Biology subjects

Spielmann, T.

Publications and source records attributed to Spielmann, T..

17 recordsLinked to original sources

bioRxiv2026

A new class of lipid transfer proteins is required for the recycling of lipids from the P. falciparum digestive vacuole

Malaria parasites endocytose large quantities of hemoglobin from the host erythrocyte, a process critical for parasite survival, leading to extensive membrane internalization. While hemoglobin degradation in the digestive vacuole (DV) is well studied, how the parasite deals with the membranes arriving within the DV is unknown. Here we identified PfTUPA, a previously uncharacterized lipid transfer protein in the DV membrane that is needed for this function. PfTUPA contains a soluble TULIP-like lipid transport domain exposed to the DV lumen and a transmembrane lipid transfer domain of bacterial origin (PqiA) in the DV membrane. Structural comparisons revealed proteins with various PqiA and TULIP-like domain combinations across distant eukaryotic clades, indicating this is a frequent functional partnership. Hence, PfTUPA belongs to a new class of eukaryotic lipid transfer proteins that in malaria parasites is needed for a key function of its biology.

microbiology↗

bioRxiv2026

Characterization of Host Cell Cytosol-filled Vesicles in the Human Malaria Parasite Plasmodium falciparum

Endocytosis of host cell cytosol is a key process in malaria blood stages. The endocytosed material consists mostly of haemoglobin (Hb) and is transported to the parasite's digestive vacuole (DV), where it is degraded. However, the endosomal transport pathway of the parasite is not well defined. A number of proteins are known that - when inactivated - lead to the appearance of Hb-filled vesicles (HbVs) in the parasite cytoplasm and prevent Hb from arriving in the DV, indicating they play a role in endosomal transport. However, despite the prominence of these HbVs, their morphology, molecular composition, and relationship to the endosomal transport pathway remain poorly understood. Here we carried out a morphological and surface proteome study of HbVs. CryoET showed HbVs are coatless, double membraned vesicles with a very narrow inter-membrane space devoid of larger protein densities. HbV surface proteomes generated by BioIDs most prominently detected DV proteases. Halo-based tracking of one of these DV protease confirmed it as a bona fide HbV cargo. The BioID also identified a number of vesicle trafficking proteins, including PfTBC8 and Rab11 proteins. Functional analysis of PfTBC8 showed its importance for the transport of Hb to the DV. This was due to a novel phenotype characterized by accumulation of diverse Hb-filled structures in the parasite cytosol and gradual decline of DV protease trafficking. PfTBC8 DiQ-BioID detected Rab11a and PfTBC8 inactivation altered Rab11a localization, suggesting it may be a Rab11a effector and that the new endosomal transport phenotype may result from a recycling defect. Together with the detection of VPS35 in the BioID and evidence from the CryoET of a disrupted inner HbV membrane in a proportion of vesicles, these findings support a model in which HbVs undergo maturation prior to fusion with the DV. Overall, our findings define morphological and molecular features of HbVs, identify protein cargo transported through this pathway, and reveal a previously unrecognized Rab-regulatory component required for endosomal trafficking in blood-stage P. falciparum parasites.

microbiology↗

bioRxiv2026

Kelch13 stochastics determine drug survival in resistant malaria parasites

As resistance to the frontline antimalarial artemisinin (ART) in the deadliest malaria species Plasmodium falciparum spreads, it threatens the gains made in reducing global malaria burden over the last decades. Mutations in the gene encoding Kelch13 (K13) hold a central role in ART resistance. Yet even in clonal populations harbouring a resistance conferring k13 mutation, only a portion of parasites survive drug exposure. Here we show that stochastic cell- to-cell variation of cellular K13 levels determines survival of individual parasites. Using isogenic parasite lines, we establish that decreased cellular K13 levels correlate with resistance and in addition a fitness cost through an increased cell cycle length. As resistance increases, parasites show a shift of the stochastic range towards lower K13 levels, increasing the proportion of drug survivors. While this range was inherited, individual parasites with differing K13 levels gave rise to progeny across the full spectrum. Hence, while the resistance fitness profile of each parasite line is defined by the range of K13 levels, the fate of individual parasites within that range is determined by stochastics. These findings provide an explanation why only a portion of genetically identical parasites survive drug exposure and reveal a system where the stochastics of a single protein determine individual parasite drug survival and fitness.

