Biology subjects

Bischoff, M.

Publications and source records attributed to Bischoff, M..

18 recordsLinked to original sources

bioRxiv2026

Copper transport to mitochondria by SLC25A3 contributes to skeletal myoblast differentiation and is required for survival of differentiated myotubes

Differentiation of skeletal muscle is associated with increased mitochondrial biogenesis and reliance of oxidative phosphorylation (OXPHOS). The terminal enzyme complex in the electron transport chain, cytochrome c oxidase (COX), requires copper for its assembly and activity, and copper delivery to mitochondria is essential for OXPHOS. However, when mitochondrial copper becomes essential during skeletal myoblast differentiation is not known. Here, we show that genetic deficiency of the mitochondrial copper and phosphate carrier SLC25A3 induced prior to myoblast differentiation leads to the formation of smaller myotubes, but SLC25A3 deficiency induced in mature myotubes leads to cell death and detachment. Both phenotypes are recapitulated upon genetic knockdown of COX17, a critical assembly protein for both COX copper cofactors, or by chemical inhibition of COX. Importantly, myotube death caused by SLC25A3 deficiency is rescued by copper supplementation or expression of an SLC25A3 variant that transports copper but not phosphate. Taken together these data support a model wherein copper transport by SLC25A3 and copper delivery to COX is critical for survival in mature myotubes.

cell biology↗

bioRxiv2026

A screen for adherens junction proteins regulating collective cell migration and testis morphogenesis reveals important roles for the Rab GAP RN-tre and the kinase Par-1

Animal tissues have diverse architectures and cell behaviors across the epithelial-mesenchymal spectrum. Cell adhesion mediated by classical cadherins is foundational. Cadherins nucleate complexes of dozens of proteins connecting junctions to the cytoskeleton and signaling downstream. Many junctional proteins are well-studied in epithelia, but less is known about roles during mesenchymal migration. The nascent myotubes of the pupal Drosophila testis provide an excellent model for N-cadherin mediated mesenchymal migration. We combined a proximity proteomics dataset of adherens junction proteins in mammalian epithelial cells with genome-wide shRNA libraries knocking down Drosophila genes to begin to define the subset of junctional proteins important in mesenchymal migration. While N-cadherin is predominant, E-cadherin plays a supporting role. Surprisingly, several proteins with key roles in epithelial morphogenesis, including Afadins homolog Canoe, ZO-1s homolog Polychaetoid, and Par3s homolog Bazooka play at most modest roles. Twenty-two genes with diverse cell biological roles had strong to moderate defects in testis morphogenesis. These will provide a community resource. We followed up two. The kinase Par-1 is important for migration and gap closure, with knockdown phenotypes paralleling those of myosin. The Rab GAP RN-tre does not have roles until after migration and works in parallel with N-cadherin during testis spiralization.

cell biology↗

bioRxiv2026

Drosophila male genitalia rotation depends on permissive remodeling of the posterior abdomen

One of the most characteristic morphogenetic processes in Drosophila is the 360{degrees} rotation of the male pupal genital disc. This movement is driven by the myosin Myo1D, whose expression in the genital disc is controlled by the Hox gene Abdominal-B. The rotation takes place in contact and relative to the posterior abdomen, yet the contribution of abdominal tissues has remained unclear. Here we show that normal genital disc circumrotation requires active remodeling of posterior abdominal larval epidermal cells that contact the rotating terminalia. Preventing apoptosis in these cells, or increasing EGFR signaling, delays their extrusion and results in incomplete rotation without altering rotational chirality. In parallel, elimination of Extracellular Matrix by Metalloproteinase 1 in these cells, although without leading to their extrusion, is also strictly required for genital disc circumrotation. Inhibition of this metalloproteinase activity leads to persistence of collagen IV and incomplete rotation, revealing an independent requirement for Extracellular Matrix clearance at the disc-abdomen interface. By contrast, genetic conditions that prevent formation or elimination of the male A7 segment do not necessarily impair genital disc rotation, demonstrating that A7 suppression and circumrotation are separable processes. These findings identify posterior abdominal tissue remodeling as an essential extrinsic requirement that enables genital disc circumrotation.

developmental biology↗

bioRxiv2026

Structure Elucidation, Biosynthesis and Biological Evaluation of Neosorangicin A, a Member of the Sorangicin Family

