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Mac Donagh J, Marchesini A, Spiga A, Fallico MJ, Arrías PN, Monzon AM, Vagiona AC, Gonçalves-Kulik M, Mier P, Andrade-Navarro MA. Structured Tandem Repeats in Protein Interactions. Int J Mol Sci 2024; 25:2994. [PMID: 38474241 DOI: 10.3390/ijms25052994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins.
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Affiliation(s)
- Juan Mac Donagh
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Abril Marchesini
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
- Biotechnology and Molecular Biology Institute (IBBM, UNLP-CONICET), Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Agostina Spiga
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maximiliano José Fallico
- Laboratory of Bioactive Compound Research and Development, Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, Via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Aimilia-Christina Vagiona
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Mariane Gonçalves-Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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Chuang CN, Liu HC, Woo TT, Chao JL, Chen CY, Hu HT, Hsueh YP, Wang TF. Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs. eLife 2024; 12:RP91405. [PMID: 38393970 PMCID: PMC10942620 DOI: 10.7554/elife.91405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including Saccharomyces cerevisiae RNA-mediated transposition and pseudohyphal growth, Candida albicans filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, Tetrahymena thermophila xylan catabolism and meiosis, Dictyostelium discoideum development and sexual cycles, Plasmodium falciparum infection, and the nervous systems of Drosophila melanogaster, Mus musculus and Homo sapiens. We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAAQ and TAGQ codons. Notably, the usage frequency of CAGQ is much lower in ciliates with reassigned TAAQ and TAGQ codons than in organisms with expanded and unstable Q runs (e.g. D. melanogaster and H. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
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Affiliation(s)
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Tai-Ting Woo
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Ju-Lan Chao
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Chiung-Ya Chen
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Hisao-Tang Hu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
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Raghavan M, Kalantar KL, Duarte E, Teyssier N, Takahashi S, Kung AF, Rajan JV, Rek J, Tetteh KKA, Drakeley C, Ssewanyana I, Rodriguez-Barraquer I, Greenhouse B, DeRisi JL. Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections. eLife 2023; 12:e81401. [PMID: 36790168 PMCID: PMC10005774 DOI: 10.7554/elife.81401] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 02/14/2023] [Indexed: 02/16/2023] Open
Abstract
Protection against Plasmodium falciparum, which is primarily antibody-mediated, requires recurrent exposure to develop. The study of both naturally acquired limited immunity and vaccine induced protection against malaria remains critical for ongoing eradication efforts. Towards this goal, we deployed a customized P. falciparum PhIP-seq T7 phage display library containing 238,068 tiled 62-amino acid peptides, covering all known coding regions, including antigenic variants, to systematically profile antibody targets in 198 Ugandan children and adults from high and moderate transmission settings. Repeat elements - short amino acid sequences repeated within a protein - were significantly enriched in antibody targets. While breadth of responses to repeat-containing peptides was twofold higher in children living in the high versus moderate exposure setting, no such differences were observed for peptides without repeats, suggesting that antibody responses to repeat-containing regions may be more exposure dependent and/or less durable in children than responses to regions without repeats. Additionally, short motifs associated with seroreactivity were extensively shared among hundreds of antigens, potentially representing cross-reactive epitopes. PfEMP1 shared motifs with the greatest number of other antigens, partly driven by the diversity of PfEMP1 sequences. These data suggest that the large number of repeat elements and potential cross-reactive epitopes found within antigenic regions of P. falciparum could contribute to the inefficient nature of malaria immunity.
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Affiliation(s)
- Madhura Raghavan
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Elias Duarte
- University of California, BerkeleyBerkeleyUnited States
| | - Noam Teyssier
- University of California, San FranciscoSan FranciscoUnited States
| | - Saki Takahashi
- University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- University of California, San FranciscoSan FranciscoUnited States
| | - Jayant V Rajan
- University of California, San FranciscoSan FranciscoUnited States
| | - John Rek
- Infectious Diseases Research CollaborationKampalaUganda
| | - Kevin KA Tetteh
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Chris Drakeley
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isaac Ssewanyana
- Infectious Diseases Research CollaborationKampalaUganda
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isabel Rodriguez-Barraquer
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Bryan Greenhouse
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph L DeRisi
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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Khurana J, Shrivastava A, Singh A, Gupta A. Exploring potential of Plasmodium RUVBL proteins as anti-malarial drug target. J Biomol Struct Dyn 2023; 41:736-752. [PMID: 34877896 DOI: 10.1080/07391102.2021.2011418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although malaria related cases and deaths have consistently declined over time, growing resistance to existing anti-malarial drugs in Plasmodium remains a matter of extreme concern. Since we rely so heavily on use of chemotherapy for malaria treatment and knowing that all the available anti-malarial drug will become virtually useless in the near future, we have to increase our understanding of basic biology of the parasite as well as characterize new molecular targets that can be exploited for anti-malarial therapy. In the present study, PfRUVBLs (AAA family member proteins) were evaluated for their potential as novel anti-malarial drug target candidates, using computational approaches. Virtual High-throughput screening of various pharmacophore libraries obtained from three different databases (which included, Asinex, ZINC15 & PubChem) followed by extra precision docking, resulted in identification of relevant hit compounds that showed binding affinity with the active region of PfRUVBL1 protein. Based on molecular docking data, MD simulations, and protein-ligand interaction studies, combined with toxicity assessment & ADME profiling data, at least three best hits were eventually identified that could be novel potent inhibitors of PfRUVBL1 protein and can be further tested for anti-malarial activity using in vitro protocols. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juhi Khurana
- Epigenetics and Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashish Shrivastava
- Bioinformatics Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashutosh Singh
- Bioinformatics Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Ashish Gupta
- Epigenetics and Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
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Nema S, Krishna S, Tiwari A, Bharti PK. Limited genetic diversity and expression profile of Plasmodium falciparum haem detoxification protein: a possible diagnostic target. Trans R Soc Trop Med Hyg 2022; 116:1162-1171. [PMID: 35724244 DOI: 10.1093/trstmh/trac055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/11/2022] [Accepted: 05/21/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Haem detoxification protein (HDP) is a significant protein in the erythrocytic stage of the Plasmodium lifecycle. HDP could be of paramount interest as a diagnostic biomarker for accurate diagnosis of malaria. We thus explored HDP genetic variation, expression levels of HDP and immune response. METHODS Phylogenetic analysis was carried out using Pfhdp orthologues sequences of various Plasmodium species. Blood samples were collected from patients in central India. Pfhdp gene was amplified, and sequenced by sanger DNA sequencing. B-cell epitopes were identified in PfHDP using Bepipred Linear Epitope Prediction 2.0, and median-joining network was constructed using global PfHDP sequences. Pfhdp expression levels during erythrocytic stage were assessed using real-time qPCR at 4-h intervals. An IgG immune response against synthetic PfHDP peptides was analysed using ELISA. RESULTS Phylogenetic analysis revealed the conserved nature of Pfhdp gene. Diversity analysis revealed one non-synonymous mutation (F91L) among all isolates. Neutrality tests indicated negative selection for Pfhdp gene. HDP was expressed throughout the erythrocytic cycle, and comparatively, high expression was observed in the late trophozoite and schizont stages. High IgG response against both peptides was observed, and no polymorphism was seen in any of the seven predicted B-cell epitopes. CONCLUSIONS Findings of the present study indicate the possibility of HDP being exploited as a diagnostic biomarker for Plasmodium falciparum malaria after proteomic validation studies.