microbiology↗

bioRxiv2025

Protein landscape of the chromatin states in the malaria parasite Plasmodium falciparum

Epigenetic regulation is essential for development and adaptation across eukaryotes. However, a comprehensive overview of the molecular framework of chromatin-mediated regulation, particularly in non-model organisms, is lacking. Here, we present a systematic proteomic characterization of the chromatin states in P. falciparum, an ancient human pathogen with unique genome composition and epigenetic blueprint. We adapted and systematically employed three proximity-labelling approaches to provide a high-confidence and comprehensive proteome of heterochromatin, euchromatin and (peri)centromeric chromatin comprised of 214 proteins, including both expected and new chromatin components. Characterization of 20 proteins validated our approach and i) uncovered a protein influencing parasite transmission, ii) defined complexes relevant for histone variant exchange and chromatin-RNA interactions and iii) provided evidence for the so far believed to be absent spindle assembly checkpoint and the corresponding Bub1-like kinase. This study hence offers a reference proteome of the chromatin states and a resource to uncover novel chromatin biology.

cell biology↗

bioRxiv2025

A bridge-like lipid transfer protein is critical for generation of invasive stages in malaria parasites

Malaria blood stages build and maintain an intricate system of membranes during their cycle of rapid growth and schizogony (daughter-cell formation), requiring precise mechanisms of lipid synthesis and trafficking. Lipid transfer proteins (LTPs) at ER membrane contact sites (MCSs) have emerged as key for lipid distribution processes but remain largely unexplored in protozoans. Here we use the ER adaptor VAP to identify essential mechanisms of lipid transfer at ER-MCSs in P. falciparum. One PfVAP-interacting LTP was the bridge-like PfVPS13L1, which allows bulk flow of lipids between two apposed membranes. PfVPS13L1 bridges the ER with the nascent inner membrane complex (IMC), a de novo-generated organelle required for schizogony. Its loss-of-function reduced IMC growth and led to smaller anucleated progeny, impairing schizogony. Our data supports a model in which VPS13L1 is critical for the formation of apicomplexan invasive stages by mediating bulk transfer of lipids from the ER to the growing IMC.

cell biology↗

bioRxiv2024

Malaria parasite HOPS/CORVET complexes are critical for endocytosis and invasion organelles function

The tethering complexes HOPS/CORVET are central for vesicular fusion through the eukaryotic endolysosomal system, but the functions of these complexes in the intracellular development of malaria parasites are unknown. Here we show that early inactivation of core HOPS/CORVET complex subunits in Plasmodium falciparum leads to developmental arrest and accumulation of cytosolic vesicles, indicating a role of HOPS/CORVET in parasite endocytosis and fusion of endosomes to the digestive vacuole membrane. Late inactivation of the core HOPS/CORVET subunits led to the mislocalization of luminal rhoptry and microneme proteins, and to a severe defect in merozoite invasion. Ultra-expansion microscopy revealed a reduced rhoptry volume and the accumulation of numerous vesicles, further supporting a role of HOPS/CORVET in protein trafficking to the apical organelles. Malaria parasites have therefore repurposed HOPS/CORVET to perform dual functions consistent with a canonical endocytosis pathway for delivery of host cell material to the digestive vacuole in trophozoite stages and a parasite specific role in trafficking of protein cargo to the apical organelles required for invasion in schizont stages.

cell biology↗

bioRxiv2024

CUT&Tag and DiBioCUT&Tag enable investigation of the AT-rich and dynamic epigenome of Plasmodium falciparum from low input samples.

