Biology subjects

Schauer, K.

Publications and source records attributed to Schauer, K..

10 recordsLinked to original sources

bioRxiv2026

Endosomal membrane state governs trafficking and cell migration under TFEB control

Transcription Factor EB (TFEB) regulates the biogenesis of lysosomes, which are acidic organelles of the endosomal network. While its role in cellular clearance is well established, the pleiotropic functions of TFEB across diverse cellular processes, as well as its activation in several cancer types, remain incompletely understood. Investigating TFEB in a bladder cancer model, we found that its depletion selectively impaired cell migration and adhesion. This phenotype was associated with the retention of the adhesion molecule integrin {beta}5 (ITG{beta}5), in central intracellular compartments identified as multivesicular bodies (MVBs) upon TFEB knockdown (KD). Mechanistically, TFEB regulated cellular lipid composition and membrane fluidity of acidic endosomes that controlled ITG{beta}5 trafficking. Remarkably, exogenous supplementation with a monounsaturated fatty acid (MUFA) that increased MVB membrane fluidity was sufficient to phenocopy the intracellular trapping of ITG{beta}5 in 2D culture and 3D tumoroids. We further showed that TFEB-dependent maintenance of MVB membrane fluidity relies on ESCRT-0 subcomplex, HGS/Hrs, which retains cholesterol at MVBs. Together, these findings reveal how transcriptional programs shape endosomal membrane states to control cargo trafficking and cell behavior.

cell biology↗

bioRxiv2026

Contributions of plasmid p1AB5075-encoded antibiotic resistance genes to multidrug resistance of Acinetobacter baumannii AB5075

Infections with multidrug resistant Acinetobacter baumannii are considered a threat to human and animal health. The widely studied A. baumannii strain AB5075 displays a high degree of antibiotic resistance. In this study, we experimentally validated that antibiotic resistance is largely mediated by resistance genes located on plasmid p1AB5075. We used a p1AB5075-deficient AB5075 strain to assess individual contributions of p1AB5075-encoded antibiotic resistance genes by ectopically (over-)expressing each gene in the {Delta}p1AB5075 background. By determining individual contributions of seven p1AB5075-encoded antibiotic resistance genes, we show individual and overlapping roles of genes for aminoglycoside resistance and uncover the importance of extended-spectrum {beta}-lactamase blaGES-11 for cephalosporin resistance in A. baumannii AB5075. We discovered that aminoglycoside N-acetyltransferase aaC(6)-Ib3 (aacA4), which was considered a potential pseudogene in A. baumannii AB5075, to be functional providing broad resistance to gentamicin, kanamycin, amikacin, streptomycin and tobramycin when overexpressed in A. baumannii AB5075. Because p1AB5075 is transferrable to a wide range of environmental and clinical A. baumannii strains and non-baumannii Acinetobacter species, the relevance of our findings extends beyond A. baumannii AB5075.

microbiology↗

bioRxiv2025

Microtubule deacetylation drives kinesin-1 mediated mitochondrial transport accelerating breast cancer cell migration

Mitochondrial trafficking is reprogrammed in metastatic breast cancer cells to sustain their migratory and invasive behavior. Mitochondria repositioning to sites of high energy demand is governed by a balance between opposing dynein and kinesin-1 (KIF5B) molecular motors whose regulation remains incompletely understood. Here, we identify the SYBU gene as a candidate prognostic marker downregulated in metastatic disease. SYBU encodes syntabulin, a mitochondria outer membrane protein that interacts with dynein to counterbalance KIF5B-dependent anterograde transport to the cell cortex. Loss of SYBU disrupts the balance, causing excessive KIF5B-driven mitochondria movement, microtubule damage and deacetylation. In turn, microtubule deacetylation reinforces KIF5B-mediated transport, creating a positive feedback loop that drives mitochondria distribution close to the cell periphery and enhances cancer cell migration. Pharmacological inhibition of the tubulin deacetylase HDAC6 restores mitochondrial positioning and reduces cell migration in SYBU-deficient cells. Our findings identify SYBU as a key regulator of mitochondrial trafficking and pave the way to personalized therapeutic approaches for metastatic breast tumors with low SYBU expression.

