Biology subjects

Gubbels, M.-J.

Publications and source records attributed to Gubbels, M.-J..

15 recordsLinked to original sources

bioRxiv2026

A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii

Understanding how T. gondii builds an invasion-competent cell has been limited by its rapid, asynchronous division cycle, incomplete gene function annotation, and studies that have examined one regulator or complex at a time. Here, we placed acute perturbation of 21 transcriptional and epigenetic factors, promoter occupancy, chromatin accessibility, and molecular validation on a common single-cell clock. The resulting consensus map links the lytic-cycle programs to candidate activating and repressive inputs, organizes genes into 108 co-regulated communities, and nominates regulatory partnerships that would not have emerged from any single data type. The work bridges three longstanding gaps: it resolves perturbation responses in cell-cycle time, distinguishes promoter occupancy from perturbation-linked regulation, and turns a large multidimensional dataset into an experimentally navigable map. We indeed confirmed known factor interactions such as MORC/HDAC3 and recovered combinations such as the Cdc5/SNIP1 and DMAP1/EPL1 as coregulatory nodes (that in other systems have been described to cooperate). Furthermore, we discovered a novel apicomplexan specific combination of AAF1/AP2XI-5 that provides mechanistic insights of the unique AP2 transcription factor family.

microbiology↗

bioRxiv2025

Toxoplasma gondii AAP7 is essential for functionally connecting the IMC embedded apical annuli to the plasma membrane

The Toxoplasma gondii cytoskeleton contains an intermediate filament network, supporting a quilt of alveolar sheets forming the inner membrane complex (IMC), undergirded by 22 subpellicular microtubules (SPMTs). Embedded within the IMC are the apical annuli: 5-6 ring-shaped pores facilitating dense granule exocytosis. Here we describe a novel apical annuli protein, AAP7. AAP7 depletion causes a severe fitness defect. In stable AAP7-depleted (ATc-resistant) parasites, LMBD3 no longer traffics to the annuli, but accumulates among the secretory organelles. This suggests AAP7 is required to traffic LMDB3 to the plasma membrane through a novel route. Moreover, it indicated that AAP7 connects plasma membrane embedded LMDB3 to the AAP proteins embedded in the IMC sutures. Functionally, AAP7 depletion results in reduced secretion of dense granule proteins. Specifically, parasitophorous vacuole membrane pore forming GRA17 secretion is reduced, causing bubble vacuoles. GRA17 overexpression overcomes AAP7 depletion and reduces bubble vacuoles revealing the critical defect. An additional AAP7 depletion phenotype is the accumulation of polyglutamylated SPMTs at the basal end, indicating slow turnover. Lastly, from a comparative angle, we investigated annuli in Sarcocystis neurona, revealing 6 apical annuli. This is surprising considering S. neuronas 11 alveolar vesicles and expected 11 annuli. Ergo, annuli architecture does not take cues from IMC suture positioning. In summary, our analysis of AAP7 led to equally versatile and novel insights in apical annuli architecture, their assembly (uncovering a potentially novel trafficking process), how they interface with the IMC and impact the SPMTs, and their critical function in facilitating GRA17 secretion required for the pore across the parasitophorous vacuole membrane

microbiology↗

bioRxiv2024

Co-dependent formation of the Toxoplasma gondii subpellicular microtubules and inner membrane skeleton

