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Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections. Nat Commun 2021; 12:909. [PMID: 33568678 PMCID: PMC7875998 DOI: 10.1038/s41467-021-21269-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/15/2021] [Indexed: 01/30/2023] Open
Abstract
Malaria control may be enhanced by targeting reservoirs of Plasmodium falciparum transmission. One putative reservoir is asymptomatic malaria infections and the scale of their contribution to transmission in natural settings is not known. We assess the contribution of asymptomatic malaria to onward transmission using a 14-month longitudinal cohort of 239 participants in a high transmission site in Western Kenya. We identify P. falciparum in asymptomatically- and symptomatically-infected participants and naturally-fed mosquitoes from their households, genotype all parasites using deep sequencing of the parasite genes pfama1 and pfcsp, and use haplotypes to infer participant-to-mosquito transmission through a probabilistic model. In 1,242 infections (1,039 in people and 203 in mosquitoes), we observe 229 (pfcsp) and 348 (pfama1) unique parasite haplotypes. Using these to link human and mosquito infections, compared with symptomatic infections, asymptomatic infections more than double the odds of transmission to a mosquito among people with both infection types (Odds Ratio: 2.56; 95% Confidence Interval (CI): 1.36-4.81) and among all participants (OR 2.66; 95% CI: 2.05-3.47). Overall, 94.6% (95% CI: 93.1-95.8%) of mosquito infections likely resulted from asymptomatic infections. In high transmission areas, asymptomatic infections are the major contributor to mosquito infections and may be targeted as a component of transmission reduction.
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202
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Ricaurte-Contreras LA, Lovera A, Moreno-Pérez DA, Bohórquez MD, Suárez CF, Gutiérrez-Vásquez E, Cuy-Chaparro L, Garzón-Ospina D, Patarroyo MA. Two 20-Residue-Long Peptides Derived from Plasmodium vivax Merozoite Surface Protein 10 EGF-Like Domains Are Involved in Binding to Human Reticulocytes. Int J Mol Sci 2021; 22:ijms22041609. [PMID: 33562650 PMCID: PMC7915351 DOI: 10.3390/ijms22041609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Plasmodium parasites’ invasion of their target cells is a complex, multi-step process involving many protein-protein interactions. Little is known about how complex the interaction with target cells is in Plasmodium vivax and few surface molecules related to reticulocytes’ adhesion have been described to date. Natural selection, functional and structural analysis were carried out on the previously described vaccine candidate P. vivax merozoite surface protein 10 (PvMSP10) for evaluating its role during initial contact with target cells. It has been shown here that the recombinant carboxyl terminal region (rPvMSP10-C) bound to adult human reticulocytes but not to normocytes, as validated by two different protein-cell interaction assays. Particularly interesting was the fact that two 20-residue-long regions (388DKEECRCRANYMPDDSVDYF407 and 415KDCSKENGNCDVNAECSIDK434) were able to inhibit rPvMSP10-C binding to reticulocytes and rosette formation using enriched target cells. These peptides were derived from PvMSP10 epidermal growth factor (EGF)-like domains (precisely, from a well-defined electrostatic zone) and consisted of regions having the potential of being B- or T-cell epitopes. These findings provide evidence, for the first time, about the fragments governing PvMSP10 binding to its target cells, thus highlighting the importance of studying them for inclusion in a P. vivax antimalarial vaccine.
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Affiliation(s)
- Laura Alejandra Ricaurte-Contreras
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
- MSc Programme in Microbiology, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Andrea Lovera
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Darwin Andrés Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Michel David Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Carlos Fernando Suárez
- Biomathematics Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia;
| | - Elizabeth Gutiérrez-Vásquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Laura Cuy-Chaparro
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Diego Garzón-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá 111321, Colombia; (L.A.R.-C.); (A.L.); (D.A.M.-P.); (M.D.B.); (E.G.-V.); (L.C.-C.); (D.G.-O.)
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Carrera 9#51-11, Bogotá 110231, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
- Correspondence:
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203
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Gunnarsson S, Prabakaran S. In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework. Malar J 2021; 20:71. [PMID: 33546698 PMCID: PMC7866754 DOI: 10.1186/s12936-021-03598-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Plasmodium falciparum causes the deadliest form of malaria, which remains one of the most prevalent infectious diseases. Unfortunately, the only licensed vaccine showed limited protection and resistance to anti-malarial drug is increasing, which can be largely attributed to the biological complexity of the parasite’s life cycle. The progression from one developmental stage to another in P. falciparum involves drastic changes in gene expressions, where its infectivity to human hosts varies greatly depending on the stage. Approaches to identify candidate genes that are responsible for the development of infectivity to human hosts typically involve differential gene expression analysis between stages. However, the detection may be limited to annotated proteins and open reading frames (ORFs) predicted using restrictive criteria. Methods The above problem is particularly relevant for P. falciparum; whose genome annotation is relatively incomplete given its clinical significance. In this work, systems proteogenomics approach was used to address this challenge, as it allows computational detection of unannotated, novel Open Reading Frames (nORFs), which are neglected by conventional analyses. Two pairs of transcriptome/proteome were obtained from a previous study where one was collected in the mosquito-infectious oocyst sporozoite stage, and the other in the salivary gland sporozoite stage with human infectivity. They were then re-analysed using the proteogenomics framework to identify nORFs in each stage. Results Translational products of nORFs that map to antisense, intergenic, intronic, 3′ UTR and 5′ UTR regions, as well as alternative reading frames of canonical proteins were detected. Some of these nORFs also showed differential expression between the two life cycle stages studied. Their regulatory roles were explored through further bioinformatics analyses including the expression regulation on the parent reference genes, in silico structure prediction, and gene ontology term enrichment analysis. Conclusion The identification of nORFs in P. falciparum sporozoites highlights the biological complexity of the parasite. Although the analyses are solely computational, these results provide a starting point for further experimental validation of the existence and functional roles of these nORFs,
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Affiliation(s)
- Sophie Gunnarsson
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
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204
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Knöckel J, Dundas K, Yang ASP, Galaway F, Metcalf T, Gemert GJV, Sauerwein RW, Rayner JC, Billker O, Wright GJ. Systematic Identification of Plasmodium Falciparum Sporozoite Membrane Protein Interactions Reveals an Essential Role for the p24 Complex in Host Infection. Mol Cell Proteomics 2021; 20:100038. [PMID: 33515807 PMCID: PMC7950211 DOI: 10.1074/mcp.ra120.002432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Sporozoites are a motile form of malaria-causing Plasmodium falciparum parasites that migrate from the site of transmission in the dermis through the bloodstream to invade hepatocytes. Sporozoites interact with many cells within the host, but the molecular identity of these interactions and their role in the pathology of malaria is poorly understood. Parasite proteins that are secreted and embedded within membranes are known to be important for these interactions, but our understanding of how they interact with each other to form functional complexes is largely unknown. Here, we compile a library of recombinant proteins representing the repertoire of cell surface and secreted proteins from the P. falciparum sporozoite and use an assay designed to detect extracellular interactions to systematically identify complexes. We identify three protein complexes including an interaction between two components of the p24 complex that is involved in the trafficking of glycosylphosphatidylinositol-anchored proteins through the secretory pathway. Plasmodium parasites lacking either gene are strongly inhibited in the establishment of liver-stage infections. These findings reveal an important role for the p24 complex in malaria pathogenesis and show that the library of recombinant proteins represents a valuable resource to investigate P. falciparum sporozoite biology.
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Key Words
- avexis, avidity-based extracellular interaction screen
- csp, circumsporozoite protein
- gpi, glycosylphosphatidylinositol
- hbs, hepes-buffered saline
- hek, human embryonic kidney
- ivis, in vivo imaging system
- msp, merozoite surface protein
- piesp15, parasite-infected erythrocyte surface protein 15
- spr, surface plasmon resonance
- trap, thrombospondin-related anonymous protein
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Affiliation(s)
- Julia Knöckel
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom; Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Kirsten Dundas
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom; Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Annie S P Yang
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom; Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Tom Metcalf
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Geert-Jan van Gemert
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert W Sauerwein
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julian C Rayner
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Oliver Billker
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom; The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom; Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom; Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom.
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205
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Gurung P, Gomes AR, Martins RM, Juranek SA, Alberti P, Mbang-Benet DE, Urbach S, Gazanion E, Guitard V, Paeschke K, Lopez-Rubio JJ. PfGBP2 is a novel G-quadruplex binding protein in Plasmodium falciparum. Cell Microbiol 2021; 23:e13303. [PMID: 33340385 DOI: 10.1111/cmi.13303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
Guanine-quadruplexes (G4s) are non-canonical DNA structures that can regulate key biological processes such as transcription, replication and telomere maintenance in several organisms including eukaryotes, prokaryotes and viruses. Recent reports have identified the presence of G4s within the AT-rich genome of Plasmodium falciparum, the protozoan parasite causing malaria. In Plasmodium, potential G4-forming sequences (G4FS) are enriched in the telomeric and sub-telomeric regions of the genome where they are associated with telomere maintenance and recombination events within virulence genes. However, there is a little understanding about the biological role of G4s and G4-binding proteins. Here, we provide the first snapshot of G4-interactome in P. falciparum using DNA pull-down assay followed by LC-MS/MS. Interestingly, we identified ~24 potential G4-binding proteins (G4-BP) that bind to a stable G4FS (AP2_G4). Furthermore, we characterised the role of G-strand binding protein 2 (PfGBP2), a putative telomere-binding protein in P. falciparum. We validated the interaction of PfGBP2 with G4 in vitro as well as in vivo. PfGBP2 is expressed throughout the intra-erythrocytic developmental cycle and is essential for the parasites in the presence of G4-stabilising ligand, pyridostatin. Gene knockout studies showed the role of PfGBP2 in the expression of var genes. Taken together, this study suggests that PfGBP2 is a bona fide G4-binding protein, which is likely to be involved in the regulation of G4-related functions in these malarial parasites. In addition, this study sheds light on this understudied G4 biology in P. falciparum.