Antimicrobial resistance represents an escalating global health crisis, with drug-resistant infections predicted to cause up to 10 million deaths annually by 2050, underscoring the urgent need for novel antibiotics. Natural products play a crucial role in the discovery and development of antibiotics, with myxobacteria emerging as a particularly promising source due to their ability to produce structurally diverse and bioactive compounds. One prominent example of antibiotics from myxobacteria are the sorangicins, potent inhibitors of the bacterial RNA polymerase (RNAP). Here, we report the isolation of two unprecedented compounds, neosorangicin A (1) and neosorangioside A (2), from Sorangium cellulosum strain Soce439, elucidated their molecular structures, thereby revealing significant structural variation in comparison to sorangicin, and describe their biosynthetic pathway. Neosorangicin A (1) exhibited strong activity against various Gram-positive bacteria, with enhanced potency on intracellular Staphylococcus aureus. In a murine wound infection model, a head-to-head comparison of neosorangicin A (1) and sorangicin A (3) provided useful insights into how the altered physicochemical properties, arising from the shortened side chain and the lack of the free carboxylic acid of neosorangicin A, influence the in vivo efficacy of sorangicin derivatives.

microbiology↗

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↗

bioRxiv2024

Melanocyte differentiation and mechanosensation are differentially modulated by distinct extracellular matrix proteins

Dysfunctions in melanocytes can lead to pigmentation disorders, such as albinism, or contribute to the development of melanoma, the most aggressive form of skin cancer. Epidermal melanocytes typically interact with the collagen IV-rich basement membrane, but upon injury or in pathological conditions, they can encounter environments rich in collagen I or fibronectin. While alterations in extracellular matrix (ECM) composition and stiffness are known to impact cell behavior, the specific roles of each of these cues for melanocyte functions remain unclear. To explore the impact of these extrinsic cues, we here exposed murine melanocytes to different ECM proteins as well as varying substrate stiffnesses. This study identified MITF, a key regulator of melanocyte differentiation and function, as an ECM- and mechanosensitive transcription factor. We further revealed that distinct ECM proteins and substrate stiffness engage a FAK/MEK/ERK/MITF signaling axis to control melanocyte functions. Exposure of melanocytes to collagen I restricted FAK and ERK activation, promoting high nuclear MITF levels associated with melanocyte proliferation and differentiation. Conversely, fibronectin elicited elevated FAK and ERK activation, leading to low nuclear MITF, correlating with a dedifferentiated and motile phenotype. Consistent with these observations, RNA sequencing revealed that collagen I supports a differentiated gene expression program, whereas fibronectin induces a dedifferentiated transcriptomic signature. Importantly, inhibiting MEK or ERK activity in melanocytes cultured on fibronectin led to increased MITF nuclear localization and enhanced melanogenesis. Additionally, on fibronectin FAK inhibition reduced ERK activation and enhanced melanogenesis, supporting a role for FAK upstream of ERK. Finally, we uncovered that melanocyte mechanoresponses differ depending on the specific ECM environment. Together, these findings reveal a substantial effect of extrinsic cues on melanocyte function, with a context-dependent MITF regulation downstream of ERK, offering new perspectives for our understanding of melanocyte-related pathologies.

cell biology↗

bioRxiv2024

An active matter model captures the spatial dynamics of actomyosin oscillations during morphogenesis

The apicomedial actomyosin network is crucial for generating mechanical forces in cells. Oscillatory behaviour of this contractile network is commonly observed before or during significant morphogenetic events. For instance, during the development of the Drosophila adult abdominal epidermis, larval epithelial cells (LECs) undergo pulsed contractions before being replaced by histoblasts. These contractions involve the formation of contracted regions of concentrated actin and myosin. However, the emergence and control of pulsed contractions are not fully understood. Here, we combined in vivo 4D microscopy with numerical simulations of an active elastomer model applied to realistic cell geometries and boundary conditions to study LEC actomyosin dynamics. The active elastomer model was able to reproduce in vivo observations quantitatively. We also characterised the relationship between cell shape, cell polarity, and actomyosin network parameters with the spatiotemporal characteristics of the contractile network both in vivo and in simulations. Our results show that cell geometry, accompanied by boundary conditions which reflect the cells polarity, is essential to understand the dynamics of the apicomedial actomyosin network. Moreover, our findings support the notion that spatiotemporal oscillatory behaviour of the actomyosin network is an emergent property of the actomyosin network, rather than driven by upstream signalling.