One of the defining features of apicomplexan parasites is their cytoskeleton composed of alveolar vesicles, known as the inner membrane complex (IMC) undergirded by intermediate-like filament network and an array of subpellicular microtubules (SPMTs). In Toxoplasma gondii, this specialized cytoskeleton is involved in all aspects of the disease-causing lytic cycle, and notably acting as a scaffold for parasite offspring in the internal budding process. Despite advances in our understanding of the architecture and molecular composition, insights pertaining to the coordinated assembly of the scaffold are still largely elusive. Here, T. gondii tachyzoites were dissected by advanced, iterative expansion microscopy (pan-ExM) revealing new insights into the very early sequential formation steps of the tubulin scaffold. A comparative study of the related parasite Sarcocystis neurona revealed that different MT bundling organizations of the nascent SPMTs correlate with the number of central and basal alveolar vesicles. In absence of a so far identified MT nucleation mechanism, we genetically dissected T. gondii {gamma}-tubulin and {gamma}-tubulin complex protein 4 (GCP4). While {gamma}-tubulin depletion abolished the formation of the tubulin scaffold, a set of MTs still formed that suggests SPMTs are nucleated at the outer core of the centrosome. Depletion of GCP4 interfered with the correct assembly of SPMTs into the forming daughter buds, further indicating that the parasite utilizes the {gamma}-tubulin complex in tubulin scaffold formation.

microbiology↗

bioRxiv2023

Single cell expression and chromatin access of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential pivotal controller of a ribosome regulon

Sequential lytic cycles driven by cascading transcriptional waves underlie pathogenesis in the apicomplexan parasite Toxoplasma gondii. This parasites unique division by internal budding, short cell cycle, and jumbled up classically defined cell cycle stages have restrained in-depth transcriptional program analysis. Here, unbiased transcriptome and chromatin accessibility maps throughout the lytic cell cycle were established at the single cell level. Correlated pseudo-timeline assemblies of expression and chromatin profiles mapped transcriptional versus chromatin level transition points promoting the cell division cycle. Sequential clustering analysis identified putatively functionally related gene groups facilitating parasite division. Promoter DNA motif mapping revealed patterns of combinatorial regulation. Pseudo-time trajectory analysis revealed transcriptional bursts at different cell cycle points. The dominant burst in G1 was driven by transcription factor AP2XII-8, which engages TGCATGCG/A and TATAAGCCG motifs, and promoted the expression of a regulon encoding 40 ribosomal proteins. Overall, the study provides integrated, multi-level insights into apicomplexan transcriptional regulation.

microbiology↗

bioRxiv2022

Toxoplasma gondii-s basal complex: the other apicomplexan business end is multifunctional

The Apicomplexa are famously named for their apical complex, a constellation of organelles at their apical end dedicated to invasion of their host cells. In contrast, at the other end of the cell, the basal complex (BC) has been in the limelight since it is much less prominent and specific functions were not immediately obvious. However, in the past decade a staggering array of functions have been associated with the BC, and strides have been made in understanding its structure. Here, these collective insights are supplemented with new data to provide an overview of the understanding of the BC in Toxoplasma gondii. The emerging picture is that the BC is a dynamic and multifunctional complex, with a series of (putative) functions. The BC has multiple roles in cell division: it is the site where building blocks are added to the cytoskeleton scaffold; it exerts a two-step stretch and constriction mechanism as contractile ring; and it is key in organelle division. Furthermore, the BC has numerous putative roles in import, such as the recycling of mother cell remnants, the acquisition of host-derived vesicles, possibly the uptake of lipids derived from the extracellular medium, and the endocytosis of micronemal proteins. The latter process ties the BC to motility, whereas an additional role in motility is conferred by Myosin C. Furthermore, the BC acts on the assembly and/or function of the intravacuolar network, which may directly or indirectly contribute to the establishment of chronic tissue cysts. Here we provide experimental support for molecules acting in several of these processes, and identify several new BC proteins critical to maintaining the cytoplasmic bridge between divided parasites. However, the dispensable nature of many BC components leaves many questions unanswered regarding its function. In conclusion, the BC in T. gondii is a dynamic and multifunctional structure at the posterior end of the parasite.

