Biology subjects

van den Heuvel, S.

Publications and source records attributed to van den Heuvel, S..

9 recordsLinked to original sources

bioRxiv2025

The First of Us: Ophiocordyceps use a novel scramblase-binding peptide to manipulate zombie ants

Parasite-adaptive manipulation of behavior is a widespread natural phenomenon. While Ophiocordyceps zombie fungi are well-known for hijacking ant behavior to increase their fitness, functionally characterizing the biomolecules involved in behavior manipulation remains difficult in these non-model organisms. To circumvent this problem, we have adopted the powerful genetics toolbox of Caenorhabditis elegans to identify molecular targets and neurophysiological effects of candidate Ophiocordyceps effectors. With this approach, we discovered a novel cysteine-rich, small secreted fungal peptide that binds to well-conserved calcium-dependent scramblase channels in neurons, particularly those associated with sensory tissues. This binding suppressed nematode motor coordination and dampened ant olfactory systems vital for communication. Our findings are the first to directly connect an Ophiocordyceps effector with its extended phenotype, while demonstrating the neuroethological role of Scramblase-1.

molecular biology↗

bioRxiv2024

Probing DNA damage sites reveals context-dependent and novel DNA damage response factors

DNA damage is a constant threat to genome integrity and function. Diminished capacity for DNA repair is linked to many human diseases, therefore understanding the molecular pathways responding to DNA damage is key for developing novel therapies. Lack of unbiased probes to report DNA damage dynamics and the associated proteins in living cells and animals limit our current efforts to completely understand DNA repair processes. In this study we overcome these limitations by engineering protein probes containing the tandem-BRCT domain of MCPH1, which we show to have a specific affinity for the DNA-damage-associated histone mark {gamma}H2AX. We employ these probes to track DNA damage dynamics in living cells exposed to a panel of different genotoxic insults and to visualize programmed double strand breaks during gametogenesis in living animals. We further utilize the binding selectivity of our probe to tether TurboID biotin ligases to chromatin and identify the DNA damage-associated proteome via proximity ligation. By comparing five different DNA damaging agents, we reveal the proteome associated with specific lesions, and identify multiple novel proteins with potential implications in damage response and repair. Among these novel proteins, we characterize the ubiquitin ligase UBE3A, the methyl-binding and proteasome-recruiting protein L3MBTL3, and the spliceosomal factor U2SURP, as previously uncharacterized effectors of DNA damage response. These functional datasets reveal the DNA damage-dependent proteomes and reveal novel insights into DNA damage response.

molecular biology↗

bioRxiv2024

Quantitative modelling of fate specification in the C. elegans postembryonicM lineage reveals a missing spatiotemporal signal

The invariant lineages of C. elegans provide tractable cell fate models to study how developing organisms robustly integrate spatial signals at the single-cell level via gene regulatory networks. For instance, during postembryonic development, a mesoderm lineage arises through a sequence of oriented cell divisions from a single progenitor. This mesoblast initially gives rise to 18 cells with three distinct fates - 14 body wall muscles (BWMs), 2 coelomocytes (CCs; dorsal), and 2 sex myoblasts (SMs; ventral). The latter cells migrate and then proliferate to contribute 16 smooth muscles to the nematodes reproductive organs. Prior work identified key symmetry breaking cues: i) ventrally restricted activation of the LIN-12 Notch pathway promoting SM over CC fate and ii) asymmetric re-distribution of SYS-1 {beta}-catenin and POP-1 TCF among daughter cells along the anteroposterior (A-P) axis, i.e. the Wnt/{beta}-catenin asymmetry pathway. However, it remains unclear whether these pathways are sufficient to specify all cell fates accordingly or whether additional symmetry breaking cues are necessary. In this study, we use quantitative modelling to better understand fate specification in the postembryonic M lineage. Specifically, we focus on the anteroposterior symmetry break by creating increasingly complex models towards robustly reproducing fate specification in wild type larvae and mutants. This iterative process resulted in two alternative models that explain the experimental observations by either introducing an additional spatial (spatial symmetry break) or temporal cue (temporal symmetry break). Finally, we evaluate their plausibility and propose a series of experiments to provide support for alternative models. Overall, our study highlights how a quantitative examination of mechanistic ideas can identify knowledge gaps and guide experimental follow-up.

