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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 613 records · Page 34Linked to original sources

bioRxiv2024

E-cadherin endocytosis promotes non-canonical EGFR:STAT signalling to induce cell death and inhibit heterochromatinisation

Signalling molecules often contribute to several signalling pathways that produce distinct transcriptional outputs and cellular phenotypes. One of the major unanswered questions in cell biology is how multiple activities of signalling molecules are coordinated in space and time in vivo. Here, we focus on the Signal Transducer and Activator of Transcription (STAT) protein as a paradigm of signalling molecules involved in several independent signalling pathways. In addition to the canonical pathways, whereby STAT is phosphorylated and activated by Janus Kinases, STAT is involved in at least two non-canonical pathways. In one pathway, STAT is activated by the Epidermal Growth Factor Receptor (EGFR) promoting apoptosis. In another, it binds the Heterochromatin Protein 1 (HP1) to enhance heterochromatin formation. Using Drosophila wing discs as an epithelial system, we demonstrate that all three STAT activities coexist in this tissue. We provide evidence that while the canonical STAT signalling is dominant over non-canonical pathways, EGFR:STAT and HP1:STAT pathways compete for the availability of unphosphorylated STAT. We also describe the role of the cell-cell adhesion protein E-cadherin in EGFR:STAT signalling. Both EGFR and STAT colocalise with E-cadherin at cell-cell junctions and on intracellular vesicles. Elevated intracellular E-cadherin promotes EGFR:STAT pathway leading to apoptosis, whereas blocking E-cadherin endocytosis prevents apoptosis induction. Altogether, we propose that E-cadherin endocytosis controls the balance between two non-canonical STAT activities in a potential tumour-suppressive mechanism - junctional disassembly in dysregulated epithelial-to-mesenchymal transitions would shift this balance towards the EGFR:STAT signalling to promote apoptosis.

cell biology↗

bioRxiv2019

The mechanisms of dynamin-actin interaction

Cell-cell fusion is an indispensable process in the conception, development and physiology of multicellular organisms. Here we demonstrate a direct and noncanonical role for dynamin, best known as a fission GTPase in endocytosis, in cell-cell fusion. Our genetic and cell biological analyses show that dynamin colocalizes within the F-actin-enriched podosome-like structures at the fusogenic synapse, which is required for generating invasive membrane protrusions and myoblast fusion in vivo, in an endocytosis-independent manner. Biochemical, negative stain EM and cryo-electron tomography (cryo-ET) analyses revealed that dynamin forms helices that directly bundles actin filaments by capturing multiple actin filaments at their outer rim via interactions with dynamins proline-rich domain. GTP hydrolysis by dynamin triggers disassembly of the dynamin helix, exposes the sides of the actin filaments, promotes dynamic Arp2/3-mediated branched actin polymerization, and generates a mechanically stiff actin network. Thus, dynamin functions as a unique actin-bundling protein that enhances mechanical force generation by the F-actin network in a GTPase-dependent manner. Our findings have universal implications for understanding dynamin-actin interactions in various cellular processes beyond cell-cell fusion.

cell biology↗

bioRxiv2025

Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants

G protein-coupled receptors (GPCRs) exhibit signaling bias, or preferential activation of heterotrimeric G proteins versus GPCR receptor kinase (GRK)-mediated {beta}-arrestin signaling. The protease-activated receptor-1 (PAR1) GPCR activates both G protein and {beta}-arrestin in response to thrombin, but only {beta}-arrestin in response to activated protein C (APC). Thrombin-activated PAR1-G protein signaling is desensitized by {beta}-arrestin-1, whereas APC-activated PAR1 signaling is propagated by {beta}-arrestin-2. The mechanisms underlying PAR1 biased signaling are not known. Here, using computational modeling and cell biology studies, we reveal the molecular basis of signaling by thrombin- and APC-activated PAR1. Although both thrombin- and APC-induced PAR1 signaling are regulated by the same GRK isoform, GRK5, the two types of signaling are differentially dependent on GRK5 membrane anchoring, PAR1 C-terminal phosphorylation, and the binding mode of {beta}-arrestin-2. These differences translate into distinct {beta}-arrestin-2 conformations and define the cytoprotective signaling signature by APC which contrasts with thrombin inflammatory signaling.