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Affiliation(s)
- Pratima Gurung
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Ana Rita Gomes
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Rafael M Martins
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Patrizia Alberti
- Laboratory Genome Structure and Instability, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U 1154, Paris, France
| | - Diane-Ethna Mbang-Benet
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Serge Urbach
- BioCampus Montpellier, CNRS UMR 5203, IGF, Montpellier, France
| | - Elodie Gazanion
- Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Vincent Guitard
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jose-Juan Lopez-Rubio
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
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206
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Neal ML, Wei L, Peterson E, Arrieta-Ortiz ML, Danziger S, Baliga N, Kaushansky A, Aitchison J. A systems-level gene regulatory network model for Plasmodium falciparum. Nucleic Acids Res 2021; 49:4891-4906. [PMID: 33450011 PMCID: PMC8136813 DOI: 10.1093/nar/gkaa1245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022] Open
Abstract
Many of the gene regulatory processes of Plasmodium falciparum, the deadliest malaria parasite, remain poorly understood. To develop a comprehensive guide for exploring this organism's gene regulatory network, we generated a systems-level model of P. falciparum gene regulation using a well-validated, machine-learning approach for predicting interactions between transcription regulators and their targets. The resulting network accurately predicts expression levels of transcriptionally coherent gene regulatory programs in independent transcriptomic data sets from parasites collected by different research groups in diverse laboratory and field settings. Thus, our results indicate that our gene regulatory model has predictive power and utility as a hypothesis-generating tool for illuminating clinically relevant gene regulatory mechanisms within P. falciparum. Using the set of regulatory programs we identified, we also investigated correlates of artemisinin resistance based on gene expression coherence. We report that resistance is associated with incoherent expression across many regulatory programs, including those controlling genes associated with erythrocyte-host engagement. These results suggest that parasite populations with reduced artemisinin sensitivity are more transcriptionally heterogenous. This pattern is consistent with a model where the parasite utilizes bet-hedging strategies to diversify the population, rendering a subpopulation more able to navigate drug treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - John D Aitchison
- To whom correspondence should be addressed. Tel: +1 206 884 3125; Fax: +1 206 884 3104;
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207
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An Integrative Computational Approach for the Prediction of Human- Plasmodium Protein-Protein Interactions. BIOMED RESEARCH INTERNATIONAL 2021; 2020:2082540. [PMID: 33426052 PMCID: PMC7771252 DOI: 10.1155/2020/2082540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/08/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022]
Abstract
Host-pathogen molecular cross-talks are critical in determining the pathophysiology of a specific infection. Most of these cross-talks are mediated via protein-protein interactions between the host and the pathogen (HP-PPI). Thus, it is essential to know how some pathogens interact with their hosts to understand the mechanism of infections. Malaria is a life-threatening disease caused by an obligate intracellular parasite belonging to the Plasmodium genus, of which P. falciparum is the most prevalent. Several previous studies predicted human-plasmodium protein-protein interactions using computational methods have demonstrated their utility, accuracy, and efficiency to identify the interacting partners and therefore complementing experimental efforts to characterize host-pathogen interaction networks. To predict potential putative HP-PPIs, we use an integrative computational approach based on the combination of multiple OMICS-based methods including human red blood cells (RBC) and Plasmodium falciparum 3D7 strain expressed proteins, domain-domain based PPI, similarity of gene ontology terms, structure similarity method homology identification, and machine learning prediction. Our results reported a set of 716 protein interactions involving 302 human proteins and 130 Plasmodium proteins. This work provides a list of potential human-Plasmodium interacting proteins. These findings will contribute to better understand the mechanisms underlying the molecular determinism of malaria disease and potentially to identify candidate pharmacological targets.
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208
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Yu X, Feng G, Zhang Q, Cao J. From Metabolite to Metabolome: Metabolomics Applications in Plasmodium Research. Front Microbiol 2021; 11:626183. [PMID: 33505389 PMCID: PMC7829456 DOI: 10.3389/fmicb.2020.626183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023] Open
Abstract
Advances in research over the past few decades have greatly improved metabolomics-based approaches in studying parasite biology and disease etiology. This improves the investigation of varied metabolic requirements during life stages or when following transmission to their hosts, and fulfills the demand for improved diagnostics and precise therapeutics. Therefore, this review highlights the progress of metabolomics in malaria research, including metabolic mapping of Plasmodium vertebrate life cycle stages to investigate antimalarials mode of actions and underlying complex host-parasite interactions. Also, we discuss current limitations as well as make several practical suggestions for methodological improvements which could drive metabolomics progress for malaria from a comprehensive perspective.
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Affiliation(s)
- Xinyu Yu
- 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.,Medical College of Soochow University, Suzhou, China
| | - Gaoqian Feng
- Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Qingfeng Zhang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Cao
- 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.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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209
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Ferreira JL, Heincke D, Wichers JS, Liffner B, Wilson DW, Gilberger TW. The Dynamic Roles of the Inner Membrane Complex in the Multiple Stages of the Malaria Parasite. Front Cell Infect Microbiol 2021; 10:611801. [PMID: 33489940 PMCID: PMC7820811 DOI: 10.3389/fcimb.2020.611801] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/30/2020] [Indexed: 01/31/2023] Open
Abstract
Apicomplexan parasites, such as human malaria parasites, have complex lifecycles encompassing multiple and diverse environmental niches. Invading, replicating, and escaping from different cell types, along with exploiting each intracellular niche, necessitate large and dynamic changes in parasite morphology and cellular architecture. The inner membrane complex (IMC) is a unique structural element that is intricately involved with these distinct morphological changes. The IMC is a double membrane organelle that forms de novo and is located beneath the plasma membrane of these single-celled organisms. In Plasmodium spp. parasites it has three major purposes: it confers stability and shape to the cell, functions as an important scaffolding compartment during the formation of daughter cells, and plays a major role in motility and invasion. Recent years have revealed greater insights into the architecture, protein composition and function of the IMC. Here, we discuss the multiple roles of the IMC in each parasite lifecycle stage as well as insights into its sub-compartmentalization, biogenesis, disassembly and regulation during stage conversion of P. falciparum.
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Affiliation(s)
- Josie Liane Ferreira
- Centre for Structural Systems Biology, Hamburg, Germany
- Heinrich Pette Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - Dorothee Heincke
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Jan Stephan Wichers
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Benjamin Liffner
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Danny W. Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Burnet Institute, Melbourne, VIC, 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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210
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Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Res 2021; 49:D998-D1003. [PMID: 33084874 PMCID: PMC7779042 DOI: 10.1093/nar/gkaa884] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.
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Affiliation(s)
- Sanathoi Gurumayum
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Puzi Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Xiaowen Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peer Bork
- European molecular biology laboratory (EMBL), Meyerhof Strasse 1, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, 200433 Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | - Li-jie He
- Department of Medical Oncology, People's Hospital of Liaoning Province, 110016 Shenyang, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
- College of Life Science, Henan Normal University, 453007 Xinxiang, Henan, China
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211
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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212
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Role of the J Domain Protein Family in the Survival and Pathogenesis of Plasmodium falciparum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:97-123. [PMID: 34569022 DOI: 10.1007/978-3-030-78397-6_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plasmodium falciparum has dedicated an unusually large proportion of its genome to molecular chaperones (2% of all genes), with the heat shock protein 40 (Hsp40) family (now called J domain proteins, JDPs) exhibiting evolutionary radiation into 49 members. A large number of the P. falciparum JDPs (PfJDPs) are predicted to be exported, with certain members shown experimentally to be present in the erythrocyte cytosol (PFA0660w and PFE0055c) or erythrocyte membrane (ring-infected erythrocyte surface antigen, RESA). PFA0660w and PFE0055c are associated with an exported plasmodial Hsp70 (PfHsp70-x) within novel mobile structures called J-dots, which have been proposed to be dedicated to the trafficking of key membrane proteins such as erythrocyte membrane protein 1 (PfEMP1). Well over half of the PfJDPs appear to be essential, including the J-dot PfJDP, PFE0055c, while others have been found to be required for growth under febrile conditions (e.g. PFA0110w, the ring-infected erythrocyte surface antigen protein [RESA]) or involved in pathogenesis (e.g. PF10_0381 has been shown to be important for protrusions of the infected red blood cell membrane, the so-called knobs). Here we review what is known about those PfJDPs that have been well characterised, and may be directly or indirectly involved in the survival and pathogenesis of the malaria parasite.
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213
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Jonsdottir TK, Gabriela M, Gilson PR. The Role of Malaria Parasite Heat Shock Proteins in Protein Trafficking and Remodelling of Red Blood Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:141-167. [PMID: 34569024 DOI: 10.1007/978-3-030-78397-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The genus Plasmodium comprises intracellular eukaryotic parasites that infect many vertebrate groups and cause deadly malaria disease in humans. The parasites employ a suite of heat shock proteins to help traffic other proteins to different compartments within their own cells and that of the host cells they parasitise. This review will cover the role of these chaperones in protein export and host cell modification in the asexual blood stage of the human parasite P. falciparum which is the most deadly and well-studied parasite species. We will examine the role chaperones play in the import of proteins into the secretory pathway from where they are escorted to the vacuole space surrounding the intraerythrocytic parasite. Here, other heat shock proteins unfold protein cargoes and extrude them into the red blood cell (RBC) cytosol from where additional chaperones of parasite and possibly host origin refold the cargo proteins and guide them to their final functional destinations within their RBC host cells. The secretory pathway also serves as a launch pad for proteins targeted to the non-photosynthetic apicoplast organelle of endosymbiotic origin, and the role of heat shock proteins in trafficking proteins here will be reviewed. Finally, the function of chaperones in protein trafficking into the mitochondrion, the remaining organelle of endosymbiotic origin, will be discussed.
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Affiliation(s)
- Thorey K Jonsdottir
- Burnet Institute, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Mikha Gabriela
- Burnet Institute, Melbourne, VIC, Australia.,School of Medicine, Deakin University, Waurn Ponds, VIC, Australia
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214
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Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite. Biochem J 2020; 477:2153-2177. [PMID: 32484216 DOI: 10.1042/bcj20200145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022]
Abstract
Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
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215
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Gao D, Chen Q, Zeng Y, Jiang M, Zhang Y. Applications of Machine Learning in Drug Target Discovery. Curr Drug Metab 2020; 21:790-803. [PMID: 32723266 DOI: 10.2174/1567201817999200728142023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/12/2020] [Accepted: 05/13/2020] [Indexed: 12/15/2022]
Abstract
Drug target discovery is a critical step in drug development. It is the basis of modern drug development because it determines the target molecules related to specific diseases in advance. Predicting drug targets by computational methods saves a great deal of financial and material resources compared to in vitro experiments. Therefore, several computational methods for drug target discovery have been designed. Recently, machine learning (ML) methods in biomedicine have developed rapidly. In this paper, we present an overview of drug target discovery methods based on machine learning. Considering that some machine learning methods integrate network analysis to predict drug targets, network-based methods are also introduced in this article. Finally, the challenges and future outlook of drug target discovery are discussed.
