Biology subjects

Holzer, E.

Publications and source records attributed to Holzer, E..

4 recordsLinked to original sources

bioRxiv2025

Pathway and gates for ATG2A-mediated lipid transport in autophagy

Autophagy is a complex process in which eukaryotic cells degrade cytosolic components by delivering them to lysosomes via double-membrane autophagosomes. The lipid transfer protein ATG2A plays a crucial role in autophagosome formation by tethering the phagophore membrane to the ER and delivering a significant fraction of the required lipids. The mechanism by which ATG2A shuttles lipids from one membrane to the other, however, remains elusive. Here, we combine structural predictions, molecular dynamics simulations and in vitro lipid transfer assays to gain mechanistic insights into ATG2A-mediated lipid transport. Using this integrative approach, we characterize the contact sites of the protein with donor and acceptor membranes. Our simulations capture multiple events of lipid uptake and delivery from and to the bound membrane. Conformational rearrangements of N-terminal amphipathic helices emerge as a critical factor for facile lipid transport. With this insight, we designed an ATG2A mutant that transfers lipids three times faster than the wild type in vitro. In complex with ATG9A, ATG2A forms a bridge between two parallel membranes at 12 nm separation. Overall, our findings suggest that ATG2A is a lipid transporter gated at the N-terminus by blocking helices that, upon release, act as additional membrane tethers.

biophysics↗

bioRxiv2025

A lipid transfer-dependent feedback loop activates ATG9A compartments in autophagy initiation

Autophagy degrades cellular material by sequestering it within autophagosomes, which form de novo from precursors called phagophores. Phagophore assembly and expansion require ATG9A-positive seed compartments, the lipid transfer protein ATG2A, and the class III phosphatidylinositol 3-phosphate kinase complex I (PI3KC3-C1). PI3KC3-C1 synthesizes phosphatidylinositol 3-phosphate (PI3P), a key lipid that drives downstream processes for phagophore expansion, including ATG8 lipidation. We find that ATG9A compartments contain only traces of phosphatidylinositol (PI), likely insufficient for efficient PI3P production or recruitment of PI3P-binding effectors. Nevertheless, ATG2A is recruited to these compartments and mediates lipid transfer, including PI, into them. Remarkably, even without detectable PI3P, ATG9A compartments are direct substrates for ATG8 lipidation, and ATG8 proteins themselves enhance ATG2A-mediated lipid transfer. In cells, ATG2A is essential for the appearance of PI3P on ATG9A compartments. Our findings support a model in which a lipid transfer-driven feedback loop activates ATG9A compartments for phagophore expansion.

cell biology↗

bioRxiv2021

A Modified TurboID Approach Identifies Tissue-Specific Centriolar Components In C. elegans

Proximity-dependent labeling approaches such as BioID have been a great boon to studies of protein-protein interactions in the context of cytoskeletal structures such as centrosomes which are poorly amenable to traditional biochemical approaches like immunoprecipitation and tandem affinity purification. Yet, these methods have so far not been applied extensively to invertebrate experimental models such as C. elegans given the long labeling times required for the original promiscuous biotin ligase variant BirA*. Here, we show that the recently developed variant TurboID successfully probes the interactomes of both stably associated (SPD-5) and dynamically localized (PLK-1) centrosomal components. We further develop an indirect proximity labeling method employing a GFP nanobody-TurboID fusion, which allows the identification of protein interactors in a tissue-specific manner in the context of the whole animal. Critically, this approach utilizes available endogenous GFP fusions, avoiding the need to generate multiple additional strains for each target protein and the potential complications associated with overexpressing the protein from transgenes. Using this method, we identify homologs of two highly conserved centriolar components, Cep97 and Bld10/Cep135, which are present in various somatic tissues of the worm. Surprisingly, neither protein is expressed in early embryos, likely explaining why these proteins have escaped attention until now. Our work expands the experimental repertoire for C. elegans and opens the door for further studies of tissue-specific variation in centrosome architecture.

cell biology↗

bioRxiv2020

An Acentriolar Centrosome At The C. elegans Ciliary Base

In animal cells the functions of the cytoskeleton are coordinated by centriole-based centrosomes via microtubule-nucleating {gamma}-tubulin complexes embedded in the pericentriolar material or PCM [1]. PCM assembly has been best studied in the context of mitosis, where centriolar SPD-2 recruits PLK-1, which in turn phosphorylates key scaffolding components such as SPD-5 and CNN to promote expansion of the PCM polymer [2-4]. To what extent these mechanisms apply to centrosomes in interphase or in differentiated cells remains unclear [5]. Here, we examine a novel type of centrosome found at the ciliary base of C. elegans sensory neurons, which we show plays important roles in neuronal morphogenesis, cellular trafficking and ciliogenesis. These centrosomes display similar dynamic behavior to canonical, mitotic centrosomes, with a stable PCM scaffold and dynamically localized client proteins. Unusually, however, they are not organized by centrioles, which degenerate early in terminal differentiation [6]. Yet, PCM not only persists but continues to grow with key scaffolding proteins including SPD-5 expressed under control of the RFX transcription factor DAF-19. This assembly occurs in the absence of the mitotic regulators SPD-2, AIR-1 and PLK-1, but requires tethering by PCMD-1, a protein which also plays a role in the initial, interphase recruitment of PCM in early embryos [7]. These results argue for distinct mechanisms for mitotic and non-mitotic PCM assembly, with only the former requiring PLK-1 phosphorylation to drive rapid expansion of the scaffold polymer. ETOC BLURBCentrioles play a critical role in mitotic centrosome assembly. Here, Garbrecht et al. show that pericentriolar material (PCM) persists at the ciliary base of C. elegans sensory neurons after centriole degeneration, where it contributes to neuronal morphogenesis and cellular trafficking. Remarkably, this PCM displays dynamic properties similar to canonical centrosomes, yet its continued assembly and maintenance is independent of known mitotic regulators, suggesting differential mechanisms for mitotic and non-mitotic centrosome assembly. HIGHLIGHTSO_LIPCM persists at the acentriolar ciliary base in C. elegans C_LIO_LIPCM assembles in a SPD-2, AIR-1 and PLK-1-independent manner C_LIO_LIPCMD-1 tethers PCM at the ciliary base in the absence of centrioles C_LIO_LIPCM is required for neuronal morphogenesis and cilium assembly C_LI

cell biology↗