Martin Zoltner

African trypanosomes employ specialized mechanisms of membrane trafficking as a strategy to persist in both the mammalian host and insect vector. Their survival relies on continuous synthesis and surface delivery of extremely abundant surface coat proteins, imposing an extraordinary biosynthetic burden on the secretory pathway. Despite this, their ER and Golgi luminal proteomes remain incompletely characterized. Here, we exploit proximity biotinylation, using the abundant ER chaperone BiP as bait to map the ER proteome in bloodstream and procyclic lifecycle stages. Comparison with BiPN, a truncated secretory form of BiP that escapes the ER and transits the Golgi, provides differential compartmental labelling. Quantitative ranking of BiP labelling intensity identifies a candidate BiP interactor cohort including a divergent homologue to the mammalian BiP nucleotide exchange inhibitor MANF. Reciprocal manipulation of TbMANF abundance produces opposing shifts in cellular sensitivity to ER stress. These data are consistent with a role in regulating BiP ATPase cycling in an organism that, unlike opisthokonts, lacks a canonical unfolded protein response, making TbMANF the first regulator of BiP activity identified in kinetoplastids. Finally, proximity labelling anchored at the inner face of the nuclear pore via NUP65 extends our endomembrane map to the inner nuclear membrane, identifying candidate proteins of this specialized ER-continuous domain.

African trypanosomes employ specialised mechanisms of membrane trafficking as a key strategy to persist in both the mammalian host and insect vector. Their survival and pathogenicity rely on the continuous synthesis and surface delivery of extremely abundant surface coat proteins, imposing an extraordinary biosynthetic burden on the secretory pathway. Despite this, the luminal proteome of the T. brucei endoplasmic reticulum (ER) and Golgi apparatus remains incompletely characterised. Here, we exploit TurboID proximity biotinylation, using the abundant ER chaperone BiP (Binding-immunoglobulin protein) as luminal bait to map the ER proteome in bloodstream and procyclic lifecycle stages of Trypanosoma brucei . Comparison with BiPN, a truncated secretory form of BiP that transits the Golgi, provides differential compartmental labelling, together identifying 366 (BiP) and 428 (BiPN) proximity partners respectively and encompassing established ER quality control machinery, secretory cargo, and Golgi proteins. Quantitative ranking of BiP labelling intensity identifies a cohort of candidate BiP interactors: the most strongly enriched is Tb927.5.1160, a protein sharing structural homology with the mammalian BiP nucleotide exchange inhibitor MANF (mesencephalic astrocyte-derived neurotrophic factor). Endogenous mNeonGreen tagging confirms ER localisation of TbMANF in both life cycle stages, and reciprocal manipulation of its abundance by RNAi and inducible expression produces opposing shifts in cellular sensitivity to ER stress. These data are consistent with a role in regulating BiP ATPase cycling in an organism that, unlike yeast and mammals, lacks a canonical unfolded protein response, making TbMANF the first candidate regulator of BiP activity identified in kinetoplastids. Finally, TurboID proximity labelling anchored at the inner face of the nuclear pore via NUP65 extends our endomembrane map to the inner nuclear membrane, identifying candidate proteins of this specialised ER-continuous domain. AUTHOR SUMMARY: African sleeping sickness is caused by Trypanosoma brucei , a parasite that survives in the mammalian bloodstream by constantly renewing its protective protein coat. To synthesise and export this surface coat, the parasite relies on two intracellular compartments, the endoplasmic reticulum (ER) and the Golgi apparatus, which function as a quality control and sorting factory for proteins entering the secretory pathway. However, the identity of the proteins that populate these compartments in blood-stage parasites, and that maintain functioning under stress conditions, has remained poorly mapped. Here, we used an enzyme-based proximity labelling strategy that identifies neighbouring proteins in live cells without disturbing their targeting signals, generating a comprehensive protein inventory of both compartments across the two main T. brucei lifecycle stages. Among the most strongly labelled proteins was Tb927.5.1160, a protein structurally related to a mammalian regulator of the master ER chaperone BiP. Reducing or increasing the abundance of Tb927.5.1160 in parasites produced opposite changes in ER stress tolerance, identifying it as a candidate modulator of ER homeostasis in a lineage that regulates protein quality control through mechanisms distinct from those operating in yeast or human cells. Together, our findings provide a new molecular resource for understanding how T. brucei sustains secretory pathway function under the biosynthetic demands of mammalian and insect host infection.

5´ends of eukaryotic mRNAs are protected by the m7G cap, connected to the mRNA via a three-phosphate bridge. In mRNA decay, the pyrophosphate bond between the α and β phosphate is cleaved by the nudix hydrolase DCP2. Uniquely among eukaryotes, Kinetoplastida lack DCP2 and instead employ the ApaH-like phosphatase ALPH1 for mRNA decapping. ALPH1 consists of an unstructured N-terminus, a catalytic domain, and a structured C-terminus that mediates ALPH1 dimerisation. Here, we have analysed Trypanosoma brucei ALPH1 in greater detail. We find that the enzyme has broad substrate specificity and accepts different cap types and even cap analogues. Strikingly, cap-analogues and RNAs without the m7G-methyl group are turned over significantly faster than m7G methylated substrates. Moreover, all methylated and non-methylated cap analogues tested, with at least one additional nucleotide 3´ to the NpppN moiety, are cleaved at the β-γ pyrophosphate bond, producing the equivalent of a 5′ diphosphate-RNA. While the presence of the ALPH1 C-terminal domain is essential for cell viability and increases enzyme activity in vitro, substrate preferences are determined solely by the catalytic domain. Altogether, these ALPH1 enzymatic properties exhibit intriguing differences to the canonical eukaryotic decapping enzyme DCP2, which we critically discuss and which potentially have biotechnological applications.