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Affiliation(s)
- Dongrui Gao
- School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China
| | - Qingyuan Chen
- School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China
| | - Yuanqi Zeng
- School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China
| | - Meng Jiang
- School of Mechanical Automotive Engineering, Nanyang Institute of Technology, Nanyang 473000, China
| | - Yongqing Zhang
- School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China
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216
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Structure of the Plasmodium-interspersed repeat proteins of the malaria parasite. Proc Natl Acad Sci U S A 2020; 117:32098-32104. [PMID: 33257570 PMCID: PMC7749308 DOI: 10.1073/pnas.2016775117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Plasmodium parasites that cause malaria replicate within blood cells of an infected host. These parasites send a small number of proteins to infected blood cell surfaces, allowing them to bind host molecules but also risking their detection by the host immune system. These proteins have diversified into large families, allowing the parasite to avoid detection by using antigenic variation. The most ubiquitous of these families is the Plasmodium-interspersed repeat (PIR) protein family. Here we present the structure of a PIR protein, revealing the architecture of its ectodomain and showing how it has diversified. Finally, we use structure-guided methods to understand which small variant surface antigen families are PIRs and to understand their evolution across malaria parasites. The deadly symptoms of malaria occur as Plasmodium parasites replicate within blood cells. Members of several variant surface protein families are expressed on infected blood cell surfaces. Of these, the largest and most ubiquitous are the Plasmodium-interspersed repeat (PIR) proteins, with more than 1,000 variants in some genomes. Their functions are mysterious, but differential pir gene expression associates with acute or chronic infection in a mouse malaria model. The membership of the PIR superfamily, and whether the family includes Plasmodium falciparum variant surface proteins, such as RIFINs and STEVORs, is controversial. Here we reveal the structure of the extracellular domain of a PIR from Plasmodium chabaudi. We use structure-guided sequence analysis and molecular modeling to show that this fold is found across PIR proteins from mouse- and human-infective malaria parasites. Moreover, we show that RIFINs and STEVORs are not PIRs. This study provides a structure-guided definition of the PIRs and a molecular framework to understand their evolution.
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217
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The Key Glycolytic Enzyme Phosphofructokinase Is Involved in Resistance to Antiplasmodial Glycosides. mBio 2020; 11:mBio.02842-20. [PMID: 33293381 PMCID: PMC7733947 DOI: 10.1128/mbio.02842-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, continues to be a devastating global health issue, causing 405,000 deaths and 228 million cases in 2018. Understanding key metabolic processes in malaria parasites is critical to the development of new drugs to combat this major infectious disease. The Plasmodium glycolytic pathway is essential to the malaria parasite, providing energy for growth and replication and supplying important biomolecules for other essential Plasmodium anabolic pathways. Despite this overreliance on glycolysis, no current drugs target glycolysis, and there is a paucity of information on critical glycolysis targets. Our work addresses this unmet need, providing new mechanistic insights into this key pathway. Plasmodium parasites rely heavily on glycolysis for ATP production and for precursors for essential anabolic pathways, such as the methylerythritol phosphate (MEP) pathway. Here, we show that mutations in the Plasmodium falciparum glycolytic enzyme, phosphofructokinase (PfPFK9), are associated with in vitro resistance to a primary sulfonamide glycoside (PS-3). Flux through the upper glycolysis pathway was significantly reduced in PS-3-resistant parasites, which was associated with reduced ATP levels but increased flux into the pentose phosphate pathway. PS-3 may directly or indirectly target enzymes in these pathways, as PS-3-treated parasites had elevated levels of glycolytic and tricarboxylic acid (TCA) cycle intermediates. PS-3 resistance also led to reduced MEP pathway intermediates, and PS-3-resistant parasites were hypersensitive to the MEP pathway inhibitor, fosmidomycin. Overall, this study suggests that PS-3 disrupts core pathways in central carbon metabolism, which is compensated for by mutations in PfPFK9, highlighting a novel metabolic drug resistance mechanism in P. falciparum.
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218
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Development of novel anti-malarial from structurally diverse library of molecules, targeting plant-like CDPK1, a multistage growth regulator of P. falciparum. Biochem J 2020; 477:1951-1970. [PMID: 32401306 DOI: 10.1042/bcj20200045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023]
Abstract
Upon Plasmodium falciparum merozoites exposure to low [K+] environment in blood plasma, there is escalation of cytosolic [Ca2+] which activates Ca2+-Dependent Protein Kinase 1 (CDPK1), a signaling hub of intra-erythrocytic proliferative stages of parasite. Given its high abundance and multidimensional attributes in parasite life-cycle, this is a lucrative target for designing antimalarials. Towards this, we have virtually screened MyriaScreenII diversity collection of 10,000 drug-like molecules, which resulted in 18 compounds complementing ATP-binding pocket of CDPK1. In vitro screening for toxicity in mammalian cells revealed that these compounds are non-toxic in nature. Furthermore, SPR analysis demonstrated differential binding affinity of these compounds towards recombinantly purified CDPK1 protein. Selection of lead compound 1 was performed by evaluating their inhibitory effects on phosphorylation and ATP binding activities of CDPK1. Furthermore, in vitro biophysical evaluations by ITC and FS revealed that binding of compound 1 is driven by formation of energetically favorable non-covalent interactions, with different binding constants in presence and absence of Ca2+, and TSA authenticated stability of compound 1 bound CDPK1 complex. Finally, compound 1 strongly inhibited intra-erythrocytic growth of P. falciparum in vitro. Conceivably, we propose a novel CDPK1-selective inhibitor, step towards developing pan-CDPK kinase inhibitors, prerequisite for cross-stage anti-malarial protection.
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219
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Prajapati SK, Ayanful-Torgby R, Pava Z, Barbeau MC, Acquah FK, Cudjoe E, Kakaney C, Amponsah JA, Obboh E, Ahmed AE, Abuaku BK, McCarthy JS, Amoah LE, Williamson KC. The transcriptome of circulating sexually committed Plasmodium falciparum ring stage parasites forecasts malaria transmission potential. Nat Commun 2020; 11:6159. [PMID: 33268801 PMCID: PMC7710746 DOI: 10.1038/s41467-020-19988-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022] Open
Abstract
Malaria is spread by the transmission of sexual stage parasites, called gametocytes. However, with Plasmodium falciparum, gametocytes can only be detected in peripheral blood when they are mature and transmissible to a mosquito, which complicates control efforts. Here, we identify the set of genes overexpressed in patient blood samples with high levels of gametocyte-committed ring stage parasites. Expression of all 18 genes is regulated by transcription factor AP2-G, which is required for gametocytogenesis. We select three genes, not expressed in mature gametocytes, to develop as biomarkers. All three biomarkers we validate in vitro using 6 different parasite lines and develop an algorithm that predicts gametocyte production in ex vivo samples and volunteer infection studies. The biomarkers are also sensitive enough to monitor gametocyte production in asymptomatic P. falciparum carriers allowing early detection and treatment of infectious reservoirs, as well as the in vivo analysis of factors that modulate sexual conversion. Malaria gametocytes are sexual-stage parasites transmitted from mammalian host’s blood back to their insect vector. Here, Prajapati et al. identify gametocyte-committed ring-stage biomarkers allowing to forecast malaria transmission potential.
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Affiliation(s)
- Surendra K Prajapati
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
| | - Ruth Ayanful-Torgby
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michelle C Barbeau
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,University of Virginia, Charlottesville, VA, USA
| | - Festus K Acquah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Elizabeth Cudjoe
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Courage Kakaney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Jones A Amponsah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Anwar E Ahmed
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Benjamin K Abuaku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Linda E Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kim C Williamson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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220
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Sharma AI, Shin SH, Bopp S, Volkman SK, Hartl DL, Wirth DF. Genetic background and PfKelch13 affect artemisinin susceptibility of PfCoronin mutants in Plasmodium falciparum. PLoS Genet 2020; 16:e1009266. [PMID: 33370279 PMCID: PMC7793257 DOI: 10.1371/journal.pgen.1009266] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 01/08/2021] [Accepted: 11/10/2020] [Indexed: 11/21/2022] Open
Abstract
Malaria continues to impose a significant health burden in the continent of Africa with 213 million cases in 2018 alone, representing 93% of cases worldwide. Because of high transmission of malaria within the continent, the selection pressures to develop drug resistance in African parasites are distinct compared to the rest of the world. In light of the spread of resistance to artemisinin conferred by the C580Y mutation in the PfKelch13 propeller domain in Southeast Asia, and its independent emergence in South America, it is important to study genetic determinants of resistance in the African context using African parasites. Through in vitro evolution of Senegalese parasites, we had previously generated the artemisinin-resistant parasites Pikine_R and Thiès_R and established pfcoronin mutations to be sufficient to confer artemisinin resistance in the standard ring-stage survival assay (RSA). In the current study, we used genetic analysis of revertants to demonstrate pfcoronin to be the major driver of elevated RSA in the artemisinin-resistant parasites Pikine_R and Thiès_R evolved in vitro. We interrogated the role of a second gene PF3D7_1433800, which also had mutations in both the Pikine_R and Thiès_R selected lines, but found no evidence of a contribution to reduced susceptibility in the RSA survival assay. Nevertheless, our genetic analysis demonstrates that parasite genetic background is important in the level of pfcoronin mediated RSA survival, and therefore we cannot rule out a role for PF3D7_1433800 in other genetic backgrounds. Finally, we tested the potential synergy between the mutations of pfcoronin and pfkelch13 through the generation of single and double mutants in the Pikine genetic background and found that the contribution of pfcoronin to reduced susceptibility is masked by the presence of pfkelch13. This phenomenon was also observed in the 3D7 background, suggesting that pfcoronin may mediate its effects via the same pathway as pfkelch13. Investigating the biology of proteins containing the beta-propeller domain could further elucidate the different pathways that the parasite could use to attain resistance.