biophysics↗

bioRxiv2024

Monovalent Pseudo-Natural Product Degraders Supercharge the Native Degradation of IDO1 by KLHDC3

Targeted protein degradation (TPD) modulates protein function beyond inhibition of enzyme activity or protein-protein interactions. Most degrader drugs function by directly mediating proximity between a neosubstrate and hijacked E3 ligase. Here, we identified pseudo-natural products derived from (-)-myrtanol, termed iDegs that inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs boost IDO1 ubiquitination and degradation by the cullin-RING E3 ligase CRL2KLHDC3, which we identified to natively mediate ubiquitin-mediated degradation of IDO1. Therefore, iDegs increase IDO1 turnover using the native proteolytic pathway. In contrast to clinically explored IDO1 inhibitors, iDegs reduce formation of kynurenine by both inhibition and induced degradation of the enzyme and, thus, would also modulate non-enzymatic functions of IDO1. This unique mechanism of action may open up new therapeutic opportunities for the treatment of cancer beyond classical inhibition of IDO1.

cell biology↗

bioRxiv2024

Estimating full-field displacement in biological images using deep learning

The estimation of full-field displacement between biological image frames or in videos is important for quantitative analyses of motion, dynamics and biophysics. However, the often weak signals, poor biological contrast and a multitude of noise processes typical to microscopy make this a formidable challenge for many contemporary methods. Here, we present a deep-learning method, termed Displacement Estimation FOR Microscopy (DEFORM-Net), that outperforms traditional digital image correlation and optical flow methods, as well as recent learned approaches, offering simultaneous high accuracy, spatial sampling and speed. DEFORM-Net is experimentally unsupervised, relying on displacement simulation based on a random fractal Perlin-noise process and optimised training loss functions, without the need for experimental ground truth. We demonstrate its performance on real biological videos of beating neonatal mouse cardiomyocytes and pulsed contractions in Drosophila pupae, and in various microscopy modalities. We provide DEFORM-Net as open source, including inference in the ImageJ/FIJI platform, for rapid evaluation, which will empower new quantitative applications in biology and medicine.

biophysics↗

bioRxiv2023

Extracellular release of a disintegrin and metalloproteinases orchestrates periodontal disease severity

Periodontal diseases are amongst the most common pathologies worldwide with a high risk for the development of systemic complications. Periodontal disease is driven by oral pathogens such as Porphyromonas gingivalis and the release of inflammatory cytokines. These cytokines (e.g. TNF) or their receptors (IL-1R) are substrates of a disintegrin and metalloproteinases (ADAMs). In a comparative approach, we observed an increase of ADAM8 protein expression and activity in the sulcus fluid of periodontal disease patients correlating with the disease stage. In contrast, the induced ADAM10 expression was decreased. In vitro mechanistic studies revealed that both Porphyromonas gingivalis infection and the resulting cytokine release orchestrated the release of soluble ADAM8 by keratinocytes and neutrophils as soluble ectodomain and on exosomes, respectively. Furthermore, ADAM8 regulated the release of ADAM10 and MMP9, thereby potentially influencing wound healing and tissue destruction. Thus, the dysregulation of the cell-associated and extracellular ADAM proteolytic activity mainly driven by ADAM8 may be an essential regulatory element in periodontal disease onset and progression. This potential as novel local treatment option should be addressed in future translational studies.

immunology↗

bioRxiv2022

The Secreted Tyrosine Phosphatase PtpA promotes Staphylococcus aureus Intramacrophagic Survival Through Decrease of the SUMOylation Host Response

S. aureus is a human pathogen that is extremely adaptable and is the cause of a variety of nosocomial and community-acquired infectious illnesses. During infection, S. aureus affect the host cell in many ways to enable its own multiplication, spread, and evasion of host immune defense. One of S. aureus mechanism to survive is to inhibit the SUMOylation of host proteins in order to increase its intracellular survival and persistence for longer period of time. Here, we show that the reduction in the levels of cellular SUMO-conjugated proteins is associated to the PtpA secreted virulence factor, which results in a reduction of Ubc9 protein level, the essential enzyme of the SUMOylation modification. In addition, we demonstrated that the critical residue D120A, essential for PtpA phosphatase activity, is required. This study shows for the first time that the secreted phosphatase PtpA impedes the host SUMOylation response, thus promoting S. aureus survival at long-term infection.

