Ccz1 (MC1) is a key step in the maturation of endosomes and autophagosomes. This process is tightly regulated and subject to precise spatiotemporal control of MC1 localization. We here identify and characterize an amphipathic helix in Ccz1, which is required for the function of Mon-Ccz1 in autophagy, but not endosomal maturation. Furthermore, our data show that the interaction of the Ccz1 amphipathic helix with lipid packing defects, binding of Mon1 basic patches to positively charged lipids and association of MC1 with recruiter proteins collectively govern membrane recruitment of the complex in a synergistic and redundant manner. The data demonstrate that specific protein and lipid cues convey the differential targeting of MC1 to endosomes and autophagosomes. We reveal the molecular mechanism how MC1 is adapted to recognizes distinct target compartments by exploiting the unique biophysical properties of organelle membranes and thus provide a model how the complex is regulated and activated independently in different functional contexts.

biochemistry↗