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Affiliation(s)
- Aabha I. Sharma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Sara H. Shin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Selina Bopp
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Sarah K. Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, United States of America
- College of Natural, Behavioral and Health Sciences, Simmons University, Boston, United States of America
| | - Daniel L. Hartl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States of America
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, United States of America
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221
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Guttery DS, Pandey R, Ferguson DJ, Wall RJ, Brady D, Gupta D, Holder AA, Tewari R. Plasmodium DEH is ER-localized and crucial for oocyst mitotic division during malaria transmission. Life Sci Alliance 2020; 3:e202000879. [PMID: 33106323 PMCID: PMC7652392 DOI: 10.26508/lsa.202000879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 11/24/2022] Open
Abstract
Cells use fatty acids (FAs) for membrane biosynthesis, energy storage, and the generation of signaling molecules. 3-hydroxyacyl-CoA dehydratase-DEH-is a key component of very long chain fatty acid synthesis. Here, we further characterized in-depth the location and function of DEH, applying in silico analysis, live cell imaging, reverse genetics, and ultrastructure analysis using the mouse malaria model Plasmodium berghei DEH is evolutionarily conserved across eukaryotes, with a single DEH in Plasmodium spp. and up to three orthologs in the other eukaryotes studied. DEH-GFP live-cell imaging showed strong GFP fluorescence throughout the life-cycle, with areas of localized expression in the cytoplasm and a circular ring pattern around the nucleus that colocalized with ER markers. Δdeh mutants showed a small but significant reduction in oocyst size compared with WT controls from day 10 postinfection onwards, and endomitotic cell division and sporogony were completely ablated, blocking parasite transmission from mosquito to vertebrate host. Ultrastructure analysis confirmed degeneration of Δdeh oocysts, and a complete lack of sporozoite budding. Overall, DEH is evolutionarily conserved, localizes to the ER, and plays a crucial role in sporogony.
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Affiliation(s)
- David S Guttery
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- The Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, Leicester, UK
| | - Rajan Pandey
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - David Jp Ferguson
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard J Wall
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
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222
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Boateng RA, Tastan Bishop Ö, Musyoka TM. Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study. Malar J 2020; 19:442. [PMID: 33256744 PMCID: PMC7756947 DOI: 10.1186/s12936-020-03512-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodial transketolase (PTKT) enzyme is one of the novel pharmacological targets being explored as potential anti-malarial drug target due to its functional role and low sequence identity to the human enzyme. Despite this, features contributing to such have not been exploited for anti-malarial drug design. Additionally, there are no anti-malarial drugs targeting PTKTs whereas the broad activity of these inhibitors against PTKTs from other Plasmodium spp. is yet to be reported. This study characterises different PTKTs [Plasmodium falciparum (PfTKT), Plasmodium vivax (PvTKT), Plasmodium ovale (PoTKT), Plasmodium malariae (PmTKT) and Plasmodium knowlesi (PkTKT) and the human homolog (HsTKT)] to identify key sequence and structural based differences as well as the identification of selective potential inhibitors against PTKTs. METHODS A sequence-based study was carried out using multiple sequence alignment, phylogenetic tree calculations and motif discovery analysis. Additionally, TKT models of PfTKT, PmTKT, PoTKT, PmTKT and PkTKT were modelled using the Saccharomyces cerevisiae TKT structure as template. Based on the modelled structures, molecular docking using 623 South African natural compounds was done. The stability, conformational changes and detailed interactions of selected compounds were accessed viz all-atom molecular dynamics (MD) simulations and binding free energy (BFE) calculations. RESULTS Sequence alignment, evolutionary and motif analyses revealed key differences between plasmodial and the human TKTs. High quality homodimeric three-dimensional PTKTs structures were constructed. Molecular docking results identified three compounds (SANC00107, SANC00411 and SANC00620) which selectively bind in the active site of all PTKTs with the lowest (better) binding affinity ≤ - 8.5 kcal/mol. MD simulations of ligand-bound systems showed stable fluctuations upon ligand binding. In all systems, ligands bind stably throughout the simulation and form crucial interactions with key active site residues. Simulations of selected compounds in complex with human TKT showed that ligands exited their binding sites at different time steps. BFE of protein-ligand complexes showed key residues involved in binding. CONCLUSIONS This study highlights significant differences between plasmodial and human TKTs and may provide valuable information for the development of novel anti-malarial inhibitors. Identified compounds may provide a starting point in the rational design of PTKT inhibitors and analogues based on these scaffolds.
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Affiliation(s)
- Rita Afriyie Boateng
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa.
| | - Thommas Mutemi Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa.
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223
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Amegashie EA, Amenga-Etego L, Adobor C, Ogoti P, Mbogo K, Amambua-Ngwa A, Ghansah A. Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana. Malar J 2020; 19:437. [PMID: 33246470 PMCID: PMC7694917 DOI: 10.1186/s12936-020-03510-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria-endemic areas such as Ghana. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6–59 months presenting with clinical malaria at health facilities in Cape Coast (in the coastal belt) and Navrongo (Guinea savannah region), respectively, in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting higher within-host and population-level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences, respectively. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.
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Affiliation(s)
- Elikplim A Amegashie
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucas Amenga-Etego
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Courage Adobor
- Parasitology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, , Legon, Ghana
| | - Peter Ogoti
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Kevin Mbogo
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination, Medical Research Council Unit, The Gambia Unit, Bakau, The Gambia
| | - Anita Ghansah
- Parasitology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, , Legon, Ghana.
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224
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Bansod S, Bung N, Singh P, Suthram N, Choudhury H, Roy A, Bulusu G, Bhattacharyya S. Elucidation of an essential function of the unique charged domain of Plasmodium topoisomerase III. Biochem J 2020; 477:BCJ20200318. [PMID: 33241842 DOI: 10.1042/bcj20200318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/27/2020] [Accepted: 11/26/2020] [Indexed: 12/28/2022]
Abstract
Topoisomerase III (TopoIII) along with RecQ helicases are required for the resolution of abnormal DNA structures that result from the stalling of replication forks. Sequence analyses have identified a putative TopoIII in the Plasmodium falciparum genome (PfTopoIII). PfTopoIII shows dual nuclear and mitochondrial localization. The expression and association of PfTopoIII with mtDNA is tightly linked to the asexual replication of the parasite. In this study, we observed that PfTopoIII physically interacts with PfBlm and PfWrn. Sequence alignment and domain analyses have revealed that it contains a unique positively charged region, spanning 85 amino acids, within domain II. A molecular dynamics simulation study revealed that this unstructured domain communicates with DNA and attains a thermodynamically stable state upon DNA binding. Here, we found that the association between PfTopoIII and the mitochondrial genome is negatively affected by the absence of the charged domain. Our study shows that PfTOPOIII can completely rescue the slow growth phenotype of the ΔtopoIII strain in Saccharomyces cerevisiae, but neither PfY421FtopoIII (catalytic-active site mutant) nor Pf(Δ259-337)topoIII (charged region deletion mutant) can functionally complement ScTOPOIII. Hydroxyurea (HU) led to stalling of the replication fork during the S phase, caused moderate toxicity to the growth of P. falciparum, and was associated with concomitant transcriptional upregulation of PfTOPOIII. In addition, ectopic expression of PfTOPOIII reversed HU-induced toxicity. Interestingly, the expression of Pf(Δ259-337)topoIII failed to reverse HU-mediated toxicity. Taken together, our results establish the importance of TopoIII during Plasmodium replication and emphasize the essential requirement of the charged domain in PfTopoIII function.
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Affiliation(s)
- Shephali Bansod
- University of Hyderabad, School of Life Sciences, Hyderabad, India
| | - Navneet Bung
- Tata Consultancy Services Limited, Hyderabad, India, India
| | - Priyanka Singh
- University of Hyderabad, School of Life Sciences, Hyderabad, India
| | | | | | - Arijit Roy
- Tata Consultancy Services Limited, Hyderabad, India
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225
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Rojas-Pirela M, Andrade-Alviárez D, Rojas V, Kemmerling U, Cáceres AJ, Michels PA, Concepción JL, Quiñones W. Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. Open Biol 2020; 10:200302. [PMID: 33234025 PMCID: PMC7729029 DOI: 10.1098/rsob.200302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Verónica Rojas
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Universidad de Chile, Facultad de Medicina, Santiago de Chile 8380453, Santigo de Chile
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Paul A Michels
- Centre for Immunity, Infection and Evolution, The King's Buildings, Edinburgh EH9 3FL, UK.,Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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226
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Morahan BJ, Abrie C, Al-Hasani K, Batty MB, Corey V, Cowell AN, Niemand J, Winzeler EA, Birkholtz LM, Doerig C, Garcia-Bustos JF. Human Aurora kinase inhibitor Hesperadin reveals epistatic interaction between Plasmodium falciparum PfArk1 and PfNek1 kinases. Commun Biol 2020; 3:701. [PMID: 33219324 PMCID: PMC7679417 DOI: 10.1038/s42003-020-01424-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/07/2020] [Indexed: 12/23/2022] Open
Abstract
Mitosis has been validated by numerous anti-cancer drugs as being a druggable process, and selective inhibition of parasite proliferation provides an obvious opportunity for therapeutic intervention against malaria. Mitosis is controlled through the interplay between several protein kinases and phosphatases. We show here that inhibitors of human mitotic kinases belonging to the Aurora family inhibit P. falciparum proliferation in vitro with various potencies, and that a genetic selection for mutant parasites resistant to one of the drugs, Hesperadin, identifies a resistance mechanism mediated by a member of a different kinase family, PfNek1 (PF3D7_1228300). Intriguingly, loss of PfNek1 catalytic activity provides protection against drug action. This points to an undescribed functional interaction between Ark and Nek kinases and shows that existing inhibitors can be used to validate additional essential and druggable kinase functions in the parasite. Morahan et al. investigate inhibitors of human mitotic kinases in P. falciparum and show a resistance mechanism to the drug Hesperadin through an epistatic interaction between the PfArk1 and PfNek1 kinases. This study demonstrates that existing inhibitors can be used to validate additional essential and druggable kinase functions in the parasite.