cell biology↗

bioRxiv2022

Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases

A unique aspect of apicomplexan biology is the requirement for egress from and invasion into host red blood cells (RBCs). The cellular mechanisms and molecular mediators of RBC egress and invasion remain poorly characterized in Babesia spp., a group of parasites of veterinary importance and emerging cause of zoonotic disease. Through the use of video microscopy, transcriptomics, and chemical genetics we have implicated signaling, proteases and gliding motility in egress and/or invasion by Babesia divergens. We developed CRISPR/Cas9 and two inducible knockdown systems to perform a genetic screen of putative mediators of egress. We found that proteases ASP2 and ASP3 are required for invasion, and the latter is also required for egress. Strikingly, parasites continue to replicate intracellularly in the absence of the protein kinases, PKG or CDPK4, indicating that they are required for exit from the replication cycle and egress. These essential molecules present druggable targets for Babesia spp. All together we have established a molecular framework for the spread of infection through host RBCs, with egress of B. divergens more closely resembling T. gondii than the more evolutionarily related Plasmodium spp. HighlightsO_LIEgress in Babesia divergens requires host cell lysis and parasite motility C_LIO_LITranscriptomics can be used to identify egress and invasion proteins C_LIO_LIKnockdown of the proteases, ASP2 and ASP3, inhibit egress and invasion C_LIO_LIInhibition of PKG or CDPK4 signaling results in continued intracellular replication C_LI

microbiology↗

bioRxiv2022

Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles

Babesia is a genus of Apicomplexan parasites that infect red blood cells in vertebrate hosts. Pathology occurs during rapid replication cycles in the asexual blood-stage of infection. Current knowledge of Babesia replication cycle progression and regulation is limited and relies mostly on comparative studies with related parasites. Due to limitations in synchronizing Babesia parasites, fine-scale time-course transcriptomic resources are not readily available. Single-cell transcriptomics provides a powerful unbiased alternative for profiling asynchronous cell populations. Here, we applied single-cell RNA sequencing to three Babesia species (B. divergens, B. bovis, and B. bigemina). We used analytical approaches and algorithms to map the replication cycle and construct pseudo-synchronized time-course gene expression profiles. We identify clusters of co-expressed genes showing just-in-time expression profiles, with gradually cascading peaks throughout asexual development. Moreover, clustering analysis of reconstructed gene curves reveals coordinated timing of peak expression in epigenetic markers and transcription factors. Using a regularized Gaussian Graphical Model, we reconstructed co-expression networks and identified conserved and species-specific nodes. Motif analysis of a co-expression interactome of AP2 transcription factors identified specific motifs previously reported to play a role in DNA replication in Plasmodium species. Finally, we present an interactive web-application to visualize and interactively explore the datasets.

bioinformatics↗

bioRxiv2021

A more complex basal complex: novel components mapped to the Toxoplasma gondii cytokinesis machinery portray an expanded hierarchy of its assembly and function

The basal complex (BC) of Toxoplasma gondii has an essential role in cell division but details on the mechanism are lacking. To promote insights in this process, reciprocal proximity based biotinylation was used to map the basal complex proteome. An assembled protein map was interrogated by spatiotemporal characterization of critical components as well as functionally by disrupting the expression of the components. Spatially, this revealed four proteins sub-complexes with distinct sub-structural BC localization. Temporally, several patterns were differentiated based on their first appearance and/or disappearance from the BC corresponding with different steps in BC development (initiation, expansion, constriction, maturation). We also identified a protein pre-ceding BC formation (BCC0) laid out in a 5-fold symmetry. This symmetry marks the apical annuli and site of alveolar suture formation. From here, it was determined that the apical cap is assembled in the apical direction, whereas the rest of the IMC expands in the basal direction, inspiring a new bi-directional daughter budding process. Furthermore, we discovered BCC4, an essential protein exclusively localizing to the BC during cell division. Although depletion of BCC4 did not prevent BC formation, it led to BC fragmentation at the mid-point of cell division. Based on these data, a model is presented wherein BCC4 and MORN1 stabilize each other and form a rubber band that implies an essential role for the BC in preventing the fraying of the basal end of the assembling daughter cytoskeleton scaffolds. Furthermore, one new component of the Myosin J and Centrin2 cluster was BCC1, a hypothetical protein whose depletion prevents the non-essential last step of BC constriction. Overall, the BC is a highly dynamic, multi-functional structure that is critical to the hierarchical assembly of the daughter parasites.

