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Luque Navarro PM, Carrasco-Jiménez MP, Parisini E, Lanari D, Odina LM, Jekabsons A, Perales S, Zelencova-Gopejenko D, Pérez-Moreno G, Bosch-Navarrete C, González-Pacanowska D, López-Cara LC. Biological evaluation as antimalarial of two families of biscationic compounds featuring two different sulphur linkers. Bioorg Med Chem Lett 2025; 123:130241. [PMID: 40246180 DOI: 10.1016/j.bmcl.2025.130241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 04/07/2025] [Accepted: 04/14/2025] [Indexed: 04/19/2025]
Abstract
Plasmodium falciparum kinases have been widely studied due to their potential as targets for the discovery of alternatives to artemisinin-combined therapies. Their role in parasite blood-stage replication and their homology with human kinases has led to the exploitation of already tested antitumoral kinase inhibitors as antiplasmodial drugs. Plasmodium falciparum choline kinase (PfCK), a cytosolic enzyme involved in phospholipid synthesis, is a promising target for parasite resistant strains. PfCK uses the host choline and catalyzes its transformation in phosphocholine, a key step for the formation of the lipid membranes required by the new parasite progeny inside the erythrocyte. Previously, we described the synthesis of two libraries (PL and FP) of human choline kinase (hCK) inhibitors, which we generated following a green by design approach. Some of these compounds were found to exhibit antitumoral properties. Here, we evaluated the same compounds as potential inhibitors of PfCK and antimalarial agents. Interestingly, while the compounds of the FP library, which feature a disulphide linker, show PfCK inhibition in the nM range independently of the cationic head (FP3 being the most active compound, PfCK IC50 = 0.16 μM), they show no effect on infected erythrocytes. On the other hand, the compounds of the PL library, which feature a dithioethane linker, show in vitro activity against the parasite but no inhibitory activity against the isolated enzyme (PL40 exhibits the highest antimalarial activity, with IC50 = 10 nM). This lack of correlation could be due to either cellular disulphide degradation in vitro or to the existence of alternative targets for the dithioethane library. Considering the previously reported anticancer potential of the PL family and the antiparasitic activity reported herein, these compounds may be considered as good starting points for the development of multifunctional drugs.
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Affiliation(s)
- Pilar M Luque Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada 18071, Spain; Department of Pharmaceutical Sciences, University of Perugia, Perugia 06123, Italy
| | - M Paz Carrasco-Jiménez
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada 18071, Spain
| | - Emilio Parisini
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV 1006, Latvia; Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, Bologna 40126, Italy
| | - Daniela Lanari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia 06123, Italy
| | - Laura M Odina
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV 1006, Latvia
| | - Atis Jekabsons
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV 1006, Latvia
| | - Sonia Perales
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada 18071, Spain
| | - Diana Zelencova-Gopejenko
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV 1006, Latvia
| | - Guiomar Pérez-Moreno
- Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine "López-Neyra", Spanish National Research Council, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 17, 18016 Granada, Spain
| | - Cristina Bosch-Navarrete
- Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine "López-Neyra", Spanish National Research Council, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 17, 18016 Granada, Spain
| | - Dolores González-Pacanowska
- Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine "López-Neyra", Spanish National Research Council, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 17, 18016 Granada, Spain
| | - Luisa Carlota López-Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada 18071, Spain
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2
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Truong A, Hu R, Quan B, Bailey MA, Schroeder EA, Sylvester K, Neveu G, Kafsack BF, Fitzgerald MC, Derbyshire ER. Covalent inhibition of Plasmodium falciparum Ubc13 impairs global protein synthesis. iScience 2025; 28:112545. [PMID: 40491475 PMCID: PMC12146557 DOI: 10.1016/j.isci.2025.112545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 03/05/2025] [Accepted: 04/24/2025] [Indexed: 06/11/2025] Open
Abstract
The ubiquitin-conjugating enzyme 13 (Ubc13) has an essential function and putative role in artemisinin activity against Plasmodium falciparum. Ubc13 conjugates lysine 63-linked ubiquitin (K63-Ub) to proteins, but the role of this modification in Plasmodium remains largely unknown. Herein, we characterize and deploy NSC697923 to interrogate PfUbc13 function. We demonstrate that NSC697923 covalently targets the PfUbc13 catalytic cysteine and exhibits nanomolar inhibitory potency. NSC697923 inhibits multiple life stages and synergizes with the malaria drug dihydroartemisinin. NSC697923 specifically reduces K63-Ub in blood stage parasites, and subsequent chemoproteomic studies identified 31 putative PfUbc13 substrates. These proteins were enriched in transcription, translation, and proteasome processes, and 90% overlapped with previous Plasmodium ubiquitinome studies. Nascent protein synthesis was reduced following NSC697923 exposure, supporting a role for PfUbc13 and K63-Ub in mediating protein translation. These findings expand our knowledge of PfUbc13-dependent processes in these pathogenic parasites and highlight this enzyme as a potential antimalarial drug target.
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Affiliation(s)
- Anna Truong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Ruitian Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Baiyi Quan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | | | - Erin A. Schroeder
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kayla Sylvester
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Gaëlle Neveu
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Björn F.C. Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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3
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Macdonald JR, Arnold MS, Luth MR, Cihalova D, Quinn RJ, Winzeler EA, Lee MC, van Dooren GG, Maier AG, Skinner-Adams TS, Andrews KT, Fisher GM. Inner-mitochondrial membrane protein PfMPV17 is linked to P. falciparum in vitro resistance to the indoloquinolizidine alkaloid alstonine. J Antimicrob Chemother 2025:dkaf141. [PMID: 40432501 DOI: 10.1093/jac/dkaf141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 04/27/2025] [Indexed: 05/29/2025] Open
Abstract
BACKGROUND There are an estimated 260 million malaria cases and ∼600 000 deaths annually. Challenges to malaria eradication include the lack of highly effective and broadly applicable vaccines and parasite drug resistance. This is driving the need for new tools, including novel drugs and drug targets. The indoloquinolizidine alkaloid alstonine was previously shown to have in vitro activity against Plasmodium falciparum malaria parasites and a slow-action activity that is different from other slow-action antiplasmodial compounds such as clindamycin. OBJECTIVES To investigate the action of the antiplasmodial compound alstonine by validating a putative resistance mutation and determining whether the activity of alstonine is linked to the mitochondrial electron transport chain. MATERIALS AND METHODS In vitro evolution of resistance was used to generate alstonine-resistant P. falciparum, followed by whole-genome sequencing and CRISPR/Cas9 gene editing of wildtype parasites to validate a putative resistance-associated mutation. Links to mitochondrial function were assessed using oxygen consumption rate measurements and activity of alstonine in P. falciparum expressing the yeast dihydroorotate dehydrogenase. RESULTS P. falciparum parasites were selected with ∼20-fold reduced sensitivity to alstonine compared to wild-type parasites. Whole-genome sequencing of alstonine-resistant P. falciparum sub-clones identified several mutations including a copy number variation and point mutation (A318P) in a gene encoding a putative inner-mitochondrial membrane protein (PfMPV17). Introduction of the A318P mutation into the PfMPV17 gene in wild-type P. falciparum yielded parasites with reduced alstonine sensitivity. While a direct link between alstonine action and mitochondrial respiratory function was not found, a transgenic P. falciparum line resistant to the cytochrome bc1 inhibitor atovaquone and pyrimidine synthesis inhibitor DSM265 had reduced sensitivity to alstonine. CONCLUSIONS These data demonstrate that PfMPV17 is linked to alstonine resistance and suggest that alstonine action is linked to the mitochondria and/or pyrimidine biosynthesis pathways.
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Affiliation(s)
- J R Macdonald
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
| | - M S Arnold
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
| | - M R Luth
- Department of Pediatrics, University of California, San Diego, USA
| | - D Cihalova
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - R J Quinn
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
| | - E A Winzeler
- Department of Pediatrics, School of Medicine, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA
| | - M C Lee
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - G G van Dooren
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - A G Maier
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - T S Skinner-Adams
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
| | - K T Andrews
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
| | - G M Fisher
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, Queensland, Australia
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Liu J, Vidilaseris K, Johansson NG, Ribeiro O, Dreano L, Yli-Kauhaluoma J, Xhaard H, Goldman A. Expression, purification and preliminary pharmacological characterization of the Plasmodium falciparum membrane-bound pyrophosphatase type 1. PLoS One 2025; 20:e0322756. [PMID: 40424284 PMCID: PMC12111632 DOI: 10.1371/journal.pone.0322756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Accepted: 04/30/2025] [Indexed: 05/29/2025] Open
Abstract
Membrane-bound pyrophosphatases are integral membrane proteins that catalyze the hydrolysis of pyrophosphate into orthophosphate, while simultaneously facilitating the pumping of protons and/or sodium ions. Since mPPases are absent in humans but play a critical role in the life cycle of protist parasite, they represent promising therapeutic targets. We successfully expressed the Plasmodium falciparum type 1 mPPase in the baculovirus/insect cell expression system and purified the protein, yielding 0.3 mg per liter cell culture. Various detergents were tested for solubilization, with the protein remaining active under all selected detergents. n-dodecyl-β-D-maltoside combined with cholesteryl hemisuccinate provided the highest solubility (88%). Finally, the PfPPase-VP1 was assayed against a set of fourteen antimalarial drugs, along with seven Thermotoga maritima mPPase inhibitors and fourteen compounds of unknown activity against mPPases. Only three compounds, all pyrazolo[1,5-a]pyrimidine-based TmPPase inhibitors, retained micromolar IC50 activity against PfPPase-VP1. The expression and purification of the PfPPase-VP1 will allow to conduct structural studies as well as to develop target-based screens, two steps necessary for the development of inhibitors to combat parasite disease.
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Affiliation(s)
- Jianing Liu
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Keni Vidilaseris
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Niklas G. Johansson
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Orquidea Ribeiro
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Loïc Dreano
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Adrian Goldman
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
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5
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Rawat A, Antil N, Meenakshi, Deshmukh B, Rai AB, Nagar A, Kumar N, Prasad TSK, Karmodiya K, Sharma P. PfPPM2 signalling regulates asexual division and sexual conversion of human malaria parasite Plasmodium falciparum. Nat Commun 2025; 16:4790. [PMID: 40410154 PMCID: PMC12102381 DOI: 10.1038/s41467-025-59476-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 04/24/2025] [Indexed: 05/25/2025] Open
Abstract
Malaria parasite undergoes interesting developmental transition in human and mosquito host. While it divides asynchronously in the erythrocytes, it switches to sexual forms, which is critical for disease transmission. We report a novel signalling pathway involving Protein Phosphatase PfPPM2, which regulates asexual division of Plasmodium falciparum as well as its conversion to sexual forms. PfPPM2 may regulate the phosphorylation of key proteins involved in chromatin remodelling and protein translation. One of the key PfPPM2-targets was Heterochromatin Protein 1 (HP1), a regulator of heritable gene silencing which contributes to both mitotic proliferation as well as sexual commitment of the parasite. PfPPM2 promotes sexual conversion by regulating the interaction between HP1, H3K9me3 and chromatin and it achieves this by dephosphorylating S33 of HP1. PfPPM2 also regulates protein synthesis in the parasite by repressing the phosphorylation of initiation factor eIF2α, which is likely to contribute to parasite division and possibly sexual differentiation.
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Affiliation(s)
- Akanksha Rawat
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neelam Antil
- Center for Systems Biology and Molecular Medicine [an ICMR Collaborating Centre of Excellence 2024 (ICMR-CCoE 2024)], Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Meenakshi
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Bhagyashree Deshmukh
- Immunoinformatics Laboratory, National Institute of Immunology, New Delhi, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine [an ICMR Collaborating Centre of Excellence 2024 (ICMR-CCoE 2024)], Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Annu Nagar
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Narendra Kumar
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- Immunoinformatics Laboratory, National Institute of Immunology, New Delhi, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine [an ICMR Collaborating Centre of Excellence 2024 (ICMR-CCoE 2024)], Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Krishanpal Karmodiya
- Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, 411008, India
| | - Pushkar Sharma
- Eukaryotic Gene Expression Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
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6
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Probst AS, Paton DG, Appetecchia F, Bopp S, Adams KL, Rinvee TA, Pou S, Winter R, Du EW, Yahiya S, Vidoudez C, Singh N, Rodrigues J, Castañeda-Casado P, Tammaro C, Chen D, Godinez-Macias KP, Jaramillo JL, Poce G, Rubal MJ, Nilsen A, Winzeler EA, Baum J, Burrows JN, Riscoe MK, Wirth DF, Catteruccia F. In vivo screen of Plasmodium targets for mosquito-based malaria control. Nature 2025:10.1038/s41586-025-09039-2. [PMID: 40399670 DOI: 10.1038/s41586-025-09039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Accepted: 04/17/2025] [Indexed: 05/23/2025]
Abstract
The decline in malaria deaths has recently stalled owing to several factors, including the widespread resistance of Anopheles vectors to the insecticides used in long-lasting insecticide-treated nets (LLINs)1,2. One way to mitigate insecticide resistance is to directly kill parasites during their mosquito-stage of development by incorporating antiparasitic compounds into LLINs. This strategy can prevent onward parasite transmission even when insecticides lose efficacy3,4. Here, we performed an in vivo screen of compounds against the mosquito stages of Plasmodium falciparum development. Of the 81 compounds tested, which spanned 28 distinct modes of action, 22 were active against early parasite stages in the mosquito midgut lumen, which in turn prevented establishment of infection. Medicinal chemistry was then used to improve antiparasitic activity of the top hits from the screen. We generated several endochin-like quinolones (ELQs) that inhibited the P. falciparum cytochrome bc1 complex (CytB). Two lead compounds that targeted separate sites in CytB (Qo and Qi) showed potent, long-lasting and stable activity when incorporated and/or extruded into bed net-like polyethylene films. ELQ activity was fully preserved in insecticide-resistant mosquitoes, and parasites resistant to these compounds had impaired development at the mosquito stage. These data demonstrate the promise of incorporating ELQ compounds into LLINs to counteract insecticide resistance and to reduce malaria transmission.
