Biology subjects

Doerig, C.

Publications and source records attributed to Doerig, C..

14 recordsLinked to original sources

bioRxiv2026

FIKK1, a member of the FIKK kinase family, phosphorylates VAR2CSA and regulates adhesion of Plasmodium falciparum-infected erythrocytes to the placental receptor CSA

Plasmodium falciparum promotes the adhesion of infected erythrocytes (IEs) to host cells by extensively remodeling their surface. For this process, the parasite exports a large number of proteins to its host erythrocyte, including members of the P. falciparum Erythrocyte Membrane Protein-1 (PfEMP1) adhesin family and members of the FIKK family. Several FIKK have been shown to play a role in P. falciparum virulence, notably affecting IES cell surface remodeling, rigidity and cytoadhesion. VAR2CSA, a member of the PfEMP1 adhesin family, is associated with IES sequestration in the placenta and has been shown to be phosphorylated. In view of the previously described importance of VAR2CSA phosphorylation, we investigated the role of FIKK1. We show that FIKK1 is capable of phosphorylating VAR2CSA in vitro, and that this phosphorylation increases the binding of recombinant VAR2CSA to the placental receptor chondroitin sulphate A (CSA). In an inducible transgenic cell line expressing HA-tagged FIKK1, immunofluorescence assays indicate that the kinase localizes to punctuated foci within Maurers Cleft, similarly to VAR2CSA. Rapamycin-induced knock out of FIKK1 reduces IEs cytoadhesion to CSA, even though levels of VAR2CSA are not affected. In vitro phosphorylation assays show that FIKK1 can phosphorylate recombinant DBL1-3 domains on several residues, including S429 and T934, previously implicated in in vitro binding and IES cytoadhesion to CSA. Taken together, these data support a model whereby FIKK1 contributes to placental malaria virulence through IEs sequestration mediated by VAR2CSA phosphorylation. Having no orthologs in mammals, this orphan kinase therefore represents an attractive target for the development of drugs against placental malaria. Author summarySequestration of Plasmodium falciparum infected erythrocytes (IEs) in the placenta is a hallmark of placental malaria and a major driver of adverse maternofetal outcomes. This process is mediated by VAR2CSA, a member of the P. falciparum Erythrocyte Membrane Protein (PfEMP1) family. VAR2CSA binds to chondroitin sulfate A (CSA) on the placental syncytium, facilitating IEs sequestration. In a previous study, we demonstrated that endogenous VAR2CSA is phosphorylated and identified specific phosphosites important for its cytoadhesive function. To elucidate the molecular mechanisms underlying these post-translational modifications, we examined the role of the P. falciparum FIKK1 kinase in VAR2CSA phosphorylation and its impact on IEs adhesion. Using a FIKK1::HA conditional knockout transgenic line, we found that FIKK1 deletion impairs IEs cytoadhesion, likely due to altered VAR2CSA phosphorylation. Importantly, both endogenous and recombinant FIKK1 interact with and phosphorylate the extracellular region of VAR2CSA. Furthermore, recombinant FIKK1 also enhances VAR2CSA binding to CSA in vitro and phosphorylates a residue previously identified as important for CSA binding and IEs adhesion. Collectively, these findings highlight a pivotal role for FIKK1 in placental adhesion and underscore the potential of targeting this kinase family for interventions against placental malaria.

biochemistry↗

bioRxiv2025

Plasmodium falciparum exploits NUAK1 to establish infection in human erythrocytes

The malaria parasite Plasmodium falciparum continues to demonstrate growing drug resistance, raising the need for innovative treatments. Host-directed therapeutics are emerging as a promising approach for many infectious diseases, but knowledge of critical host factors for malaria is limited. P. falciparum is an obligate intracellular parasite of human erythrocytes, suggesting it has evolved to exploit specific host pathways to establish infection. Here, we report that the AMPK-related kinase NUAK1 is a critical host factor for P. falciparum in erythrocytes and has potential as a therapeutic target. We show that NUAK1 is present in human erythrocytes and undergoes increased phosphorylation in P. falciparum-infected cells. Two highly selective NUAK1 inhibitors, HTH-01-015 and WZ4003, inhibited P. falciparum growth throughout its asexual life cycle, including during erythrocyte invasion. Chemoproteomic profiling confirmed the inhibitors selectivity for human NUAK1. We further show that treatment with the inhibitors reduces phosphorylation of the well-characterized NUAK1 substrate MYPT1 in erythroid cells. Moreover, we find that genetic overexpression of NUAK1 in erythroid cells partially rescues both the signaling and invasion phenotypes elicited by the small molecule inhibitors. These results establish a critical role for the NUAK1 signaling pathway in P. falciparum-infected erythrocytes and highlight its potential as a vulnerable target for host-directed malaria control.

