Biology subjects

Doerr, S.

Publications and source records attributed to Doerr, S..

8 recordsLinked to original sources

bioRxiv2026

SHIP1 partitions between cortical oscillations and membrane puncta to regulate neutrophil chemotaxis

As frontline defenders in the innate immune system, neutrophils traffic to sites of infection by detecting chemical gradients, polarizing, and migrating towards foreign pathogens. This requires communication between small GTPases, phosphatidylinositol phosphate (PIP) lipids, and the actin cytoskeleton to generate forces that drive leading-edge membrane protrusions. Central to the coordination of these signaling events is the hematopoietic-cell-specific 5-inositol lipid phosphatase SHIP1 (or INPP5D), which shapes PIP lipid domains by dephosphorylating phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) to generate PI(3,4)P2. To decipher mechanisms controlling SHIP1 membrane localization during neutrophil chemotaxis, we combined genetic manipulation of SHIP1 with live cell Total Internal Reflection Fluorescence (TIRF) microscopy. Our results reveal two modes of SHIP1 localization: (1) cortical oscillations regulated by the membrane curvature sensing protein FBP17, and (2) dynamic membrane puncta organized by the adaptor protein Nck1. Localization to both membrane structures requires the proline-rich C-terminal domain (CTD) of SHIP1. Neutrophil-differentiated HL60 cells solely expressing a cytoplasmic localized SHIP1 CTD deletion mutant exhibit chemotaxis defects that phenocopy complete SHIP1 loss of function. Overall, this work reveals a dual mechanism by which SHIP1 integrates signals from membrane curvature sensing and adaptor proteins to control neutrophil cell migration.

cell biology↗

bioRxiv2026

Postnatal Maturation of Dendritic Epidermal T Cells and Langerhans Cells Follows Distinct Differentiation Trajectories Independent of Microbiota

The mouse epidermis harbors two key resident immune populations--dendritic epidermal T cells (DETCs), a subset of invariant {gamma}{delta} T cells, and Langerhans cells (LCs), specialized tissue-resident macrophages--both of which play critical roles in immune surveillance, barrier integrity, and tissue homeostasis. While the fetal origin of both cell types has been defined, the cellular and molecular mechanisms that govern their postnatal fates following colonization of the epidermis around birth remain incompletely understood. Here, we present a combination of immunophenotyping- and transcriptome-resolved single-cell map of DETC and LC development in the mouse epidermis from late embryogenesis through adulthood. We delineate differentiation trajectories for both cell types, marked by distinct changes in morphology, proliferation, and transcriptional programming. Using mice deficient in {gamma}{delta} T cells, which lack canonical DETCs, we demonstrate that LCs develop independently of canonical DETCs likely due to the presence of {beta}DETCs. Moreover, analysis of germ-free mice and wildlings reveals that the postnatal development of both DETCs and LCs is independent of microbial colonization. Together, our findings define the core principles underlying the establishment of the mouse epidermal immune niche. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/716534v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@18088a0org.highwire.dtl.DTLVardef@189e0f2org.highwire.dtl.DTLVardef@10f37d6org.highwire.dtl.DTLVardef@1ad59c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Phosphorylation of the C-terminus of PI4KA inhibits lipid kinase activity

Phosphatidylinositol 4-kinase alpha (PI4KA) is a lipid kinase that generates phosphatidylinositol 4-phosphate (PI4P) from phosphatidylinositol (PI) at the plasma membrane (PM). PI4P generated by PI4KA is essential for both plasma membrane identity and for PIP2 and PIP3 signalling driven by the PLC and PI3K family of enzymes. While the structure of PI4KA is known, the regulatory mechanisms that control its activity are undefined. Here, we discovered PI4KA can be inhibited through phosphorylation of Y2090 in the kinase domain, which can be phosphorylated by multiple tyrosine kinases. Y2090 phosphorylation causes local conformational changes in the k12 C-terminal helix. PI4KA activity is predominantly controlled through membrane recruitment by EFR3, with Y2090 phosphorylation inhibiting EFR3 bound PI4KA. Phosphorylation of the k12 C-terminal helix is found in PI3Ks and PI4Ks, suggesting an evolutionarily conserved regulatory mechanism for diverse phosphoinositide kinases. Overall, our work reveals novel molecular insight into inhibitory post-translational regulation of PI4KA.

biochemistry↗

bioRxiv2026

Reconstitution of Ras-PI3Kγ membrane communication and feedback using light-induced signaling inputs

Biochemical reactions involving phosphatidylinositol phosphate (PIP) lipids and small GTPases serve essential roles in signal transduction immediately downstream of cell surface receptor activation. Interconnected positive and negative feedback loops link these distinct classes of reactions and allow for the rapid establishment of the steep and precisely oriented intracellular activity gradients that are hallmarks of cell polarity. Although genetic approaches have identified numerous molecules that potentially regulate feedback between GTPases and PIP lipids in cells, it is unclear how different types of feedback modulate the spatiotemporal dynamics of membrane signaling reactions. Here, we reconstitute communication and feedback between Ras GTPase and phosphatidylinositol 3-kinase gamma (PI3K{gamma})-mediated generation of PIP3 on supported membranes. We employ light-induced membrane recruitment of a guanine nucleotide exchange factor (GEF) to rapidly and reversibly shift steady-state conditions and monitor corresponding Ras activation and PIP3 production in time and space. Alone, the Ras-PI3K{gamma} module exhibits weak and transient activation due to global inhibitors. However, the introduction of GEF-mediated positive feedback drives local amplification of Ras activation and PIP3 generation, resulting in a wave of activity that propagates across the membrane surface. Spatial coupling between activated Ras and PIP3 molecules depends on their respective diffusion coefficients and the species involved in the feedback circuit. This work identifies activation thresholds, membrane diffusion, and feedback architecture as key factors that determine how small GTPases and PIP lipid modifying enzymes amplify membrane signaling reactions in the presence of global inhibitors.