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Affiliation(s)
- Alexandra S Probst
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Douglas G Paton
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Infectious Disease, University of Georgia, Athens, GA, USA
| | - Federico Appetecchia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Selina Bopp
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey L Adams
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tasneem A Rinvee
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Esrah W Du
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sabrina Yahiya
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Naresh Singh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Chiara Tammaro
- Department of Chemistry and Pharmaceutical Technologies, Sapienza University of Rome, Rome, Italy
| | - Daisy Chen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Giovanna Poce
- Department of Chemistry and Pharmaceutical Technologies, Sapienza University of Rome, Rome, Italy
| | | | - Aaron Nilsen
- VA Medical Center, Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London, UK
- School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Michael K Riscoe
- VA Medical Center, Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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7
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Rajaram K, Rangel GW, Munro JT, Nair SC, Elahi R, Llinás M, Prigge ST. MULTIPLE, REDUNDANT CARBOXYLIC ACID TRANSPORTERS SUPPORT MITOCHONDRIAL METABOLISM IN PLASMODIUM FALCIPARUM. J Biol Chem 2025:110248. [PMID: 40398604 DOI: 10.1016/j.jbc.2025.110248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 05/09/2025] [Accepted: 05/14/2025] [Indexed: 05/23/2025] Open
Abstract
The mitochondrion of the deadliest human malaria parasite, Plasmodium falciparum, is an essential source of cellular acetyl-CoA during the asexual blood-stage of the parasite life cycle. Blocking mitochondrial acetyl-CoA synthesis leads to a hypoacetylated proteome and parasite death. We previously determined that mitochondrial acetyl-CoA is primarily synthesized from glucose-derived pyruvate by α-ketoacid dehydrogenases. Here, we asked if inhibiting the import of glycolytic pyruvate across the mitochondrial inner membrane would affect acetyl-CoA production and, thus, could be a potential target for antimalarial drug development. We selected the two predicted mitochondrial pyruvate carrier proteins, PfMPC1 (PF3D7_1340800) and PfMPC2 (PF3D7_1470400), for genetic knockout and isotopic metabolite tracing via HPLC-MS metabolomic analysis. Surprisingly, we observed that asexual blood-stage parasites could survive the loss of either or both PfMPCs with only minor growth defects, despite a substantial reduction in the amount of glucose-derived isotopic labelling into acetyl-CoA. Furthermore, genetic deletion of two additional mitochondrial carboxylic acid transporters - DTC (PF3D7_0823900, di/tricarboxylic acid carrier) and YHM2 (PF3D7_1223800, a putative citrate/α-ketoglutarate carrier protein) - only mildly affected blood-stage replication, even in the context of PfMPC deficiency. Although we observed no added impact on the incorporation of glucose carbon into acetyl-CoA in these quadruple knockout mutants, we noted a large decrease in glutamine-derived label in tricarboxylic acid cycle metabolites, suggesting that DTC and YHM2 both import glutamine derivatives into the mitochondrion. Altogether, our results demonstrate that redundant routes are used to fuel the blood-stage malaria parasite mitochondrion with imported carbon from two major sources - glucose and glutamine.
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Affiliation(s)
- Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205; Present address: Department of Microbiology, The Ohio State University, Columbus, OH 43210
| | - Gabriel W Rangel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802
| | - Justin T Munro
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802; Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Sethu C Nair
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Rubayet Elahi
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802; Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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8
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Al Monla R, Penzo M, Vallentin A, Lohia R, Vincent J, Berry L, Gomes AR, Cerdan R, Wengelnik K. PI3-kinase has multiple functions in asexual blood stages of Plasmodium falciparum. Sci Rep 2025; 15:16762. [PMID: 40369090 PMCID: PMC12078608 DOI: 10.1038/s41598-025-01397-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 05/06/2025] [Indexed: 05/16/2025] Open
Abstract
All symptoms of malaria are caused during the replication of the parasite Plasmodium falciparum in human red blood cells. The parasite digests the host cell cytoplasm in its food vacuole, a pathway of particular interest as drug target. The Vps34-type PI3-kinase in P. falciparum produces PI3-monophophate (PI3P) and has been linked to haemoglobin digestion, to resistance to the current first line antimalarial artemisinin and to biology of the apicoplast. Here we dissect the functions of PfPI3-kinase by inducible deletion of its gene using the loxP-DiCre system and find that PfPI3-kinase is essential for parasite survival. Mutant parasites accumulate undigested haemoglobin (Hb) confirming a defect in the pathway of Hb uptake and digestion, the most likely reason for parasite death. Some parasites are affected in apicoplast inheritance demonstrating that PI3P-dependent processes are important for apicoplast biology in P. falciparum. Finally, we discover that in PI3-kinase mutant parasites carrying a mutation conferring resistance to artemisinin, the lower amounts of PI3P correlate with lower levels of artemisinin resistance. We suggest that the reduced levels of PI3P in the PI3-kinase mutant dampen repair mechanisms like the autophagic processes normally associated with Kelch13 mutations, leading to a proteotoxic stress and to an increase in susceptibility to artemisinin.
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Affiliation(s)
- Reem Al Monla
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Maria Penzo
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Alice Vallentin
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Rakhee Lohia
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Jeremy Vincent
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Laurence Berry
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Ana Rita Gomes
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Rachel Cerdan
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Kai Wengelnik
- LPHI, CNRS, INSERM, University of Montpellier, Montpellier, France.
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9
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Khim M, Montgomery J, Laureano De Souza M, Delvillar M, Weible LJ, Prabakaran M, Hulverson MA, Eck T, Bheemanabonia RY, Alday PH, Rotella DP, Doggett JS, Staker BL, Ojo KK, Bhanot P. Versatile Imidazole Scaffold with Potent Activity against Multiple Apicomplexan Parasites. ACS Infect Dis 2025. [PMID: 40339062 DOI: 10.1021/acsinfecdis.5c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2025]
Abstract
Malaria, toxoplasmosis, and cryptosporidiosis are caused by apicomplexan parasites Plasmodium spp., Toxoplasma gondii, and Cryptosporidium parvum, respectively, and pose major health challenges. Their therapies are inadequate, ineffective or threatened by drug resistance. The development of novel drugs against them requires innovative and resource-efficient strategies. We exploited the kinome conservation of these parasites to determine the cellular targets and effects of two Plasmodium falciparum inhibitors in T. gondii and C. parvum. The imidazoles, (R)-RY-1-165 and (R)-RY-1-185, were developed to target the cGMP dependent protein kinase of P. falciparum (PfPKG), orthologs of which are present in T. gondii and C. parvum. Using structural and modeling approaches we determined that the molecules bind stereospecifically and interact with PfPKG in a manner unique among described inhibitors. We used enzymatic assays and mutant P. falciparum expressing PfPKG with a substituted "gatekeeper" residue to determine that cellular activity of the molecules is mediated through targets additional to PfPKG. These likely include P. falciparum calcium dependent protein kinase 1 and 4 (PfCDPK-1, -4), kinases that, like PfPKG, have small amino acids at the "gatekeeper" position. The molecules are active against T. gondii and C. parvum, with T. gondii tachyzoites being particularly sensitive. Using mutant parasites, enzyme assays and modeling studies we demonstrate that targets in T. gondii include TgPKG, TgCDPK1, TgCDPK4 and the mitogen activated kinase-like 1 (MAPKL-1). Our results suggest that this scaffold holds promise for the development of new toxoplasmosis drugs.
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Affiliation(s)
- Monique Khim
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center for Global Infectious Disease ResearchSeattle Children's Research Institute, Seattle, Washington 98109, United States
| | - Jemma Montgomery
- Divisions of Infectious Diseases and ResearchVA Portland Healthcare System, Portland, Oregon 97239, United States
| | - Mariana Laureano De Souza
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Melvin Delvillar
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Lyssa J Weible
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious DiseasesUniversity of Washington, Seattle, Washington 98109, United States
| | - Mayuri Prabakaran
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious DiseasesUniversity of Washington, Seattle, Washington 98109, United States
| | - Matthew A Hulverson
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious DiseasesUniversity of Washington, Seattle, Washington 98109, United States
| | - Tyler Eck
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life SciencesMontclair State University, Montclair, New Jersey 07043, United States
| | - Rammohan Y Bheemanabonia
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life SciencesMontclair State University, Montclair, New Jersey 07043, United States
| | - P Holland Alday
- Divisions of Infectious Diseases and ResearchVA Portland Healthcare System, Portland, Oregon 97239, United States
- Division of Infectious Diseases,Oregon Health & Science University School of Medicine, Portland, Oregon 97239, United States
| | - David P Rotella
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life SciencesMontclair State University, Montclair, New Jersey 07043, United States
| | - J Stone Doggett
- Divisions of Infectious Diseases and ResearchVA Portland Healthcare System, Portland, Oregon 97239, United States
- Division of Infectious Diseases,Oregon Health & Science University School of Medicine, Portland, Oregon 97239, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center for Global Infectious Disease ResearchSeattle Children's Research Institute, Seattle, Washington 98109, United States
| | - Kayode K Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious DiseasesUniversity of Washington, Seattle, Washington 98109, United States
- Department of Global HealthUniversity of Washington, Seattle, Washington 98195, United States
| | - Purnima Bhanot
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, United States
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10
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Elahi R, Mesones Mancilla S, Sievert ML, Ribeiro Dinis L, Adewale-Fasoro O, Mann A, Zur Y, Prigge ST. Decoding the Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance. J Mol Biol 2025:169156. [PMID: 40335414 DOI: 10.1016/j.jmb.2025.169156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 03/28/2025] [Accepted: 04/09/2025] [Indexed: 05/09/2025]
Abstract
Post-transcriptional tRNA modifications are essential for accurate and efficient protein translation across all organisms. The apicoplast organelle genome of Plasmodium falciparum contains a minimal set of 25 complete tRNA isotypes, making it an ideal model for studying minimal translational machinery. Efficient decoding of mRNA codons by this limited tRNA set depends on post-transcriptional modifications. In this study, we sought to define the minimal set of tRNA-modifying enzymes. Using comparative genomics and apicoplast protein localization prediction tools, we identified 16 nucleus-encoded tRNA-modifying enzymes predicted to localize to the apicoplast. Experimental studies confirmed apicoplast localization for 14 enzymes, including two with dual localization. Combining an apicoplast metabolic bypass parasite line with gene disruption tools, we disrupted 12 of the 14 apicoplast-localized enzymes. Six of these enzymes were found to be essential for parasite survival, and six were dispensable. All six essential enzymes are thought to catalyze modifications in the anticodon loop of tRNAs, and their deletions resulted in apicoplast disruption. Of the two genes refractory to deletion, one exhibited dual localization, suggesting essential functions outside the apicoplast. The other, which appears to localize solely to the apicoplast, may play an indispensable role that is not circumvented by our metabolic bypass. Our findings suggest the apicoplast translation system relies on a minimal set of tRNA modifications concentrated in the anticodon loop. This work advances our understanding of minimal translational machinery in reduced organelles, such as the apicoplast, with promising applications in synthetic biology.
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Affiliation(s)
- Rubayet Elahi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Sebastian Mesones Mancilla
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Montana L Sievert
- Johns Hopkins Malaria Research Institute, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Luciana Ribeiro Dinis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Opeoluwa Adewale-Fasoro
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Alexis Mann
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Yonatan Zur
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins Malaria Research Institute, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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11
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Balakrishnan A, Hunziker M, Tiwary P, Pandey V, Drew D, Billker O. A CRISPR homing screen finds a chloroquine resistance transporter-like protein of the Plasmodium oocyst essential for mosquito transmission of malaria. Nat Commun 2025; 16:3895. [PMID: 40274854 PMCID: PMC12022033 DOI: 10.1038/s41467-025-59099-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 04/10/2025] [Indexed: 04/26/2025] Open
Abstract
Genetic screens with barcoded PlasmoGEM vectors have identified thousands of Plasmodium berghei gene functions in haploid blood stages, gametocytes and liver stages. However, the formation of diploid cells by fertilisation has hindered similar research on the parasites' mosquito stages. In this study, we develop a scalable genetic system that uses barcoded gene targeting vectors equipped with a CRISPR-mediated homing mechanism to generate homozygous loss-of-function mutants after one parent introduces a modified allele into the zygote. To achieve this, we use vectors additionally expressing a target gene specific gRNA. When integrated into one of the parental alleles it directs Cas9 to the intact allele after fertilisation, leading to its disruption. This homing strategy is 90% effective at generating homozygous gene editing of a fluorescence-tagged reporter locus in the oocyst. A pilot screen identifies PBANKA_0916000 as a chloroquine resistance transporter-like protein (CRTL) essential for oocyst growth and sporogony, pointing to an unexpected importance for malaria transmission of the poorly understood digestive vacuole of the oocyst that contains hemozoin granules. Homing screens provide a method for the systematic discovery of malaria transmission genes whose first essential functions are after fertilisation in the bloodmeal, enabling their potential as targets for transmission-blocking interventions to be assessed.
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Affiliation(s)
- Arjun Balakrishnan
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mirjam Hunziker
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Puja Tiwary
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Vikash Pandey
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Oliver Billker
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden.
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umea Centre for Microbial Research, Umeå University, Umeå, Sweden.