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Affiliation(s)
- Belinda J Morahan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Clarissa Abrie
- Faculty of Natural and Agricultural Sciences, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, 0028, South Africa
| | - Keith Al-Hasani
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.,Department of Diabetes, Monash University Central Clinical School, Alfred Centre, Melbourne, VIC, 3004, Australia
| | - Mitchell B Batty
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.,Department of Diabetes, Monash University Central Clinical School, Alfred Centre, Melbourne, VIC, 3004, Australia
| | - Victoria Corey
- Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, MC 0760, La Jolla, CA, 92093-0760, USA.,Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Anne N Cowell
- Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, MC 0760, La Jolla, CA, 92093-0760, USA.,Department of Medicine, University of California San Diego School of Medicine, 9444 Medical Center Drive, MC 0879, La Jolla, CA, 92093-0879, USA
| | - Jandeli Niemand
- Faculty of Natural and Agricultural Sciences, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, 0028, South Africa
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, MC 0760, La Jolla, CA, 92093-0760, USA
| | - Lyn-Marie Birkholtz
- Faculty of Natural and Agricultural Sciences, Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, 0028, South Africa
| | - Christian Doerig
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia. .,School of Health and Biomedical Sciences, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
| | - Jose F Garcia-Bustos
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
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227
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Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates. Sci Rep 2020; 10:20220. [PMID: 33214620 PMCID: PMC7677368 DOI: 10.1038/s41598-020-77001-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
A variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles during parasite development. NEDD8 is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulates diverse cellular processes. Although neddylation is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. We characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Ala/Gly76Ala) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 (rub1Δ) or NEDD8 conjugating E2 enzyme (ubc12Δ). The PfNEDD8 immunoprecipitate also contained S. cerevisiae cullin cdc53, further substantiating cullins as physiological substrates of PfNEDD8. Our findings lay ground for investigation of specific roles and drug target potential of neddylation in malaria parasites.
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228
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Absalon S, Dvorin JD. Depletion of the mini-chromosome maintenance complex binding protein allows the progression of cytokinesis despite abnormal karyokinesis during the asexual development of Plasmodium falciparum. Cell Microbiol 2020; 23:e13284. [PMID: 33124706 DOI: 10.1111/cmi.13284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022]
Abstract
The eukaryotic cell cycle is typically divided into distinct phases with cytokinesis immediately following mitosis. To ensure proper cell division, each phase is tightly coordinated via feedback controls named checkpoints. During its asexual replication cycle, the malaria parasite Plasmodium falciparum undergoes multiple asynchronous rounds of mitosis with segregation of uncondensed chromosomes followed by nuclear division with intact nuclear envelope. The multi-nucleated schizont is then subjected to a single round of cytokinesis that produces dozens of daughter cells called merozoites. To date, no cell cycle checkpoints have been identified that regulate the Plasmodium spp. mode of division. Here, we identify the Plasmodium homologue of the Mini-Chromosome Maintenance Complex Binding Protein (PfMCMBP), which co-purified with the Mini-Chromosome Maintenance (MCM) complex, a replicative helicase required for genomic DNA replication. By conditionally depleting PfMCMBP, we disrupt nuclear morphology and parasite proliferation without causing a block in DNA replication. By immunofluorescence microscopy, we show that PfMCMBP depletion promotes the formation of mitotic spindle microtubules with extensions to more than one DNA focus and abnormal centrin distribution. Strikingly, PfMCMBP-deficient parasites complete cytokinesis and form aneuploid merozoites with variable cellular and nuclear sizes. Our study demonstrates that the parasite lacks a robust checkpoint response to prevent cytokinesis following aberrant karyokinesis.
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Affiliation(s)
- Sabrina Absalon
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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229
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Barylyuk K, Koreny L, Ke H, Butterworth S, Crook OM, Lassadi I, Gupta V, Tromer E, Mourier T, Stevens TJ, Breckels LM, Pain A, Lilley KS, Waller RF. A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host Microbe 2020; 28:752-766.e9. [PMID: 33053376 PMCID: PMC7670262 DOI: 10.1016/j.chom.2020.09.011] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Apicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to highly specialized cell compartments and structures. These adaptations drive their recognition, nondestructive penetration, and elaborate reengineering of the host's cells to promote their growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty. Consequently, half of apicomplexan proteins are unique and uncharacterized. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasite Toxoplasma gondii. This provides unprecedented comprehensive molecular definition of these unicellular eukaryotes and their specialized compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.
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Affiliation(s)
| | - Ludek Koreny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Huiling Ke
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Simon Butterworth
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Oliver M Crook
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK; MRC Biostatistics Unit, Cambridge Institute for Public Health, Cambridge CB2 0SR, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Vipul Gupta
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Eelco Tromer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Tobias Mourier
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; Global Station for Zoonosis Control, Gi-CoRE, Hokkaido University, Sapporo 060-0808, Japan; Nuffield Division of Clinical Laboratory Sciences (NDCLS), University of Oxford, Oxford OX3 9DU, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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230
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An ELISA method to assess HDAC inhibitor-induced alterations to P. falciparum histone lysine acetylation. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:249-256. [PMID: 33279862 PMCID: PMC7724001 DOI: 10.1016/j.ijpddr.2020.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
The prevention and treatment of malaria requires a multi-pronged approach, including the development of drugs that have novel modes of action. Histone deacetylases (HDACs), enzymes involved in post-translational protein modification, are potential new drug targets for malaria. However, the lack of recombinant P. falciparum HDACs and suitable activity assays, has made the investigation of compounds designed to target these enzymes challenging. Current approaches are indirect and include assessing total deacetylase activity and protein hyperacetylation via Western blot. These approaches either do not allow differential compound effects to be determined or suffer from low throughput. Here we investigated dot blot and ELISA methods as new, higher throughput assays to detect histone lysine acetylation changes in P. falciparum parasites. As the ELISA method was found to be superior to the dot blot assay using the control HDAC inhibitor vorinostat, it was used to evaluate the histone H3 and H4 lysine acetylation changes mediated by a panel of six HDAC inhibitors that were shown to inhibit P. falciparum deacetylase activity. Vorinostat, panobinostat, trichostatin A, romidepsin and entinostat all caused an ~3-fold increase in histone H4 acetylation using a tetra-acetyl lysine antibody. Tubastatin A, the only human HDAC6-specific inhibitor tested, also caused H4 hyperacetylation, but to a lesser extent than the other compounds. Further investigation revealed that all compounds, except tubastatin A, caused hyperacetylation of the individual N-terminal H4 lysines 5, 8, 12 and 16. These data indicate that tubastatin A impacts P. falciparum H4 acetylation differently to the other HDAC inhibitors tested. In contrast, all compounds caused hyperacetylation of histone H3. In summary, the ELISA developed in this study provides a higher throughput approach to assessing differential effects of antiplasmodial compounds on histone acetylation levels and is therefore a useful new tool in the investigation of HDAC inhibitors for malaria. P. falciparum histone lysine acetylation was compared using dot blot and ELISA. ELISA was more reproducible than dot blot in acetylation assays. ELISA was used to assess acetylation changes induced by anti-cancer HDAC inhibitors. Tubastatin A showed a different histone H4 acetylation profile to other compounds. This new method will facilitate the study of HDAC inhibitors for malaria.
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231
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Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites. Commun Biol 2020; 3:624. [PMID: 33116247 PMCID: PMC7595149 DOI: 10.1038/s42003-020-01349-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022] Open
Abstract
Pathogen multiplication rate is theoretically an important determinant of virulence, although often poorly understood and difficult to measure accurately. We show intrinsic asexual blood stage multiplication rate variation of the major human malaria parasite Plasmodium falciparum to be associated with blood-stage infection intensity in patients. A panel of clinical isolates from a highly endemic West African population was analysed repeatedly during five months of continuous laboratory culture, showing a range of exponential multiplication rates at all timepoints tested, mean rates increasing over time. All isolates had different genome sequences, many containing within-isolate diversity that decreased over time in culture, but increases in multiplication rates were not primarily attributable to genomic selection. New mutants, including premature stop codons emerging in a few isolates, did not attain sufficiently high frequencies to substantially affect overall multiplication rates. Significantly, multiplication rate variation among the isolates at each of the assayed culture timepoints robustly correlated with parasite levels seen in patients at clinical presentation, indicating innate parasite control of multiplication rate that contributes to virulence. Lindsay Stewart et al. analyze clinical isolates of the human malaria parasite Plasmodium falciparum from a highly endemic West African population and show that intrinsic multiplication rate variation is associated with blood-stage infection intensity. Their results indicate that parasite control of multiplication contributes to virulence.
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232
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Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. Malar J 2020; 19:382. [PMID: 33109193 PMCID: PMC7592540 DOI: 10.1186/s12936-020-03448-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.
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Kassegne K, Komi Koukoura K, Shen HM, Chen SB, Fu HT, Chen YQ, Zhou XN, Chen JH, Cheng Y. Genome-Wide Analysis of the Malaria Parasite Plasmodium falciparum Isolates From Togo Reveals Selective Signals in Immune Selection-Related Antigen Genes. Front Immunol 2020; 11:552698. [PMID: 33193320 PMCID: PMC7645038 DOI: 10.3389/fimmu.2020.552698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022] Open
Abstract
Malaria is a public health concern worldwide, and Togo has proven to be no exception. Effective approaches to provide information on biological insights for disease elimination are therefore a research priority. Local selection on malaria pathogens is due to multiple factors including host immunity. We undertook genome-wide analysis of sequence variation on a sample of 10 Plasmodium falciparum (Pf) clinical isolates from Togo to identify local-specific signals of selection. Paired-end short-read sequences were mapped and aligned onto > 95% of the 3D7 Pf reference genome sequence in high fold coverage. Data on 266 963 single nucleotide polymorphisms were obtained, with average nucleotide diversity π = 1.79 × 10−3. Both principal component and neighbor-joining tree analyses showed that the Togo parasites clustered according to their geographic (Africa) origin. In addition, the average genome-wide diversity of Pf from Togo was much higher than that from other African samples. Tajima’s D value of the Togo isolates was −0.56, suggesting evidence of directional selection and/or recent population expansion. Against this background, within-population analyses identifying loci of balancing and recent positive selections evidenced that host immunity has been the major selective agent. Importantly, 87 and 296 parasite antigen genes with Tajima’s D values > 1 and in the top 1% haplotype scores, respectively, include a significant representation of membrane proteins at the merozoite stage that invaded red blood cells (RBCs) and parasitized RBCs surface proteins that play roles in immunoevasion, adhesion, or rosetting. This is consistent with expectations that elevated signals of selection due to allele-specific acquired immunity are likely to operate on antigenic targets. Collectively, our data suggest a recent expansion of Pf population in Togo and evidence strong host immune selection on membrane/surface antigens reflected in signals of balancing/positive selection of important gene loci. Findings from this study provide a fundamental basis to engage studies for effective malaria control in Togo.