cell biology↗

bioRxiv2023

A conserved pressure-driven mechanism for regulating cytosolic osmolarity

Controlling intracellular osmolarity is essential to all cellular life. Cells that live in hypo-osmotic environments like freshwater must constantly battle water influx to avoid swelling until they burst. Many eukaryotic cells use contractile vacuoles to collect excess water from the cytosol and pump it out of the cell. Although contractile vacuoles are essential to many species, including important pathogens, the mechanisms that control their dynamics remain unclear. To identify basic principles governing contractile vacuole function, we here investigate the molecular mechanisms of two species with distinct vacuolar morphologies from different eukaryotic lineages--the discoban Naegleria gruberi, and the amoebozoan slime mold Dictyostelium discoideum. Using quantitative cell biology we find that, although these species respond differently to osmotic challenges, they both use actin for osmoregulation, as well as vacuolar-type proton pumps for filling contractile vacuoles. We also use analytical modeling to show that cytoplasmic pressure is sufficient to drive water out of contractile vacuoles in these species, similar to findings from the alveolate Paramecium multimicronucleatum. Because these three lineages diverged well over a billion years ago, we propose that this represents an ancient eukaryotic mechanism of osmoregulation.

cell biology↗

bioRxiv2025

A key role for Canoes intrinsically disordered region in linking cell junctions to the cytoskeleton

AbstractAdherens junctions are key to tissue architecture, mediating robust yet dynamic cell-cell adhesion and, via cytoskeletal linkage, allowing cells to change shape and move. Adherens junctions contain thousands of molecules linked by multivalent interactions of folded protein domains and Intrinsically Disordered Regions (IDRs). One key challenge is defining mechanisms conferring robust linkage and mechanosensing. Drosophila Canoe and mammalian Afadin provide superb entrypoints to explore how their complex protein structures and shared IDRs enable function. We combined genetic, cell biological and biochemical tools to define how Canoes IDR functions during morphogenesis. Unlike many of Canoes folded domains, the IDR is critical for junctional localization, mechanosensing and function. We took the IDR apart, identifying two conserved stickers in the IDR that directly bind F-actin, separated by less-conserved spacers. Surprisingly, while mutants lacking the IDR die as embryos with morphogenesis defects, no sub-region of the IDR is essential for viability. Instead, IDR stickers and spacers act combinatorially to ensure localization, mechanosensing and function.

cell biology↗

bioRxiv2026

Defining redundancy in the stickers and spacers of the cell-cell junction protein Canoe's intrinsically disordered region

Cell-cell adherens junctions (AJs) and their dynamic cytoskeletal linkage power morphogenesis. AJs are enormous complexes with hundreds of proteins linked by multivalent interactions. Like other biomolecular condensates, intrinsically disordered regions (IDRs) in junctional proteins play important roles in AJ assembly and function, using spacer elements to span distances, and stickers to engage targets. To define molecular mechanisms, we need to define the functional units within IDRs. Drosophila Canoe, homolog of human Afadin, is our model. Canoe mediates morphogenesis and has an extensive IDR, with two conserved F-actin-binding stickers and two poorly conserved spacers. We combined biochemical, genetic and cell biological approaches to define the function of these IDR elements. While no single element is essential, deleting the full IDR essentially eliminates Canoe function. By scrambling the amino acid sequence of the spacers, we find that length and composition are more important than amino acid sequences, though sequences in the C-terminal spacer affect Canoe localization. Finally, we test redundancy of the F-actin-binding stickers. Deleting both reduces but does not eliminate viability, and sensitized assays reveal their redundant roles. These data reveal the robustness of IDRs.

cell biology↗

bioRxiv2021

Shaping liposomes by cell-free expressed bacterial microtubules

Genetic control over a cytoskeletal network inside lipid vesicles offers a potential route to controlled shape changes and DNA segregation in synthetic cell biology. Bacterial microtubules (bMTs) are protein filaments found in bacteria of the genus Prosthecobacter. They are formed by the tubulins BtubA and BtubB which polymerize in the presence of GTP. Here, we show that the tubulins BtubA/B can be functionally expressed from DNA templates in a reconstituted transcription-translation system, thus providing a cytosol-like environment to study their biochemical and biophysical properties. We found that bMTs spontaneously interact with lipid membranes and display treadmilling. When compartmentalized inside liposomes, de novo synthesized BtubA/B tubulins self-organize into cytoskeletal structures of different morphologies. Moreover, bMTs can exert a pushing force on the membrane and deform liposomes, a phenomenon that can be reversed by light-activated disassembly of the filaments. Our work establishes bMTs as a new building block in synthetic biology. In the context of creating a synthetic cell, bMTs could help shape the lipid compartment, establish polarity or directional transport, and assist the division machinery.