microbiology↗

bioRxiv2021

The extracellular milieu of Toxoplasma-s lytic cycle drives lab-adaptation and promotes changes in lipid metabolism primarily driven by transcriptional reprogramming

To map host-independent in vitro virulence traits of Toxoplasma gondii, evolve and resequencing (E&R) during the lab-adaption was applied. Phenotypic assessments of the lytic cycle revealed that only traits needed in the extracellular milieu evolved. Surprisingly, only non-synonymous mutations in a P4 flippase fixed in two populations. However, dramatic changes in the transcriptional signature of extracellular parasites revealed a "pro-tachyzoite" profile as well as upregulation of fatty acid biosynthesis (FASII) pathway genes. More general, a set of 300 genes which expression profile changes during evolution mapped to specific traits. Validation of a select number of genes in this set by knock-outs indeed confirmed their role in lab-adaptation. Finally, assembly of an ApiAP2 and Myb transcription factor network revealed the transcriptional program underlying the adapting extracellular state. Overall, E&R is a new genomic tool successfully applied to map the development of polygenic traits underlying in vitro virulence of T. gondii.

microbiology↗

bioRxiv2020

Toxoplasma ferlin1 is a versatile and dynamic mediator of microneme trafficking and secretion

Toxoplasma gondii is a polarized cell concentrating several secretory organelles at the apical pole. The secretory micronemes come in two sub-populations differentiated by dependence on the Rab5A/C in their biogenesis. Calcium-dependent exocytosis of micronemes occurs at the very apical tip and is critical for parasite egress from its host cell, adhesion and invasion of the next cell. Ferlins represent a protein family with roles in exocytosis containing multiple Ca2+-sensing C2 domains. We determined that T. gondiis ferlin 1 (FER1) localized dynamically to the parasites secretory pathway. FER1 function was dissected by dominant negative overexpression strategies. We demonstrated that FER1 traffics microneme organelles along the following trajectories:1. From the trans-Golgi-endosomes network to the subpellicular cortex; 2. Along the cortex to the apical end; 3. To the apical tip for fusion with the plasma membrane; 4. Retrograde transport allowing microneme recycling from mother to daughter; 5. Differential microneme sub-population traffic. Finally, FER1 overexpression triggers a microneme exocytosis burst, supporting the notion that the radially organized micronemes at the apical tip comprise a readily-releasable microneme pool. In summary, FER1 is pivotal for dynamic microneme trafficking, acts differently on the two microneme subpopulations, and acts on the plasma membrane fusion step during microneme exocytosis.

cell biology↗

bioRxiv2020

Fussing about fission: defining variety among mainstream and exotic apicomplexan cell division modes