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Affiliation(s)
- Shrikant Nema
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India.,School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University of Madhya Pradesh), Bhopal, 462 023, Madhya Pradesh, India
| | - Sri Krishna
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India
| | - Archana Tiwari
- School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University of Madhya Pradesh), Bhopal, 462 023, Madhya Pradesh, India
| | - Praveen Kumar Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India
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Cascarina SM, Ross ED. The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins. Bioinformatics 2022; 38:5446-5448. [PMID: 36282522 PMCID: PMC9750097 DOI: 10.1093/bioinformatics/btac699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 12/25/2022] Open
Abstract
SUMMARY Low-complexity domains (LCDs) in proteins are regions enriched in a small subset of amino acids. LCDs exist in all domains of life, often have unusual biophysical behavior, and function in both normal and pathological processes. We recently developed an algorithm to identify LCDs based predominantly on amino acid composition thresholds. Here, we have integrated this algorithm with a webserver and augmented it with additional analysis options. Specifically, users can (i) search for LCDs in whole proteomes by setting minimum composition thresholds for individual or grouped amino acids, (ii) submit a known LCD sequence to search for similar LCDs, (iii) search for and plot LCDs within a single protein, (iv) statistically test for enrichment of LCDs within a user-provided protein set and (v) specifically identify proteins with multiple types of LCDs. AVAILABILITY AND IMPLEMENTATION The LCD-Composer server can be accessed at http://lcd-composer.bmb.colostate.edu. The corresponding command-line scripts can be accessed at https://github.com/RossLabCSU/LCD-Composer/tree/master/WebserverScripts.
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Affiliation(s)
| | - Eric D Ross
- To whom correspondence should be addressed. or
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7
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de Jong RM, Singh SK, Teelen K, van de Vegte-Bolmer M, van Gemert GJ, Stone WJR, Locke E, Plieskatt J, Theisen M, Bousema T, Jore MM. Heterologous Expression and Evaluation of Novel Plasmodium falciparum Transmission Blocking Vaccine Candidates. Front Immunol 2022; 13:909060. [PMID: 35812379 PMCID: PMC9259988 DOI: 10.3389/fimmu.2022.909060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022] Open
Abstract
Malaria transmission blocking vaccines (TBV) aim to induce antibodies that can interrupt Plasmodium falciparum development in the mosquito midgut and thereby prevent onward malaria transmission. A limited number of TBV candidates have been identified and only three (Pfs25, Pfs230 and Pfs48/45) have entered clinical testing. While one of these candidates may emerge as a highly potent TBV candidate, it is premature to determine if they will generate sufficiently potent and sustained responses. It is therefore important to explore novel candidate antigens. We recently analyzed sera from naturally exposed individuals and found that the presence and/or intensity of antibodies against 12 novel putative surface expressed gametocyte antigens was associated with transmission reducing activity. In this study, protein fragments of these novel TBV candidates were designed and heterologously expressed in Drosophila melanogaster S2 cells and Lactococcus lactis. Eleven protein fragments, covering seven TBV candidates, were successfully produced. All tested antigens were recognized by antibodies from individuals living in malaria-endemic areas, indicating that native epitopes are present. All antigens induced antigen-specific antibody responses in mice. Two antigens induced antibodies that recognized a native protein in gametocyte extract, and antibodies elicited by four antigens recognized whole gametocytes. In particular, we found that antigen Pf3D7_0305300, a putative transporter, is abundantly expressed on the surface of gametocytes. However, none of the seven novel TBV candidates expressed here induced an antibody response that reduced parasite development in the mosquito midgut as assessed in the standard membrane feeding assay. Altogether, the antigen fragments used in this study did not prove to be promising transmission blocking vaccine constructs, but led to the identification of two gametocyte surface proteins that may provide new leads for studying gametocyte biology.