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Affiliation(s)
- Kokouvi Kassegne
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Komi Komi Koukoura
- Laboratoire des Sciences Biomédicales, Alimentaires et Santé Environnementale, Département des Analyses Biomédicales, Ecole Supérieure des Techniques Biologiques et Alimentaires, Université de Lomé, Lomé, Togo
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Hai-Tian Fu
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yong-Quan Chen
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention, Chinese Centre for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, National Centre for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Centre for Disease Control and Prevention-Shenzhen Centre for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,The School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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234
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Tagliamonte MS, Yowell CA, Elbadry MA, Boncy J, Raccurt CP, Okech BA, Goss EM, Salemi M, Dame JB. Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America. mSphere 2020; 5:e00937-20. [PMID: 33087522 PMCID: PMC7580960 DOI: 10.1128/msphere.00937-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, was introduced into Hispaniola and other regions of the Americas through the slave trade spanning the 16th through the 19th centuries. During this period, more than 12 million Africans were brought across the Atlantic to the Caribbean and other regions of the Americas. Since malaria is holoendemic in West Africa, a substantial percentage of these individuals carried the parasite. St. Domingue on Hispaniola, now modern-day Haiti, was a major port of disembarkation, and malaria is still actively transmitted there. We undertook a detailed study of the phylogenetics of the Haitian parasites and those from Colombia and Peru utilizing whole-genome sequencing. Principal-component and phylogenetic analyses, based upon single nucleotide polymorphisms (SNPs) in protein coding regions, indicate that, despite the potential for millions of introductions from Africa, the Haitian parasites share an ancestral relationship within a well-supported monophyletic clade with parasites from South America, while belonging to a distinct lineage. This result, in stark contrast to the historical record of parasite introductions, is best explained by a severe population bottleneck experienced by the parasites introduced into the Americas. Here, evidence is presented for targeted selection of rare African alleles in genes which are expressed in the mosquito stages of the parasite's life cycle. These genetic markers support the hypothesis that the severe population bottleneck was caused by the required adaptation of the parasite to transmission by new definitive hosts among the Anopheles (Nyssorhynchus) spp. found in the Caribbean and South America.IMPORTANCE Historical data suggest that millions of P. falciparum parasite lineages were introduced into the Americas during the trans-Atlantic slave trade, which would suggest a paraphyletic origin of the extant isolates in the Western Hemisphere. Our analyses of whole-genome variants show that the American parasites belong to a well-supported monophyletic clade. We hypothesize that the required adaptation to American vectors created a severe bottleneck, reducing the effective introduction to a few lineages. In support of this hypothesis, we discovered genes expressed in the mosquito stages of the life cycle that have alleles with multiple, high-frequency or fixed, nonsynonymous mutations in the American populations which are rarely found in African isolates. These alleles appear to be in gene products critical for transmission through the anopheline vector. Thus, these results may inform efforts to develop novel transmission-blocking vaccines by identifying parasite proteins functionally interacting with the vector that are important for successful transmission. Further, to the best of our knowledge, these are the first whole-genome data available from Haitian P. falciparum isolates. Defining the genome of these parasites provides genetic markers useful for mapping parasite populations and monitoring parasite movements/introductions.
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Affiliation(s)
- Massimiliano S Tagliamonte
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Charles A Yowell
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Maha A Elbadry
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jacques Boncy
- Laboratoire National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Christian P Raccurt
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, University of Quisqueya, Port-au-Prince, Haiti
| | - Bernard A Okech
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, College of Agricultural and Life Sciences, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - John B Dame
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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235
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Yang T, Yeoh LM, Tutor MV, Dixon MW, McMillan PJ, Xie SC, Bridgford JL, Gillett DL, Duffy MF, Ralph SA, McConville MJ, Tilley L, Cobbold SA. Decreased K13 Abundance Reduces Hemoglobin Catabolism and Proteotoxic Stress, Underpinning Artemisinin Resistance. Cell Rep 2020; 29:2917-2928.e5. [PMID: 31775055 DOI: 10.1016/j.celrep.2019.10.095] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/08/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Increased tolerance of Plasmodium falciparum to front-line artemisinin antimalarials (ARTs) is associated with mutations in Kelch13 (K13), although the precise role of K13 remains unclear. Here, we show that K13 mutations result in decreased expression of this protein, while mislocalization of K13 mimics resistance-conferring mutations, pinpointing partial loss of function of K13 as the relevant molecular event. K13-GFP is associated with ∼170 nm diameter doughnut-shaped structures at the parasite periphery, consistent with the location and dimensions of cytostomes. Moreover, the hemoglobin-peptide profile of ring-stage parasites is reduced when K13 is mislocalized. We developed a pulse-SILAC approach to quantify protein turnover and observe less disruption to protein turnover following ART exposure when K13 is mislocalized. Our findings suggest that K13 regulates digestive vacuole biogenesis and the uptake/degradation of hemoglobin and that ART resistance is mediated by a decrease in heme-dependent drug activation, less proteotoxicity, and increased survival of parasite ring stages.
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Affiliation(s)
- Tuo Yang
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lee M Yeoh
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Matthew W Dixon
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paul J McMillan
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia; Biological Optical Microscopy Platform, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stanley C Xie
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jessica L Bridgford
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David L Gillett
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael F Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Simon A Cobbold
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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236
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Wang C, Gibbons J, Adapa SR, Oberstaller J, Liao X, Zhang M, Adams JH, Jiang RHY. The human malaria parasite genome is configured into thousands of coexpressed linear regulatory units. J Genet Genomics 2020; 47:513-521. [PMID: 33272860 DOI: 10.1016/j.jgg.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/07/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
The human malaria parasite Plasmodium falciparum thrives in radically different host environments in mosquitoes and humans, with only a limited set of transcription factors. The nature of regulatory elements or their target genes in the P. falciparum genome remains elusive. Here, we found that this eukaryotic parasite uses an efficient way to maximally use genetic and epigenetic regulation to form regulatory units (RUs) during blood infections. Genes located in the same RU tend to have the same pattern of expression over time and are associated with open chromatin along regulatory elements. To precisely define and quantify these RUs, a novel hidden Markov model was developed to capture the regulatory structure in a genome-wide fashion by integrating expression and epigenetic evidence. We successfully identified thousands of RUs and cross-validated with previous findings. We found more genes involved in red blood cell (RBC) invasion located in the same RU as the PfAP2-I (AP2-I) transcription factor, demonstrating that AP2-I is responsible for regulating RBC invasion. Our study has provided a regulatory mechanism for a compact eukaryotic genome and offers new insights into the in vivo transcriptional regulation of the P. falciparum intraerythrocytic stage.
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Affiliation(s)
- Chengqi Wang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Justin Gibbons
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Min Zhang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - John H Adams
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Rays H Y Jiang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
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237
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Abuga KM, Jones-Warner W, Hafalla JCR. Immune responses to malaria pre-erythrocytic stages: Implications for vaccine development. Parasite Immunol 2020; 43:e12795. [PMID: 32981095 PMCID: PMC7612353 DOI: 10.1111/pim.12795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/26/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
Radiation-attenuated sporozoites induce sterilizing immunity and remain the 'gold standard' for malaria vaccine development. Despite practical challenges in translating these whole sporozoite vaccines to large-scale intervention programmes, they have provided an excellent platform to dissect the immune responses to malaria pre-erythrocytic (PE) stages, comprising both sporozoites and exoerythrocytic forms. Investigations in rodent models have provided insights that led to the clinical translation of various vaccine candidates-including RTS,S/AS01, the most advanced candidate currently in a trial implementation programme in three African countries. With advances in immunology, transcriptomics and proteomics, and application of lessons from past failures, an effective, long-lasting and wide-scale malaria PE vaccine remains feasible. This review underscores the progress in PE vaccine development, focusing on our understanding of host-parasite immunological crosstalk in the tissue environments of the skin and the liver. We highlight possible gaps in the current knowledge of PE immunity that can impact future malaria vaccine development efforts.
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Affiliation(s)
- Kelvin Mokaya Abuga
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - William Jones-Warner
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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238
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Siegel SV, Chappell L, Hostetler JB, Amaratunga C, Suon S, Böhme U, Berriman M, Fairhurst RM, Rayner JC. Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions. Sci Rep 2020; 10:16667. [PMID: 33028892 PMCID: PMC7541449 DOI: 10.1038/s41598-020-73562-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022] Open
Abstract
Plasmodium vivax gene regulation remains difficult to study due to the lack of a robust in vitro culture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol “DAFT-seq” to sequence the transcriptome of four P. vivax field isolates that were cultured for a short period ex vivo before using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5′ and 3′ untranslated regions, some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity between P. vivax schizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lack Plasmodium falciparum homologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity within P. vivax transcriptomes will be essential for the prioritisation of novel vaccine targets.
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Affiliation(s)
- Sasha V Siegel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Lia Chappell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jessica B Hostetler
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chanaki Amaratunga
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bankgok, Thailand.,Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Ulrike Böhme
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK. .,Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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239
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Khairallah A, Ross CJ, Tastan Bishop Ö. Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites. Front Mol Biosci 2020; 7:575196. [PMID: 33102524 PMCID: PMC7546909 DOI: 10.3389/fmolb.2020.575196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/20/2020] [Indexed: 11/13/2022] Open
Abstract
The de novo folate synthesis pathway is a well-established drug target in the treatment of many infectious diseases. Antimalarial antifolate drugs have proven to be effective against malaria, however, rapid drug resistance has emerged on the two primary targeted enzymes: dihydrofolate reductase and dihydroptoreate synthase. The need to identify alternative antifolate drugs and novel metabolic targets is of imminent importance. The 6-pyruvol tetrahydropterin synthase (PTPS) enzyme belongs to the tunneling fold protein superfamily which is characterized by a distinct central tunnel/cavity. The enzyme catalyzes the second reaction step of the parasite’s de novo folate synthesis pathway and is responsible for the conversion of 7,8-dihydroneopterin to 6-pyruvoyl-tetrahydropterin. In this study, we examine the structural dynamics of Plasmodium falciparum PTPS using the anisotropic network model, to elucidate the collective motions that drive the function of the enzyme and identify potential sites for allosteric modulation of its binding properties. Based on our modal analysis, we identified key sites in the N-terminal domains and central helices which control the accessibility to the active site. Notably, the N-terminal domains were shown to regulate the open-to-closed transition of the tunnel, via a distinctive wringing motion that deformed the core of the protein. We, further, combined the dynamic analysis with motif discovery which revealed highly conserved motifs that are unique to the Plasmodium species and are located in the N-terminal domains and central helices. This provides essential structural information for the efficient design of drugs such as allosteric modulators that would have high specificity and low toxicity as they do not target the PTPS active site that is highly conserved in humans.