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12
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Awalt JK, Ooi ZK, Ashton TD, Mansouri M, Calic PPS, Zhou Q, Vasanthan S, Lee S, Loi K, Jarman KE, Penington JS, Qiu D, Zhang X, Lehane AM, Mao EY, Gancheva MR, Wilson DW, Giannangelo C, MacRaild CA, Creek DJ, Yeo T, Sheth T, Fidock DA, Churchyard A, Baum J, Famodimu MT, Delves MJ, Kristan M, Stewart L, Sutherland CJ, Coyle R, Jagoe H, Lee MCS, Chowdury M, de Koning-Ward TF, Baud D, Brand S, Jackson PF, Cowman AF, Dans MG, Sleebs BE. Optimization and Characterization of N-Acetamide Indoles as Antimalarials That Target PfATP4. J Med Chem 2025; 68:8933-8966. [PMID: 40228810 PMCID: PMC12035806 DOI: 10.1021/acs.jmedchem.5c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 03/19/2025] [Accepted: 03/25/2025] [Indexed: 04/16/2025]
Abstract
To discover new antimalarials, a screen of the Janssen Jumpstarter library against Plasmodium falciparum uncovered the N-acetamide indole hit class. The structure-activity relationship of this chemotype was defined and culminated in the optimized frontrunner analog WJM664, which exhibited potent asexual stage activity and high metabolic stability. Resistant selection and whole-genome sequencing revealed mutations in PfATP4, which was validated as the target by showing that analogs exhibited reduced potency against parasites with resistance-conferring mutations in PfATP4, a metabolomic signature similar to that of the PfATP4 inhibitor KAE609, and inhibition of Na+-dependent ATPase activity consistent with on-target inhibition of PfATP4. WJM664 inhibited gamete development and blocked parasite transmission to mosquitoes but exhibited low efficacy in aPlasmodium berghei mouse model, which was attributed to ATP4 species differentiation and its moderate systemic exposure. Optimization of these attributes is required for N-acetamide indoles to be pursued for development as a curative and transmission-blocking therapy.
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Affiliation(s)
- Jon Kyle Awalt
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Zi Kang Ooi
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Trent D. Ashton
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Mahta Mansouri
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Petar P. S. Calic
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Qingmiao Zhou
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Santhya Vasanthan
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Serena Lee
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Katie Loi
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Kate E. Jarman
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Jocelyn S. Penington
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Deyun Qiu
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Xinxin Zhang
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Adele M. Lehane
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Emma Y. Mao
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Maria R. Gancheva
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Danny W. Wilson
- Research
Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Carlo Giannangelo
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville 3052, Australia
| | | | - Darren J. Creek
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville 3052, Australia
| | - Tomas Yeo
- Department
of Microbiology & Immunology, Columbia
University Irving Medical Center, New York, New York 10032, United States
- Center
for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanaya Sheth
- Department
of Microbiology & Immunology, Columbia
University Irving Medical Center, New York, New York 10032, United States
- Center
for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David A. Fidock
- Department
of Microbiology & Immunology, Columbia
University Irving Medical Center, New York, New York 10032, United States
- Center
for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division
of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Alisje Churchyard
- Department
of Life Sciences, Imperial College London, South Kensington SW7 2AZ, U.K.
| | - Jake Baum
- Department
of Life Sciences, Imperial College London, South Kensington SW7 2AZ, U.K.
- School
of Biomedical Sciences, University of New
South Wales, Sydney 2031, Australia
| | | | - Michael J. Delves
- London School of
Hygiene and Tropical Medicine, London WC1E 7HT, U.K.
| | - Mojca Kristan
- London School of
Hygiene and Tropical Medicine, London WC1E 7HT, U.K.
| | - Lindsay Stewart
- London School of
Hygiene and Tropical Medicine, London WC1E 7HT, U.K.
| | | | - Rachael Coyle
- London School of
Hygiene and Tropical Medicine, London WC1E 7HT, U.K.
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton CB10 1SA, U.K.
| | - Hannah Jagoe
- London School of
Hygiene and Tropical Medicine, London WC1E 7HT, U.K.
| | - Marcus C. S. Lee
- Wellcome Sanger Institute, Wellcome Genome Campus Hinxton CB10 1SA, U.K.
- Wellcome
Centre for Anti-Infectives Research, Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Mrittika Chowdury
- School
of Medicine, Deakin University, Waurn Ponds 3216, Australia
- Institute
for Mental and Physical Health and Clinical Translation, Deakin University, Geelong 3216, Australia
| | - Tania F. de Koning-Ward
- School
of Medicine, Deakin University, Waurn Ponds 3216, Australia
- Institute
for Mental and Physical Health and Clinical Translation, Deakin University, Geelong 3216, Australia
| | - Delphine Baud
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Stephen Brand
- Medicines for Malaria Venture, Geneva 1215, Switzerland
| | - Paul F. Jackson
- Emerging
Science & Innovation, Discovery Sciences, Janssen R&D LLC, La Jolla 92121, United States
| | - Alan F. Cowman
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Madeline G. Dans
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Brad E. Sleebs
- The
Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department
of Medical Biology, The University of Melbourne, Parkville 3010, Australia
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13
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Blatch GL, Edkins AL. New insights into Sti1/Hop's cochaperone function highlight the complexity of proteostatic regulation. FEBS J 2025. [PMID: 40259657 DOI: 10.1111/febs.70108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Accepted: 04/11/2025] [Indexed: 04/23/2025]
Abstract
Sti1/Hop is a cochaperone that regulates Hsp70 and Hsp90 chaperones. Sti1/Hop function is perceived as limited to scaffolding chaperone complexes, although recent studies suggest a broader function. Rutledge et al. show that while Sti1/Hop functions within chaperone complexes under basal conditions, during high stress, it operates independently to sequester soluble misfolded protein in the cytoplasm, a function typically associated with chaperones rather than cochaperones. Furthermore, the localisation and levels of Sti1/Hop are finely tuned to ensure orderly sequestration and resolution of misfolded proteins. These data support a role for Sti1/Hop as a cochaperone specialised for stressed proteostasis networks.
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Affiliation(s)
- Gregory Lloyd Blatch
- The Vice Chancellery, The University of Notre Dame Australia, Fremantle, Australia
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
| | - Adrienne Lesley Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
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14
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Zadow ME, MacRaild CA, Creek DJ, Wilson DW. Alba protein-mediated gene and protein regulation in protozoan parasites. Int J Parasitol 2025:S0020-7519(25)00076-1. [PMID: 40246164 DOI: 10.1016/j.ijpara.2025.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 02/21/2025] [Accepted: 04/10/2025] [Indexed: 04/19/2025]
Abstract
The success of protozoan parasites relies heavily on regulation of gene and protein expression to facilitate their persistence in harsh and often changing environments. These parasites display biology that is highly divergent from model eukaryotes, unfortunately leaving our understanding of these parasites' critical regulatory mechanisms incomplete. Alba proteins, a highly diverse group of DNA/RNA-binding proteins, are found across all domains of life and it has become increasingly apparent that these proteins play key regulatory roles in many protozoan parasite species including Plasmodium, Leishmania, Toxoplasma, and Trypanosoma. This review focusses on a subset of clinically relevant protozoan parasites and highlights the key biological processes known to have Alba protein involvement in these organisms including parasite development, survival, and virulence. In order to gain greater insight into these proteins, we also undertook a bioinformatic exploration of their protein sequences, leading us to identify previously unreported C-terminal Alba domain motifs and propose annotations for several currently unannotated protozoan Alba-like proteins. This collation of information allows us to observe common themes in Alba protein function across this group of parasites while also identifying areas of opportunity for further study.
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Affiliation(s)
- Meghan E Zadow
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide 5005 SA, Australia.
| | - Christopher A MacRaild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide 5005 SA, Australia; Burnet Institute, Melbourne 3004 Victoria, Australia.
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15
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García-Guerrero AE, Marvin RG, Blackwell AM, Sigala PA. Biogenesis of Cytochromes c and c1 in the Electron Transport Chain of Malaria Parasites. ACS Infect Dis 2025; 11:813-826. [PMID: 39481007 PMCID: PMC11991887 DOI: 10.1021/acsinfecdis.4c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2024]
Abstract
Plasmodium malaria parasites retain an essential mitochondrional electron transport chain (ETC) that is critical for growth within humans and mosquitoes and is a key antimalarial drug target. ETC function requires cytochromes c and c1, which are unusual among heme proteins due to their covalent binding to heme via conserved CXXCH sequence motifs. Heme attachment to these proteins in most eukaryotes requires the mitochondrial enzyme holocytochrome c synthase (HCCS) that binds heme and the apo cytochrome to facilitate the biogenesis of the mature cytochrome c or c1. Although humans encode a single bifunctional HCCS that attaches heme to both proteins, Plasmodium parasites are like yeast and encode two separate HCCS homologues thought to be specific for heme attachment to cyt c (HCCS) or cyt c1 (HCC1S). To test the function and specificity of Plasmodium falciparum HCCS and HCC1S, we used CRISPR/Cas9 to tag both genes for conditional expression. HCC1S knockdown selectively impaired cyt c1 biogenesis and caused lethal ETC dysfunction that was not reversed by the overexpression of HCCS. Knockdown of HCCS caused a more modest growth defect but strongly sensitized parasites to mitochondrial depolarization by proguanil, revealing key defects in ETC function. These results and prior heterologous studies in Escherichia coli of cyt c hemylation by P. falciparum HCCS and HCC1S strongly suggest that both homologues are essential for mitochondrial ETC function and have distinct specificities for the biogenesis of cyt c and c1, respectively, in parasites. This study lays a foundation to develop novel strategies to selectively block ETC function in malaria parasites.
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Affiliation(s)
- Aldo E. García-Guerrero
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA 84112
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA 84112
| | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA 84112
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA 84112
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16
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Hirai M, Arai M, Hayamichi S, Uchida A, Sudo M, Kubota R, Shinzawa N, Mita T. Deletion of the chloroquine resistance transporter gene confers reduced piperaquine susceptibility to the rodent malaria parasite Plasmodium berghei. Antimicrob Agents Chemother 2025; 69:e0158924. [PMID: 39992104 PMCID: PMC11963562 DOI: 10.1128/aac.01589-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 01/17/2025] [Indexed: 02/25/2025] Open
Abstract
Malaria parasites acquire drug resistance through genetic changes, the mechanisms of which remain incompletely understood. Understanding the mechanisms of drug resistance is crucial for the development of effective treatments against malaria, and for this purpose, new genetic tools are needed. In a previous study, as a forward genetic tool, we developed the rodent malaria parasite Plasmodium berghei mutator (PbMut) line, which has a greatly increased rate of mutation accumulation and from which we isolated a mutant with reduced susceptibility to piperaquine (PPQ). We identified a mutation in the chloroquine resistance transporter (PbCRT N331I) as responsible for this phenotype. In the current study, we generated a marker-free PbMut to enable further genetic manipulation of the isolated mutants. Here, we screened again for PPQ-resistant mutants in marker-free PbMut and obtained a parasite population with reduced susceptibility to PPQ. Of five isolated clones, none had the mutation PbCRT N331I; rather, they possessed a nonsense mutation at amino acid 119 (PbCRT Y119*), which would truncate the protein before eight of its ten predicted transmembrane domains. The PbCRT orthologue in the human malaria parasite Plasmodium falciparum, PfCRT, is an essential membrane transporter. To address the essentiality of PbCRT, we successfully deleted the full PbCRT gene [PbCRT(-)] from wild-type parasites. PbCRT(-) parasites exhibited reduced susceptibility to PPQ, along with compromised fitness in mice and following transmission to mosquitoes. Taken together, our findings provide the first evidence that P. berghei can acquire reduced PPQ susceptibility through complete loss of PbCRT function.
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Affiliation(s)
- Makoto Hirai
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Bunkyo-ku Hongo, Tokyo, Japan
| | - Meiji Arai
- Department of International Medical Zoology, School of Medicine, Kagawa University, Kida, Kagawa, Japan
| | - Soki Hayamichi
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Bunkyo-ku Hongo, Tokyo, Japan
| | - Ayako Uchida
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Bunkyo-ku Hongo, Tokyo, Japan
| | - Megumi Sudo
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Bunkyo-ku Hongo, Tokyo, Japan
| | - Rie Kubota
- Department of Parasitology and Tropical Medicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, Bunkyo-ku Yushima, Tokyo, Japan
| | - Naoaki Shinzawa
- Department of Parasitology and Tropical Medicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, Bunkyo-ku Yushima, Tokyo, Japan
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Bunkyo-ku Hongo, Tokyo, Japan
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17
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Saharan K, Baral S, Gandhi S, Singh AK, Ghosh S, Das R, Nagaraj VA, Vasudevan D. Structure-function studies of a nucleoplasmin isoform from Plasmodium falciparum. J Biol Chem 2025; 301:108379. [PMID: 40049416 PMCID: PMC11993163 DOI: 10.1016/j.jbc.2025.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 02/14/2025] [Accepted: 02/27/2025] [Indexed: 04/01/2025] Open
Abstract
An organized regulation of gene expression and DNA replication is vital for the progression of the complex life cycle of Plasmodium falciparum (Pf), involving multiple hosts and various stages. These attributes rely on the dynamic architecture of chromatin governed by several factors, including histone chaperones. Nucleoplasmin class of histone chaperones perform histone chaperoning function and participate in various developmental processes in eukaryotes. Here, our crystal structure confirmed that Pf indeed possesses a nucleoplasmin isoform (PfNPM), and the N-terminal core domain (NTD) adopts the characteristic pentameric doughnut conformation. Furthermore, PfNPM exists as a pentamer in solution, and the N-terminal core domain exhibits thermal and chemical stability. PfNPM interacts individually with assembled H2A/H2B and H3/H4 with an equimolar stoichiometry, wherein the acidic tracts of PfNPM were found to be necessary for these interactions. Further, H3/H4 displays a higher binding affinity for PfNPM than H2A/H2B, potentially due to stronger electrostatic interactions. The interaction studies also suggested that H2A/H2B and H3/H4 might share the same binding site on the PfNPM distal face, wherein H3/H4 could substitute H2A/H2B due to a higher binding affinity. Intriguingly, PfNPM neither demonstrated direct interaction with the nucleosome core particles nor displayed nucleosome assembly function, suggesting it may not be directly associated with histone deposition on the parasite genomic DNA. Furthermore, our immunofluorescence results suggested that PfNPM predominantly localizes in the nucleus and exhibits expression only in the early blood stages, such as ring and trophozoite. Altogether, we provide the first report on the structural and functional characterization of PfNPM.