microbiology↗

bioRxiv2025

The environmental stress response controls the biophysical properties of the cytoplasm and is critical for survival in quiescence

All organisms have evolved survival strategies to cope with changes in environmental conditions. Nutrient deprivation, one of the most frequently encountered stresses in nature, causes haploid budding yeast to enter a reversible state of non-proliferation known as quiescence, which entails extensive remodeling of gene expression, metabolism and the cellular biophysical properties. Yeast cells can adapt to and survive long periods of time in glucose starvation-induced quiescence, provided they are able to respire in the early stages of glucose withdrawal. When respiration is blocked during glucose withdrawal, cells prematurely age and exhibit markedly reduced survival and cytoplasmic diffusion. We find here that respiration is required to induce a quiescence-related gene expression program. Induction of this program prior to withdrawing glucose in respiration-inhibited cells bypasses the need for respiration and rescues survival and biophysical properties to levels seen in glucose-starved but respiration-competent cells. This rescue effect relies on proteomic adaptation, which partially occurs through inactivation of Ras/PKA signaling and activation of the environmental stress response via the transcription factors Msn2/4. This signaling cascade triggers the expression of stress response genes and modulates the cytoplasmic diffusion state of cells, ensuring long-term survival in quiescence even in the absence of respiration. Our results highlight the importance of stress adaptation in quiescence and aging, integrating gene expression control and modulation of cytoplasmic properties to maintain cell fitness.

cell biology↗

bioRxiv2024

Casein Kinases 2-dependent phosphorylation of the placental ligand VAR2CSA regulates Plasmodium falciparum-infected erythrocytes cytoadhesion

Placental malaria is characterized by the massive accumulation and sequestration of infected erythrocytes in the placental intervillous blood spaces, causing severe birth outcomes. The variant surface antigen VAR2CSA is associated with Plasmodium falciparum sequestration in the placenta via its capacity to adhere to chondroitin sulfate A. We have previously shown that the extracellular region of VAR2CSA is phosphorylated on several residues and that the phosphorylation enhances the adhesive properties of CSA-binding infected erythrocytes. Here, we aimed to identify the kinases mediating this phosphorylation. Here, we report that human and Plasmodium falciparum Casein Kinase 2 are involved in the phosphorylation of the extracellular region of VAR2CSA. We notably show that both CK2 can phosphorylate the extracellular region of recombinant and immunoprecipitated VAR2CSA. Mass spectrometry analysis of recombinant VAR2CSA phosphorylated by recombinant Human and P. falciparum CK2 combined with site-directed mutagenesis led to the identification of residue S1068 in VAR2CSA, which is phosphorylated by both enzymes and is associated with CSA binding. Furthermore, using CRISPR/Cas9 we generated a parasite line in which phosphoresidue, S1068, was changed to alanine. This mutation strongly impairs infected erythrocytes adhesion by abolishing VAR2CSA translocation to the surface of infected erythrocytes. We also report that two specific CK2 inhibitors reduce infected erythrocytes adhesion to CSA and decrease the phosphorylation of the recombinant extracellular region of VAR2CSA using either infected erythrocytes lysates as a source of kinases or recombinant Human and P. falciparum casein kinase 2. Taken together, these results undoubtedly demonstrate that host and P. falciparum CK2 phosphorylate the extracellular region of VAR2CSA and that this post-translational modification is important for VAR2CSA trafficking and for infected erythrocytes adhesion to CSA.

microbiology↗

bioRxiv2024

Enhancing the biological insight from limited proteolysis-coupled mass spectrometry