microbiology↗

bioRxiv2021

Hydroxyapatite pellets as versatile model surfaces for systematic studies on enamel

Research into materials for medical application draws inspiration from naturally occurring or synthesized surfaces, just like many other research directions. For medical application of materials, particular attention has to be paid to biocompatibility, osseointegration and bacterial adhesion behavior. To understand their properties and behavior, experimental studies with natural materials such as teeth are strongly required. The results, however, may be highly case-dependent because natural surfaces have the disadvantage of being subject to wide variations, for instance in their chemical composition, structure, morphology, roughness, and porosity. A synthetic surface which mimics enamel in its performance with respect to bacterial adhesion and biocompatibility would, therefore, facilitate systematic studies much better. In this study, we discuss the possibility of using hydroxyapatite (HAp) pellets to simulate the surfaces of teeth and show the possibility and limitations of using a model surface. We performed single-cell force spectroscopy with single Staphylococcus aureus cells to measure adhesion-related parameters such as adhesion force and rupture length of adhesins binding to HAp and enamel. We also examine the influence of blood plasma and saliva on the adhesion properties of S. aureus. The results of these measurements are matched to water wettability, elemental composition of the samples and the change in the macromolecules adsorbed over time. We found that the adhesion properties of S. aureus were similar on both samples under all conditions: Significant decreases in adhesion strength were found equally in the presence of saliva or blood plasma on both surfaces. We therefore conclude that HAp pellets are a good alternative for natural dental material. This is especially true when slight variations in the physicochemical properties of the natural materials may affect the experimental series.

biophysics↗

bioRxiv2021

T cell stiffness is enhanced upon formation of immunological synapse

T cells are activated by cognate target cells via an intimate contact, termed immunological synapse (IS). Cellular mechanical properties, especially stiffness, are essential to regulate cell functions, T cell stiffness at a subcellular level at the IS still remains largely elusive. In this work, we established an atomic force microscopy (AFM)-based elasticity mapping method on whole T cells to obtain an overview of the stiffness with a resolution of ~ 60 nm. Using Jurkat T-cells and primary human CD4+ T cells, we show that in the T cells in contact with functionalized surfaces, the lamellipodia are stiffer than the cell body. Upon IS formation, T cell stiffness is substantially enhanced both at the lamellipodia and in cell body. Chelation of intracellular Ca2+ abolishes IS-induced stiffening at the lamellipodia but has no influence on cell body-stiffening, suggesting different regulatory mechanism of IS-induced stiffening between the lamellipodia and the cell body.

biophysics↗

bioRxiv2021

The adhesion capability of S. aureus cells is heterogeneously distributed over the cell envelope

Understanding and controlling microbial adhesion is an important biomedical problem. However, many properties of the adhesion process of bacteria are still unknown, for example the distribution of adhesive strength over the cell wall. While a patchy colloid model for adhesion has been developed recently for Gram-negative Escherichia coli cells, a comparable model for Grampositive cells is unknown. Here, we use single-cell force spectroscopy to measure the adhesion of Staphylococcus aureus at different positions on tailored surfaces. We find heterogeneous adhesion profiles with varying degrees of intensity. By comparing these results to simulations, we find that locally increased adhesion can be explained by several distinct spots of high adhesion capabilities, similar to the patchy colloid model. Only for the underlying profile without local adhesive spots simple geometric considerations are insufficient. Rather, strong angle-dependent molecule-substratum interactions are necessary to explain the bathtub-like adhesion profiles seen for Staphylococcus aureus on a sinusoidal surface. We discuss implications of our results for the development of new materials and the design and analysis of future studies.

biophysics↗

bioRxiv2020

Filopodia-based contact stimulated collective migration drives tissue morphogenesis