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Affiliation(s)
- Roos M. de Jong
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susheel K. Singh
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Karina Teelen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Geert-Jan van Gemert
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Will J. R. Stone
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emily Locke
- PATH‘s Malaria Vaccine Initiative, Washington, DC, United States
| | - Jordan Plieskatt
- PATH‘s Malaria Vaccine Initiative, Washington, DC, United States
| | - Michael Theisen
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Matthijs M. Jore
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- *Correspondence: Matthijs M. Jore,
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Jaramillo Ponce JR, Kapps D, Paulus C, Chicher J, Frugier M. Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein. J Biol Chem 2022; 298:101987. [PMID: 35487244 PMCID: PMC9136112 DOI: 10.1016/j.jbc.2022.101987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multisynthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that participates in tRNA trafficking; we show that tRip also functions as an AIMP. We identified three aaRSs, the glutamyl-tRNA synthetase (ERS), glutaminyl-tRNA synthetase (QRS), and methionyl-tRNA synthetase (MRS), which were specifically coimmunoprecipitated with tRip in Plasmodium berghei blood stage parasites. All four proteins contain an N-terminal glutathione-S-transferase (GST)-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip-ERS-QRS) and the M-complex (tRip-ERS-MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together, our results demonstrate that neither the singular homodimerization of tRip nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.
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Affiliation(s)
- José R Jaramillo Ponce
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Delphine Kapps
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Caroline Paulus
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Johana Chicher
- Strasbourg-Esplanade Proteomics Facility, Université de Strasbourg, Strasbourg, France
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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Genetic Diversity, Repeat Motifs, and Natural Selection at the C-Terminal Knob-Associated Histidine Rich Protein (KAHRP) of Plasmodium falciparum Clinical Samples from Saudi Arabia. J Trop Med 2022; 2022:3740889. [PMID: 35387278 PMCID: PMC8979686 DOI: 10.1155/2022/3740889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Malaria is still a public health problem in Saudi Arabia specifically in the Jazan region. Plasmodium falciparum knob-associated histidine-rich proteins (PfKAHRPs) play an important role in cerebral malaria pathophysiology as well as pathogenesis of P. falciparum infections. The repeat region of PfKAHRP C-terminal interaction domain has been found to bind to the infected red blood cells and the vascular endothelium. Thus, this study aimed to assess the allelic variations, genetic diversity, and natural selection acting at the C-terminal PfKAHRP between parasite isolates from Saudi Arabia. Materials and Methods The PfKHARP C-terminal interaction domain was successfully PCR-amplified and sequence data from 441 clinical isolates from Saudi Arabia were obtained. The DnaSP v5.10 software was used to determine the genetic diversity, polymorphism, haplotype, and natural selection. Haplotype network analysis was constructed by using the median-joining method in the NETWORK version 5.0.0.1 software. Results Alignment and analysis of 441 C-terminal PfKAHRP-deduced amino acid sequences identified 5 genotypes (I–V) based on the decapeptide repeat arrangements (TKEASTSKEA, TKEASTSKGA, TKEASTTEGA, and TKEASTSKRA). Among the repeat types, Type I (49.43%, 218/441) was the most abundant in Saudi Arabia, followed by Type II (48.29%, 213/441). Overall, the nucleotide diversity in the PfKHARP C-terminal region was found to be low in Saudi Arabia (π = 0.00142); however, natural selection tests indicated positive selection (dN-dS = 1.64, P < 0.05) which was due to the variations within the repeat motifs. Genealogical relationship haplotype network of PfKAHRP from 4 different countries (i.e., Saudi Arabia, Iran, Burundi, and India) revealed 1 major shared haplotype cluster (H_1) with samples representative from all 4 countries (Saudi Arabia; n = 441, Burundi; n = 4, Iran; n = 13, and India; n = 1). Conclusion Since this is the first study to report on genetic diversity of C-terminal PfKAHRP interaction domain and the repeat motifs from clinical samples in Saudi Arabia, it will contribute towards the rational design of antiadhesion drug therapies for P. falciparum malaria.
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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Affiliation(s)
- Myo T. Naung
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Elijah Martin
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Jacob Munro
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Somya Mehra
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Andrew J. Guy
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - G. L. Abby Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Livingstone Tavul
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel Hetzel
- Swiss Tropical Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dominic Kwiatkowski
- Sanger Institute, Hinxton, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Division of Parasites and Insect Vectors, Pasteur Institute, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
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11
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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12
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Dumetz F, Chow EYC, Harris LM, Liew SW, Jensen A, Umar MI, Chung B, Chan TF, Merrick CJ, Kwok CK. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2021; 49:12486-12501. [PMID: 34792144 PMCID: PMC8643661 DOI: 10.1093/nar/gkab1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
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Affiliation(s)
- Franck Dumetz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eugene Yui-Ching Chow
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Anders Jensen
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Betty Chung
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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13
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Cook AD, Roberts AJ, Atherton J, Tewari R, Topf M, Moores CA. Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. J Biol Chem 2021; 297:101063. [PMID: 34375637 PMCID: PMC8526983 DOI: 10.1016/j.jbc.2021.101063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
Plasmodium parasites cause malaria and are responsible annually for hundreds of thousands of deaths. Kinesins are a superfamily of microtubule-dependent ATPases that play important roles in the parasite replicative machinery, which is a potential target for antiparasite drugs. Kinesin-5, a molecular motor that cross-links microtubules, is an established antimitotic target in other disease contexts, but its mechanism in Plasmodium falciparum is unclear. Here, we characterized P. falciparum kinesin-5 (PfK5) using cryo-EM to determine the motor's nucleotide-dependent microtubule-bound structure and introduced 3D classification of individual motors into our microtubule image processing pipeline to maximize our structural insights. Despite sequence divergence in PfK5, the motor exhibits classical kinesin mechanochemistry, including ATP-induced subdomain rearrangement and cover neck bundle formation, consistent with its plus-ended directed motility. We also observed that an insertion in loop5 of the PfK5 motor domain creates a different environment in the well-characterized human kinesin-5 drug-binding site. Our data reveal the possibility for selective inhibition of PfK5 and can be used to inform future exploration of Plasmodium kinesins as antiparasite targets.
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Affiliation(s)
- Alexander D Cook
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Joseph Atherton
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Rita Tewari
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom.