systems biology↗

bioRxiv2022

Caenorhabditis elegans MES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12

Polycomb Repressive Complex 2 (PRC2) catalyzes the mono-, di, and trimethylation of histone protein H3 on lysine 27 (H3K27), which is strongly associated with transcriptionally silent chromatin. The functional core of PRC2 is highly conserved in animals and consists of four subunits. One of these, SUZ12, has not been identified in the genetic model Caenorhabditis elegans, whereas C. elegans PRC2 contains the clade-specific MES-3 protein. Through unbiased sensitive sequence similarity searches complemented by high-quality structure predictions of monomers and multimers, we here demonstrate that MES-3 is a highly divergent ortholog of SUZ12. MES-3 shares protein folds and conserved residues of key domains with SUZ12 and is predicted to interact with core PRC2 members similar to SUZ12 in human PRC2. Thus, in agreement with previous genetic and biochemical studies, we provide evidence that C. elegans contains a diverged yet evolutionary conserved core PRC2, like other animals.

evolutionary biology↗

bioRxiv2021

Caenorhabditis elegans LET-413 Scribble is essential in the epidermis for growth, viability, and directional outgrowth of epithelial seam cells

The conserved adapter protein Scribble (Scrib) plays essential roles in a variety of cellular processes, including polarity establishment, proliferation, and directed cell migration. While the mechanisms through which Scrib promotes epithelial polarity are beginning to be unraveled, its roles in other cellular processes including cell migration remain enigmatic. In C. elegans, the Scrib ortholog LET-413 is essential for apical-basal polarization and junction formation in embryonic epithelia. However, whether LET-413 is required for postembryonic development or plays a role in migratory events is not known. Here, we use inducible protein degradation to investigate the functioning of LET-413 in larval epithelia. We find that LET-413 is essential in the epidermal epithelium for growth, viability, and junction maintenance. In addition, we identify a novel role for LET-413 in the polarized outgrowth of the epidermal seam cells. These stem cell-like epithelial cells extend anterior and posterior directed apical protrusions in each larval stage to reconnect to their neighbors. We show that the role of LET-413 in seam cell outgrowth is mediated at least in part by the junctional component DLG-1 discs large, which appears to restrict protrusive activity to the apical domain. Finally, we demonstrate that the Rho-family GTPases CED-10 Rac and CDC-42 can regulate seam cell outgrowth and may also function downstream of LET-413. Our data uncover multiple essential functions for LET-413 in larval development and shed new light on the regulation of polarized outgrowth of the seam cells.

developmental biology↗

bioRxiv2019

Dose-dependent functions of SWI/SNF BAF in permitting and inhibiting cell proliferation in vivo

SWI/SNF complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb-group (PcG) proteins. Genes that encode SWI/SNF subunits are frequently mutated in human cancer. The selective advantage, subunit bias, and common heterozygosity of such mutations remains poorly understood. Here, we characterized how functional loss of various SWI/SNF subunits and PcG EZH2 affect proliferation-differentiation decisions in vivo, making use of the reproducible development of the nematode C. elegans. We applied a lineage-specific genetics strategy to create partial or complete SWI/SNF subunit loss, as well as double gene knockout with PcG EZH2. Our data show that a high SWI/SNF BAF dosage is needed to oppose Polycomb-mediated transcriptional repression and to arrest cell division during differentiation. In contrast, even in the absence of the PcG EZH2-related methyltransferase, a low level of the SWI/SNF BAF complex is necessary and sufficient to sustain cell proliferation and hyperplasia. Our data provide experimental support for the theory that during carcinogenesis partial SWI/SNF BAF loss-of-function mutations are selected because they eliminate a tumor suppressor activity while maintaining an essential transcription regulatory function.