Cells migrate collectively to form tissues and organs during morphogenesis. Contact inhibition of locomotion (CIL) drives collective migration by inhibiting lamellipodial protrusions at cell-cell contacts and promoting polarization at the leading edge. Here, we report on a CIL-related collective cell behavior of myotubes that lack lamellipodial protrusions, but instead use filopodia to move as a cohesive cluster in a formin-dependent manner. Genetic, pharmacological and mechanical perturbation analyses reveal essential roles of Rac2, Cdc42 and Rho1 in myotube migration. They differentially control not only protrusion dynamics but also cell-matrix adhesion formation. Here, active Rho1 GTPase localizes at retracting free edge filopodia. Rok-dependent actomyosin contractility does not mediate a contraction of protrusions at cell-cell contacts but likely plays an important role in the constriction of supracellular actin cables. We propose that contact-dependent asymmetry of cell-matrix adhesion drives directional movement, whereas contractile actin cables contribute to the integrity of the migrating cell cluster.

cell biology↗

bioRxiv2020

Single-particle cryo-EM at atomic resolution

The three-dimensional positions of atoms in protein molecules define their structure and provide mechanistic insights into the roles they perform in complex biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more knowledge about protein function may be inferred. With breakthroughs in electron detection and image processing technology, electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years1,2. However, obtaining cryo-EM reconstructions with sufficient resolution to visualise individual atoms in proteins has thus far been elusive. Here, we show that using a new electron source, energy filter and camera, we obtained a 1.7 [A] resolution cryo-EM reconstruction for a prototypical human membrane protein, the {beta}3 GABAA receptor homopentamer3. Such maps allow a detailed understanding of small molecule coordination, visualisation of solvent molecules and alternative conformations for multiple amino acids, as well as unambiguous building of ordered acidic side chains and glycans. Applied to mouse apo-ferritin, our strategy led to a 1.2 [A] resolution reconstruction that, for the first time, offers a genuine atomic resolution view of a protein molecule using single particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualised in difference maps, allowing a direct analysis of hydrogen bonding networks. Combination of the technological advances described here with further approaches to accelerate data acquisition and improve sample quality provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery.

biophysics↗

bioRxiv2019

Cellular contractility coordinates cytoskeletal dynamics and cell behaviour during Drosophila abdominal morphogenesis

During morphogenesis, cells undergo various behaviours, such as migration and constriction, which need to be coordinated. How this is achieved remains elusive. During morphogenesis of the Drosophila adult abdominal epidermis, larval epithelial cells (LECs) migrate directedly before constricting apically and undergoing apoptosis. Here, we study the mechanisms underlying the transition from migration to constriction. We show that LECs possess a pulsatile apical actomyosin network and that a change in network polarity underlies behavioural change. Exploring the properties of the contractile network, we find that the level of cell contractility impacts on the networks behaviour, as well as on overall cytoskeletal architecture and cell behaviour. We also find that pulsed contractions occur only in cells with intermediate levels of contractility. Furthermore, increasing levels of the small Rho GTPase Rho1 disrupts pulsed contractions, and instead leading to cells that cycle between two states, characterised by a junctional cortical and an apicomedial actin network. Our results highlight that behavioural change relies on tightly controlled cellular contractility. Moreover, we show that constriction can occur without pulsed contractions, raising questions about their contribution to constriction.

cell biology↗

bioRxiv2018

Apical caspase reporters uncover unknown stages of apoptosis and enable ready visualization of undead cells

The caspase-mediated regulation of many cellular processes, including apoptosis, justifies the substantial interest in understanding all of the biological features of these enzymes. To complement functional assays, it is critical to identify caspase-activating cells in live tissues. Our work describes new caspase-reporters that, for the first time, provide direct information concerning the initial steps of the caspase activation cascade in Drosophila tissues. One of our caspase-sensors has capitalized on the rapid subcellular localization change of a fluorescent marker to uncover novel cellular apoptotic events. These refer to the actin-mediated positioning of the nucleus before cell delamination. The other construct has benefited from a caspase-induced nuclear translocation of a QF transcription factor. This feature enables the genetic manipulation of caspase-activating cells, whilst showing the spatio-temporal patterns of apical caspase activation. Collectively, our sensors offer new experimental opportunities that are already illuminating unknown aspects of caspase-dependent processes in apoptotic and non-apoptotic cellular scenarios.\n\nSummary statementWe describe a novel set of caspase sensors that directly detect early caspase activation. The exclusive features of our reporters uncovered unknown stages of apoptosis and properties of caspase-activating cells.

cell biology↗