Biology subjects

Kroeger, B.

Publications and source records attributed to Kroeger, B..

7 recordsLinked to original sources

bioRxiv2026

The mechanosensitive protein Zyxin influences Hippo signalling and tissue growth via adherens junctions and basal spot junctions in Drosophila

Physical forces like tension and compression have a central role in the growth and morphogenesis of tissues. Cell-cell junctions and the actin cytoskeleton are key mediators of physical forces and influence activity of signalling networks like the Hippo pathway. Here, we show that the mechanosensitive proteins Zyxin and Ajuba work in concert to limit Hippo signalling and promote Drosophila epithelial tissue growth. Zyxin recruits both Ajuba and the central Hippo pathway kinase Warts to adherens junctions and basal spot junctions, and limit Warts activity by segregating it from Hippo pathway activator proteins. Zyxin also promotes the transmission of actomyosin tension to adherens junctions in growing epithelial tissues, indicating conservation of this function. Thus, we provide new insights into how Zyxin couples mechanical cues and Hippo pathway-dependent tissue growth and highlight the importance of basal spot junctions and their associated actomyosin network in epithelial tissue development.

developmental biology↗

bioRxiv2025

Hippo signalling regulates the nuclear behaviour and DNA dwell times of YAP and TEAD to control transcription

Over the past two decades, genetic and proteomic screens have enabled the discovery and elucidation of the Hippo pathway as a complex signalling network that controls tissue growth and cell fate and which is of major importance for human cancers. Despite these advances, our understanding of how Hippo signalling regulates transcription is less clear. To address this, we used live microscopy approaches to study the nuclear behaviour of the major transcription effectors of the human Hippo pathway, YAP and TEADs. Our experiments revealed that TEADs are a major determinant of YAPs nuclear biophysical behaviour, whilst YAP only has a minor influence on TEAD behaviour. Acute chemical inhibition of Hippo signalling stimulated an increase in the DNA residence time of both YAP and TEAD1. Consistently, YAP and TEAD1 bound DNA for longer periods in cells with high intrinsic YAP/TEAD activity (induced trophoblast stem cells) than in cells with low intrinsic YAP/TEAD activity (induced pluripotent stem cells). TEAD1 bound the genome on a broad range of timescales, and this is extended substantially in nuclear condensates. Finally, single molecule tracking experiments revealed that a fusion protein encoded by a cancer-associated YAP allele exhibits substantially different nuclear biophysical behaviour than either YAP or TEAD1. These live microscopy experiments reveal that Hippo signalling regulates transcription at least in part by influencing the DNA dwell times of both YAP and TEAD.

cell biology↗

bioRxiv2023

Basal spot junctions of epithelial tissues respond to morphogenetic forces and regulate Hippo signalling

Organ size is controlled by numerous factors including mechanical forces, which are mediated in part by the Hippo pathway. In growing Drosophila melanogaster epithelial tissues, cytoskeletal tension influences Hippo signalling by modulating the subcellular localisation of key pathway proteins in different apical domains, namely adherens junctions, the sub-apical region and the medial apical cortex. Here, using both electron and light microscopy, we have discovered the existence of basal spot junctions in D. melanogaster epithelial tissues, and that they respond to morphogenetic forces and also influence Hippo signalling. Like adherens junctions, the Warts kinase is recruited to basal spot junctions via Ajuba and E-cadherin, which prevent Warts activation by segregating it from upstream Hippo pathway proteins. Basal spot junctions are prominent when tissues undergo morphogenesis and are highly sensitive to fluctuations in cytoskeletal tension. Basal spot junctions are distinct from focal adhesions, but the latter profoundly influences the abundance of spot junctions by modulating the basal-medial actomyosin network and tension experienced by spot junctions. Thus, basal spot junctions potentially couple morphogenetic forces to Hippo pathway activity and organ growth.

cell biology↗

bioRxiv2022

LambdaPP: Fast and accessible protein-specific phenotype predictions

The availability of accurate and fast Artificial Intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first internet server making AI protein predictions available in 1992. Given a protein sequence as input, LambdaPP provides easily accessible visualizations of protein 3D structure, along with predictions at the protein level (GeneOntology, subcellular location), and the residue level (binding to metal ions, small molecules, and nucleotides; conservation; intrinsic disorder; secondary structure; alpha-helical and beta-barrel transmembrane segments; signal-peptides; variant effect) in seconds. The structure prediction provided by LambdaPP - leveraging ColabFold and computed in minutes - is based on MMseqs2 multiple sequence alignments. All other feature prediction methods are based on the pLM ProtT5. Queried by a protein sequence, LambdaPP computes protein and residue predictions almost instantly for various phenotypes, including 3D structure and aspects of protein function. Accessibility StatementLambdaPP is freely available for everyone to use under embed.predictprotein.org, the interactive results for the case study can be found under https://embed.predictprotein.org/o/Q9NZC2. The frontend of LambdaPP can be found on GitHub (github.com/sacdallago/embed.predictprotein.org), and can be freely used and distributed under the academic free use license (AFL-2). For high-throughput applications, all methods can be executed locally via the bio-embeddings (bioembeddings.com) python package, or docker image at ghcr.io/bioembeddings/bio_embeddings, which also includes the backend of LambdaPP. Impact StatementWe introduce LambdaPP, a webserver integrating fast and accurate sequence-only protein feature predictions based on embeddings from protein Language Models (pLMs) available in seconds along with high-quality protein structure predictions. The intuitive interface invites experts and novices to benefit from the latest machine learning tools. LambdaPPs unique combination of predicted features may help in formulating hypotheses for experiments and as input to bioinformatics pipelines.