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Affiliation(s)
- Ketul Saharan
- Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Somanath Baral
- Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Surajit Gandhi
- Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Ajit Kumar Singh
- Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Sourav Ghosh
- Malaria Parasite Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Rahul Das
- Malaria Parasite Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Viswanathan Arun Nagaraj
- Malaria Parasite Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Dileep Vasudevan
- Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India; Structural Biology Laboratory, BRIC-Rajiv Gandhi Centre for Biotechnology (BRIC-RGCB), Thiruvananthapuram, India.
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18
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Mesén-Ramírez JP, Fuchs G, Burmester J, Farias GB, Alape-Flores AM, Singla S, Alder A, Cubillán-Marín J, Castro-Peña C, Lemcke S, Sondermann H, Prado M, Spielmann T, Wilson D, Gilberger TW. HOPS/CORVET tethering complexes are critical for endocytosis and protein trafficking to invasion related organelles in malaria parasites. PLoS Pathog 2025; 21:e1013053. [PMID: 40198740 PMCID: PMC12011295 DOI: 10.1371/journal.ppat.1013053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 04/21/2025] [Accepted: 03/18/2025] [Indexed: 04/10/2025] Open
Abstract
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 still unknown. Here we show that the HOPS/CORVET core subunits are critical for the intracellular proliferation of the malaria parasite Plasmodium falciparum. We demonstrate that HOPS/CORVET are required for parasite endocytosis and host cell cytosol uptake, as early functional depletion of the complex led to developmental arrest and accumulation of endosomes that failed to fuse to the digestive vacuole membrane. Late depletion of the core HOPS/CORVET subunits led to a severe defect in merozoite invasion as a result of the mistargeting of proteins destined to the apical secretory organelles, the rhoptries and micronemes. Ultrastructure-expansion microscopy revealed a reduced rhoptry volume and the accumulation of numerous vesicles in HOPS/CORVET deficient schizonts, further supporting a role of HOPS/CORVET in post-Golgi protein cargo trafficking to the invasion related organelles. Hence, malaria parasites have repurposed HOPS/CORVET to perform dual functions across the intraerythrocytic cycle, consistent with a canonical endocytic 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.
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Affiliation(s)
- Joëlle Paolo Mesén-Ramírez
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Gwendolin Fuchs
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Jonas Burmester
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Guilherme B. Farias
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Ana María Alape-Flores
- Microbiology Faculty and Center for Research in Tropical Diseases (CIET), University of Costa Rica, San José, Costa Rica
| | - Shamit Singla
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia
| | - Arne Alder
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | | | | | - Sarah Lemcke
- Centre for Structural Systems Biology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Holger Sondermann
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Mónica Prado
- Microbiology Faculty and Center for Research in Tropical Diseases (CIET), University of Costa Rica, San José, Costa Rica
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Danny Wilson
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, Australia
| | - Tim-Wolf Gilberger
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
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19
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Smith C, Hajisadeghian M, van Noort GJVDH, Deery MJ, Pinto-Fernández A, Kessler BM, Artavanis-Tsakonas K. Activity-based protein profiling reveals both canonical and novel ubiquitin pathway enzymes in Plasmodium. PLoS Pathog 2025; 21:e1013032. [PMID: 40249735 PMCID: PMC12007708 DOI: 10.1371/journal.ppat.1013032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 03/11/2025] [Indexed: 04/20/2025] Open
Abstract
The ubiquitin-proteasome system (UPS) is essential for Plasmodium falciparum survival and represents a potential target for antimalarial therapies. We utilised a ubiquitin- activity based probe (Ub-Dha) to capture active components of the ubiquitin conjugating machinery during asexual blood-stage development. Several E2 ubiquitin-conjugating enzymes, the E1 activating enzyme, and the HECT E3 ligase PfHEUL were identified and validated through in vitro ubiquitination assays. We also demonstrate selective functional interactions between PfHEUL and a subset of both human and P. falciparum E2s. Additionally, the Ub-Dha probe captured an uncharacterized protein, PF3D7_0811400 (C0H4U0) with no known homology to ubiquitin-pathway enzymes in other organisms. Through structural and biochemical analysis, we validate it as a novel E2 enzyme, capable of binding ubiquitin in a cysteine-specific manner. These findings contribute to our understanding of the P. falciparum UPS, identifying promising novel drug targets and highlighting the evolutionary uniqueness of the Ub-proteasome system in this parasite.
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Affiliation(s)
- Cameron Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Michael J. Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adán Pinto-Fernández
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
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20
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Sundararaman SA, Miller JJ, Daley EC, O’Brien KA, Kasak P, Daniels AM, Edwards RL, Heidel KM, Bague DA, Wilson MA, Koelper AJ, Kourtoglou EC, White AD, August SA, Apple GA, Rouamba RW, Durand AJ, Esteb JJ, Muller FL, Johnson RJ, Hoops GC, Dowd CS, Odom John AR. Prodrug activation in malaria parasites mediated by an imported erythrocyte esterase, acylpeptide hydrolase (APEH). Proc Natl Acad Sci U S A 2025; 122:e2417682122. [PMID: 40035755 PMCID: PMC11912422 DOI: 10.1073/pnas.2417682122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 01/24/2025] [Indexed: 03/06/2025] Open
Abstract
The continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by undesirable drug-like properties of lead compounds. Prodrug approaches temporarily mask undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin (Fsm), exhibit significantly higher antimalarial potency than their parent compounds [R.L. Edwards et al., Sci. Rep. 7, 8400 (2017)]. However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH), is the major activating enzyme of multiple lipophilic ester prodrugs. Surprisingly, this enzyme is taken up by the malaria parasite, Plasmodium falciparum, where it localizes to the parasite cytoplasm and retains enzymatic activity. Using a fluorogenic ester library, we characterize the structure-activity relationship of APEH and compare it to that of P. falciparum esterases. We show that parasite-internalized APEH plays an important role in the activation of substrates with branching at the alpha carbon, in keeping with its exopeptidase activity. Our findings highlight a mechanism for antimicrobial prodrug activation, relying on a host-derived enzyme to yield activation at a microbial target. Mutations in prodrug-activating enzymes are a common mechanism for antimicrobial drug resistance [E. S. Istvan et al., Nat. Commun. 8, 14240 (2017); K. M. V. Sindhe et al., mBio 11, e02640-19 (2020); J. H. Butler et al., Acs Infect Dis. 6, 2994-3003 (2020)]. Leveraging an internalized host enzyme would circumvent this, enabling the design of prodrugs with higher barriers to drug resistance.
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Affiliation(s)
- Sesh A. Sundararaman
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Justin J. Miller
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA19104
| | - Ellora C. Daley
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Kelsey A. O’Brien
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Paulina Kasak
- College of Health Professions, Thomas Jefferson University, Philadelphia, PA19107
| | - Abigail M. Daniels
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Rachel L. Edwards
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO63110
- Omniose, Saint Louis, MO63110
| | - Kenneth M. Heidel
- Department of Chemistry, George Washington University, Washington, DC20052
| | - Darean A. Bague
- Department of Chemistry, George Washington University, Washington, DC20052
| | - Madeleine A. Wilson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Andrew J. Koelper
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Elexi C. Kourtoglou
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Alex D. White
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Sloan A. August
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Georgia A. Apple
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Regis W. Rouamba
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Anthony J. Durand
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - John J. Esteb
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | | | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Geoffrey C. Hoops
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, IN46208
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC20052
| | - Audrey R. Odom John
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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21
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Windle ST, Neal ML, Mast FD, Kappe SHI, Aitchison JD. A Conditional Cas9 System for Stage-Specific Gene Editing in P. falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.09.642268. [PMID: 40161752 PMCID: PMC11952345 DOI: 10.1101/2025.03.09.642268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
The malaria parasite has a complex lifecycle involving various host cell environments in both human and mosquito hosts. The parasite must tightly regulate gene expression at each stage in order to adapt to its current environment while continuing development. However, it is challenging to study gene function and regulation of essential genes across the parasite's multi-host lifecycle. Thus, we adapted a recently developed a single-plasmid dimerizable Cre recombinase system for rapamycin-controllable expression of Cas9, allowing for conditional introduction of mutations. We explored rates of gene deletion using varying repair template lengths, showing functionality of donor templates under 250bp for homology-directed repair. As a proof of concept, we conditionally disrupted two uncharacterized genes in blood and gametocyte stages, identifying new stage-specific phenotypes. Importance As progress towards eliminating malaria has stalled, there is a pressing need for new antimalarials and vaccines. Genes essential to multiple stages of development represent ideal candidates for both antimalarials and vaccines. However, much of the parasite genome remains uncharacterized. Conditional gene perturbation approaches are needed in order to study gene function across the lifecycle. Currently available tools are limited in their ability to perturb genes at the scale required for large screens. We describe a tool that allows for conditional introduction of desired mutations by controlling Cas9 with the DiCre-loxP system. We demonstrate the accessibility of this approach by designing gRNA-donor pairs that can be commercially synthesized. This toolkit provides a scalable system for identifying new drug and vaccine candidates targeting multiple stages of the parasite lifecycle.
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Affiliation(s)
- Sean T. Windle
- Department of Global Health, University of Washington, Seattle, WA, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Stefan H. I. Kappe
- Department of Global Health, University of Washington, Seattle, WA, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - John D. Aitchison
- Department of Global Health, University of Washington, Seattle, WA, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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22
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Acharya D, Bavikatte AN, Ashok VV, Hegde SR, Macpherson CR, Scherf A, Vembar SS. Ectopic overexpression of Plasmodium falciparum DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development. Microbiol Spectr 2025; 13:e0088524. [PMID: 39868986 PMCID: PMC11878077 DOI: 10.1128/spectrum.00885-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 11/27/2024] [Indexed: 01/28/2025] Open
Abstract
Alba domain-containing proteins are ubiquitously found in archaea and eukaryotes. By binding to either DNA, RNA, or DNA:RNA hybrids, these proteins function in genome stabilization, chromatin organization, gene regulation, and/or translational modulation. In the malaria parasite Plasmodium falciparum, six Alba domain proteins PfAlba1-6 have been described, of which PfAlba1 has emerged as a "master regulator" of translation during parasite intra-erythrocytic development (IED). Given that a tight control of gene expression is especially important during IED, when malaria pathogenesis manifests, in this study, we focus on three other P. falciparum Albas, PfAlba2-4. Because genetic manipulation of the genomic loci of PfAlba2-4 was unsuccessful, we overexpressed each of these proteins from an episome under a strong constitutive promoter. We observed that PfAlba2 or PfAlba3 overexpression strongly reduced parasite growth and impacted IED stage transitions. In contrast, elevated levels of PfAlba4 were well-tolerated by the parasite. In keeping with this, differential gene expression analysis using RNA-seq of PfAlba2 or PfAlba3 overexpressing strains revealed a significant misregulation of mRNAs encoding virulence factors, such as those related to erythrocyte invasion; a general repression of var gene expression was also apparent. PfAlba4 overexpression, on the other hand, did not significantly perturb the steady-state transcriptome of IED stages and appeared to enhance var mRNA levels. Moreover, distinct sets of genes were targeted by each PfAlba for regulation. Taken together, this study highlights the nonredundant roles of PfAlba proteins in the P. falciparum IED, emphasizing their importance in subtelomeric chromatin biology and RNA regulation.IMPORTANCEThe malaria parasite Plasmodium falciparum tightly controls the expression of its genes at the epigenetic, transcriptional, post-transcriptional, and translational levels to synthesize essential proteins, including virulence factors, in a timely and spatially coordinated manner. A family of six proteins implicated in this process is called PfAlba, characterized by the presence of the DNA-, RNA- or DNA:RNA hybrid-binding Alba domain. To better understand the cellular pathways regulated by this protein family, we overexpressed three PfAlbas during P. falciparum intra-erythrocytic growth and found that high levels of PfAlba2 and PfAlba3 were detrimental to parasite development. This was accompanied by significant changes in the parasite's transcriptome, either with regards to mRNA steady-state levels or expression timing. PfAlba4 overexpression, on the other hand, was well-tolerated by the parasite. Overall, our results delineate specific pathways targeted by individual PfAlbas for regulation and link PfAlba2/PfAlba3 to mutually exclusive expression of the virulence-promoting surface antigen PfEMP1.