Phenotypic variation between malaria parasites is one of the major contributors to the pathogens success and is regulated by differences in heterochromatin-mediated gene silencing. Currently, the heterochromatin landscape is mostly profiled utilising chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). However this technique has drawbacks regarding AT-content-related artifacts and requires substantial material and time investment, severely limiting profiling of scarce sample types (e.g. field isolates). In order to facilitate assessments of epigenetic states in low-input samples, we adopted the epigenetic profiling technique Cleavage Under Targets and Tagmentation (CUT&Tag) to Plasmodium falciparum parasites. Performing the reaction with 100,000 or even only 10,000 nuclei yielded reproducible results coherent with bulk-ChIP-seq data while using significantly less material. We also optimised sample preparation, permitting the use of crude saponin lysates, which decreases sample loss due to inefficient nuclei isolation and increases versatility of the protocol. Finally, we developed DiBioCUT&Tag, a novel way of utilising dimerisation-induced recruitment of biotin ligases for signal amplification prior to anti-biotin CUT&Tag, which we successfully deployed to profile both heterochromatin occupancy and a dynamically chromatin-associated protein (BDP5). Methods described here hence provide substantially improved means for epigenetic profiling of (transiently) chromatin-associated proteins from low-input samples in the malaria parasite and beyond.

genomics↗

bioRxiv2024

A system for functional studies of the major virulence factor of malaria parasites

PfEMP1 is a variable antigen displayed on erythrocytes infected with the malaria parasite Plasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a cause of severe malaria. Each parasite encodes [~]60 different PfEMP1 variants but only one is expressed at a time. Switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 is difficult to study due to expression heterogeneity between parasites which also renders genetic modification approaches ineffective. Here, we used selection linked integration (SLI) to generate parasites all expressing the same PfEMP1 variant and genome edit the expressed locus. Moving this system from the reference strain 3D7 to IT4 resulted in PfEMP1 expressor parasites with effective receptor binding capacities. We also introduce a second version of SLI (SLI2) to introduce additional genome edits. Using these systems, we study PfEMP1 trafficking, generate cell lines binding to the most common endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell and identify new proteins needed for PfEMP1 mediated sequestration. These findings show the usefulness of the system to study the key virulence factor of malaria parasites.

microbiology↗

bioRxiv2023

Identification of domains in Plasmodium falciparum proteins of unknown function using DALI search on Alphafold predictions

Plasmodium falciparum, the causative agent of malaria, poses a significant global health challenge, yet much of its biology remains elusive. A third of the genes in the P. falciparum genome lack annotations regarding their function, impeding our understanding of the parasites biology. In this study, we employed structure predictions and the DALI search algorithm to analyse proteins encoded by uncharacterized genes in the reference strain 3D7 of P. falciparum. By comparing Alphafold predictions to experimentally determined protein structures in the Protein Data Bank, we found similarities to known domains in 353 proteins of unknown function, shedding light on their potential functions. The lowest-scoring 5% of similarities were additionally validated using the size-independent TM-align algorithm, confirming the detected similarities in 88% of the cases. Notably, in over 70 P. falciparum proteins the presence of domains resembling heptatricopeptide repeats, which are typically involvement in RNA binding and processing, was detected. This suggests this family, which is important in transcription in mitochondria and apicoplasts, is much larger in Plasmodium parasites than previously thought. The results of this domain search provide a resource to the malaria research community that is expected to inform and enable experimental studies.

cell biology↗

bioRxiv2023

Identification of a Rabenosyn-5 like protein and Rab5b in host cell cytosol uptake reveals conservation of endosomal transport in malaria parasites

Vesicular trafficking, including secretion and endocytosis, plays fundamental roles in the unique biology of P. falciparum blood-stage parasites. Endocytosis of host cell cytosol (HCC) provides nutrients and room for parasite growth and is critical for the action of antimalarial drugs and parasite drug resistance. Previous work showed that PfVPS45 functions in endosomal transport of HCC to the parasites food vacuole, raising the possibility that malaria parasites possess a canonical endolysosomal system. However, the seeming absence of VPS45-typical functional interactors such as rabenosyn 5 (Rbsn5) and the re-purposing of Rab5 isoforms and other endolysosomal proteins for secretion in apicomplexans question this idea. Here we identified a parasite Rbsn5-like protein and show that it functions with VPS45 in the endosomal transport of HCC. We also show that PfRab5b but not PfRab5a is involved in the same process. Inactivation of PfRbsn5L resulted in PI3P and PfRab5b decorated HCC-filled vesicles, typical for endosomal compartments. Overall, this indicates that despite the low sequence conservation of PfRbsn5 and the unusual N-terminal modification of PfRab5b, principles of endosomal transport in malaria parasite are similar to that of model organisms. Using a conditional double protein inactivation system, we further provide evidence that the PfKelch13 compartment, an unusual apicomplexa-specific endocytosis structure at the parasite plasma membrane, is connected upstream of the Rbsn5/VPS45/Rab5b-dependent endosomal route. Altogether, this work indicates that HCC-uptake consists of a highly parasite-specific part that feeds endocytosed material into an endosomal system containing more canonical elements, leading to the delivery of HCC to the food vacuole.