synthetic biology↗

bioRxiv2022

A cell size threshold triggers commitment to stomatal fate in Arabidopsis

How flexible developmental programs integrate information from internal and external factors to modulate stem cell behavior is a fundamental question in developmental biology. Cells of the Arabidopsis stomatal lineage modify the balance of stem cell proliferation and differentiation to adjust the size and cell type composition of mature leaves. Here, we report that meristemoids, one type of stomatal lineage stem cell, trigger the transition from asymmetric self-renewing divisions to commitment and terminal differentiation by crossing a critical cell size threshold. Through computational simulation, we demonstrate that this cell size-mediated transition allows robust, yet flexible termination of stem cell proliferation and we observe adjustments in the number of divisions before the differentiation threshold under several genetic manipulations. We experimentally evaluate several mechanisms for cell size sensing, and our data suggest that cell size is sensed via a chromatin ruler acting in the nucleus.

developmental biology↗

bioRxiv2025

The BUB1 and BUBR1 paralogs scaffold the kinetochore fibrous corona

The kinetochore corona, a polymeric fibrous structure, facilitates chromosome biorientation and mitotic checkpoint signaling during mitosis. How its main building block, the RZZ complex, assembles on the outer kinetochore remains poorly understood. Harnessing corona biochemical reconstitutions and cell biology, we reveal the paralogous checkpoint proteins BUB1 and BUBR1 promote non-redundant branches of corona assembly. MPS1-kinase-dependent kinetochore docking of BUB1 and subsequent recruitment of BUBR1 initiates assembly. Disrupting the first branch by depleting CENP-E, a kinesin that links BUBR1 to RZZ, uncovered a second assembly pathway mediated by a direct interaction between BUB1 and ROD. Discovery of a direct interaction with the RZZ explains how the SAC protein MAD1 fits this corona assembly scheme. Our findings solve the long-standing puzzle of corona assembly and demonstrate the intimate interweaving of chromosome biorientation and checkpoint signaling.

cell biology↗

bioRxiv2020

Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation

O-linked {beta}-N-acetylglucosamine (O-GlcNAc) is a dynamic form of intracellular glycosylation common in animals, plants and other organisms. O-GlcNAcylation is essential in mammalian cells and is dysregulated in myriad human diseases, such as cancer, neurodegeneration and metabolic syndrome. Despite this pathophysiological significance, key aspects of O-GlcNAc signaling remain incompletely understood, including its impact on fundamental cell biological processes. Here, we investigate the role of O-GlcNAcylation in the coat protein II complex (COPII), a system universally conserved in eukaryotes that mediates anterograde vesicle trafficking from the endoplasmic reticulum. We identify new O-GlcNAcylation sites on Sec24C, Sec24D and Sec31A, core components of the COPII system, and provide evidence for potential nutrient-sensitive pathway regulation through site-specific glycosylation. Our work suggests a new connection between metabolism and trafficking through the conduit of COPII protein O-GlcNAcylation.

cell biology↗

bioRxiv2023

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells

Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSC) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary time scales.

developmental biology↗

bioRxiv2022

Condensin dysfunction is a reproductive isolating barrier in mice

Reproductive isolation occurs when the genomes of two populations accumulate genetic incompatibilities that prevent inter-breeding. Cell biological understanding of such hybrid incompatibility is limited, especially for hybrid female sterility. Here we find that species divergence in condensin regulation and centromere organization between two mouse species, Mus musculus and Mus spretus, drives chromosome de-condensation and mis-segregation in their F1 hybrid oocytes, reducing female fertility. The chromosome condensation defects in hybrid oocytes were especially prominent at Mus musculus centromeres due to their highly abundant major satellite DNA, leading to species-specific chromosome mis-segregation. This study provides the first mechanistic insights into hybrid incompatibility in female meiosis and demonstrates that condensin mis-regulation can be a reproductive isolating barrier in mammals.

cell biology↗

bioRxiv2026

Activation of the bridge-like lipid transfer protein Atg2 by Atg1-mediated phosphorylation

Bridge-like lipid transfer proteins (BLTPs) have emerged as major contributors to lipid flux and thus cellular organization. BLTPs harbor a hydrophobic channel connecting two membranes to enable the bulk flow of lipids between them. The regulation of BLTPs is incompletely understood. Employing in vitro reconstitution, molecular dynamics simulations, and cell biology, we discovered that the BLTP Atg2, which mediates lipid transfer during autophagosome biogenesis, is activated by the Atg1 kinase. Atg1 phosphorylates two serines in the N-terminal region of Atg2. This triggers membrane binding and opening of the channel to enable lipid transfer. The Atg1 kinase complex is localized to the endoplasmic reticulum through binding of its Atg13 subunit to the VAP protein Scs2. Phosphorylated Atg2 can subsequently establish contacts with Atg9 vesicles. Our study delineates a pathway for the Atg1 kinase mediated activation of the BLTP Atg2 to establish membrane contact site formation and lipid flux.

cell biology↗

bioRxiv2019

Phase separation of zonula occludens proteins drives formation of tight junctions