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Affiliation(s)
- Dimple Acharya
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | | | - Vishnu Vinayak Ashok
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Shubhada R. Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Cameron Ross Macpherson
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France
- CNRS ERM9195, Paris, France
- INSERM U1201, Paris, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France
- CNRS ERM9195, Paris, France
- INSERM U1201, Paris, France
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23
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Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Godoy Magalhaes L, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean KJ, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. NPJ DRUG DISCOVERY 2025; 2:3. [PMID: 40066064 PMCID: PMC11892419 DOI: 10.1038/s44386-025-00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 01/22/2025] [Indexed: 03/19/2025]
Abstract
Identification of novel drug targets is a key component of modern drug discovery. While antimalarial targets are often identified through the mechanism of action studies on phenotypically derived inhibitors, this method tends to be time- and resource-consuming. The discoverable target space is also constrained by existing compound libraries and phenotypic assay conditions. Leveraging recent advances in protein structure prediction, we systematically assessed the Plasmodium falciparum genome and identified 867 candidate protein targets with evidence of small-molecule binding and blood-stage essentiality. Of these, 540 proteins showed strong essentiality evidence and lack inhibitors that have progressed to clinical trials. Expert review and rubric-based scoring of this subset based on additional criteria such as selectivity, structural information, and assay developability yielded 27 high-priority antimalarial target candidates. This study also provides a genome-wide data resource for P. falciparum and implements a generalizable framework for systematically evaluating and prioritizing novel pathogenic disease targets.
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Affiliation(s)
| | - Daisy Chen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | | | | | - Anna Adam
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Selina Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Krypton Carolino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | - Lauren B. Coulson
- Holistic Drug Discovery and Development (H3D) Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Greg Durst
- Lgenia, Inc., 412 S Maple St, Fortville, IN USA
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY USA
| | - Lisl Esherick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Madeline A. Farringer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA USA
| | | | - Barbara Forte
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Tiqing Liu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | - Luma Godoy Magalhaes
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Anil K. Gupta
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Eva S. Istvan
- Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
| | - Tiantian Jiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | - Krittikorn Kumpornsin
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Karen Lobb
- Lgenia, Inc., 412 S Maple St, Fortville, IN USA
| | - Kyle J. McLean
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Igor M. R. Moura
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY USA
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY USA
| | - N. Connor Payne
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA USA
| | - Andrew Plater
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | | | - Jair L. Siqueira-Neto
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | | | - Robert L. Summers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | - Rumin Zhang
- Global Health Drug Discovery Institute, Beijing, China
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
| | | | - Brice Campo
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Beatriz Baragaña
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - James Duffy
- MMV Medicines for Malaria Venture, 1215, Geneva, Switzerland
| | - Ian H. Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Science, University of Dundee, Dundee, UK
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Case W. McNamara
- Calibr-Skaggs Institute for Innovative Medicines, a division of The Scripps Research Institute, La Jolla, CA USA
| | - Xiu Cheng
- Global Health Drug Discovery Institute, Beijing, China
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics & Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa
| | | | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY USA
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA USA
| | - Daniel E. Goldberg
- Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO USA
| | - Marcus C. S. Lee
- Division of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA USA
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24
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Yang S, Wei Y, Quansah E, Zhang Z, Da W, Wang B, Wang K, Sun D, Tao Z, Zhang C. Cas12a is competitive for gene editing in the malaria parasites. Microb Pathog 2025; 200:107340. [PMID: 39880137 DOI: 10.1016/j.micpath.2025.107340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/22/2025] [Accepted: 01/25/2025] [Indexed: 01/31/2025]
Abstract
Malaria, caused by the Plasmodium parasites, has always been one of the worst infectious diseases that threaten human health, making it necessary for us to study the genetic function and physiological mechanisms of Plasmodium parasites from the molecular level to find more effective ways of addressing the increasingly pressing threat. The CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) is an RNA-guided adaptive immune system, which has been extensively developed and used as a genome editing tool in many organisms, including Plasmodium parasites. However, due to the physiological characteristics and special genomic characteristics of Plasmodium parasites, most of the tools currently used for genome editing of Plasmodium parasites have not met expectations. CRISPR-Cas12a (also known as Cpf1), one of the CRISPR-Cas systems, has attracted considerable attention because of its characteristics of being used for biological diagnosis and multiple genome editing. Recent studies have shown that its unique properties fit the genetic makeup of Plasmodium parasites making it a promising tool for gene editing in these parasites. In this review, we have summarized the relevant content of the Cas12 family, especially the frequently used Cas12a, its advantages for gene editing, and the application prospects in Plasmodium parasites.
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Affiliation(s)
- Shijie Yang
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Yiming Wei
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Elvis Quansah
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Ziyu Zhang
- The First Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Weiran Da
- The First Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Bingjie Wang
- The First Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Kaige Wang
- The First Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Danhong Sun
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, People's Republic of China.
| | - Zhiyong Tao
- Key Laboratory of Infection and Immunity of Anhui Higher Education Institutes, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui, 233030, People's Republic of China.
| | - Chao Zhang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, People's Republic of China.
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25
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Smith CJ, Eavis H, Briggs C, Henrici R, Karpiyevich M, Ansbro MR, Hoshizaki J, van der Heden van Noort GJ, Ascher DB, Sutherland CJ, Lee MCS, Artavanis-Tsakonas K. Drug resistance-associated mutations in Plasmodium UBP-1 disrupt its essential deubiquitinating activity. J Biol Chem 2025; 301:108266. [PMID: 39909372 PMCID: PMC11927682 DOI: 10.1016/j.jbc.2025.108266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/19/2025] [Accepted: 01/30/2025] [Indexed: 02/07/2025] Open
Abstract
Deubiquitinating enzymes function to cleave ubiquitin (Ub) moieties from modified proteins, serving to maintain the pool of free Ub in the cell while simultaneously impacting the fate and function of a target protein. Like all eukaryotes, Plasmodium parasites rely on the dynamic addition and removal of Ub for their own growth and survival. While humans possess around 100 deubiquitinases, Plasmodium contains ∼20 putative Ub hydrolases, many of which bear little to no resemblance to those of other organisms. In this study, we characterize Plasmodium falciparum UBP-1, a large Ub hydrolase unique to Plasmodium spp., which has been linked to endocytosis and drug resistance. We demonstrate its Ub activity, linkage specificity, and assess the repercussions of point mutations associated with drug resistance on catalytic activity and parasite fitness. We confirm that the deubiquitinating activity of UBP-1 is essential for parasite survival, implicating an important role for Ub signaling in endocytosis.
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Affiliation(s)
- Cameron J Smith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Heledd Eavis
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Carla Briggs
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ryan Henrici
- Department of Immunology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Megan R Ansbro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | - David B Ascher
- University of Queensland, School of Chemistry and Molecular Biosciences, Queensland, Australia
| | - Colin J Sutherland
- Department of Immunology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
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26
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Okombo J, Fidock DA. Towards next-generation treatment options to combat Plasmodium falciparum malaria. Nat Rev Microbiol 2025; 23:178-191. [PMID: 39367132 PMCID: PMC11832322 DOI: 10.1038/s41579-024-01099-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2024] [Indexed: 10/06/2024]
Abstract
Malaria, which is caused by infection of red blood cells with Plasmodium parasites, can be fatal in non-immune individuals if left untreated. The recent approval of the pre-erythrocytic vaccines RTS, S/AS01 and R21/Matrix-M has ushered in hope of substantial reductions in mortality rates, especially when combined with other existing interventions. However, the efficacy of these vaccines is partial, and chemotherapy remains central to malaria treatment and control. For many antimalarial drugs, clinical efficacy has been compromised by the emergence of drug-resistant Plasmodium falciparum strains. Therefore, there is an urgent need for new antimalarial medicines to complement the existing first-line artemisinin-based combination therapies. In this Review, we discuss various opportunities to expand the present malaria treatment space, appraise the current antimalarial drug development pipeline and highlight examples of promising targets. We also discuss other approaches to circumvent antimalarial resistance and how potency against drug-resistant parasites could be retained.
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Affiliation(s)
- John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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27
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Nwankwo I, Ke H. Maintenance of pyrophosphate homeostasis in multiple subcellular compartments is essential in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.20.639246. [PMID: 40027813 PMCID: PMC11870574 DOI: 10.1101/2025.02.20.639246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Pyrophosphate is a byproduct of numerous cellular reactions that use ATP or other nucleoside triphosphates to synthesize DNA, RNA, protein, and other molecules. Its degradation into monophosphate is thus crucial for the survival and proliferation of all life forms. The human malaria parasite Plasmodium falciparum encodes two classes of pyrophosphatases to hydrolyze pyrophosphate. The first consists of P. falciparum proton pumping vacuolar pyrophosphatases (PfVP1 and PfVP2), which localize to the parasite's subcellular membranes and work as proton pumps. The second includes P. falciparum soluble pyrophosphatases (PfsPPases), which have not been well characterized. Interestingly, the gene locus of PfsPPase encodes two isoforms, PfsPPase1 (PF3D7_0316300.1) and PfsPPase2 (PF3D7_0316300.2). PfsPPase2 contains a 51- amino acid organellar localization peptide that is absent in PfsPPase1. Here, we combine reverse genetics and biochemical approaches to identify the localization of PfsPPase1 and PfsPPase2 and elucidate their individual functions. We show that PfsPPases are essential for the asexual blood stage. While PfsPPase1 solely localizes to the cytoplasm, PfsPPase2 exhibits multiple localizations including the mitochondrion, the apicoplast, and, to a lesser extent, the cytoplasm. Our data suggest that P. falciparum has taken a unique evolutionary trajectory in pyrophosphate metabolism by utilizing a leader sequence to direct sPPases to the mitochondrion and apicoplast. This differs from model eukaryotes as they generally encode multiple sPPases at distinct genetic loci to facilitate pyrophosphate degradation in cytosolic and organellar compartments. Our study highlights PfsPPases as promising targets for the development of novel antimalarial drugs.
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28
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Ramaprasad A, Blackman MJ. A scaleable inducible knockout system for studying essential gene function in the malaria parasite. Nucleic Acids Res 2025; 53:gkae1274. [PMID: 39739757 PMCID: PMC11879119 DOI: 10.1093/nar/gkae1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 11/14/2024] [Accepted: 12/12/2024] [Indexed: 01/02/2025] Open
Abstract
The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously. To overcome this, we have developed SHIFTiKO (frameshift-based trackable inducible knockout), a novel scaleable strategy that uses short, easy-to-construct, barcoded repair templates to insert loxP sites around short regions in target genes. Induced DiCre-mediated excision of the flanked region causes a frameshift mutation resulting in genetic ablation of gene function. Dual DNA barcodes inserted into each mutant enables verification of successful modification and induced excision at each locus and collective phenotyping of the mutants, not only across multiple replication cycles to assess growth fitness but also within a single cycle to identify specific phenotypic impairments. As a proof of concept, we have applied SHIFTiKO to screen the functions of malarial rhomboid proteases, successfully identifying their blood stage-specific essentiality. SHIFTiKO thus offers a powerful platform to conduct inducible phenotypic screens to study essential gene function at scale in the malaria parasite.
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Affiliation(s)
- Abhinay Ramaprasad
- Malaria Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT London, UK
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29
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Moon RW, Bushell ESC. Not just monkey business. Science 2025; 387:582-583. [PMID: 39913602 DOI: 10.1126/science.adv2328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2025]
Abstract
Functional genomics in malaria unlocks comparative biology across the family tree.
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Affiliation(s)
- Robert W Moon
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ellen S C Bushell
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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30
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Sreenivasamurthy SK, Baptista CG, West CM, Blader IJ, Dvorin JD. PfFBXO1 is essential for inner membrane complex formation in Plasmodium falciparum during both asexual and transmission stages. Commun Biol 2025; 8:190. [PMID: 39915671 PMCID: PMC11802861 DOI: 10.1038/s42003-025-07619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 01/29/2025] [Indexed: 02/09/2025] Open
Abstract
Plasmodium species replicate via schizogony, which involves asynchronous nuclear divisions followed by semi-synchronous segmentation and cytokinesis. Successful segmentation requires a double-membranous structure known as the inner membrane complex (IMC). Here we demonstrate that PfFBXO1 (PF3D7_0619700) is critical for both asexual segmentation and gametocyte maturation. In Toxoplasma gondii, the FBXO1 homolog, TgFBXO1, is essential for the development of the daughter cell scaffold and a component of the daughter cell IMC. We demonstrate PfFBXO1 forming a similar IMC initiation scaffold near the apical region of developing merozoites and unilaterally positioned in gametocytes of P. falciparum. While PfFBXO1 initially localizes to the apical region of dividing parasites, it displays an IMC-like localization as segmentation progresses. Similarly, PfFBXO1 localizes to the IMC region in gametocytes. Following inducible knockout of PfFBXO1, parasites undergo abnormal segmentation and karyokinesis, generating inviable daughters. PfFBXO1-deficient gametocytes are abnormally shaped and fail to fully mature. Proteomic analysis identified PfSKP1 as one of PfBXO1's stable interacting partners, while other major proteins included multiple IMC pellicle and membrane proteins. We hypothesize that PfFBXO1 is necessary for IMC biogenesis, chromosomal maintenance, vesicular transport, and ubiquitin-mediated translational regulation of proteins in both sexual and asexual stages of P. falciparum.
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Affiliation(s)
- Sreelakshmi K Sreenivasamurthy
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Carlos Gustavo Baptista
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, NY, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Ira J Blader
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, NY, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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31
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Elsworth B, Ye S, Dass S, Tennessen JA, Sultana Q, Thommen BT, Paul AS, Kanjee U, Grüring C, Ferreira MU, Gubbels MJ, Zarringhalam K, Duraisingh MT. The essential genome of Plasmodium knowlesi reveals determinants of antimalarial susceptibility. Science 2025; 387:eadq6241. [PMID: 39913579 PMCID: PMC12104972 DOI: 10.1126/science.adq6241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 12/05/2024] [Indexed: 02/09/2025]
Abstract
Measures to combat the parasites that cause malaria have become compromised because of reliance on a small arsenal of drugs and emerging drug resistance. We conducted a transposon mutagenesis screen in the primate malaria parasite Plasmodium knowlesi, producing the most complete classification of gene essentiality in any Plasmodium spp. to date, with the resolution to define truncatable genes. We found conservation in the druggable genome between Plasmodium spp. and divergences in mitochondrial metabolism. Perturbation analyses with the frontline antimalarial artemisinin revealed modulators that both increase and decrease drug susceptibility. Our findings aid prioritization of drug and vaccine targets for the Plasmodium vivax clade and reveal mechanisms of resistance that can inform therapeutic development.