Cellular reproduction defines life, yet our textbook-level understanding of cell division is limited to a small number of model organisms centered around humans. The horizon on cell division variants is expanded here by advancing insights on the fascinating cell division modes found in the Apicomplexa, a key group of protozoan parasites. The Apicomplexa display remarkable variation in offspring number, whether karyokinesis follows each S/M-phase or not, and whether daughter cells bud in the cytoplasm or bud from the cortex. We find that the terminology used to describe the various manifestations of asexual apicomplexan cell division emphasizes either the number of offspring or site of budding, which are not directly comparable features and has led to confusion in the literature. Division modes have been primarily studied in two human pathogenic Apicomplexa, malaria-causing Plasmodium spp. and Toxoplasma gondii, a major cause of opportunistic infections. Plasmodium spp. divide asexually by schizogony, producing multiple daughters per division round through a cortical budding process, though at several life-cycle nuclear amplifications are not followed by karyokinesis. T. gondii divides by endodyogeny producing two internally budding daughters per division round. Here we add to this diversity in replication mechanisms by considering the cattle parasite Babesia bigemina and the pig parasite Cystoisospora suis. B. bigemina produces two daughters per division round by a binary fission mechanism whereas C. suis produces daughters through both endodyogeny and multiple internal budding known as endopolygeny. In addition, we provide new data from the causative agent of equine protozoal myeloencephalitis (EPM), Sarcocystis neurona, which also undergoes endopolygeny but differs from C. suis by maintaining a single multiploid nucleus. Overall, we operationally define two principally different division modes: internal budding found in cyst-forming Coccidia (comprising endodyogeny and two forms of endopolygeny) and external budding found in the other parasites studied (comprising the two forms of schizogony, binary fission and multiple fission). Progressive insights into the principles defining the molecular and cellular requirements for internal versus external budding, as well as variations encountered in sexual stages are discussed. The evolutionary pressures and mechanisms underlying apicomplexan cell division diversification carries relevance across Eukaryota. Contribution to the FieldMechanisms of cell division vary dramatically across the Tree of Life, but the mechanistic basis has only been mapped for several model organisms. Here we present cell division strategies across Apicomplexa, a group of obligate intracellular parasites with significant impact on humans and domesticated animals. Asexual apicomplexan cell division is organized around assembly of daughter buds, but division forms differ in the cellular site of budding, number of offspring per division round, whether each S-phase follows karyokinesis and if mitotic rounds progress synchronously. This varies not just between parasites, but also between different life-cycle stages of a given species. We discuss the historical context of terminology describing division modes, which has led to confusion on how different modes relate to each other. Innovations in cell culture and genetics together with light microscopy advances have opened up cell biological studies that can shed light on this puzzle. We present new data for three division modes barely studied before. Together with existing data, we show how division modes are organized along phylogenetic lines and differentiate along external and internal budding mechanisms. We also discuss new insights into how the variations in division mode are regulated at the molecular level, and possess unique cell biological requirements.

microbiology↗

bioRxiv2019

The apical annuli of Toxoplasma gondii are composed of coiled-coil and signaling proteins embedded in the IMC sutures

The apical annuli are among the most intriguing and understudied structures in the cytoskeleton of the apicomplexan parasite Toxoplasma gondii. We mapped the proteome of the annuli in Toxoplasma by reciprocal proximity biotinylation (BioID), and validated five apical annuli proteins (AAP1-5), Centrin2 and a methyltransferase (AAMT). Moreover, Inner Membrane Complex (IMC) suture proteins connecting the alveolar vesicles were also detected and support annuli residence within the sutures. Super-resolution microscopy (SR-SIM) identified a concentric organization comprising four rings with diameters ranging from 200-400 nm. The high prevalence of domain signatures shared with centrosomal proteins in the AAPs together with Centrin2 suggest that the annuli are related and/or derived from the centrosomes. Phylogenetic analysis revealed the AAPs are conserved narrowly in Coccidian, apicomplexan parasites that multiply by an internal budding mechanism. This suggests a role in replication, for example, to provide pores in the mother IMC permitting exchange of building blocks and waste products. However, presence of multiple signaling domains and proteins are suggestive of additional functions. Knockout of AAP4, the most conserved compound forming the largest ring-like structure, modestly decreased parasite fitness in vitro but had no significant impact on acute virulence in vivo. In conclusion, the apical annuli are composed of coiled-coil and signaling proteins assembled in a pore-like structure crossing the IMC barrier maintained during internal budding.

cell biology↗

bioRxiv2018

TgCep250 is dynamically processed through the division cycle and essential for structural integrity of the Toxoplasma centrosome