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14
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Cela M, Théobald-Dietrich A, Rudinger-Thirion J, Wolff P, Geslain R, Frugier M. Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip. Nucleic Acids Res 2021; 49:10618-10629. [PMID: 34530443 PMCID: PMC8501954 DOI: 10.1093/nar/gkab769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 12/19/2022] Open
Abstract
Malaria is a life-threatening and devastating parasitic disease. Our previous work showed that parasite development requires the import of exogenous transfer RNAs (tRNAs), which represents a novel and unique form of host-pathogen interaction, as well as a potentially druggable target. This import is mediated by tRip (tRNA import protein), a membrane protein located on the parasite surface. tRip displays an extracellular domain homologous to the well-characterized OB-fold tRNA-binding domain, a structural motif known to indiscriminately interact with tRNAs. We used MIST (Microarray Identification of Shifted tRNAs), a previously established in vitro approach, to systematically assess the specificity of complexes between native Homo sapiens tRNAs and recombinant Plasmodium falciparum tRip. We demonstrate that tRip unexpectedly binds to host tRNAs with a wide range of affinities, suggesting that only a small subset of human tRNAs is preferentially imported into the parasite. In particular, we show with in vitro transcribed constructs that tRip does not bind specific tRNAs solely based on their primary sequence, hinting that post-transcriptional modifications modulate the formation of our host/parasite molecular complex. Finally, we discuss the potential utilization of the most efficient tRip ligands for the translation of the parasite's genetic information.
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Affiliation(s)
- Marta Cela
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Anne Théobald-Dietrich
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, SC, USA
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000Strasbourg, France
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15
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Siqueira WF, Viana AG, Reis Cunha JL, Rosa LM, Bueno LL, Bartholomeu DC, Cardoso MS, Fujiwara RT. The increased presence of repetitive motifs in the KDDR-plus recombinant protein, a kinesin-derived antigen from Leishmania infantum, improves the diagnostic performance of serological tests for human and canine visceral leishmaniasis. PLoS Negl Trop Dis 2021; 15:e0009759. [PMID: 34534217 PMCID: PMC8480608 DOI: 10.1371/journal.pntd.0009759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/29/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Visceral leishmaniasis (VL) is caused by protozoa belonging to the Leishmania donovani complex and is considered the most serious and fatal form among the different types of leishmaniasis, if not early diagnosed and treated. Among the measures of disease control stand out the management of infected dogs and the early diagnosis and appropriate treatment of human cases. Several antigens have been characterized for use in the VL diagnosis, among them are the recombinant kinesin-derived antigens from L. infantum, as rK39 and rKDDR. The main difference between these antigens is the size of the non-repetitive kinesin region and the number of repetitions of the 39 amino acid degenerate motif (6.5 and 8.5 repeats in rK39 and rKDDR, respectively). This repetitive region has a high antigenicity score. To evaluate the effect of increasing the number of repeats on diagnostic performance, we designed the rKDDR-plus antigen, containing 15.3 repeats of the 39 amino acid degenerate motif, besides the absence of the non-repetitive portion from L. infantum kinesin. Its performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and rapid immunochromatographic test (ICT), and compared with the kinesin-derived antigens (rKDDR and rK39). In ELISA with human sera, all recombinant antigens had a sensitivity of 98%, whereas the specificity for rKDDR-plus, rKDDR and rK39 was 100%, 96% and 71%, respectively. When evaluated canine sera, the ELISA sensitivity was 97% for all antigens, and the specificity for rKDDR-plus, rKDDR and rK39 was 98%, 91% and 83%, respectively. Evaluation of the ICT/rKDDR-plus, using human sera, showed greater diagnostic sensitivity (90%) and specificity (100%), when compared to the IT LEISH (79% and 98%, respectively), which is based on the rK39 antigen. These results suggest that the increased presence of repetitive motifs in the rKDDR-plus protein improves the diagnostic performance of serological tests by increasing the specificity and accuracy of the diagnosis.
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Affiliation(s)
- Williane Fernanda Siqueira
- Programa de Pós-graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Agostinho Gonçalves Viana
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João Luís Reis Cunha
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leticia Mansur Rosa
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lilian Lacerda Bueno
- Programa de Pós-graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniella Castanheira Bartholomeu
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana Santos Cardoso
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo Toshio Fujiwara
- Programa de Pós-graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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16
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Michelow IC, Park S, Tsai SW, Rayta B, Pasaje CFA, Nelson S, Early AM, Frosch AP, Ayodo G, Raj DK, Nixon CE, Nixon CP, Pond-Tor S, Friedman JF, Fried M, Duffy PE, Le Roch KG, Niles JC, Kurtis JD. A newly characterized malaria antigen on erythrocyte and merozoite surfaces induces parasite inhibitory antibodies. J Exp Med 2021; 218:e20200170. [PMID: 34342640 PMCID: PMC8340565 DOI: 10.1084/jem.20200170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
We previously identified a Plasmodium falciparum (Pf) protein of unknown function encoded by a single-copy gene, PF3D7_1134300, as a target of antibodies in plasma of Tanzanian children in a whole-proteome differential screen. Here we characterize this protein as a blood-stage antigen that localizes to the surface membranes of both parasitized erythrocytes and merozoites, hence its designation as Pf erythrocyte membrane and merozoite antigen 1 (PfEMMA1). Mouse anti-PfEMMA1 antisera and affinity-purified human anti-PfEMMA1 antibodies inhibited growth of P. falciparum strains by up to 68% in growth inhibition assays. Following challenge with uniformly fatal Plasmodium berghei (Pb) ANKA, up to 40% of mice immunized with recombinant PbEMMA1 self-cured, and median survival of lethally infected mice was up to 2.6-fold longer than controls (21 vs. 8 d, P = 0.005). Furthermore, high levels of naturally acquired human anti-PfEMMA1 antibodies were associated with a 46% decrease in parasitemia over 2.5 yr of follow-up of Tanzanian children. Together, these findings suggest that antibodies to PfEMMA1 mediate protection against malaria.