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Affiliation(s)
- Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration: Silver Spring, MD, USA
| | - Sida Ye
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
- Department of Mathematics, University of Massachusetts Boston: Boston, MA, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston: Boston, MA, USA
| | - Sheena Dass
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Jacob A. Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Qudseen Sultana
- Center for Personalized Cancer Therapy, University of Massachusetts Boston: Boston, MA, USA
- Department of Computer Science, University of Massachusetts Boston: Boston, MA, USA
| | - Basil T. Thommen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Christof Grüring
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo: São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon: Lisbon, Portugal
| | | | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston: Boston, MA, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston: Boston, MA, USA
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health: Boston, MA
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32
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Oberstaller J, Xu S, Naskar D, Zhang M, Wang C, Gibbons J, Pires CV, Mayho M, Otto TD, Rayner JC, Adams JH. Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites. Science 2025; 387:eadq7347. [PMID: 39913589 DOI: 10.1126/science.adq7347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 12/05/2024] [Indexed: 03/27/2025]
Abstract
Malaria parasites are highly divergent from model eukaryotes. Large-scale genome engineering methods effective in model organisms are frequently inapplicable, and systematic studies of gene function are few. We generated more than 175,000 transposon insertions in the Plasmodium knowlesi genome, averaging an insertion every 138 base pairs, and used this "supersaturation" mutagenesis to score essentiality for 98% of genes. The density of mutations allowed mapping of putative essential domains within genes, providing a completely new level of genome annotation for any Plasmodium species. Although gene essentiality was largely conserved across P. knowlesi, Plasmodium falciparum, and rodent malaria model Plasmodium berghei, a large number of shared genes are differentially essential, revealing species-specific adaptations. Our results indicated that Plasmodium essential gene evolution was conditionally linked to adaptive rewiring of metabolic networks for different hosts.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Shulin Xu
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Deboki Naskar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Min Zhang
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Chengqi Wang
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Justin Gibbons
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Camilla Valente Pires
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Matthew Mayho
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas D Otto
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Laboratory of Pathogens and Host Immunity, Centre National de la Recherche Scientifique, and Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John H Adams
- Center for Global Health and Interdisciplinary Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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33
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Rawat M, Padalino G, Adika E, Okombo J, Yeo T, Brancale A, Fidock DA, Hoffmann KF, Lee MCS. Quinoxaline-based anti-schistosomal compounds have potent anti-plasmodial activity. PLoS Pathog 2025; 21:e1012216. [PMID: 39899599 PMCID: PMC11809919 DOI: 10.1371/journal.ppat.1012216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 02/10/2025] [Accepted: 01/14/2025] [Indexed: 02/05/2025] Open
Abstract
The human pathogens Plasmodium and Schistosoma are each responsible for over 200 million infections annually, especially in low- and middle-income countries. There is a pressing need for new drug targets for these diseases, driven by emergence of drug-resistance in Plasmodium and an overall dearth of drug targets against Schistosoma. Here, we explored the opportunity for pathogen-hopping by evaluating a series of quinoxaline-based anti-schistosomal compounds for their activity against P. falciparum. We identified compounds with low nanomolar potency against 3D7 and multidrug-resistant strains. In vitro resistance selections using wildtype and mutator P. falciparum lines revealed a low propensity for resistance. Only one of the series, compound 22, yielded resistance mutations, including point mutations in a non-essential putative hydrolase pfqrp1, as well as copy number amplification of a phospholipid-translocating ATPase, pfatp2, a potential target. Notably, independently generated CRISPR-edited mutants in pfqrp1 also showed resistance to compound 22 and a related analogue. Moreover, previous lines with pfatp2 copy number variations were similarly less susceptible to challenge with the new compounds. Finally, we examined whether the predicted hydrolase activity of PfQRP1 underlies its mechanism of resistance, showing that both mutation of the putative catalytic triad and a more severe loss of function mutation elicited resistance. Collectively, we describe a compound series with potent activity against two important pathogens and their potential target in P. falciparum.
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Affiliation(s)
- Mukul Rawat
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gilda Padalino
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
- Swansea University Medical School, Swansea, United Kingdom
| | - Edem Adika
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrea Brancale
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, United States of America
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Karl F. Hoffmann
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Marcus C. S. Lee
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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34
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Hildebrandt F, N Matias A, Treeck M. A CRISPR view on genetic screens in Toxoplasma gondii. Curr Opin Microbiol 2025; 83:102577. [PMID: 39778479 DOI: 10.1016/j.mib.2024.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/04/2024] [Accepted: 12/12/2024] [Indexed: 01/11/2025]
Abstract
Genome editing technologies, such as CRISPR-Cas9, have revolutionised the study of genes in a variety of organisms, including unicellular parasites. Today, the CRISPR-Cas9 technology is vastly applied in high-throughput screens to investigate interactions between the Apicomplexan parasite Toxoplasma gondii and its hosts. In vitro and in vivo T. gondii screens performed in naive and restrictive conditions have led to the discovery of essential and fitness-conferring T. gondii genes, as well as factors important for virulence and dissemination. Recent studies have adapted the CRISPR-Cas9 screening technology to study T. gondii genes based on phenotypes unrelated to parasite survival. These advances were achieved by using conditional systems coupled with imaging, as well as single-cell RNA sequencing and phenotypic selection. Here, we review the state-of-the-art of CRISPR-Cas9 screening technologies with a focus on T. gondii, highlighting strengths, current limitations and future avenues for its development, including its application to other Apicomplexan species.
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Affiliation(s)
- Franziska Hildebrandt
- Gulbenkian Institute for Molecular Medicine (GIMM), Avenida Professor Egas Moniz, Lisboa, Portugal
| | - Ana N Matias
- Gulbenkian Institute for Molecular Medicine (GIMM), Avenida Professor Egas Moniz, Lisboa, Portugal
| | - Moritz Treeck
- Gulbenkian Institute for Molecular Medicine (GIMM), Avenida Professor Egas Moniz, Lisboa, Portugal.
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Fukumoto J, Yoshida M, Tokuoka SM, H Hayakawa ES, Miyazaki S, Sakura T, Inaoka DK, Kita K, Usukura J, Shindou H, Tokumasu F. Pivotal roles of Plasmodium falciparum lysophospholipid acyltransferase 1 in cell cycle progression and cytostome internalization. Commun Biol 2025; 8:142. [PMID: 39880906 PMCID: PMC11779973 DOI: 10.1038/s42003-025-07564-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 01/16/2025] [Indexed: 01/31/2025] Open
Abstract
The rapid intraerythrocytic replication of Plasmodium falciparum, a deadly species of malaria parasite, requires a quick but constant supply of phospholipids to support marked cell membrane expansion. In the malarial parasite, many enzymes functioning in phospholipid synthesis pathway have not been identified or characterized. Here, we identify P. falciparum lysophospholipid acyltransferase 1 (PfLPLAT1) and show that PfLPLAT1 is vital for asexual parasite cell cycle progression and cytostome internalization. Deficiency in PfLPLAT1 results in decreased parasitemia and prevents transition to the schizont stage. Parasites lacking PfLPLAT1 also exhibit distinctive omega-shaped vacuoles, indicating disrupted cytostome function. Transcriptomic analyses suggest that this deficiency impacts DNA replication and cell cycle regulation. Mass spectrometry-based enzyme assay and lipidomic analysis demonstrate that recombinant PfLPLAT1 exhibits lysophospholipid acyltransferase activity with a preference for unsaturated fatty acids as its acyl donors and lysophosphatidic acids as an acceptor, with its conditional knockout leading to abnormal lipid composition and marked morphological and developmental changes including stage arrest. These findings highlight PfLPLAT1 as a potential target for antimalarial therapy, particularly due to its unique role and divergence from human orthologs.
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Affiliation(s)
- Junpei Fukumoto
- Department of Cellular Architecture Studies, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
- Research Fellow of Japan Society for the Promotion of Science, Nagasaki, Japan.
- Division of Malaria Research, Proteo-Science Center, Ehime University, Ehime, Japan.
| | - Minako Yoshida
- Department of Cellular Architecture Studies, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Molecular Infection Dynamics, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Suzumi M Tokuoka
- Department of Lipidomics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Eri Saki H Hayakawa
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Shinya Miyazaki
- Department of Cellular Architecture Studies, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Jiro Usukura
- Institute of Materials and Systems for Sustainability, Nagoya University, Aichi, Japan
| | - Hideo Shindou
- Department of Lipid Life Science, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Medical Lipid Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fuyuki Tokumasu
- Department of Cellular Architecture Studies, Division of Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
- Department of Laboratory Sciences, Graduate School of Health Sciences, Gunma University, Gunma, Japan.
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Rachuri S, Nepal B, Shukla A, Ramanathan A, Morrisey JM, Daly T, Mather MW, Bergman LW, Kortagere S, Vaidya AB. Mutational analysis of an antimalarial drug target, PfATP4. Proc Natl Acad Sci U S A 2025; 122:e2403689122. [PMID: 39773028 PMCID: PMC11745376 DOI: 10.1073/pnas.2403689122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 11/24/2024] [Indexed: 01/11/2025] Open
Abstract
Among new antimalarials discovered over the past decade are multiple chemical scaffolds that target Plasmodium falciparum P-type ATPase (PfATP4). This essential protein is a Na+ pump responsible for the maintenance of Na+ homeostasis. PfATP4 belongs to the type two-dimensional (2D) subfamily of P-type ATPases, for which no structures have been determined. To gain better insight into the structure/function relationship of this validated drug target, we generated a homology model of PfATP4 based on sarco/endoplasmic reticulum Ca2+ ATPase, a P2A-type ATPase, and refined the model using molecular dynamics in its explicit membrane environment. This model predicted several residues in PfATP4 critical for its function, as well as those that impart resistance to various PfATP4 inhibitors. To validate our model, we developed a genetic system involving merodiploid states of PfATP4 in which the endogenous gene was conditionally expressed, and the second allele was mutated to assess its effect on the parasite. Our model predicted residues involved in Na+ coordination as well as the phosphorylation cycle of PfATP4. Phenotypic characterization of these mutants involved assessment of parasite growth, localization of mutated PfATP4, response to treatment with known PfATP4 inhibitors, and evaluation of the downstream consequences of Na+ influx. Our results were consistent with modeled predictions of the essentiality of the critical residues. Additionally, our approach confirmed the phenotypic consequences of resistance-associated mutations as well as a potential structural basis for the fitness cost associated with some mutations. Taken together, our approach provides a means to explore the structure/function relationship of essential genes in haploid organisms.
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Affiliation(s)
- Swaksha Rachuri
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Binod Nepal
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Anurag Shukla
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Aarti Ramanathan
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Joanne M. Morrisey
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Thomas Daly
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Michael W. Mather
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Lawrence W. Bergman
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
| | - Akhil B. Vaidya
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, Philadelphia, PA19129
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Jonsdottir T, Paoletta M, Ishizaki T, Hernandez S, Ivanova M, Herrera Curbelo A, Saiki P, Selinger M, Das D, Henriksson J, Bushell EC. A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei. Nucleic Acids Res 2025; 53:gkaf005. [PMID: 39844455 PMCID: PMC11754126 DOI: 10.1093/nar/gkaf005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 11/30/2024] [Accepted: 01/09/2025] [Indexed: 01/24/2025] Open
Abstract
Many Plasmodium genes remain uncharacterized due to low genetic tractability. Previous large-scale knockout screens have only been able to target about half of the genome in the more genetically tractable rodent malaria parasite Plasmodium berghei. To overcome this limitation, we have developed a scalable CRISPR system called P. berghei high-throughput (PbHiT), which uses a single cloning step to generate targeting vectors with 100-bp homology arms physically linked to a guide RNA (gRNA) that effectively integrate into the target locus. We show that PbHiT coupled with gRNA sequencing robustly recapitulates known knockout mutant phenotypes in pooled transfections. Furthermore, we provide an online resource of knockout and tagging designs to target the entire P. berghei genome and scale-up vector production using a pooled ligation approach. This work presents for the first time a tool for high-throughput CRISPR screens in Plasmodium for studying the parasite's biology at scale.