The Toxoplasma centrosome is a unique bipartite structure comprising an inner- and outer-core responsible for the nuclear cycle (mitosis) and budding cycles (cytokinesis), respectively. These two cores remain associated during the cell cycle but have been proposed to function independently. Here, we describe the function of a large coiled-coil protein, TgCep250, in connecting the two centrosomal cores and promoting their structural integrity. Throughout the cell cycle TgCep250 localizes to the centrosome inner-core but resides on both inner- and outer-cores during the onset of cell division. This dynamic localization pattern is associated with proteolysis: the processed version residing on the inner-core. In the absence of TgCep250, stray centrosome inner- and outer-core foci were observed; detachment of the inner-outer-core connection resulted in nuclear partitioning defects. The detachment between centrosome inner- and outer-core was found in only one of the centrosomes during cell division, indicating distinct states of mother and daughter centrosomes. We further dissected the hierarchical organization of centrosome and kinetochore complex through depletion of kinetochore component TgNuf2, which resulted in dissociation of the intact bipolar centrosome from the nuclear periphery. Together, these data suggest that TgCep250 bridges the interaction between the centrosome cores but not between the inner-core and kinetochore.\n\nShort SummaryThe opportunistic apicomplexan parasite Toxoplasma gondii uses a bipartite centrosome to independently regulate mitosis and cytokinesis. Here we report a large coiled-coil protein that functions to integrate the two centrosomal cores for faithful cell division. This study also reveals the layered structural organization of the centrosome/kinetochore complex.

microbiology↗

bioRxiv2018

A member of the ferlin calcium sensor family is essential for Toxoplasma gondii rhoptry secretion

Invasion of host cells by apicomplexan parasites such as Toxoplasma gondii is critical for their infectivity and pathogenesis. In Toxoplasma, secretion of essential egress, motility and invasion-related proteins from microneme organelles is regulated by oscillations of intracellular Ca2+. Later stages of invasion are considered Ca2+-independent, including the secretion of proteins required for host cell entry and remodeling from the parasites rhoptries. We identified a family of three Toxoplasma proteins with homology to the ferlin family of double C2 domain-containing Ca2+ sensors. In humans and model organisms such Ca2+ sensors orchestrate Ca2+-dependent exocytic membrane fusion with the plasma membrane. One ferlin that is conserved across the Apicomplexa, TgFER2, localizes to the parasites cortical membrane skeleton, apical end, and rhoptries. Unexpectedly, conditionally TgFER2-depleted parasites secreted their micronemes normally and were completely motile. However, these parasites were unable to invade host cells and were therefore not viable. Specifically, knockdown of TgFER2 prevented rhoptry secretion and these parasites failed to form the moving junction on the parasite-host interface necessary for host cell invasion. Collectively, these data demonstrate that the putative Ca2+ sensor TgFER2 is required for the secretion of rhoptries. These findings provide the first regulatory and mechanistic insights into this critical yet poorly understood aspect of apicomplexan host cell invasion.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC=\"FIGDIR/small/304048_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@505202org.highwire.dtl.DTLVardef@138400aorg.highwire.dtl.DTLVardef@1f468beorg.highwire.dtl.DTLVardef@1089d34_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2017

Two phosphoglucomutase paralogs regulate triggered secretion of the Toxoplasma micronemes

Parafusin is a phosphoglucomutase (PGM) paralog that acts as a signaling scaffold protein in calcium mediated exocytosis across many eukaryotes. In Toxoplasma gondii the parafusin related protein 1 (PRP1) has been associated in indirect and heterologous studies with the regulated exocytosis of the micronemes, which are required for successful host cell invasion and egress. Here we directly assessed the role of PRP1 by deleting the gene from the parasite. We observed a specific defect in microneme secretion in response to high Ca2+ fluxes, but not to phosphatidic acid fluxes controlling microneme release. We observed no defect in constitutive microneme secretion which was sufficient to support completion of the lytic cycle. Furthermore, deletion of the other PGM in Toxoplasma, PGM2, as well as the double PRP1/PGM2 deletion resulted in a similar phenotype. This suggests a functional interaction between these two genes. Strikingly, tachyzoites without both paralogs are completely viable in vitro and during acute mice infections. This indicates that PGM activity is neither required for glycolysis. In conclusion, the PRP1-PGM2 pair is required for a burst in microneme secretion upon high Ca2+ fluxes, but this burst is not essential to complete the lytic cycle of the parasite.\n\nPlain Language SummaryCalcium mediated control of microneme secretion is essential for host cell invasion and egress of Toxoplasma gondii. Here it is shown that the two phosphoglucomutases in Toxoplasma both function in the translation of a spike in calcium into a burst in microneme secretion.

microbiology↗