microbiology↗

bioRxiv2022

The Kelch13 compartment is a hub of highly divergent vesicle trafficking proteins in malaria parasites

Single amino acid changes in the parasite protein Kelch13 (K13) result in reduced susceptibility of P. falciparum parasites to artemisinin and its derivatives (ART). Recent work indicated that K13 and other proteins co-localising with K13 (K13 compartment proteins) are involved in the endocytic uptake of host cell cytosol (HCCU) and that a reduction in HCCU results in ART resistance. HCCU is critical for parasite survival but is poorly understood, with the K13 compartment proteins among the few proteins so far functionally linked to this process. Here we further defined the composition of the K13 compartment by analysing more hits from a previous BioID, showing that MyoF and MCA2 as well as Kelch13 interaction candidate (KIC) 11 and 12 are found at this site. Functional analyses, tests for ART susceptibility as well as comparisons of structural similarities using AlphaFold2 predictions of these and previously identified proteins showed that canonical vesicle trafficking and endocytosis domains were frequent in proteins involved in resistance or endocytosis (or both), comprising one group of K13 compartment proteins. While this strengthened the link of the K13 compartment to endocytosis, many proteins of this group showed unusual domain combinations and large parasite-specific regions, indicating a high level of taxon-specific adaptation of this process. Another group of K13 compartment proteins did not influence endocytosis or ART susceptibility and lacked detectable vesicle trafficking domains. We here identified the first protein of this group that is important for asexual blood stage development and showed that it likely is involved in invasion. Overall, this work identified novel proteins functioning in endocytosis and at the K13 compartment. Together with comparisons of structural predictions it provides a repertoire of functional domains at the K13 compartment that indicate a high level of adaption of endocytosis in malaria parasites.

cell biology↗

bioRxiv2022

Gene-by-gene screen of the unknown proteins encoded on P. falciparum chromosome 3

Taxa-specific proteins are key determinants defining the biology of all organisms and represent prime drug targets in pathogens. However, lacking comparability with proteins in other lineages makes them particularly difficult to study. In malaria parasites this is exacerbated by technical limitations. Here, we analysed the cellular location, essentiality, function and, in selected cases, interactome of all unknown non-secretory proteins encoded on an entire P. falciparum chromosome. The nucleus was the most common localisation, indicating it is a hotspot of parasite-specific biology. More in-depth functional studies with four proteins revealed essential roles in DNA replication and mitosis. The novel mitosis proteins defined a possible orphan complex and a highly diverged complex needed for the spindle-kinetochore connection. Structure-function comparisons indicated that the taxa-specific proteins evolved by different mechanisms. This work demonstrates the feasibility of gene-by-gene screens to elucidate the biology of malaria parasites and reveal critical parasite-specific processes of interest as drug targets.

cell biology↗

bioRxiv2022

Moderate ART resistance mutations with low fitness cost in malaria parasites from Africa