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Affiliation(s)
- Thorey K Jonsdottir
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Martina S Paoletta
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA–CONICET, de Los Reseros y Dr. Nicolás Repetto s/n, P.O. Box 25 (B1712WAA), Hurlingham, Buenos Aires, Argentina
| | - Takahiro Ishizaki
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Parasitology and Zoology Unit, Department of Infection and Pathology, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai-midorimachi, Ebetsu, Hokkaido, 069-8501, Japan
| | - Sophia Hernandez
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Maria Ivanova
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Alicia Herrera Curbelo
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Paulina A Saiki
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Martin Selinger
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
| | - Debojyoti Das
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Division of Children’s and Women’s Health (BKH), Department of Biomedical and Clinical Sciences (BKV), Linköping University, Sjukhusvägen Building 511, 581 83 Linköping, Sweden
| | - Johan Henriksson
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Umeå Center for Microbial Research (UCMR), Umeå University, Universitetstorget 4, 901 87 Umeå, Sweden
- IceLab, Umeå University, Naturvetarhuset, Universitetsvägen, 901 87 Umeå, Sweden
| | - Ellen S C Bushell
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Department of Molecular Biology, Umeå University, Försörjningsvägen 2A, 901 87 Umeå, Sweden
- Umeå Center for Microbial Research (UCMR), Umeå University, Universitetstorget 4, 901 87 Umeå, Sweden
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Liu Y, Cheng S, He G, He D, Wang D, Wang S, Chen L, Zhu L, Feng Y, Cui L, Cao Y, Zhu X. An inner membrane complex protein IMC1g in Plasmodium berghei is involved in asexual stage schizogony and parasite transmission. mBio 2025; 16:e0265224. [PMID: 39576115 PMCID: PMC11708024 DOI: 10.1128/mbio.02652-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 10/23/2024] [Indexed: 01/11/2025] Open
Abstract
The inner membrane complex (IMC), a double-membrane organelle underneath the plasma membrane in apicomplexan parasites, plays a significant role in motility and invasion and confers shape to the cell. We characterized the function of PbIMC1g, a component of the IMC1 family member in Plasmodium berghei. PbIMC1g is recruited to the IMC in late schizonts, activated gametocytes, and ookinetes. Pairwise yeast two-hybrid assays demonstrate that PbIMC1g interacts with IMC1c, a component of the PHIL1 complex, and the core sub-repeat motif "EKI(V)V(I)EVP" in PbIMC1g is essential for this interaction. Localization of PbIMC1g to the IMC was dependent on its IMCp domain, while its C-terminus and palmitoylation sites were required for the full efficiency of proper IMC targeting. PbIMC1g is required for asexual stage development, and its conditional knockdown resulted in a defect in schizogony. Additionally, PbIMC1g was also important for male gametogenesis and ookinete development. As an IMC component that assists in anchoring the glideosome to the subpellicular network, PbIMC1g was also involved in ookinete motility and mosquito midgut invasion. IMC1g from the human parasite Plasmodium vivax could functionally replace PbIMC1g in P. berghei, confirming the evolutionary conservation of IMC1g proteins in Plasmodium spp. Together, this work reveals an essential role of IMC1g in the parasite life cycle and suggests that IMC1 family members likely contribute to parasite gliding and invasion. IMPORTANCE The malaria parasite's inner membrane complex is critical to maintain its structural integrity and motility. Here, we identified the function of the IMC1g protein, a member of the IMC1 family, in invasive and proliferative stages of P. berghei. We found that the IMCp domain of PbIMC1g is critical for proper IMC targeting, and PbIMC1g interacts with PbIMC1c. Conditional knockdown of PbIMC1g expression affects schizogony, gametogenesis, and ookinete conversion. PbIMC1g interacts with IMC1c to firmly anchor the glideosome to the subpellicular network. Additionally, we confirmed that IMC1g is functionally conserved in Plasmodium spp. These data reveal the function of IMC1g protein in anchoring the glideosome, providing further insight into the mechanism of the glideosome function.
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Affiliation(s)
- Yinjie Liu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Shitong Cheng
- Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gang He
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Dawei He
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Duo Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Sicong Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Lumeng Chen
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Liying Zhu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yonghui Feng
- Department of Laboratory Medicine, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xiaotong Zhu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
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Shi Q, Wang C, Yang W, Ma X, Tang J, Zhang J, Zhu G, Wang Y, Liu Y, He X. Plasmodium falciparum transcription factor AP2-06B is mutated at high frequency in Southeast Asia but does not associate with drug resistance. Front Cell Infect Microbiol 2025; 14:1521152. [PMID: 39835275 PMCID: PMC11744005 DOI: 10.3389/fcimb.2024.1521152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/02/2024] [Indexed: 01/22/2025] Open
Abstract
Introduction A continuing challenge for malaria control is the ability of Plasmodium falciparum to develop resistance to antimalarial drugs. Members within the Plasmodium transcription factor family AP2 regulate the growth and development of the parasite, and are also thought to be involved in unclear aspects of drug resistance. Here we screened for single nucleotide polymorphisms (SNPs) within the AP2 family and identified 6 non-synonymous mutations within AP2-06B (PF3D7_0613800), with allele frequencies greater than 0.05. One mutation, K3124R, was located in a PfAP2-06B AP2 domain. Methods To investigate transcriptional regulation by PfAP2-06B, ChIP-seq assays were performed on 3D7/PfAP2-06B-GFP schizonts using antibodies against GFP. The DNA sequences of the artemisinin-resistant CWX and the quinoline-resistant strains PfDd2 and Pf7G8 were analyzed for the genetic diversity of AP2-06B, compared with the Pf3D7 strain as a reference sequence. To determine whether AP2-06B can alter the expression of pfk13 and pfcrt, as well as cause artemisinin and quinoline resistance in Plasmodium, we generated both a K3124R mutation and conditional knockdown of AP2-06B in Pf3D7 using CRISPR/Cas9-mediated genome editing. Results ChIP-Seq analysis showed that AP2-06B can bind to the loci of the Plasmodium genes pfk13 and pfcrt. The AP2-06B K3124R mutation was also found in the artemisinin-resistant parasite strain CWX and the chloroquine-resistant strains Dd2 and 7G8. Contrary to expectation, Pf3D7 Plasmodium lines modified by either K3124R mutation of AP2-06B or conditional knockdown of AP2-06B did not have altered sensitivity to artemisinin or quinolines by modulating pfk13 or pfcrt expression. Discussion AP2-06B was predicted to be associated with artemisinin and quinoline resistance, but no change in resistance was observed after mutation or conditional knockdown. Given the multigenic nature of resistance, it might be difficult to recreate a resistance phenotype. In conclusion, whether AP2-06B regulates the development of artemisinin or quinoline resistance remains to be studied.
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Affiliation(s)
- Qiyang Shi
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai, China
| | - Wenluan Yang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Xiaoqin Ma
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Jiayao Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yinlong Wang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
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Stewart LB, Escolar EL, Philpott J, Claessens A, Amambua-Ngwa A, Conway DJ. Multiplication rate variation of malaria parasites from hospital cases and community infections. Sci Rep 2025; 15:666. [PMID: 39753639 PMCID: PMC11698726 DOI: 10.1038/s41598-024-82916-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 12/10/2024] [Indexed: 01/06/2025] Open
Abstract
The significance of multiplication rate variation in malaria parasites needs to be determined, particularly for Plasmodium falciparum, the species that causes most virulent infections. To investigate this, parasites from cases presenting to hospital in The Gambia and from local community infections were culture-established and then tested under exponential growth conditions in a standardised six-day multiplication rate assay. The multiplication rate distribution was lower than seen previously in clinical isolates from another area in West Africa where infection is more highly endemic. Multiplication rates were higher in cultured isolates derived from hospital cases (N = 23, mean = 2.9-fold per 48 h) than in those from community infections (N = 11, mean = 1.8-fold)(Mann-Whitney P < 0.001). There was a positive correlation between levels of parasitaemia in peripheral blood of sampled individuals and multiplication rates of the isolates in culture (Spearman's rho = 0.45, P = 0.017). There was no significant difference between isolates containing single parasite genotypes or multiple genotypes at the time of assay, suggesting that parasites do not modify their multiplication rates in response to the presence of different genotypes. It will be important to uncover the mechanisms of this intrinsic multiplication rate variation, and to also investigate the epidemiological distribution and potential associations with infection phenotypes in other populations.
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Affiliation(s)
- Lindsay B Stewart
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Elena Lantero Escolar
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - James Philpott
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Antoine Claessens
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
- LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Alfred Amambua-Ngwa
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - David J Conway
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
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Walunj SB, Mishra G, Wagstaff KM, Patankar S, Jans DA. The Ivermectin Related Compound Moxidectin Can Target Apicomplexan Importin α and Limit Growth of Malarial Parasites. Cells 2025; 14:39. [PMID: 39791740 PMCID: PMC11720742 DOI: 10.3390/cells14010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 12/22/2024] [Accepted: 12/29/2024] [Indexed: 01/12/2025] Open
Abstract
Signal-dependent transport into and out of the nucleus mediated by members of the importin (IMP) superfamily is crucial for eukaryotic function, with inhibitors targeting IMPα being of key interest as anti-infectious agents, including against the apicomplexan Plasmodium species and Toxoplasma gondii, causative agents of malaria and toxoplasmosis, respectively. We recently showed that the FDA-approved macrocyclic lactone ivermectin, as well as several other different small molecule inhibitors, can specifically bind to and inhibit P. falciparum and T. gondii IMPα functions, as well as limit parasite growth. Here we focus on the FDA-approved antiparasitic moxidectin, a structural analogue of ivermectin, for its IMPα-targeting and anti-apicomplexan properties for the first time. We use circular dichroism and intrinsic tryptophan fluorescence measurements to show that moxidectin can bind directly to apicomplexan IMPαs, thereby inhibiting their key binding functions at low μM concentrations, as well as possessing anti-parasitic activity against P. falciparum in culture. The results imply a class effect in terms of IMPα's ability to be targeted by macrocyclic lactone compounds. Importantly, in the face of rising global emergence of resistance to approved anti-parasitic agents, the findings highlight the potential of moxidectin and possibly other macrocyclic lactone compounds as antimalarial agents.
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Affiliation(s)
- Sujata B. Walunj
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; (S.B.W.); (K.M.W.)
- Molecular Parasitology Laboratory, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (G.M.); (S.P.)
| | - Geetanjali Mishra
- Molecular Parasitology Laboratory, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (G.M.); (S.P.)
| | - Kylie M. Wagstaff
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; (S.B.W.); (K.M.W.)
| | - Swati Patankar
- Molecular Parasitology Laboratory, Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (G.M.); (S.P.)
| | - David A. Jans
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; (S.B.W.); (K.M.W.)
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Le Berre M, Tubiana T, Reuterswärd Waldner P, Lazar N, Li de la Sierra-Gallay I, Santos JM, Llinás M, Nessler S. Structural characterization of the ACDC domain from ApiAP2 proteins, a potential molecular target against apicomplexan parasites. Acta Crystallogr D Struct Biol 2025; 81:38-48. [PMID: 39820027 PMCID: PMC11740583 DOI: 10.1107/s2059798324012518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Accepted: 12/28/2024] [Indexed: 01/19/2025] Open
Abstract
The apicomplexan AP2 (ApiAP2) proteins are the best characterized family of DNA-binding proteins in Plasmodium spp. malaria parasites. Apart from the AP2 DNA-binding domain, there is little sequence similarity between ApiAP2 proteins. However, a conserved AP2-coincident domain mostly at the C-terminus (ACDC domain) is observed in a subset of the ApiAP2 proteins. The structure and function of this domain remain unknown. We report two crystal structures of ACDC domains derived from distinct Plasmodium ApiAP2 proteins, revealing a conserved, unique, noncanonical, four-helix bundle architecture. We used these structures to perform in silico docking calculations against a library of known antimalarial compounds and identified potential small-molecule ligands that bind in a highly conserved hydrophobic pocket that is present in all apicomplexan ACDC domains. These ligands provide a new molecular basis for the future design of ACDC inhibitors.
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Affiliation(s)
- Marine Le Berre
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
| | - Thibault Tubiana
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
| | - Philippa Reuterswärd Waldner
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State UniversityState CollegePA16802USA
- Huck Center for Malaria ResearchThe Pennsylvania State UniversityState CollegePA16802USA
| | - Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
| | - Joana M. Santos
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
| | - Manuel Llinás
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State UniversityState CollegePA16802USA
- Huck Center for Malaria ResearchThe Pennsylvania State UniversityState CollegePA16802USA
- Department of ChemistryThe Pennsylvania State UniversityState CollegePA16802USA
| | - Sylvie Nessler
- Institute for Integrative Biology of the Cell (I2BC)Université Paris-SaclayCEA, CNRS91198Gif-sur-YvetteFrance
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Šťastný D, Balleková A, Tahotná D, Pokorná L, Holič R, Humpolíčková J, Griač P. Characterization of two Plasmodium falciparum lipid transfer proteins of the Sec14/CRAL-TRIO family. Biochim Biophys Acta Mol Cell Biol Lipids 2025; 1870:159572. [PMID: 39426587 DOI: 10.1016/j.bbalip.2024.159572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/11/2024] [Accepted: 10/13/2024] [Indexed: 10/21/2024]
Abstract
Invasion of human red blood cells by the malaria parasite Plasmodium falciparum is followed by dramatic modifications of erythrocytes properties, including de novo formation of new membrane systems. Lipid transfer proteins from both the parasite and the host cell are most likely an important part of those membrane remodeling processes. Using bioinformatics and in silico structural analysis, we have identified five P. falciparum potential lipid transfer proteins containing cellular retinaldehyde binding - triple functional domain (CRAL-TRIO). Two of these proteins, C6KTD4, encoded by the PF3D7_0629900 gene and Q8II87, encoded by the PF3D7_1127600 gene, were studied in more detail. In vitro lipid transfer assays using recombinant C6KTD4 and Q8II87 confirmed that these proteins are indeed bona fide lipid transfer proteins. C6KTD4 transfers sterols, phosphatidylinositol 4,5 bisphosphate, and, to some degree, also phosphatidylcholine between two membrane compartments. Q8II87 possesses phosphatidylserine transfer activity in vitro. In the yeast model, the expression of P. falciparumQ8II87 protein partially complements the absence of Sec14p and its closest homologue, Sfh1p. C6KTD4 protein can substitute for the collective essential function of oxysterol-binding related proteins. According to published whole genome studies in P. falciparum, absence of C6KTD4 and Q8II87 proteins has severe consequences for parasite viability. Therefore, CRAL-TRIO lipid transfer proteins of P. falciparum are potential targets of novel antimalarials, in search for which the yeast model expressing these proteins could be a valuable tool.
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Affiliation(s)
- Dominik Šťastný
- Centre of Biosciences, Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Alena Balleková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Dana Tahotná
- Centre of Biosciences, Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Lucia Pokorná
- Centre of Biosciences, Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Roman Holič
- Centre of Biosciences, Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Peter Griač
- Centre of Biosciences, Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia.