Limited proteolysis combined with mass spectrometry (LiP-MS) facilitates probing structural changes on a proteome-wide scale in situ. Distinguishing the different signal contributions, such as changes in protein abundance, from protein abundance changes remains challenging. We propose a two-step approach, first removing unwanted variations from the LiP signal that are not caused by protein structural effects and subsequently inferring the effects of variables of interest on the remaining signal. Using LiP-MS data from three species we demonstrate that our framework provides a uniquely powerful approach for deconvolving LiP-MS signals and inferring protein structural changes.

bioinformatics↗

bioRxiv2023

Plasmodium falciparum MORC protein modulates gene expression through interaction with heterochromatin

Dynamic control of gene expression is critical for blood stage development of malaria parasites. Here, we used multi-omic analyses to investigate transcriptional regulation by the chromatin-associated microrchidia protein, MORC, during asexual blood stage development of the human malaria parasite Plasmodium falciparum. We show that PfMORC (PF3D7_1468100) interacts with a suite of nuclear proteins, including APETALA2 (AP2) transcription factors (PfAP2-G5, PfAP2-O5, PfAP2-I, PF3D7_0420300, PF3D7_0613800, PF3D7_1107800, and PF3D7_1239200), a DNA helicase DS60 (PF3D7_1227100), and other chromatin remodelers (PfCHD1 and PfEELM2). Transcriptomic analysis of PfMORCHA-glmS knockdown parasites revealed 163 differentially expressed genes belonging to hypervariable multigene families, along with upregulation of genes mostly involved in host cell invasion. In vivo genome-wide chromatin occupancy analysis during both trophozoite and schizont stages of development demonstrates that PfMORC is recruited to repressed, multigene families, including the var genes in subtelomeric chromosomal regions. Collectively, we find that PfMORC is found in chromatin complexes that play a role in the epigenetic control of asexual blood stage transcriptional regulation and chromatin organization.

microbiology↗

bioRxiv2023

Mammalian cells internalize bacteriophages and utilize them as a food source to enhance cellular growth and survival

There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following eight hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage internalization led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a food source to promote cellular growth and metabolism.

microbiology↗

bioRxiv2021

Network analysis of large phospho-signalling datasets: application to Plasmodium-erythrocyte interactions

Phosphorylation based signalling is a complicated and intertwined series of pathways critical to all domains of life. This interconnectivity, though essential to life, makes understanding and decoding the interactions difficult. Large datasets of phosphorylation interactions through the activity of kinases on their numerous effectors are now being generated, however interpretation of the network environment remains challenging. In humans, many phosphorylation interactions have been identified across published works to form the known phosphorylation interaction network. We overlayed phosphorylation datasets onto this network which provided information to each of the connections. To analyse the datasets now mapped into a network, we designed a pathway analysis that uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected. This analysis highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in a given dataset. Here we used datasets of human red blood cells infected with the notable stages of Plasmodium falciparum asexual development. The analysis identified several known signalling interactions, and additional interactions which could form the basis of numerous future studies. The network analysis designed here is widely applicable to any comparative phosphorylation dataset across infection and disease and can provide a rapid and reliable analysis to guide validation studies.

microbiology↗

bioRxiv2020

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

The cellular proteome, the ensemble of proteins derived from a genome, catalyzes and controls thousands of biochemical functions that are the basis of living cells. Whereas the protein coding regions of the genome of the human and many other species are well known, the complexity and composition of proteomes largely remains to be explored. This task is challenging because mechanisms including alternative splicing and post-translational modifications generally give rise to multiple distinct, but related proteins - proteoforms - per coding gene that expand the functional capacity of a cell. Bottom-up proteomics is a mass spectrometric method that infers the identity and quantity of proteins from the measurement of peptides derived from these proteins by proteolytic digestion. Whereas bottom-up proteomics has become the method of choice for the detection of translation products from essentially any gene, the inherent missing link between measured peptides and their parental proteins has so far precluded the systematic assessment of proteoforms and thus limited the resolution of proteome maps. Here we present a novel, data-driven strategy to assign peptides to unique functional proteoform groups based on peptide correlation patterns across large bottom-up proteomic datasets. Our strategy does not fully characterize specific proteoforms, as is achievable in top-down approaches. Rather, it clusters peptides into functional proteoform groups that are directly linked to the biological context of the study. This allows the detection of tens to hundreds of proteoform groups in an untargeted fashion from bottom-up proteomics experiments. We applied the strategy to two types of bottom-up proteomic datasets. The first is a protein complex co-fractionation dataset where native complexes across two different cell cycle stages were resolved and analyzed. Here, our approach enabled the systematic detection and evaluation of assembly specific proteoforms at an unprecedented scale. The second is a protein abundance vs. sample data matrix typical for bottom-up cohort studies consisting of tissue samples from the mouse BXD genetic reference panel. In either data type the method detected state-specific proteoform groups that could be linked to distinct molecular mechanisms including proteolytic cleavage, alternative splicing and phosphorylation. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.