biochemistry↗

bioRxiv2024

Lateral cell polarization drives organization of epithelia in sea anemone embryos and embryonic cell aggregates

One of the first organizing processes during animal development is the assembly of embryonic cells into epithelia. In certain animals, including Hydra and sea anemones, epithelia also emerge when cells from dissociated tissues are aggregated back together. Although cell adhesion is required to keep cells together, it is not clear whether cell polarization plays a role as epithelia emerge from disordered aggregates. Here, we demonstrate that lateral cell polarization is essential for epithelial organization in both embryos and aggregates of the sea anemone Nematostella vectensis. Specifically, knock down of the lateral polarity protein Lgl disrupts epithelia in developing embryos and impairs the capacity of dissociated cells to epithelialize from aggregates. Cells in lgl mutant epithelia lose their columnar shape and have mispositioned mitotic spindles and ciliary basal bodies. Together, our data suggest that in Nematostella, Lgl is required to establish lateral cell polarity and position cytoskeletal organelles in cells of embryos and aggregates during de novo epithelial organization.

developmental biology↗

bioRxiv2022

Evaluation of K-Ras4B dimer interfaces and the role of Raf effectors

K-Ras4B is one the most frequently mutated proteins in cancer, yet mechanistic details of its activation such as its homodimerization on the membrane remain elusive. The structural determinants of K-Ras4B homodimerization have been debated with different conformations being proposed in the literature. Here, we perform microsecond all-atom Molecular Dynamics (MD) simulations on the K-Ras4B monomer in solution, the K-Ras4B monomer on the membrane, and two experimentally-based K-Ras4B dimer models of the 4-5 interface to investigate the stability of these structures bound to GTP on a model cell membrane. We then evaluate the complexes for their propensity to form stable dimers on the plasma membrane in the presence and absence of Raf[RBD-CRD] effectors. We find that Raf[RBD-CRD] effectors enhance dimer stability, suggesting that the presence of effectors is necessary for K-Ras4B dimers stabilization on the cell membrane. Moreover, we observe, for the first time, a dynamic water channel at the K-Ras4B dimer interface, and identify putative allosteric connections in the K-Ras4B dimer interface. To discover novel K-Ras4B interfaces, we perform coarse-grained MD simulations in two dissociated K-Ras4B monomers on the membrane, which reveal that the dominant dimer interface is the 4-5 interface. Finally, a druggability analysis is performed in the different K-Ras4B structures in the monomeric states. Strikingly, all known binding pockets of K-Ras4B are identified only in the structure that is membrane-bound, but not in the solution structure. Based on these results, we propose that modulating the protein-membrane interactions can be an alternative strategy for inhibiting K-Ras4B signaling.

molecular biology↗

bioRxiv2021

Identification of the Park Grass Experiment soil metaproteome

The Park Grass Experiment, is an international reference soil with an impressive repository of temperate grassland (meta)data, however, it still lacks documentation of its soil metaproteome. The identification of these proteins is crucial to our understanding of soil ecology and their role in major biogeochemical processes. However, protein extraction can be fraught with technical difficulties including co-extraction of humic material and lack of a compatible databases to identify proteins. To address these issues, we used two compatible soil protein extraction techniques on Park Grass soil, one that removed humic material, namely a modified freeze-dry, heat/thaw/phenol/chloroform (HTPC) method and another which co-extracted humic material, namely an established surfactant method. Proteins were identified by matching mass spectra against a tailored Park Grass metagenome database. We identified a broad range of proteins from Park Grass soil, mainly in "protein metabolism", "membrane transport", "carbohydrate metabolism", "respiration" and "ribosome associated" categories, enabling reconstitution of specific processes active in grassland soil. The soil microbiome was dominated by Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes at phyla level and Bradyrhizobium, Rhizobium, Acidobacteria, Streptomyces and Pseudolabrys at genus level. Further functional enrichment analysis enabled us to identify many proteins in regulatory and signalling networks of key biogeochemical cycles such as the nitrogen cycle. The combined extraction methods connected previous Park Grass metadata with the metaproteome, biogeochemistry and soil ecology. This could provide a base on which future targeted studies of important soil processes and their regulation can be built. HighlightsO_LIParallel protein extraction methods identified 1266 proteins from Park Grass soil C_LIO_LIProteome was enriched in ribosomal and respiration proteins for the surfactant extraction method and nitrogen associated proteins for the modified phenol/chloroform method C_LIO_LIIdentification of regulatory and signalling proteins in key biogeochemical cycles C_LIO_LILinks metaproteome to microbiome, biogeochemical cycles and Park Grass metadata C_LIO_LIProvides baseline for future targeted studies C_LI

biochemistry↗

bioRxiv2021

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

BackgroundBilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves a glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethane sulfonate) into acetaldehyde and sulfite. ResultsWe demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential ironsulfur (FeS) cluster-containing shell protein identified by sequence analysis. ConclusionsWe characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut.

microbiology↗