bioinformatics↗

bioRxiv2020

Drosophila Sex Peptide Controls the Assembly of Lipid Microcarriers in Seminal Fluid

Seminal fluid plays an essential role in promoting male reproductive success and modulating female physiology and behaviour. In the fruit fly, Drosophila melanogaster, Sex Peptide (SP) is the best-characterised protein mediator of these effects. It is secreted from the paired male accessory glands (AGs), which, like the mammalian prostate and seminal vesicles, generate most of the seminal fluid contents. After mating, SP binds to spermatozoa and is retained in the female sperm storage organs. It is gradually released by proteolytic cleavage and induces several long-term post-mating responses including ovulation, elevated feeding and reduced receptivity to remating, primarily signalling through the SP receptor (SPR). Here, we demonstrate a previously unsuspected SPR-independent function for SP. We show that, in the AG lumen, SP and secreted proteins with membrane-binding anchors are carried on abundant, large neutral lipid-containing microcarriers, also found in other SP-expressing Drosophila species. These microcarriers are transferred to females during mating, where they rapidly disassemble. Remarkably, SP is a key assembly factor for microcarriers and is also required for the female disassembly process to occur normally. Males expressing non-functional SP mutant proteins that affect SPs binding to and release from sperm in females also do not produce normal microcarriers, suggesting that this male-specific defect contributes to the resulting widespread defects in ejaculate function. Our data therefore reveal a novel role for SP in formation of seminal macromolecular assemblies, which may explain the presence of SP in Drosophila species, which lack the signalling functions seen in D. melanogaster. Significance StatementSeminal fluid plays a critical role in reprogramming female physiology and behaviour to promote male reproductive success. We show in the fruit fly that specific seminal proteins, including the archetypal female-reprogramming molecule Sex Peptide, are stored in male seminal secretions in association with large neutral lipid-containing microcarriers, which rapidly disperse in females. Related structures are also observed in other Sex Peptide-expressing Drosophila species. Males lacking Sex Peptide have structurally defective microcarriers, leading to abnormal cargo loading and transfer to females. Our data reveal that this key signalling molecule in Drosophila seminal fluid is also a microcarrier assembly factor that controls transfer of other seminal factors, and that this may be a more evolutionarily ancient role of this protein.

cell biology↗

bioRxiv2019

Glutamine deprivation regulates the origin and function of cancer cell exosomes

Exosomes are secreted extracellular vesicles (EVs) carrying diverse cargos, which can modulate recipient cell behaviour. They are thought to derive from intraluminal vesicles formed in late endosomal multivesicular bodies (MVBs). An alternate exosome formation mechanism, which is conserved from fly to human, is described here, with exosomes carrying unique cargos, including the GTPase Rab11, generated in Rab11-positive recycling endosomal MVBs. Release of these exosomes from cancer cells is increased by reducing Akt/mechanistic Target of Rapamycin (mTORC1) signalling or depleting the key metabolic substrate glutamine, which diverts membrane flux through recycling endosomes. The resulting vesicles promote tumour cell proliferation and turnover, and modulate blood vessel networks in xenograft mouse models in vivo. Their growth-promoting activity, which is also observed in vitro, is Rab11a-dependent, involves ERK-MAPK-signalling and is inhibited by antibodies against Amphiregulin, an EGFR ligand concentrated on these vesicles. Therefore, glutamine depletion or mTORC1 inhibition stimulates release of Rab11a-exosomes with pro-tumorigenic functions, which we propose promote stress-induced tumour adaptation.

cancer biology↗

bioRxiv2018

Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity

It is known that the male seminal fluid contains factors that affect female post-mating behavior and physiology. In Drosophila, most of these factors are secreted by the two epithelial cell types that make up the male accessory gland: the main and secondary cells. Although secondary cells represent only 4% of the cells of the accessory gland, their contribution to the male seminal fluid is essential for sustaining the female post-mating response. To better understand the function of the secondary cells, here we investigate their molecular organization, particularly with respect to the intracellular membrane transport machinery. We determined that large vacuole-like structures found in the secondary cells are trafficking hubs labeled by Rab6, 7, 11 and 19. Furthermore, these cell-specific organelles are essential for the long-term post-mating behavior of females and that their formation is directly dependent upon Rab6. Our discovery adds to our understanding of Rab proteins function in secretory cells. We have created an online, open-access imaging resource as a valuable tool for the intracellular membrane and protein traffic community.

cell biology↗