Tight junctions are cell adhesion complexes that seal tissues and are involved in cell polarity and signalling. Supra-molecular assembly and positioning of tight junctions as continuous networks of adhesion strands is dependent on the two membrane associated scaffolding proteins ZO1 and ZO2. To understand how ZO proteins organize junction assembly, we performed quantitative cell biology and in vitro reconstitution experiments. We discovered that ZO proteins self-organize membrane attached compartments via phase separation. We identified the multivalent interactions of the conserved PDZ-SH3-GuK supra-domain as the driver of phase separation. These interactions are regulated by phosphorylation and intra-molecular binding. Formation of condensed ZO protein compartments is sufficient to specifically enrich and localize tight junction proteins including adhesion receptors, cytoskeletal adapters and transcription factors. Our results suggest that an active phase transition of ZO proteins into a condensed membrane bound compartment drives claudin polymerization and coalescence of a continuous tight junction belt.

cell biology↗

bioRxiv2026

Medulloblastoma-Associated KBTBD4 Mutations Disrupt PP2A-A Orphan Quality Control

Medulloblastoma, the most common malignant pediatric brain tumor, arises from developmental aberrations of cerebellar precursor cells. The CUL3-RING ubiquitin ligase adaptor KBTBD4 is recurrently mutated in medulloblastoma subgroups 3 and 4. While KBTBD4 mutations confer a gain-of-function phenotype leading to aberrant degradation of transcriptional repressors, endogenous targets of this E3 ligase remain unknown. Here, we identify the PP2A-A scaffolding subunit of the PP2A phosphatase as a CRL3KBTBD4 substrate. Using a combination of proteomics, cell biology, biochemical reconstitution, and cryo-EM structural analyses, we show that CRL3KBTBD4 mediates orphan quality control by targeting free PP2A-A for degradation to safeguard phosphatase activity. Loss of KBTBD4 or its mutation in medulloblastoma cause PP2A-A accumulation, hence affecting phospho-dependent signaling pathways in cancer development. Disease mutations in KBTBD4 thus elicit a dual phenotype: gain-of-function degradation of transcriptional repressors combined with loss of PP2A quality control, which dysregulates multiple signaling events implicated in cancer, including telomere length regulation.

cell biology↗

bioRxiv2022

Bridging the light-electron resolution gap with correlative cryo-SRRF and dual-axis cryo-STEM tomography

Cryo-electron tomography (cryo-ET) is the prime method for cell biological studies in three dimensions (3D) at high resolution. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access larger 3D volumes, on the scale of 1 micron, making it ideal to study organelles and their interactions in situ. Here we introduce two relevant advances: a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy (cryo-CLEM). Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to isotropic resolution in the reconstruction without averaging. We show individual protein densities in a mitochondrion-ER contact in a cell region 850 nm thick. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.

cell biology↗

bioRxiv2020

A genetic screen identifies processes that couple oocyte maturation to proteostasis in the immortal C. elegans germ lineage

Somatic cells age and die, but the germ-cell lineage is immortal. In C. elegans, germline immortality involves proteostasis renewal at the beginning of each new generation, when oocyte-maturation signals from sperm trigger the clearance of carbonylated proteins and protein aggregates. Here, we explore the cell biology of this proteostasis renewal in the context of a whole-genome RNAi screen. Oocyte maturation signals are known to trigger protein-aggregate removal via lysosome acidification. Our findings suggest that lysosomes are acidified as a consequence of changes in ER activity that permit assembly of the lysosomal V-ATPase, which in turn allows lysosomes to clear the aggregates via microautophagy. We define two functions for mitochondria, both of which appear to be independent of ATP generation. Many genes from the screen also regulate lysosome acidification and age-dependent protein aggregation in the soma, suggesting a fundamental mechanistic link between proteostasis renewal in the germline and somatic longevity.

cell biology↗

bioRxiv2021

Molecular mechanism for kinesin-1 direct membrane recognition

The cargo-binding capabilities of cytoskeletal motor proteins have expanded during evolution through both gene duplication and alternative splicing. For the light chains of the kinesin-1 family of microtubule motors, this has resulted in an array of carboxy-terminal domain sequences of unknown molecular function. Here, combining phylogenetic analyses with biophysical, biochemical and cell biology approaches we identify a highly conserved membrane-induced curvature-sensitive amphipathic helix within this region of a newly defined subset of long kinesin light chain paralogues and splice isoforms. This helix mediates the direct binding of kinesin-1 to lipid membranes. Membrane binding requires specific anionic phospholipids and is important for kinesin-1 dependent lysosome positioning, a canonical activity that until now has been attributed exclusively the recognition of organelle-associated cargo adaptor proteins. This leads us to propose a new protein-lipid coincidence detection framework for kinesin-1 mediated organelle transport.

cell biology↗