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MESH Headings
- Animals
- Antibodies, Protozoan/immunology
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Antigens, Protozoan/metabolism
- Child, Preschool
- Erythrocyte Membrane/parasitology
- Female
- Host-Parasite Interactions/physiology
- Humans
- Infant
- Malaria Vaccines/genetics
- Malaria Vaccines/immunology
- Malaria, Falciparum/immunology
- Malaria, Falciparum/mortality
- Malaria, Falciparum/parasitology
- Merozoites/immunology
- Merozoites/metabolism
- Mice, Inbred BALB C
- Plasmodium falciparum/immunology
- Plasmodium falciparum/pathogenicity
- Plasmodium falciparum/physiology
- Polymorphism, Single Nucleotide
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Protozoan Proteins/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- Tanzania
- Mice
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Affiliation(s)
- Ian C. Michelow
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Sangshin Park
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Graduate School of Urban Public Health & Department of Urban Big Data Convergence, University of Seoul, Seoul, Republic of Korea
| | - Shu-Whei Tsai
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Bonnie Rayta
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | | | - Sara Nelson
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Angela M. Early
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Anne P. Frosch
- Department of Medicine, Hennepin Healthcare Research Institute, University of Minnesota, Minneapolis, MN
| | - George Ayodo
- Kenya Medical Research Institute, Centre of Global Health Research, Kisumu, Kenya
- Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Dipak K. Raj
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Christina E. Nixon
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Christian P. Nixon
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Sunthorn Pond-Tor
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Jennifer F. Friedman
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pediatrics, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Patrick E. Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, University of California, Riverside, Riverside, CA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Jonathan D. Kurtis
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
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17
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Structural-functional diversity of malaria parasite's PfHSP70-1 and PfHSP40 chaperone pair gives an edge over human orthologs in chaperone-assisted protein folding. Biochem J 2021; 477:3625-3643. [PMID: 32893851 DOI: 10.1042/bcj20200434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Plasmodium falciparum, the human malaria parasite harbors a metastable proteome which is vulnerable to proteotoxic stress conditions encountered during its lifecycle. How parasite's chaperone machinery is able to maintain its aggregation-prone proteome in functional state, is poorly understood. As HSP70-40 system forms the central hub in cellular proteostasis, we investigated the protein folding capacity of PfHSP70-1 and PfHSP40 chaperone pair and compared it with human orthologs (HSPA1A and DNAJA1). Despite the structural similarity, we observed that parasite chaperones and their human orthologs exhibit striking differences in conformational dynamics. Comprehensive biochemical investigations revealed that PfHSP70-1 and PfHSP40 chaperone pair has better protein folding, aggregation inhibition, oligomer remodeling and disaggregase activities than their human orthologs. Chaperone-swapping experiments suggest that PfHSP40 can also efficiently cooperate with human HSP70 to facilitate the folding of client-substrate. SPR-derived kinetic parameters reveal that PfHSP40 has higher binding affinity towards unfolded substrate than DNAJA1. Interestingly, the observed slow dissociation rate of PfHSP40-substrate interaction allows PfHSP40 to maintain the substrate in folding-competent state to minimize its misfolding. Structural investigation through small angle x-ray scattering gave insights into the conformational architecture of PfHSP70-1 (monomer), PfHSP40 (dimer) and their complex. Overall, our data suggest that the parasite has evolved functionally diverged and efficient chaperone machinery which allows the human malaria parasite to survive in hostile conditions. The distinct allosteric landscapes and interaction kinetics of plasmodial chaperones open avenues for the exploration of small-molecule based antimalarial interventions.
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18
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Songsaigath S, Makiuchi T, Putaporntip C, Pattanawong U, Kuamsab N, Tachibana H, Jongwutiwes S. Immunoglobulin G responses to variant forms of Plasmodium vivax merozoite surface protein 9 upon natural infection in Thailand. Sci Rep 2021; 11:3201. [PMID: 33547377 PMCID: PMC7864938 DOI: 10.1038/s41598-021-82928-4] [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: 09/17/2020] [Accepted: 01/25/2021] [Indexed: 11/30/2022] Open
Abstract
Merozoite surface protein 9 (MSP9) constitutes a ligand complex involved in erythrocyte invasion by malarial merozoites and is a promising vaccine target. Plasmodium vivax MSP9 (PvMSP9) is immunogenic upon natural malaria exposure. To address whether sequence diversity in PvMSP9 among field isolates could affect natural antibody responses, the recombinant proteins representing two variants each for the N- and the C-terminal domains of PvMSP-9 were used as antigens to assess antibody reactivity among 246 P. vivax-infected patients’ sera from Tak and Ubon Ratchathani Provinces in Thailand. Results revealed that the seropositivity rates of IgG antibodies to the N-terminal antigens were higher than those to the C-terminal antigens (87.80% vs. 67.48%). Most seropositive sera were reactive to both variants, suggesting the presence of common epitopes. Variant-specific antibodies to the N- and the C-terminal antigens were detected in 15.85% and 16.70% of serum samples, respectively. These seropositivity rates were not significant difference between provinces. The seropositivity rates, levels and avidity of anti-PvMSP9 antibodies exhibited positive trends towards increasing malaria episodes. The IgG isotype responses to the N- and the C-terminal antigens were mainly IgG1 and IgG3. The profile of IgG responses may have implications for development of PvMSP9-based vaccine.