cell biology↗

bioRxiv2025

Development of two compatible plasmids to assess sRNA-mediated post-transcriptional regulation in Acinetobacter baumannii

Post-transcriptional regulation can be mediated by small, regulatory RNAs in bacteria, which can act by base-pairing to a target messenger RNA. The discovery and mechanistic validation of base-pairing sRNAs in multidrug resistant Acinetobacter baumannii has been hampered by the lack of genetic tools to assess RNA-RNA interactions. Here, we created two compatible plasmids for A. baumannii, which addresses this need. The newly designed plasmids validated the known Aar sRNA-carO mRNA, and a new interaction of sRNA44 and the mRNA of the biofilm-associated protein Bap. The new plasmid system should accelerate the mechanistic characterisation of small, regulatory RNAs in A. baumannii. IMPACT STATEMENTMulti-drug resistance of pathogenic microorganisms is one of the greatest challenges for modern medicine. Carbapenem-resistant Acinetobacter baumannii are considered a highly critical organism, yet we are only beginning to understand its physiology and mechanisms of gene regulation. Post-transcriptional regulation by base-pairing, small RNAs is an understudied area, partly because of the lack of genetic tools to investigate them. In this study, we developed a 2-plasmid system to assess sRNA-mRNA interactions, which will greatly accelerate the discovery and validation of small, regulatory RNAs and their target molecules. DATA SUMMARYPlasmid sequences of pAMCK14-sRNA44 and pAMCK18-Bap have been made available in GenBank of National Center for Biotechnology Information (accession numbers PV916437 and PV916438).

microbiology↗

bioRxiv2024

Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy

Segmentation and detection of biological objects in fluorescence microscopy is of paramount importance in cell imaging. Deep learning approaches have recently shown promise to advance, automatize and accelerate analysis. However, most of the interest has been given to the segmentation of static objects of 2D/3D images whereas the segmentation of dynamic processes obtained from time-lapse acquisitions has been less explored. Here we adapted DeepFinder, a U-net originally designed for 3D noisy cryo-electron tomography (cryo-ET) data, for the detection of rare dynamic exocytosis events (termed ExoDeepFinder) observed in temporal series of 2D Total Internal Reflection Fluorescent Microscopy (TIRFM) images. ExoDeepFinder achieved good absolute performances with a relatively small training dataset of 60 cells/[~]12000 events. We rigorously compared deep learning performances with unsupervised conventional methods from the literature. ExoDeepFinder outcompeted the tested methods, but also exhibited a greater plasticity to the experimental conditions when tested under drug treatments and after changes in cell line or imaged reporter. This robustness to unseen experimental conditions did not require re-training demonstrating generalization capability of ExoDeepFinder. ExoDeepFinder, as well as the annotated training datasets, were made transparent and available through an open-source software as well as a Napari plugin and can directly be applied to custom user data. The apparent plasticity and performances of ExoDeepFinder to detect dynamic events open new opportunities for future deep-learning guided analysis of dynamic processes in live-cell imaging.

bioinformatics↗

bioRxiv2023

Peripheral positioning of lysosomes supports melanoma aggressiveness

Emerging evidences suggest that function and position of organelles are pivotal for tumor cell dissemination. Among them, lysosomes stand out as they integrate metabolic sensing with gene regulation and secretion of proteases. Yet, how their function is linked to their position and how this controls metastasis remains elusive. Here, we analyzed lysosome subcellular distribution in patient-derived melanoma cells and patient biopsies and found that lysosome spreading scales with their aggressiveness. Peripheral lysosomes promote matrix degradation and invasion of melanoma cells which is directly linked to their lysosomal and cell transcriptional programs. When controlling lysosomal positioning using chemo-genetical heterodimerization in patient-derived melanoma cells, we demonstrated that perinuclear clustering impairs lysosomal secretion, matrix degradation and invasion. Impairing lysosomal spreading in two distinct in vivo models (mouse and zebrafish) significantly reduces invasive outgrowth. Our study provides a direct demonstration that lysosomal positioning controls cell invasion, illustrating the importance of organelle adaptation in carcinogenesis and suggesting that lysosome positioning could potentially be used for the diagnosis of metastatic melanoma.