Reduced susceptibility to ART, the first-line treatment against malaria, is common in South East Asia (SEA). It is caused by point mutations, mostly in kelch13 (k13) but also in other genes, like upb1. K13 and its compartment neighbors (KICs), including UBP1, are involved in endocytosis of host cell cytosol. We tested 135 mutations in KICs but none conferred ART resistance. Double mutations of k13C580Y with k13R539T or k13C580Y with ubp1R3138H, did also not increase resistance. In contrast, k13C580Y parasites subjected to consecutive RSAs did, but the k13 sequence was not altered. Using isogenic parasites with different k13 mutations, we found correlations between K13 protein amount, resistance and fitness cost. Titration of K13 and KIC7 indicated that the cellular levels of these proteins determined resistance through the rate of endocytosis. While fitness cost of k13 mutations correlated with ART resistance, ubp1R3138H caused a disproportionately higher fitness cost. SignificanceART resistance is only a partial resistance with a proportion of ring stages surviving physiological ART levels. The correlation of resistance with fitness cost in isogenic lines indicates that fitness cost likely prevents resistance levels permitting survival of all ring stages under physiological ART concentrations. We also found no indication that double mutations in k13, including the two most common resistance mutations in SEA, or with non-k13 genes, are a threat to lead to higher resistance. However, repeated ART exposure increased resistance by mechanisms not altering k13 gene sequence, indicating changes in the background of these parasites. The disproportionally high fitness cost of ubp1R3138H may explain why kic mutations affecting resistance are rare and highlights the unique property of K13 to influence endocytosis only in ring stages.

cell biology↗

bioRxiv2021

PMRT1, a Plasmodium specific parasite plasma membrane transporter is essential for asexual and sexual blood stage development

Membrane transport proteins perform crucial roles in cell physiology. The obligate intracellular parasite Plasmodium falciparum, an agent of human malaria, relies on membrane transport proteins for the uptake of nutrients from the host, disposal of metabolic waste, exchange of metabolites between organelles and generation and maintenance of transmembrane electrochemical gradients for its growth and replication within human erythrocytes. Despite their importance for Plasmodium cellular physiology, the functional roles of a number of membrane transport proteins remain unclear, which is particularly true for orphan membrane transporters that have no or limited sequence homology to transporter proteins in other evolutionary lineages. Therefore, in the current study, we applied endogenous tagging, targeted gene disruption, conditional knockdown and knockout approaches to investigate the subcellular localization and essentiality of six membrane transporters during intraerythrocytic development of P. falciparum parasites. They are localized at different subcellular structures - the food vacuole, the apicoplast, and the parasite plasma membrane - and four out of the six membrane transporters are essential during asexual development. Additionally, the plasma membrane resident transporter 1 (PMRT1, PF3D7_1135300), a unique Plasmodium-specific plasma membrane transporter, was shown to be essential for gametocytogenesis and functionally conserved within the genus Plasmodium. Overall, we reveal the importance of four orphan transporters to blood stage P. falciparum development, which have diverse intracellular localizations and putative functions. ImportancePlasmodium falciparum-infected erythrocytes possess multiple compartments with designated membranes. Transporter proteins embedded in these membranes do not only facilitate movement of nutrients, metabolites and other molecules between these compartments, but are common therapeutic targets and can also confer antimalarial drug resistance. Orphan membrane transporter in P. falciparum without sequence homology to transporters in other evolutionary lineages and divergent to host transporters may constitute attractive targets for novel intervention approaches. Here, we localized six of these putative transporters at different subcellular compartments and probed into their importance during asexual parasite growth using reverse genetic approaches. In total, only two candidates turned out to be dispensable for the parasite, highlighting four candidates as putative targets for therapeutic interventions. This study reveals the importance of several orphan transporters to blood stage P. falciparum development.

molecular biology↗

bioRxiv2021

An unusual trafficking domain in MSRP6 defines a complex needed for Maurer's clefts anchoring and maintenance in P. falciparum infected red blood cells

Intracellular malaria blood stage parasites remodel their host cell, a process essential for parasite survival and a cause of pathology in malaria infections. Host cell remodeling depends on the export of different classes of exported parasite proteins into the infected red blood cell (RBC). Here we show that members of a recently discovered group of difficult to predict exported proteins harbor an N-terminal export domain, similar to other classes of exported proteins, indicating that this is a common theme among all classes of exported proteins. For one such protein, MSRP6 (MSP-7 related protein 6), we identified a second, untypical export-mediating domain that corresponded to its MSP7-like region. In addition to its function in export, this domain also mediated attachment to the Maurers clefts, prominent parasite-induced structures in the host cell where MSRP6 is located. Using BioID with the Maurers clefts attachment domain of MSRP6 to identify interactors and compartment neighbors in live parasites we discovered a novel complex of proteins at the Maurers clefts. We show that this complex is necessary for the anchoring and maintaining the structural integrity of the Maurers clefts. The Maurers clefts are believed to be involved in the transport of the major virulence factor PfEMP1 to the host cell surface where it mediates cytoadherence of infected RBCs to endothelial cells, a main reason for the importance of host cell modifications for parasite virulence in the human host. Taking advantage of MSRP6 complex mutants and IT4 parasites that we modified to express only one specific PfEMP1 we find that abolishing Maurers clefts anchoring was neither needed for PfEMP1 transport to the host cell surface nor for cytoadherence. Altogether, this work reveals parasite proteins involved in Maurers clefts anchoring and maintenance and unexpectedly finds that these functions seem to be dispensable for virulence factor transport and surface display.