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Affiliation(s)
- Sunisa Songsaigath
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Takashi Makiuchi
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Urassaya Pattanawong
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Napaporn Kuamsab
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hiroshi Tachibana
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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19
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Mills B, Isaac RE, Foster R. Metalloaminopeptidases of the Protozoan Parasite Plasmodium falciparum as Targets for the Discovery of Novel Antimalarial Drugs. J Med Chem 2021; 64:1763-1785. [PMID: 33534577 DOI: 10.1021/acs.jmedchem.0c01721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Malaria poses a significant threat to approximately half of the world's population with an annual death toll close to half a million. The emergence of resistance to front-line antimalarials in the most lethal human parasite species, Plasmodium falciparum (Pf), threatens progress made in malaria control. The prospect of losing the efficacy of antimalarial drugs is driving the search for small molecules with new modes of action. Asexual reproduction of the parasite is critically dependent on the recycling of amino acids through catabolism of hemoglobin (Hb), which makes metalloaminopeptidases (MAPs) attractive targets for the development of new drugs. The Pf genome encodes eight MAPs, some of which have been found to be essential for parasite survival. In this article, we discuss the biological structure and function of each MAP within the Pf genome, along with the drug discovery efforts that have been undertaken to identify novel antimalarial candidates of therapeutic value.
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Affiliation(s)
- Belinda Mills
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
| | - R Elwyn Isaac
- School of Biology, University of Leeds, Leeds, U.K., LS2 9JT
| | - Richard Foster
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
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20
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Kucharska I, Thai E, Srivastava A, Rubinstein JL, Pomès R, Julien JP. Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11. eLife 2020; 9:e59018. [PMID: 33253113 PMCID: PMC7704109 DOI: 10.7554/elife.59018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, and the partial efficacy of RTS,S/AS01 - the leading malaria vaccine against P. falciparum (Pf) - has been associated with the humoral response against the repeats. Although structural details of antibody recognition of PfCSP have recently emerged, the molecular basis of antibody-mediated inhibition of other Plasmodium species via CSP binding remains unclear. Here, we analyze the structure and molecular interactions of potent monoclonal antibody (mAb) 3D11 binding to P. berghei CSP (PbCSP) using molecular dynamics simulations, X-ray crystallography, and cryoEM. We reveal that mAb 3D11 can accommodate all subtle variances of the PbCSP repeating motifs, and, upon binding, induces structural ordering of PbCSP through homotypic interactions. Together, our findings uncover common mechanisms of antibody evolution in mammals against the CSP repeats of Plasmodium sporozoites.
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Affiliation(s)
- Iga Kucharska
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
| | - Elaine Thai
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Ananya Srivastava
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - John L Rubinstein
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Medical Biophysics, University of TorontoTorontoCanada
| | - Régis Pomès
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Immunology, University of TorontoTorontoCanada
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21
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Subdominance in Antibody Responses: Implications for Vaccine Development. Microbiol Mol Biol Rev 2020; 85:85/1/e00078-20. [PMID: 33239435 DOI: 10.1128/mmbr.00078-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vaccines work primarily by eliciting antibodies, even when recovery from natural infection depends on cellular immunity. Large efforts have therefore been made to identify microbial antigens that elicit protective antibodies, but these endeavors have encountered major difficulties, as witnessed by the lack of vaccines against many pathogens. This review summarizes accumulating evidence that subdominant protein regions, i.e., surface-exposed regions that elicit relatively weak antibody responses, are of particular interest for vaccine development. This concept may seem counterintuitive, but subdominance may represent an immune evasion mechanism, implying that the corresponding region potentially is a key target for protective immunity. Following a presentation of the concepts of immunodominance and subdominance, the review will present work on subdominant regions in several major human pathogens: the protozoan Plasmodium falciparum, two species of pathogenic streptococci, and the dengue and influenza viruses. Later sections are devoted to the molecular basis of subdominance, its potential role in immune evasion, and general implications for vaccine development. Special emphasis will be placed on the fact that a whole surface-exposed protein domain can be subdominant, as demonstrated for all of the pathogens described here. Overall, the available data indicate that subdominant protein regions are of much interest for vaccine development, not least in bacterial and protozoal systems, for which antibody subdominance remains largely unexplored.
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Kanoi BN, Nagaoka H, Morita M, Tsuboi T, Takashima E. Leveraging the wheat germ cell-free protein synthesis system to accelerate malaria vaccine development. Parasitol Int 2020; 80:102224. [PMID: 33137499 DOI: 10.1016/j.parint.2020.102224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/04/2020] [Accepted: 09/16/2020] [Indexed: 01/29/2023]
Abstract
Vaccines against infectious diseases have had great successes in the history of public health. Major breakthroughs have occurred in the development of vaccine-based interventions against viral and bacterial pathogens through the application of classical vaccine design strategies. In contrast the development of a malaria vaccine has been slow. Plasmodium falciparum malaria affects millions of people with nearly half of the world population at risk of infection. Decades of dedicated research has taught us that developing an effective vaccine will be time consuming, challenging, and expensive. Nevertheless, recent advancements such as the optimization of robust protein synthesis platforms, high-throughput immunoscreening approaches, reverse vaccinology, structural design of immunogens, lymphocyte repertoire sequencing, and the utilization of artificial intelligence, have renewed the prospects of an accelerated discovery of the key antigens in malaria. A deeper understanding of the major factors underlying the immunological and molecular mechanisms of malaria might provide a comprehensive approach to identifying novel and highly efficacious vaccines. In this review we discuss progress in novel antigen discoveries that leverage on the wheat germ cell-free protein synthesis system (WGCFS) to accelerate malaria vaccine development.
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Affiliation(s)
- Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
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23
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Insights into the molecular diversity of Plasmodium vivax merozoite surface protein-3γ (pvmsp3γ), a polymorphic member in the msp3 multi-gene family. Sci Rep 2020; 10:10977. [PMID: 32620822 PMCID: PMC7335089 DOI: 10.1038/s41598-020-67222-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Plasmodium vivax merozoite surface protein 3 (PvMSP3) is encoded by a multi-gene family. Of these, PvMSP3α, PvMSP3β and PvMSP3γ, are considered to be vaccine targets. Despite comprehensive analyses of PvMSP3α and PvMSP3β, little is known about structural and sequence diversity in PvMSP3γ. Analysis of 118 complete pvmsp3γ sequences from diverse endemic areas of Thailand and 9 reported sequences has shown 86 distinct haplotypes. Based on variation in insert domains, pvmsp3γ can be classified into 3 types, i.e. Belem, Salvador I and NR520. Imperfect nucleotide repeats were found in six regions of the gene; none encoded tandem amino acid repeats. Predicted coiled-coil heptad repeats were abundant in the protein and displayed variation in length and location. Interspersed phase shifts occurred in the heptad arrays that may have an impact on protein structure. Polymorphism in pvmsp3γ seems to be generated by intragenic recombination and driven by natural selection. Most P. vivax isolates in Thailand exhibit population structure, suggesting limited gene flow across endemic areas. Phylogenetic analysis has suggested that insert domains could have been subsequently acquired during the evolution of pvmsp3γ. Sequence and structural diversity of PvMSP3γ may complicate vaccine design due to alteration in predicted immunogenic epitopes among variants.