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Pires CV, Chawla J, Sollelis L, Oberstaller J, Zhang M, Wang C, Gibbons J, Rayner JC, Otto TD, Marti M, Adams JH. Genetic factors regulating Plasmodium falciparum gametocytogenesis identified by phenotypic screens. Sci Rep 2024; 14:31010. [PMID: 39730700 PMCID: PMC11680961 DOI: 10.1038/s41598-024-82133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 12/03/2024] [Indexed: 12/29/2024] Open
Abstract
Successful transmission of Plasmodium falciparum from one person to another relies on the complete intraerythrocytic development of non-pathogenic sexual gametocytes infectious for anopheline mosquitoes. Understanding the genetic factors that regulate gametocyte development is vital for identifying transmission-blocking targets in the malaria parasite life cycle. Toward this end, we conducted a forward genetic study to characterize the development of gametocytes from sexual commitment to mature stage V. We described a new analysis pipeline for the piggyBac transposon-based mutagenesis phenotypic screen to identify genes that influence both early and late gametocyte stages. We classified individual mutants that increased or decreased parasite abundance as the hypoproducer and hyperproducer phenotypes, respectively, revealing distinctive temporal genetic factors early and late in the sexual development cycle. The study identifies that disruption in factors involved in transcription, protein trafficking and DNA repair are associated with decreasing gametocyte production, while modifications in phosphatase activity are linked to hyperproduction of gametocytes. Our study provides an optimized approach on genotype-phenotype evaluation, offering a new resource for understanding potential targets for therapeutic intervention strategies to disrupt transmission.
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Affiliation(s)
- Camilla V Pires
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Jyotsna Chawla
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Lauriane Sollelis
- Institute of Parasitology Zurich, VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jenna Oberstaller
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Min Zhang
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Chengqi Wang
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Justin Gibbons
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Thomas D Otto
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Institute of Parasitology Zurich, VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - John H Adams
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, FL, USA.
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Ritaparna P, Dhal AK, Mahapatra RK. An in-silico study of FIKK9.5 protein of Plasmodium falciparum for identification of therapeutics. J Biomol Struct Dyn 2024:1-14. [PMID: 39727019 DOI: 10.1080/07391102.2024.2446671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/04/2024] [Indexed: 12/28/2024]
Abstract
The FIKK protein family, encompassing 21 serine-threonine protein kinases, is a distinctive cluster exclusive to the Apicomplexa phylum. Predominantly located in Plasmodium falciparum which is a malarial parasite, with a solitary gene identified in a distinct apicomplexan species, this family derives its nomenclature from - phenylalanine, isoleucine, lysine, lysine (FIKK), a conserved amino acid motif. Integral to the parasite's life cycle and consequential to malaria pathogenesis, the absence of orthologous proteins in eukaryotic organisms designates it as a promising antimalarial drug target. Among the FIKKs, FIKK9.5 plays a pivotal role in the parasite's development within red blood cells (RBCs). This investigation acquired the three-dimensional structure of FIKK9.5 and its ligands through extensive database searches and literature review. Computational screening of natural phytochemicals derived from plants traditionally used in antimalarial remedies was conducted by employing the Glide docking suite. AutoDock Vina was utilized to discern the inhibitor exhibiting optimal binding affinity. Subsequently, Molecular Dynamics (MD) simulations employing GROMACS validated Rufigallol as the most potent inhibitory compound against FIKK9.5. The robustness of the protein-ligand complex was scrutinized through a 200 nanosecond molecular dynamics (MD) trajectory. Trajectory analysis and determination of binding free energies were accomplished using MM-GBSA and MM-PBSA approaches. The ligand-binding exhibited sustained stability throughout the simulation, manifesting an approximate binding free energy of -25.5986 kcal/mol. This comprehensive computational study lays the groundwork for potential experimental validation in the laboratory, paving the way for the development of novel therapeutics targeting FIKK9.5 in the pursuit of innovative antimalarial.
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Affiliation(s)
- Prajna Ritaparna
- School of Biotechnology, KIIT Deemed To be University, Bhubaneswar, Odisha, India
- National Innovation Foundation-India, TBI-KIIT, Bhubaneswar, Odisha, India
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed To be University, Bhubaneswar, Odisha, India
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Zhang Z, Lyu M, Han X, Bandara S, Cui M, Istvan ES, Geng X, Tringides ML, Gregor WD, Miyagi M, Oberstaller J, Adams JH, Zhang Y, Nieman MT, von Lintig J, Goldberg DE, Yu EW. The Plasmodium falciparum NCR1 transporter is an antimalarial target that exports cholesterol from the parasite's plasma membrane. SCIENCE ADVANCES 2024; 10:eadq6651. [PMID: 39693420 PMCID: PMC11654669 DOI: 10.1126/sciadv.adq6651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 11/12/2024] [Indexed: 12/20/2024]
Abstract
Malaria, a devastating parasitic infection, is the leading cause of death in many developing countries. Unfortunately, the most deadliest causative agent of malaria, Plasmodium falciparum, has developed resistance to nearly all currently available antimalarial drugs. The P. falciparum Niemann-Pick type C1-related (PfNCR1) transporter has been identified as a druggable target, but its structure and detailed molecular mechanism are not yet available. Here, we present three structures of PfNCR1 with and without the functional inhibitor MMV009108 at resolutions between 2.98 and 3.81 Å using single-particle cryo-electron microscopy (cryo-EM), suggesting that PfNCR1 binds cholesterol and forms a cholesterol transport tunnel to modulate the composition of the parasite plasma membrane. Cholesterol efflux assays show that PfNCR1 is an exporter capable of extruding cholesterol from the membrane. Additionally, the inhibition mechanism of MMV009108 appears to be due to a direct blockage of PfNCR1, preventing this transporter from shuttling cholesterol.
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Affiliation(s)
- Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Xu Han
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Sepalika Bandara
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, MA 02115, USA
| | - Eva S. Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinran Geng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marios L. Tringides
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - William D. Gregor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - John H. Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Youwei Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marvin T. Nieman
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Johannes von Lintig
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Daniel E. Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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47
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Blauwkamp J, Ambekar SV, Hussain T, Mair GR, Beck JR, Absalon S. Nuclear pore complexes undergo Nup221 exchange during blood-stage asexual replication of Plasmodium parasites. mSphere 2024; 9:e0075024. [PMID: 39526784 DOI: 10.1128/msphere.00750-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 10/11/2024] [Indexed: 11/16/2024] Open
Abstract
Plasmodium parasites, the causative agents of malaria, undergo closed mitosis without breakdown of the nuclear envelope. Unlike closed mitosis in yeast, Plasmodium berghei parasites undergo multiple rounds of asynchronous nuclear divisions in a shared cytoplasm. This results in a multinucleated organism prior to the formation of daughter cells within an infected red blood cell. During this replication process, intact nuclear pore complexes (NPCs) and their component nucleoporins play critical roles in parasite growth, facilitating selective bi-directional nucleocytoplasmic transport and genome organization. Here, we utilize ultrastructure expansion microscopy to investigate P. berghei nucleoporins at the single nucleus level throughout the 24-hour blood-stage replication cycle. Our findings reveal that these nucleoporins are distributed around the nuclei and organized in a rosette structure previously undescribed around the centriolar plaque, responsible for intranuclear microtubule nucleation during mitosis. By adapting the recombination-induced tag exchange system to P. berghei through a single plasmid tagging system, which includes the tagging plasmid as well as the Cre recombinase, we provide evidence of NPC formation dynamics, demonstrating Nup221 turnover during parasite asexual replication. Our data shed light on the distribution of NPCs and their homeostasis during the blood-stage replication of P. berghei parasites. IMPORTANCE Malaria, caused by Plasmodium species, remains a critical global health challenge, with an estimated 249 million cases and over 600,000 deaths in 2022, primarily affecting children under five. Understanding the nuclear dynamics of Plasmodium parasites, particularly during their unique mitotic processes, is crucial for developing novel therapeutic strategies. Our study leverages advanced microscopy techniques, such as ultrastructure expansion microscopy, to reveal the organization and turnover of nuclear pore complexes (NPCs) during the parasite's asexual replication. By elucidating these previously unknown aspects of NPC distribution and homeostasis, we provide valuable insights into the molecular mechanisms governing parasite mitosis. These findings deepen our understanding of parasite biology and may inform future research aimed at identifying new targets for anti-malarial drug development.
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Affiliation(s)
- James Blauwkamp
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sushma V Ambekar
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Tahir Hussain
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Gunnar R Mair
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Josh R Beck
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Sakura T, Ishii R, Yoshida E, Kita K, Kato T, Inaoka DK. Accelerating Antimalarial Drug Discovery with a New High-Throughput Screen for Fast-Killing Compounds. ACS Infect Dis 2024; 10:4115-4126. [PMID: 39561299 DOI: 10.1021/acsinfecdis.4c00328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
The urgent need for rapidly acting compounds in the development of antimalarial drugs underscores the significance of such compounds in overcoming resistance issues and improving patient adherence to antimalarial treatments. The present study introduces a high-throughput screening (HTS) approach using 1536-well plates, employing Plasmodium falciparum lactate dehydrogenase (PfLDH) combined with nitroreductase (NTR) and fluorescent probes to evaluate inhibition of the growth of the asexual blood stage of malaria parasites. This method was adapted to efficiently assess the speed of action profiling (SAP) in a 384-well plate format, streamlining the traditionally time-consuming screening process. By successfully screening numerous compounds, this approach identified fast-killing hits early in the screening process, addressing challenges associated with artemisinin-based combination therapies. The high-throughput SAP method is expected to be of value in continuously monitoring fast-killing properties during structure-activity relationship studies, expediting the identification and development of novel, rapidly acting antimalarial drugs within phenotypic drug discovery campaigns.
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Affiliation(s)
- Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
| | - Ryuta Ishii
- Department of Cellular Architecture Studies, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Eri Yoshida
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Teruhisa Kato
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
- Exploratory Research for Drug Discovery, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto, Nagasaki 852-8523, Japan
- Department of Infection Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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49
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Blackwell AM, Jami-Alahmadi Y, Nasamu AS, Kudo S, Senoo A, Slam C, Tsumoto K, Wohlschlegel JA, Manuel Martinez Caaveiro J, Goldberg DE, Sigala PA. Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis. eLife 2024; 13:RP100256. [PMID: 39660822 PMCID: PMC11634067 DOI: 10.7554/elife.100256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024] Open
Abstract
Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 Å-resolution X-ray structure that revealed a highly α-helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.
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Affiliation(s)
- Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
| | - Armiyaw S Nasamu
- Departments of Medicine and Molecular Microbiology, Washington University School of MedicineSt. LouisUnited States
| | - Shota Kudo
- Department of Chemistry & Biotechnology, The University of TokyoTokyoJapan
| | - Akinobu Senoo
- Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu UniversityFukuokaJapan
| | - Celine Slam
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Kouhei Tsumoto
- Department of Chemistry & Biotechnology, The University of TokyoTokyoJapan
- Department of Bioengineering, University of TokyoTokyoJapan
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
| | | | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of MedicineSt. LouisUnited States
| | - Paul A Sigala
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
- Departments of Medicine and Molecular Microbiology, Washington University School of MedicineSt. LouisUnited States
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50
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Zerebinski J, Margerie L, Han NS, Moll M, Ritvos M, Jahnmatz P, Ahlborg N, Ngasala B, Rooth I, Sjöberg R, Sundling C, Yman V, Färnert A, Plaza DF. Naturally acquired IgG responses to Plasmodium falciparum do not target the conserved termini of the malaria vaccine candidate Merozoite Surface Protein 2. Front Immunol 2024; 15:1501700. [PMID: 39717775 PMCID: PMC11663719 DOI: 10.3389/fimmu.2024.1501700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 11/15/2024] [Indexed: 12/25/2024] Open
Abstract
Introduction Malaria remains a significant burden, and a fully protective vaccine against Plasmodium falciparum is critical for reducing morbidity and mortality. Antibody responses against the blood-stage antigen Merozoite Surface Protein 2 (MSP2) are associated with protection from P. falciparum malaria, but its extensive polymorphism is a barrier to its development as a vaccine candidate. New tools, such as long-read sequencing and accurate protein structure modelling allow us to study the genetic diversity and immune responses towards antigens from clinical isolates with unprecedented detail. This study sought to better understand naturally acquired MSP2-specific antibody responses. Methods IgG responses against recombinantly expressed full-length, central polymorphic regions, and peptides derived from the conserved termini of MSP2 variants sequenced from patient isolates, were tested in plasma from travelers with recent, acute malaria and from individuals living in an endemic area of Tanzania. Results IgG responses towards full MSP2 and truncated MSP2 antigens were variant specific. IgG antibodies in the plasma of first-time infected or previously exposed travelers did not recognize the conserved termini of expressed MSP2 variants by ELISA, but they bound 13-amino acid long linear epitopes from the termini in a custom-made peptide array. Alphafold3 modelling suggests extensive structural heterogeneity in the conserved termini upon antigen oligomerization. IgG from individuals living in an endemic region, many who were asymptomatically infected, did not recognize the conserved termini by ELISA. Discussion Our results suggest that responses to the variable regions are critical for the development of naturally acquired immunity towards MSP2.
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Affiliation(s)
- Julia Zerebinski
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Lucille Margerie
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Nan Sophia Han
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maximilian Moll
- University Hospital of Bonn, Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University of Bonn, Bonn, Germany
| | - Matias Ritvos
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ingegerd Rooth
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling Unit, SciLifeLab, Solna, Sweden
| | - Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Victor Yman
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Södersjukhuset, Stockholm, Sweden
- Department of Global Health, Infectious Disease Epidemiology & Analytics Unit, Institut Pasteur Paris, Paris, France
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - David Fernando Plaza
- Division of Infectious Diseases, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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