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Affiliation(s)
- Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Caroline J Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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240
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Trivedi R, Nagarajaram HA. Substitution scoring matrices for proteins - An overview. Protein Sci 2020; 29:2150-2163. [PMID: 32954566 DOI: 10.1002/pro.3954] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023]
Abstract
Sequence analysis is the primary and simplest approach to discover structural, functional and evolutionary details of related proteins. All the alignment based approaches of sequence analysis make use of amino acid substitution matrices, and the accuracy of the results largely depends on the type of scoring matrices used to perform alignment tasks. An amino acid substitution matrix is a 20 × 20 matrix in which the individual elements encapsulate the rates at which each of the 20 amino acid residues in proteins are substituted by other amino acid residues over time. In contrast to most globular/ordered proteins whose amino acids composition is considered as standard, there are several classes of proteins (e.g., transmembrane proteins) in which certain types of amino acid (e.g., hydrophobic residues) are enriched. These compositional differences among various classes of proteins are manifested in their underlying residue substitution frequencies. Therefore, each of the compositionally distinct class of proteins or protein segments should be studied using specific scoring matrices that reflect their distinct residue substitution pattern. In this review, we describe the development and application of various substitution scoring matrices peculiar to proteins with standard and biased compositions. Along with most commonly used standard matrices (PAM, BLOSUM, MD and VTML) that act as default parameters in various homologs search and alignment tools, different substitution scoring matrices specific to compositionally distinct class of proteins are discussed in detail.
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Affiliation(s)
- Rakesh Trivedi
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana, India.,Graduate School, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.,Centre for Modelling, Simulation and Design, University of Hyderabad, Hyderabad, Telangana, India
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241
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Krishnan K, Ziniel P, Li H, Huang X, Hupalo D, Gombakomba N, Guerrero SM, Dotrang T, Lu X, Caridha D, Sternberg AR, Hughes E, Sun W, Bargieri DY, Roepe PD, Sciotti RJ, Wilkerson MD, Dalgard CL, Tawa GJ, Wang AQ, Xu X, Zheng W, Sanderson PE, Huang W, Williamson KC. Torin 2 Derivative, NCATS-SM3710, Has Potent Multistage Antimalarial Activity through Inhibition of P. falciparum Phosphatidylinositol 4-Kinase ( Pf PI4KIIIβ). ACS Pharmacol Transl Sci 2020; 3:948-964. [PMID: 33073193 DOI: 10.1021/acsptsci.0c00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Drug resistance is a constant threat to malaria control efforts making it important to maintain a good pipeline of new drug candidates. Of particular need are compounds that also block transmission by targeting sexual stage parasites. Mature sexual stages are relatively resistant to all currently used antimalarials except the 8-aminoquinolines that are not commonly used due to potential side effects. Here, we synthesized a new Torin 2 derivative, NCATS-SM3710 with increased aqueous solubility and specificity for Plasmodium and demonstrate potent in vivo activity against all P. berghei life cycle stages. NCATS-SM3710 also has low nanomolar EC50s against in vitro cultured asexual P. falciparum parasites (0.38 ± 0.04 nM) and late stage gametocytes (5.77 ± 1 nM). Two independent NCATS-SM3710/Torin 2 resistant P. falciparum parasite lines produced by growth in sublethal Torin 2 concentrations both had genetic changes in PF3D7_0509800, annotated as a phosphatidylinositol 4 kinase (Pf PI4KIIIβ). One line had a point mutation in the putative active site (V1357G), and the other line had a duplication of a locus containing Pf PI4KIIIβ. Both lines were also resistant to other Pf PI4K inhibitors. In addition NCATS-SM3710 inhibited purified Pf PI4KIIIβ with an IC50 of 2.0 ± 0.30 nM. Together the results demonstrate that Pf PI4KIIIβ is the target of Torin 2 and NCATS-SM3710 and provide new options for potent multistage drug development.
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Affiliation(s)
- Karthik Krishnan
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Peter Ziniel
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Hao Li
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Xiuli Huang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Daniel Hupalo
- Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Nita Gombakomba
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Sandra Mendoza Guerrero
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Thoai Dotrang
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Xiao Lu
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Diana Caridha
- Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Anna R Sternberg
- Departments of Chemistry and of Biochemistry, Cellular and Molecular Biology, Georgetown University, Washington, DC 20057, United States
| | - Emma Hughes
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wei Sun
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Daniel Y Bargieri
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, 05508, Brazil
| | - Paul D Roepe
- Departments of Chemistry and of Biochemistry, Cellular and Molecular Biology, Georgetown University, Washington, DC 20057, United States
| | - Richard J Sciotti
- Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, United States
| | - Matthew D Wilkerson
- Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
| | - Gregory J Tawa
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Amy Q Wang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Xin Xu
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wei Zheng
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Philip E Sanderson
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wenwei Huang
- National Center for Advancing Translational Science, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Kim C Williamson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
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242
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Njila Tchoufack EJ, Hahnfeld L, Pitschelatow G, Bennink S, Pradel G. The endoplasmic reticulum-resident serpentine receptor SR10 has important functions for asexual and sexual blood stage development of Plasmodium falciparum. Mol Biochem Parasitol 2020; 239:111315. [PMID: 32890576 DOI: 10.1016/j.molbiopara.2020.111315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/13/2020] [Accepted: 07/28/2020] [Indexed: 11/28/2022]
Abstract
Serpentine receptors (SRs) are transmembrane proteins generally acting as mediators to facilitate the communication between a cell and its environment. At least six putative SR-like proteins are encoded in the genome of the malaria parasite Plasmodium falciparum. For two of them, roles in cell stress control were reported; however, for most of the SR-like proteins the functions are not yet known. In this study, we provide a first phenotypic analysis of the plasmodial SR10. The transmembrane protein is expressed in the asexual and sexual blood stages of P. falciparum. Co-localization and co-immunoprecipitation assays demonstrated an association of SR10 with the endoplasmic reticulum protein ERC. Gene disruption of SR10 leads to impaired intraerythrocytic replication and strongly reduces gametocyte numbers. We thus propose that SR10 is a protein associated with the endoplasmic reticulum that has important functions for asexual and sexual blood stage development.
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Affiliation(s)
| | - Lena Hahnfeld
- Division of Cellular and Applied Infection Biology, Institute of Biology 2, RWTH Aachen University, Aachen, Germany
| | - Georg Pitschelatow
- Division of Cellular and Applied Infection Biology, Institute of Biology 2, RWTH Aachen University, Aachen, Germany
| | - Sandra Bennink
- Division of Cellular and Applied Infection Biology, Institute of Biology 2, RWTH Aachen University, Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Biology 2, RWTH Aachen University, Aachen, Germany.
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243
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The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. Microorganisms 2020; 8:microorganisms8081252. [PMID: 32824654 PMCID: PMC7463849 DOI: 10.3390/microorganisms8081252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 11/21/2022] Open
Abstract
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62× up to 263×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.
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244
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Camponovo F, Campo JJ, Le TQ, Oberai A, Hung C, Pablo JV, Teng AA, Liang X, Sim BKL, Jongo S, Abdulla S, Tanner M, Hoffman SL, Daubenberger C, Penny MA. Proteome-wide analysis of a malaria vaccine study reveals personalized humoral immune profiles in Tanzanian adults. eLife 2020; 9:53080. [PMID: 32662772 PMCID: PMC7386907 DOI: 10.7554/elife.53080] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 07/10/2020] [Indexed: 12/31/2022] Open
Abstract
Tanzanian adult male volunteers were immunized by direct venous inoculation with radiation-attenuated, aseptic, purified, cryopreserved Plasmodium falciparum (Pf) sporozoites (PfSPZ Vaccine) and protective efficacy assessed by homologous controlled human malaria infection (CHMI). Serum immunoglobulin G (IgG) responses were analyzed longitudinally using a Pf protein microarray covering 91% of the proteome, providing first insights into naturally acquired and PfSPZ Vaccine-induced whole parasite antibody profiles in malaria pre-exposed Africans. Immunoreactivity was identified against 2239 functionally diverse Pf proteins, showing a wide breadth of humoral response. Antibody-based immune ‘fingerprints’ in these individuals indicated a strong person-specific immune response at baseline, with little changes in the overall humoral immunoreactivity pattern measured after immunization. The moderate increase in immunogenicity following immunization and the extensive and variable breadth of humoral immune response observed in the volunteers at baseline suggest that pre-exposure reduces vaccine-induced antigen reactivity in unanticipated ways.
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Affiliation(s)
- Flavia Camponovo
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Amit Oberai
- Antigen Discovery Inc, Irvine, United States
| | | | | | - Andy A Teng
- Antigen Discovery Inc, Irvine, United States
| | | | | | - Said Jongo
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Salim Abdulla
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Marcel Tanner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Melissa A Penny
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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245
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Klug D, Goellner S, Kehrer J, Sattler J, Strauss L, Singer M, Lu C, Springer TA, Frischknecht F. Evolutionarily distant I domains can functionally replace the essential ligand-binding domain of Plasmodium TRAP. eLife 2020; 9:57572. [PMID: 32648541 PMCID: PMC7351488 DOI: 10.7554/elife.57572] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/25/2020] [Indexed: 02/02/2023] Open
Abstract
Inserted (I) domains function as ligand-binding domains in adhesins that support cell adhesion and migration in many eukaryotic phyla. These adhesins include integrin αβ heterodimers in metazoans and single subunit transmembrane proteins in apicomplexans such as TRAP in Plasmodium and MIC2 in Toxoplasma. Here we show that the I domain of TRAP is essential for sporozoite gliding motility, mosquito salivary gland invasion and mouse infection. Its replacement with the I domain from Toxoplasma MIC2 fully restores tissue invasion and parasite transmission, while replacement with the aX I domain from human integrins still partially restores liver infection. Mutations around the ligand binding site allowed salivary gland invasion but led to inefficient transmission to the rodent host. These results suggest that apicomplexan parasites appropriated polyspecific I domains in part for their ability to engage with multiple ligands and to provide traction for emigration into diverse organs in distant phyla. Malaria is an infectious disease caused by single-celled parasites known as Plasmodium. Humans and other animals with backbones – such as birds, reptiles and rodents – can become hosts for these parasites if an infected female mosquito feeds on their blood. Likewise, healthy mosquitoes can in turn become infected with Plasmodium if they feed on the blood of an infected animal. To complete their life cycle, Plasmodium parasites within a mosquito must become spore-like cells called sporozoites. These sporozoites are highly mobile and can get into the mosquitoes’ salivary glands, meaning they can be passed on to a new host when the insect feeds. During a mosquito bite the sporozoites are spat into the skin of the potential host, where they then need to migrate rapidly to enter the bloodstream. Once in the blood, the sporozoites can then get into liver cells and begin a new infection. One protein called TRAP, which is found on the surface of the sporozoites, is important for their migration and the infection of the salivary glands or liver. Yet it was not known how this happens at the level of the individual proteins involved. Klug et al. have now tested how a part of the TRAP protein, called the I domain, contributes to the infection process. In the experiments, the I domain of TRAP was deleted which showed that the sporozoites need this domain to be able to move around and get into the host tissues. Without the I domain the sporozoites were stuck and could not successfully infect either the mosquitoes, the livers of mice, or human liver cells grown in the laboratory. Klug et al. then replaced the Plasmodium I domain of TRAP with the I domain from a distantly related parasite called Toxoplasma gondii, which causes a condition known as toxoplasmosis. The I domain from Toxoplasma allowed the Plasmodium parasites to infect the host tissues again. This observation was unexpected because Toxoplasma and Plasmodium parasites have evolved separately over the last 800 million years and Toxoplasma does not infect insects. These findings suggest that the I domain of TRAP evolved to bind several other proteins in different tissues and hosts. Future studies will investigate which other parasite proteins TRAP works with to guide sporozoites to the salivary glands or liver. Knowledge of how these proteins act together may lead to new approaches for treating or preventing malaria. For example, some treatments could stop sporozoites from entering liver cells.