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Mier P, Elena-Real C, Urbanek A, Bernadó P, Andrade-Navarro MA. The importance of definitions in the study of polyQ regions: A tale of thresholds, impurities and sequence context. Comput Struct Biotechnol J 2020; 18:306-313. [PMID: 32071707 PMCID: PMC7016039 DOI: 10.1016/j.csbj.2020.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/13/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
Polyglutamine (polyQ) regions are one of the most prevalent homorepeats in eukaryotes. It is however difficult to evaluate their prevalence because various studies claim different results. The reason is the lack of a consensus to define what is indeed a polyQ region. We have tackled this issue by studying how the use of different thresholds (i.e., minimum number of glutamines required in a protein region of a given size), to detect polyQ regions in the human proteome influences not only their prevalence but also their general features and sequence context. Threshold definition shapes the length distribution of the polyQ dataset, and changes the observed number and position of impurities (amino acids other than glutamine) within polyQ regions. Irrespective of the chosen threshold, leucine and proline residues are enriched both within and around polyQ. While leucine is enriched at the N-terminus of polyQ and specially at position -1 (amino acid preceding the polyQ), proline is prevalent in the C-terminus (positions +1 to +5, that is, the first five amino acids after the polyQ). We also checked the suitability of these thresholds for other species, and compared their polyQ features with those found in humans. As the sequence context and features of polyQ regions are threshold-dependent, we propose a method to quickly scan the polyQ landscape of a proteome. We complement our results with a summarized overview about which biases are to be expected per threshold when studying polyQ regions.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Carlos Elena-Real
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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25
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Pramanik S, Thaker M, Perumal AG, Ekambaram R, Poondla N, Schmidt M, Kim PS, Kutzner A, Heese K. Proteomic Atomics Reveals a Distinctive Uracil-5-Methyltransferase. Mol Inform 2020; 39:e1900135. [PMID: 31943843 DOI: 10.1002/minf.201900135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022]
Abstract
Carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and sulfur (S) atoms intrigue as they are the foundation for amino acid (AA) composition and the folding and functions of proteins and thus define and control the survival of a cell, the smallest unit of life. Here, we calculated the proteomic atom distribution in >1500 randomly selected species across the entire current phylogenetic tree and identified uracil-5-methyltransferase (U5MTase) of the protozoan parasite Plasmodium falciparum (Pf, strain Pf3D7), with a distinct atom and AA distribution pattern. We determined its apicoplast location and in silico 3D protein structure to refocus attention exclusively on U5MTase with tremendous potential for therapeutic intervention in malaria. Around 300 million clinical cases of malaria occur each year in tropical and subtropical regions of the world, resulting in over one million deaths annually, placing malaria among the most serious infectious diseases. Genomic and proteomic research of the clades of parasites containing Pf is progressing slowly and the functions of most of the ∼5300 genes are still unknown. We applied a 'bottom-up' comparative proteomic atomics analysis across the phylogenetic tree to visualize a protein molecule on its actual basis - i. e., its atomic level. We identified a protruding Pf3D7-specific U5MTase, determined its 3D protein structure, and identified potential inhibitory drug molecules through in silico drug screening that might serve as possible remedies for the treatment of malaria. Besides, this atomic-based proteome map provides a unique approach for the identification of parasite-specific proteins that could be considered as novel therapeutic targets.
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Affiliation(s)
- Subrata Pramanik
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 1, 33-791, Republic of Korea.,Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, Aachen, 52074, Germany
| | - Manisha Thaker
- Department of Medicine, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Ananda Gopu Perumal
- Technology Business Incubator, Periyar Maniammai Institute of Science and Technology, Vallam, Thanjavur, 613403, Tamil Nadu, India
| | - Rajasekaran Ekambaram
- Department of Chemistry, V.S.B. Engineering College, 67 Covai Road, Karudayampalayam Post, Karur, 639111, Tamil Nadu, India
| | - Naresh Poondla
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 1, 33-791, Republic of Korea
| | - Markus Schmidt
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Pok-Son Kim
- Department of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 1, 36-702, Republic of Korea
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 1, 33-791, Republic of Korea
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26
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Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to immune escape mechanisms. BMC STRUCTURAL BIOLOGY 2019; 19:6. [PMID: 30917807 PMCID: PMC6437935 DOI: 10.1186/s12900-019-0104-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/07/2019] [Indexed: 01/24/2023]
Abstract
Background Plasmodium vivax merozoite surface protein 3α (PvMSP3α) is a promising vaccine candidate which has shown strong association with immunogenicity and protectiveness. Its use is however complicated by evolutionary plasticity features which enhance immune evasion. Low complexity regions (LCRs) provide plasticity in surface proteins of Plasmodium species, but its implication in vaccine design remain unexplored. Here population genetic, comparative phylogenetic and structural biology analysis was performed on the gene encoding PvMSP3α. Results Three LCRs were found in PvMSP3α block II. Both the predicted tertiary structure of the protein and the phylogenetic trees based on this region were influenced by the presence of the LCRs. The LCRs were mainly B cell epitopes within or adjacent. In addition a repeat motif mimicking one of the B cell epitopes was found within the PvMSP3a block II low complexity region. This particular B cell epitope also featured rampant alanine substitutions which might impair antibody binding. Conclusion The findings indicate that PvMSP3α block II possesses LCRs which might confer a strong phenotypic plasticity. The phenomenon of phenotypic plasticity and implication of LCRs in malaria immunology in general and vaccine candidate genes in particular merits further exploration. Electronic supplementary material The online version of this article (10.1186/s12900-019-0104-0) contains supplementary material, which is available to authorized users.