Immunofluorescence experiments in Euglenozoa are more challenging than in cultured mammalian cells because they are smaller, often possess a protein-dense cellular envelope and antibodies are not commercially available. Here, we present streptavidin imaging as an alternative to immunofluorescence, that circumvents the above-mentioned problems, has several additional advantages and is applicable to all cells that can be genetically manipulated.For streptavidin imaging, the protein of interest is expressed fused to the biotin ligase TurboID and the (auto)biotinylation is detected with fluorescent streptavidin. In most cases, the streptavidin signal gives the same protein localization as an antibody but is superior to a classical immunofluorescence for three reasons. First, there is a significant enhancement of the signal due to multiple biotinylation sites, which is particularly useful when antigen levels are low, either due to low-level protein expression or as a result of procedures that reduce the antigen density as in expansion microscopy or correlative light and electron microscopy. Second, there is usually less unspecific signal in comparison to antibody labeling, as the streptavidin-biotin interaction is strong and highly specific. Third, streptavidin can access regions of the cell that are impermeable to most antibodies, in particular phase-separated areas like the nucleolus or the inner nuclear pore channel. In some cases, the streptavidin signal differs from the signal obtained by an antibody or a GFP fusion. The reasons are dynamic protein interactions with localization changes of either the bait protein or (some) interacting proteins. These differences between streptavidin and antibody signal can be exploited to understand protein dynamics and interactions in temporal and spatial resolution.Here, we present the protocol for streptavidin imaging: an all-in-one solution to antibody accessibility and low signal problems with the additional potential to study the dynamics of protein interactions.

5′ends of eukaryotic mRNAs are protected by the m ⁷ G cap, connected to the mRNA via a three-phosphate-bridge. In mRNA decay, the pyrophosphate bond between the α and β phosphate is cleaved by the nudix hydrolase DCP2. Uniquely among eukaryotes, Kinetoplastida lack DCP2 and instead employ the ApaH-like phosphatase ALPH1 for mRNA decapping. ALPH1 consists of an unstructured N-terminus, a catalytic domain and a structured C-terminus that mediates ALPH1 dimerisation. Here, we have analysed Trypanosoma brucei ALPH1 in greater detail. We find that the enzyme has broad substrate specificity and accepts different cap types and even cap analogues. Strikingly, cap-analogues and RNAs without the m ⁷ G-methyl group are turned over significantly faster than m ⁷ G methylated substrates. Moreover, all methylated and non-methylated cap analogues tested, with at least one additional nucleotide 3′ to the NpppN moiety are cleaved at the β-γ pyrophosphate bond, producing the equivalent to a 5’ diphosphate-RNA. While the presence of the ALPH1 C-terminal domain is essential for cell viability and increases enzyme activity in vitro, substrate preferences are determined solely by the catalytic domain. Altogether, these ALPH1 enzymatic properties exhibit intriguing differences to the canonical eukaryotic decapping enzyme DCP2, which we critically discuss and which potentially have biotechnological applications.

Parasitic protozoa exhibit a high demand for iron, with mitochondrial iron metabolism representing a vulnerable target for chemotherapeutic intervention. We recently demonstrated that mitochondrial targeting of the iron chelator deferoxamine (DFO) via triphenylphosphonium (TPP) conjugation enhances its antiparasitic efficacy. To expand upon this strategy, mitochondrially targeted derivatives of DFO and deferasirox (DFX) were synthesized and evaluated for their activity against important human parasites. The DFX derivative mitoDFX was effective against Trypanosoma spp. and Toxoplasma gondii with remarkable selectivity. The fact that mitoDFX is a promising anticancer agent, which is likely safe to use in the context of human health, highlights the potential for drug repurposing in parasitology. Structure-activity relationship (SAR) studies and iron distribution analyses in trypanosomes revealed that mitochondrial targeting of the compounds, rather than iron chelation per se, is the main driver of the antiparasitic effects, underscoring the critical role of phosphonium salts in bioactivity.