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Affiliation(s)
- Dennis Klug
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Université de Strasbourg, CNRS UPR9022, INSERM U963, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Sarah Goellner
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Department of Molecular Virology, Heidelberg University Medical School, Heidelberg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Julia Sattler
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Léanne Strauss
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Mirko Singer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Chafen Lu
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
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246
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Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood. mSystems 2020; 5:5/4/e00116-20. [PMID: 32636334 PMCID: PMC7343306 DOI: 10.1128/msystems.00116-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts. Children are highly susceptible to clinical malaria, and in regions where malaria is endemic, their immune systems must face successive encounters with Plasmodium falciparum parasites before they develop immunity, first against severe disease and later against uncomplicated malaria. Understanding cellular and molecular interactions between host and parasites during an infection could provide insights into the processes underlying this gradual acquisition of immunity, as well as to how parasites adapt to infect hosts that are successively more malaria experienced. Here, we describe methods to analyze the host and parasite gene expression profiles generated simultaneously from blood samples collected from five consecutive symptomatic P. falciparum infections in three Malian children. We show that the data generated enable statistical assessment of the proportions of (i) each white blood cell subset and (ii) the parasite developmental stages, as well as investigations of host-parasite gene coexpression. We also use the sequences generated to analyze allelic variations in transcribed regions and determine the complexity of each infection. While limited by the modest sample size, our analyses suggest that host gene expression profiles primarily clustered by individual, while the parasite gene expression profiles seemed to differentiate early from late infections. Overall, this study provides a solid framework to examine the mechanisms underlying acquisition of immunity to malaria infections using whole-blood transcriptome sequencing (RNA-seq). IMPORTANCE We show that dual RNA-seq from patient blood samples allows characterization of host/parasite interactions during malaria infections and can provide a solid framework to study the acquisition of antimalarial immunity, as well as the adaptations of P. falciparum to malaria-experienced hosts.
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247
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Mahapatra RK, Das M. A computational approach to validate novel drug targets of gentianine from Swertiya chirayita in Plasmodium falciparum. Biosystems 2020; 196:104175. [PMID: 32593550 DOI: 10.1016/j.biosystems.2020.104175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 11/27/2022]
Abstract
Gentianine is one of the compounds found in the plant Swertiya chirayita that is known for its antimalarial activity. However, its exact molecular mechanism of action is yet to be understood. In our present study, we applied several computational approaches to filter out and determine possible targets of gentianine in Plasmodium falciparum 3D7. Protein-protein networks formed the basis of one of our strategies along with orthologous protein analysis to establish essentiality. Out of 6 essential proteins from unique pathways, haloacid dehalogenase like-hydrolase (PfHAD1), phosphoenolpyruvate carboxykinase (PfPEPCK) and fumarate hydratase (PfFH) were screened as drug targets through this approach. Through our other strategy we established the predicted IC50 (PIC50) value of gentianine with a set of molecular descriptors from 123 Pathogen Box anti-malarial compounds. Afterwards through 2D structural similarity, L-lactate dehydrogenase (PfLDH) was established as another possible target. In our work, we performed in silico docking and analysed the binding of gentianine to the proteins. All of the proteins were reported with favourable binding results and were considered for complex molecular dynamics simulation approach. Our research clears up the molecular mechanism of antimalarial activity of gentianine to some extent paving way for experimental validation of the same in future.
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Affiliation(s)
- Rajani Kanta Mahapatra
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, 751024, Odisha, India.
| | - Mahin Das
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, 751024, Odisha, India
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248
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Gazanion E, Lacroix L, Alberti P, Gurung P, Wein S, Cheng M, Mergny JL, Gomes AR, Lopez-Rubio JJ. Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites. PLoS Genet 2020; 16:e1008917. [PMID: 32628663 PMCID: PMC7365481 DOI: 10.1371/journal.pgen.1008917] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/16/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, especially within the var gene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in the Plasmodium falciparum genome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved within the closely related Laverania Plasmodium parasites. Under G4-stabilizing conditions, i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that a bona fide G4 found in the non-coding strand of var promoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role in Plasmodium gene expression regulation, sub-telomeric recombination and var gene biology.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
| | - Laurent Lacroix
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Patrizia Alberti
- "Structure and Instability of Genomes" laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, Paris, France
| | - Pratima Gurung
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Sharon Wein
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Mingpan Cheng
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
| | - Jean-Louis Mergny
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
- Institute of Biophysics of the Czech Academy of Sciences, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, France
| | - Ana Rita Gomes
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Jose-Juan Lopez-Rubio
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
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Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase. Nat Commun 2020; 11:3228. [PMID: 32591529 PMCID: PMC7320144 DOI: 10.1038/s41467-020-17013-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/28/2020] [Indexed: 11/21/2022] Open
Abstract
Plasmodium falciparum (Pf) relies solely on the salvage pathway for its purine nucleotide requirements, making this pathway indispensable to the parasite. Purine nucleotide levels are regulated by anabolic processes and by nucleotidases that hydrolyse these metabolites into nucleosides. Certain apicomplexan parasites, including Pf, have an IMP-specific-nucleotidase 1 (ISN1). Here we show, by comprehensive substrate screening, that PfISN1 catalyzes the dephosphorylation of inosine monophosphate (IMP) and is allosterically activated by ATP. Crystal structures of tetrameric PfISN1 reveal complex rearrangements of domain organization tightly associated with catalysis. Immunofluorescence microscopy and expression of GFP-fused protein indicate cytosolic localization of PfISN1 and expression in asexual and gametocyte stages of the parasite. With earlier evidence on isn1 upregulation in female gametocytes, the structures reported in this study may contribute to initiate the design for possible transmission-blocking agents. Plasmodium falciparum IMP-specific 5′-nucleotidase 1 (PfISN1) is of interest as a potential malaria drug target. Here, the authors report that IMP is a substrate, and ATP an allosteric activator, of PfISN1 and present PfISN1 crystal structures in the ligand-free state and bound to either IMP or ATP.
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Muh F, Kim N, Nyunt MH, Firdaus ER, Han JH, Hoque MR, Lee SK, Park JH, Moon RW, Lau YL, Kaneko O, Han ET. Cross-species reactivity of antibodies against Plasmodium vivax blood-stage antigens to Plasmodium knowlesi. PLoS Negl Trop Dis 2020; 14:e0008323. [PMID: 32559186 PMCID: PMC7304578 DOI: 10.1371/journal.pntd.0008323] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is caused by multiple different species of protozoan parasites, and interventions in the pre-elimination phase can lead to drastic changes in the proportion of each species causing malaria. In endemic areas, cross-reactivity may play an important role in the protection and blocking transmission. Thus, successful control of one species could lead to an increase in other parasite species. A few studies have reported cross-reactivity producing cross-immunity, but the extent of cross-reactive, particularly between closely related species, is poorly understood. P. vivax and P. knowlesi are particularly closely related species causing malaria infections in SE Asia, and whilst P. vivax cases are in decline, zoonotic P. knowlesi infections are rising in some areas. In this study, the cross-species reactivity and growth inhibition activity of P. vivax blood-stage antigen-specific antibodies against P. knowlesi parasites were investigated. Bioinformatics analysis, immunofluorescence assay, western blotting, protein microarray, and growth inhibition assay were performed to investigate the cross-reactivity. P. vivax blood-stage antigen-specific antibodies recognized the molecules located on the surface or released from apical organelles of P. knowlesi merozoites. Recombinant P. vivax and P. knowlesi proteins were also recognized by P. knowlesi- and P. vivax-infected patient antibodies, respectively. Immunoglobulin G against P. vivax antigens from both immune animals and human malaria patients inhibited the erythrocyte invasion by P. knowlesi. This study demonstrates that there is extensive cross-reactivity between antibodies against P. vivax to P. knowlesi in the blood stage, and these antibodies can potently inhibit in vitro invasion, highlighting the potential cross-protective immunity in endemic areas. In recent years, malaria initiatives have increasingly shifted focus from achieving malaria control to achieving malaria elimination. However, the interventions used are leading to drastic changes in the proportions of different Plasmodium species causing clinical infection, particularly within Southeast Asia. Little is known about how these different parasite species interact/compete in nature or whether exposure to one species could cause some level of protection against another. We examined cross-reactive antibody responses to key parasite proteins with roles in red blood cell invasion and identified novel cross-species reactivity among the closest of malaria affecting the human population (P. vivax and P. knowlesi). This comprehensive analysis provides evidence that cross-reactive immunity could play an important role in areas where species distributions are perturbed by malaria control measures, and future efforts to identify the specific cross-reactive epitopes involved would be invaluable both to our understanding of malaria immunity and vaccine development.
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Affiliation(s)
- Fauzi Muh
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Namhyeok Kim
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | | | - Egy Rahman Firdaus
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Mohammad Rafiul Hoque
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Robert W. Moon
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
- * E-mail:
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