systems biology↗

bioRxiv2020

GDV1 C-terminal truncation of 39 amino acids disrupts sexual commitment in Plasmodium falciparum

Malaria is a mosquito-borne disease caused by apicomplexan parasites of the genus Plasmodium. Completion of the parasites life cycle depends on the transmission of sexual stages, the gametocytes, from an infected human host to the mosquito vector. Sexual commitment occurs in only a small fraction of asexual blood stage parasites and is initiated by external cues. The gametocyte development protein 1 (GDV1) has been described as a key facilitator to trigger sexual commitment. GDV1 interacts with the silencing factor heterochromatin protein 1 (HP1), leading to its dissociation from heterochromatic DNA at the genomic locus encoding AP2-G, the master transcription factor of gametocytogenesis. How this process is regulated is not known. In this study we have addressed the role of protein kinases implicated in gametocyte development. From a pool of available protein kinase KO lines, we identified two kinase knockout lines which fail to produce gametocytes. However, independent genetic verification revealed that both kinases are not required for gametocytogenesis but both lines harbour the same mutation that leads to a truncation in the extreme C-terminus of GDV1. Introduction of the identified nonsense mutation into the genome of wild type parasite lines replicates the observed phenotype. Using a GDV1 overexpression line we show that the truncation in the GDV1 C-terminus does neither interfere with the nuclear import of GDV1 nor its interaction with HP1 in vitro, but appears important to sustain GDV1 protein levels and thereby sexual commitment. ImportanceTransmission of malaria causing Plasmodium species by mosquitos requires the parasite to change from a continuously growing asexual parasite form growing in the blood, to a sexually differentiated form, the gametocyte. Only a small subset of asexual parasites differentiates into gametocytes that are taken up by the mosquito. Transmission represents a bottleneck in the lifecycle of the parasite, so a molecular understanding of the events that lead to stage conversion may identify novel intervention points. Here we screened a subset of kinases we hypothesized to play a role in this process. While we did not identify kinases required for sexual conversion, we identified a mutation in the C-terminus of the Gametocyte Development 1 protein (GDV1), which abrogates sexual development. The mutation destabilises the protein but not its interaction with its cognate binding partner HP1. This suggest an important role for the GDV1 C-terminus beyond trafficking and protein stability.

microbiology↗

bioRxiv2020

Signalome-wide assessment of erythrocyte response to Plasmodium reveals novel targets for host-directed antimalarial intervention

Intracellular pathogens are known to mobilise host signaling pathways to manipulate gene expression in their host cell to promote their own survival. Surprisingly, evidence is emerging that specific signal transduction elements are activated in a-nucleated erythrocytes in response to infection with malaria parasites, but the extent of this phenomenon remains unknown. Here, we fill this knowledge gap by providing a comprehensive and dynamic assessment of host erythrocyte signaling during the course of infection with Plasmodium falciparum. We used an antibody microarray that comprises 878 antibodies directed against human signaling proteins, >600 of which are phospho-specific, to interrogate the status of host erythrocyte signaling pathways at three stages of parasite development during the asexual cycle. This confirmed the pre-existing fragmentary data on the activation of a PAK-MEK pathway, and revealed the modulation of a large number of additional signaling elements during infection. We focussed on the receptor tyrosine kinase c-MET, also known as the hepatocyte growth factor receptor, and the MAP kinase pathway component B-Raf that is reported to lie downstream of c-MET in a number of cell types. Array data validated by Western blotting revealed that activation sites of c-MET are phosphorylated in trophozoite-infected erythrocytes, and we show that treatment of parasite cultures with c-MET or B-Raf selective inhibitors have nanomolar potency against in vitro proliferation of P. falciparum and the phylogenetically distant species P. knowlesi. Furthermore, we demonstrate that a c-MET inhibitor impairs in vivo proliferation of the rodent malaria parasite P. berghei in mice. Overall, we provide a comprehensive dataset on the modulation of host erythrocyte signaling during infection with malaria parasites, as well as a proof of concept that human signaling kinases identified as activated by malaria infection represent attractive targets for antimalarial intervention.