developmental biology↗

bioRxiv2019

C. elegans Runx/CBFβ suppresses POP-1(TCF) to convert asymmetric to proliferative division of stem cell-like seam cells

A correct balance between proliferative and asymmetric cell divisions underlies normal development, stem cell maintenance and tissue homeostasis. What determines whether cells undergo symmetric or asymmetric cell division is poorly understood. To gain insight in the mechanisms involved, we studied the stem cell-like seam cells in the Caenorhabditis elegans epidermis. Seam cells go through a reproducible pattern of asymmetric divisions, instructed by non-canonical Wnt/{beta}-catenin asymmetry signaling, and symmetric divisions that increase the seam cell number. Using time-lapse fluorescence microscopy, we show that symmetric cell divisions maintain the asymmetric localization of Wnt/{beta}-catenin pathway components. Observations based on lineage-specific knockout and GFP-tagging of endogenous pop-1 support the model that POP-1TCF induces differentiation at a high nuclear level, while low nuclear POP-1 promotes seam cell self-renewal. Before symmetric division, the transcriptional regulator rnt-1Runx and cofactor bro-1CBF{beta} temporarily bypass Wnt/{beta}-catenin asymmetry by downregulating pop-1 expression. Thereby, RNT-1/BRO-1 appears to render POP-1 below the level required for its repressor function, which converts differentiation into self-renewal. Thus, opposition between the C. elegans Runx/CBF{beta} and TCF stem-cell regulators controls the switch between asymmetric and symmetric seam cell division.

developmental biology↗

bioRxiv2018

Optogenetic dissection of mitotic spindle positioning in vivo

The position of the mitotic spindle determines the plane of cell cleavage, and thereby the location, size, and content of daughter cells. Spindle positioning is driven by dynein-mediated pulling forces exerted on astral microtubules. This process requires an evolutionarily conserved complex of G-GDP, GPR-1/2Pins/LGN, and LIN-5Mud/NuMA proteins. It remains unknown whether this complex merely forms a membrane anchor for dynein, or whether the individual components have additional functions, for instance through G-GTP or dynein activation. To functionally dissect this system, we developed a genetic strategy for light-controlled localization of endogenous proteins in C. elegans embryos. Controlled germline expression and membrane recruitment of the G regulators RIC-8Ric-8A and RGS-7Loco/RGS3, and replacement of G with a light-inducible membrane anchor demonstrated that G-GTP signaling is dispensable for pulling force generation. In the absence of G, cortical recruitment of GPR-1/2 or LIN-5, but not dynein itself, induced high pulling forces. Local recruitment of LIN-5 overruled normal cell-cycle and polarity regulation, and provided experimental control over the spindle and cell cleavage plane. Our results define G*GDP-GPR-1/2Pins/LGN as a regulatable membrane anchor, and LIN-5Mud/NuMA as a potent activator of dynein-dependent spindle positioning forces. This study also highlights the possibilities for optogenetic control of endogenous proteins within an animal system.

cell biology↗

bioRxiv2017

The tumor suppressor APC is an attenuator of spindle-pulling forces during C. elegans asymmetric cell division

The adenomatous polyposis coli (APC) tumor suppressor has dual functions in Wnt/{beta}-catenin signaling and accurate chromosome segregation, and is frequently mutated in colorectal cancers. Although APC contributes to proper cell division, the underlying mechanisms remain poorly understood. Here we show that C. elegans APR-1/APC is an attenuator of the pulling forces acting on the mitotic spindle. During asymmetric cell division of the C. elegans zygote, a LIN-5/NuMA protein complex localizes dynein to the cell cortex to generate pulling forces on astral microtubules that position the mitotic spindle. We found that APR-1 localizes to the anterior cell cortex in a Par-aPKC polarity-dependent manner and suppresses anterior centrosome movements. Our combined cell biological and mathematical analyses support the conclusion that cortical APR-1 reduces force generation by stabilizing microtubule plus ends at the cell cortex. Furthermore, APR-1 functions in coordination with LIN-5 phosphorylation to attenuate spindle pulling forces. Our results document a physical basis for spindle-pulling force attenuation, which may be generally used in asymmetric cell division, and when disrupted potentially contributes to division defects in cancer.\n\nSignificance StatementAPC (adenomatous polyposis coli) is a Wnt signaling component as well as a microtubule-associated protein, and its mutations are frequently associated with colorectal cancers in humans. Although APC stabilizes microtubules (MTs), its mechanical role during cell division is largely unknown. Here we show that APC is an attenuator of forces acting on the mitotic spindle during asymmetric cell division of the C. elegans zygote. We performed live-imaging, laser-microsurgery, and numerical simulation to show how APC suppresses spindle pulling force generation by stabilizing microtubule plus-ends and reducing microtubule catastrophe frequency at the cell cortex. Our study is the first to document a mechanical role for the APC protein, and provides a physical basis for spindle-pulling force attenuation.

cell biology↗