microbiology↗

bioRxiv2021

Characterization of apicomplexan amino acid transporters (ApiATs) in the malaria parasite Plasmodium falciparum

During the symptomatic human blood phase, malaria parasites replicate within red blood cells. Parasite proliferation relies on the uptake of nutrients, such as amino acids, from the host cell and the blood plasma, requiring transport across multiple membranes. Amino acids are delivered to the parasite through the parasite surrounding vacuolar compartment by specialized nutrient-permeable channels of the erythrocyte membrane and the parasitophorous vacuole membrane (PVM). However, further transport of amino acid across the parasite plasma membrane (PPM) is currently not well characterized. In this study, we focused on a family of Apicomplexan amino acid transporters (ApiATs) that comprises five members in Plasmodium falciparum. First, we localized four of the PfApiATs at the PPM using endogenous GFP-tagging. Next, we applied reverse genetic approaches to probe into their essentiality during asexual replication and gametocytogenesis. Upon inducible knockdown and targeted gene disruption a reduced asexual parasite proliferation was detected for PfApiAT2 and PfApiAT4. Functional inactivation of individual PfApiATs targeted in this study had no effect on gametocyte development. Our data suggest that individual PfApiATs are partially redundant during asexual in vitro proliferation and fully redundant during gametocytogenesis of P. falciparum parasites. IMPORTANCEMalaria parasites live and multiply inside cells. To facilitate their extremely fast intracellular proliferation they hijack and transform their host cells. This also requires the active uptake of nutrients, such as amino acids, from the host cell and the surrounding environment through various membranes that are the consequence of the parasites intracellular lifestyle. In this manuscript we focus on a family of putative amino acid transporters termed ApiAT. We show expression and localization of four transporters in the parasite plasma membrane of Plasmodium falciparum-infected erythrocytes that represent one interface of the pathogen to its host cell. We probed into the impact of functional inactivation of individual transporters on parasite growth in asexual and sexual blood stages of P. falciparum and reveal that only two of them show a modest but significant reduction in parasite proliferation but no impact on gametocytogenesis pointing towards redundancy within this transporter family.

molecular biology↗

bioRxiv2021

Identification of novel inner membrane complex and apical annuli proteins of the malaria parasite Plasmodium falciparum

The inner membrane complex (IMC) is a defining feature of apicomplexan parasites, which confers stability and shape to the cell, functions as a scaffolding compartment during the formation of daughter cells and plays an important role in motility and invasion during different life cycle stages of these single celled organisms. To explore the IMC proteome of the malaria parasite Plasmodium falciparum we applied a proximity-dependent biotin identification (BioID)-based proteomics approach, using the established IMC marker protein Photosensitized INA-Labelled protein 1 (PhIL1) as bait in asexual blood-stage parasites. Subsequent mass spectrometry-based peptide identification revealed enrichment of twelve known IMC proteins and several uncharacterized candidate proteins. We validated nine of these previously uncharacterized proteins by endogenous GFP-tagging. Six of these represent new IMC proteins, while three proteins have a distinct apical localization that most likely represent structures described as apical annuli in Toxoplasma gondii. Additionally, various Kelch13 interacting candidates were identified, suggesting an association of the Kelch13 compartment and the IMC in schizont and merozoite stages. This work extends the number of validated IMC proteins in the malaria parasite and reveals for the first time the existence of apical annuli proteins in P. falciparum. Additionally, it provides evidence for a spatial association between the Kelch13 compartment and the IMC in late blood-stage parasites.

cell biology↗