cell biology↗

bioRxiv2022

Membrane tension spatially organizes lysosomal exocytosis

Lysosomal exocytosis is involved in many key cellular processes but its spatio-temporal regulation is poorly known. Using total internal reflection fluorescence microscopy (TIRFM) and spatial statistics, we observed that lysosomal exocytosis is not random at the adhesive part of the plasma membrane of RPE1 cells but clustered at different scales. Although the rate of exocytosis is regulated by the actin cytoskeleton, neither interfering with actin or microtubule dynamics by drug treatments alters its spatial organization. Exocytosis events partially co-appear at focal adhesions (FAs) and their clustering is reduced upon removal of FAs. Changes in membrane tension following a hypo-osmotic shock or treatment with methyl-{beta}-cyclodextrin was found to increase clustering. To investigate the link between FAs and membrane tension, cells were cultured on adhesive ring-shaped micropatterns, which allows to control the spatial organization of FAs. By using a combination of TIRFM and fluorescence lifetime imaging microscopy (FLIM) microscopy, we revealed the existence of a radial gradient in membrane tension. By changing the diameter of micropatterned substrates, we further showed that this gradient as well as the extent of exocytosis clustering can be controlled. Together, our data indicate that the spatial clustering of lysosomal exocytosis relies on membrane tension patterning controlled by the spatial organization of FAs.

biophysics↗

bioRxiv2021

Coupling between protrusion dynamics and polarized trafficking steers persistent cell migration

Migrating cells present a variety of paths, from random to highly directional ones. While random movement can be explained by basal intrinsic activity, persistent movement requires stable polarization. Here, we quantitatively address emergence of persistent migration in RPE1 cells over long timescales. By live-cell imaging and dynamic micropatterning, we demonstrate that the Nucleus-Golgi axis aligns with direction of migration leading to efficient cell movement. We show that polarized trafficking is directed towards protrusions with a 20 min delay, and that migration becomes random after disrupting internal cell organization. Eventually, we prove that localized optogenetic Cdc42 activation orients the Nucleus-Golgi axis. Our work suggests that polarized trafficking stabilizes the protrusive activity of the cell, while protrusive activity orients this polarity axis, leading to persistent cell migration. Using a minimal physical model, we show that this feedback is sufficient to recapitulate the quantitative properties of cell migration in the timescale of hours.

biophysics↗

bioRxiv2020

A comprehensive library of fluorescent constructs of SARS-CoV-2 proteins and their initial characterization in different cell types

Comprehensive libraries of plasmids for SARS-CoV-2 proteins with various tags (e.g. Strep, HA, Turbo) are now available. They enable the identification of numerous potential protein-protein interactions between the SARS-CoV-2 virus and host proteins. To facilitate further cellular investigations, notably by imaging techniques, we present here a large library of SARS CoV-2 protein constructs fused with green and red fluorescent proteins and their initial characterization in various human cell lines including lung epithelial cell models (A549, BEAS-2B), as well as in budding yeast. The localization of a few SARS-CoV-2 proteins matches their proposed interactions with host proteins. These include the localization of Nsp13 to the centrosome, Orf3a to late endosomes, and Orf9b to mitochondria.

cell biology↗

bioRxiv2018

MYO1C facilitates arrival at the Golgi apparatus through stabilization of branched actin

We aim at the identification of myosin motor proteins that control trafficking at the Golgi apparatus. In addition to the known Golgi-associated myosins MYO6, MYO18A and MYH9 (myosin IIA), we identify MYO1C as a novel player at the Golgi. We demonstrate that depletion of MYO1C induces Golgi apparatus fragmentation and decompaction. MYO1C accumulates at dynamic structures around the Golgi apparatus that colocalize with Golgi-associated actin dots. Interestingly, MYO1C depletion leads to loss of cellular F-actin, and Golgi apparatus decompaction is also observed after the inhibition or loss of the Arp2/3 complex. We show that the functional consequences of MYO1C depletion is a delay in the arrival of incoming transport carriers, both from the anterograde and retrograde routes. We propose that MYO1C stabilizes branched actin at the Golgi apparatus that facilitates the arrival of incoming transport at the Golgi.

cell biology↗