microbiology↗

bioRxiv2019

Interaction of Plasmodium falciparum Casein kinase 1 (PfCK1) with components of host cell protein trafficking machinery.

During infection, the Plasmodium falciparum casein kinase 1 (PfCK1) is secreted to the extracellular medium and appears on the RBC membrane during trophozoite stage of development. We attempted to identify a mechanism that describes the secretion of PfCK1 and its appearance on the RBC membrane and suspected a mechanism involving multiple host proteins may be utilised. Indeed, we found that the host proteins GTPase-activating protein and Vps9 domain-containing protein (GAPVD1) and Sorting nexin 22 (SNX22), which have described functions in membrane trafficking in higher eukaryotes, consistently co-purify with PfCK1 suggesting the parasite utilises trafficking pathways previously thought to be inactive in RBCs. Further, reciprocal immunoprecipitation experiments with GAPVD1 identified parasite proteins suggestive of a recycling pathway hitherto only described in higher eukaryotes to recycle membrane proteins. Thus, we have identified components of a trafficking pathway involving parasite proteins that act in concert with host proteins which we hypothesise coordinate the trafficking of PfCK1 during infection.

microbiology↗

bioRxiv2018

Validation of the protein kinase PfCLK3 as a multi-stage cross species malarial drug target

The requirement for next generation anti-malarials to be both curative and transmission blockers necessitate the identification of molecular pathways essential for viability of both asexual and sexual parasite life stages. Here we identify a selective inhibitor to the Plasmodium falciparum protein kinase PfCLK3 which we use in combination with chemogenetics, whole genome sequencing and transcriptomics to validate PfCLK3 as a druggable target acting at multiple parasite life stages. Consistent with the proposed role of PfCLK3 as a regulator of RNA splicing, inhibition results in the down-regulation of >400 genes essential for parasite survival. Through this mechanism, blocking PfCLK3 activity not only results in rapid killing of asexual blood stage parasites but is also effective on sporozoites and gametocytes as well as showing parasiticidal activity in all Plasmodium species tested. Hence, our data establishes PfCLK3 as a target with the potential to deliver both symptomatic treatment and transmission blocking in malaria.

microbiology↗

bioRxiv2018

Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites.

The life cycle of the malaria parasite Plasmodium falciparum is tightly regulated, oscillating between stages of intense proliferation and quiescence. Cyclic 48-hour asexual replication of Plasmodium is markedly different from cell division in higher eukaryotes, and mechanistically poorly understood. Here, we report tight synchronisation of malaria parasites during the early phases of the cell cycle by exposure to DL--difluoromethylornithine (DFMO), which results in the depletion of polyamines. This induces an inescapable cell cycle arrest in G1 (~15 hours post-invasion) by blocking G1/S transition. Cell cycle-arrested parasites enter a quiescent G0-like state but, upon addition of exogenous polyamines, re-initiate their cell cycle in a coordinated fashion. This ability to halt malaria parasites at a specific point in their cell cycle, and to subsequently trigger re-entry into the cell cycle, provides a valuable framework to investigate cell cycle regulation in these parasites. We therefore used gene expression analyses to show that re-entry into the cell cycle involves expression of Ca2+-sensitive (cdpk4 and pk2) and mitotic kinases (nima and ark2), with deregulation of the pre-replicative complex associated with expression of pk2. Changes in gene expression could be driven through transcription factors MYB1 and two ApiAP2 family members. This new approach to parasite synchronisation therefore expands our currently limited toolkit to investigate cell cycle regulation in malaria parasites.

cell biology↗