The exon junction complex (EJC) is a key player in metazoan mRNA quality control and is placed upstream of the exon-exon junction after splicing. Its inner core is composed of Magoh, Y14, eIF4AIII and BTZ and the outer core of proteins involved in mRNA splicing (CWC22), export (Yra1), translation (PYM) and nonsense mediated decay (NMD, UPF1/2/3). Trypanosoma brucei encodes only two genes with introns, but all mRNAs are processed by trans-splicing. The presence of three core EJC proteins and a potential BTZ homologue (Rbp25) in trypanosomes has been suggested to adapt of the EJC function to mark trans-spliced mRNAs. We analysed trypanosome EJC components and noticed major differences between eIF4AIII and Magoh/Y14: (i) whilst eIF4AIII is essential, knocking out both Magoh and Y14 elicits only a mild growth phenotype (ii) eIF4AIII localization is mostly nucleolar, while Magoh and Y14 are nucleolar and nucleoplasmic but excluded from the cytoplasm (iii) eIF4AIII associates with nucleolar proteins and the splicing factor CWC22, but not with Y14 or Magoh, while Magoh and Y14 associate with each other, but not with eIF4AIII, CWC22 or nucleolar proteins. Our data argue against the presence of a functional EJC in trypanosomes, but indicate that eIF4AIII adopted non-EJC related, essential functions, while Magoh and Y14 became redundant. Trypanosomes also possess homologues to the NMD proteins UPF1 and UPF2. Depletion of UPF1 causes only a minor reduction in growth and phylogenetic analyses show several independent losses of UPF1 and UPF2, as well as complete loss of UPF3 in the Kinetoplastida group, indicating that UPF1-dependent NMD is not essential. Regardless, we demonstrate that UPF1 depletion restores the mRNA levels of a PTC reporter. Altogether, we show that the almost intron-less trypanosomes are in the process of losing the canonical EJC/NMD pathways: Y14 and Magoh have become redundant and the still-functional UPF1-dependent NMD pathway is not essential.

Nuclear export of mRNAs requires loading the mRNP to the transporter Mex67/Mtr2 in the nucleoplasm, controlled access to the pore by the basket-localised TREX-2 complex and mRNA release at the cytoplasmic site by the DEAD-box RNA helicase Dbp5. Asymmetric localisation of nucleoporins (NUPs) and transport components as well as the ATP dependency of Dbp5 ensure unidirectionality of transport. Trypanosomes possess homologues of the mRNA transporter Mex67/Mtr2, but not of TREX-2 or Dbp5. Instead, nuclear export is likely fuelled by the GTP/GDP gradient created by the Ran GTPase. However, it remains unclear, how directionality is achieved since the current model of the trypanosomatid pore is mostly symmetric. We have revisited the architecture of the trypanosome nuclear pore complex using a novel combination of expansion microscopy, proximity labelling and streptavidin imaging. We could confidently assign the NUP76 complex, a known Mex67 interaction platform, to the cytoplasmic site of the pore and the NUP64/NUP98/NUP75 complex to the nuclear site. Having defined markers for both sites of the pore, we set out to map all 75 trypanosome proteins with known nuclear pore localisation to a subregion of the pore using mass spectrometry data from proximity labelling. This approach defined several further proteins with a specific localisation to the nuclear site of the pore, including proteins with predicted structural homology to TREX-2 components. We mapped the components of the Ran-based mRNA export system to the nuclear site (RanBPL), the cytoplasmic site (RanGAP, RanBP1) or both (Ran, MEX67). Lastly, we demonstrate, by deploying an auxin degron system, that NUP76 holds an essential role in mRNA export consistent with a possible functional orthology to NUP82/88. Altogether, the combination of proximity labelling with expansion microscopy revealed an asymmetric architecture of the trypanosome nuclear pore supporting inherent roles for directed transport. Our approach delivered novel nuclear pore associated components inclusive positional information, which can now be interrogated for functional roles to explore trypanosome-specific adaptions of the nuclear basket, export control, and mRNP remodelling.

Several Ranunculaceae species are used in folk medicine to eliminate pathologies associated with oxidative stress as well as parasitic infections; however, a number of studies confirming their pharmacological properties is limited. In this study, 19 ethanolic extracts obtained from 16 Ranunculaceae species were assayed for in vitro antioxidant, antiproliferative, and antiparasitic potential. The maximum antioxidant potential in both oxygen radical absorbance capacity (ORAC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays was observed for Aconitum toxicum extract [half-maximal inhibitory concentration (IC₅₀) 18.7 and 92.6 μg/mL]. Likewise, Anemone transsilvanica extract exerted the most promising antiproliferative activity against Caco-2 (IC₅₀ 46.9 μg/mL) and HT29 (IC₅₀ 70.2 μg/mL) cell lines in 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Additionally, a dual antioxidant and cytotoxicity effect was demonstrated for Aconitum moldavicum and Caltha palustris extracts. Whilst the efficacy of extracts was modest against Trypanosoma brucei (IC₅₀ ranging from 88.8 to 269.3 µg/mL), several extracts exhibited high potency against Leishmania infantum promastigotes (Aconitum vulparia IC₅₀ 18.8 µg/mL). We also tested them against the clinically relevant intracellular stage and found extract of A. vulparia to be the most effective (IC₅₀ 29.0 ± 1.1 µg/mL). All tested extracts showed no or low toxicity against FHs 74Int normal cell line (IC₅₀ ranging from 152.9 to >512 µg/mL). In conclusion, we suggest the above-mentioned plant extracts as potential candidates for development of novel plant-based antioxidant and/or antiproliferative and/or antileishmanial compounds.