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27
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Sironi M, Forni D, Clerici M, Cagliani R. Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins. Sci Rep 2018; 8:14682. [PMID: 30279439 PMCID: PMC6168477 DOI: 10.1038/s41598-018-33049-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/19/2018] [Indexed: 11/19/2022] Open
Abstract
Plasmodium parasites exerted a strong selective pressure on primate genomes and mutations in genes encoding erythrocyte cytoskeleton proteins (ECP) determine protective effects against Plasmodium infection/pathogenesis. We thus hypothesized that ECP-encoding genes have evolved in response to Plasmodium-driven selection. We analyzed the evolutionary history of 15 ECP-encoding genes in primates, as well as of their Plasmodium-encoded ligands (KAHRP, MESA and EMP3). Results indicated that EPB42, SLC4A1, and SPTA1 evolved under pervasive positive selection and that episodes of positive selection tended to occur more frequently in primate species that host a larger number of Plasmodium parasites. Conversely, several genes, including ANK1 and SPTB, displayed extensive signatures of purifying selection in primate phylogenies, Homininae lineages, and human populations, suggesting strong functional constraints. Analysis of Plasmodium genes indicated adaptive evolution in MESA and KAHRP; in the latter, different positively selected sites were located in the spectrin-binding domains. Because most of the positively selected sites in alpha-spectrin localized to the domains involved in the interaction with KAHRP, we suggest that the two proteins are engaged in an arms-race scenario. This observation is relevant because KAHRP is essential for the formation of “knobs”, which represent a major virulence determinant for P. falciparum.
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Affiliation(s)
- Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. Medea, 23842, Bosisio Parini, Lecco, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute, IRCCS E. Medea, 23842, Bosisio Parini, Lecco, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute, IRCCS E. Medea, 23842, Bosisio Parini, Lecco, Italy.
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28
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Imkeller K, Scally SW, Bosch A, Martí GP, Costa G, Triller G, Murugan R, Renna V, Jumaa H, Kremsner PG, Sim BKL, Hoffman SL, Mordmüller B, Levashina EA, Julien JP, Wardemann H. Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope. Science 2018; 360:1358-1362. [PMID: 29880723 PMCID: PMC6420115 DOI: 10.1126/science.aar5304] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 03/02/2018] [Accepted: 05/23/2018] [Indexed: 12/19/2022]
Abstract
Affinity maturation selects B cells expressing somatically mutated antibody variants with improved antigen-binding properties to protect from invading pathogens. We determined the molecular mechanism underlying the clonal selection and affinity maturation of human B cells expressing protective antibodies against the circumsporozoite protein of the malaria parasite Plasmodium falciparum (PfCSP). We show in molecular detail that the repetitive nature of PfCSP facilitates direct homotypic interactions between two PfCSP repeat-bound monoclonal antibodies, thereby improving antigen affinity and B cell activation. These data provide a mechanistic explanation for the strong selection of somatic mutations that mediate homotypic antibody interactions after repeated parasite exposure in humans. Our findings demonstrate a different mode of antigen-mediated affinity maturation to improve antibody responses to PfCSP and presumably other repetitive antigens.
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MESH Headings
- Antibodies, Protozoan/chemistry
- Antibodies, Protozoan/genetics
- Antibodies, Protozoan/immunology
- Antibody Affinity/genetics
- Antibody Affinity/immunology
- Antibody Formation/genetics
- Antibody Formation/immunology
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- B-Lymphocytes/immunology
- Epitopes, B-Lymphocyte/immunology
- Humans
- Lymphocyte Activation
- Mutation
- Plasmodium falciparum/immunology
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Repetitive Sequences, Nucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid/immunology
- Selection, Genetic
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Affiliation(s)
- Katharina Imkeller
- B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Stephen W Scally
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Alexandre Bosch
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Gemma Pidelaserra Martí
- B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Giulia Costa
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Gianna Triller
- B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany
| | - Rajagopal Murugan
- B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany
| | - Valerio Renna
- Institute of Immunology, University Medical Center Ulm, Ulm, Germany
| | - Hassan Jumaa
- Institute of Immunology, University Medical Center Ulm, Ulm, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine and German Center for Infection Research, Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | | | | | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON, Canada
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany.
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29
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Chaudhry SR, Lwin N, Phelan D, Escalante AA, Battistuzzi FU. Comparative analysis of low complexity regions in Plasmodia. Sci Rep 2018; 8:335. [PMID: 29321589 PMCID: PMC5762703 DOI: 10.1038/s41598-017-18695-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens. We find multiple lines of evidence in support of natural selection as a major evolutionary force shaping the composition and conservation of LCRs through time and signatures that their evolutionary paths are species specific. Our findings add a comparative analysis perspective to the debate on the evolution of LCRs and harness the power of sequence comparisons to identify potential functionally important LCR candidates.
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Affiliation(s)
- S R Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - N Lwin
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - D Phelan
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - A A Escalante
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - F U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI, USA. .,Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, USA.
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30
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Evidence that the Plasmodium falciparum Protein Sortilin Potentially Acts as an Escorter for the Trafficking of the Rhoptry-Associated Membrane Antigen to the Rhoptries. mSphere 2018; 3:mSphere00551-17. [PMID: 29299530 PMCID: PMC5750388 DOI: 10.1128/msphere.00551-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
The rhoptry organelle is critical for the invasion of an erythrocyte by the malaria parasite Plasmodium falciparum. Despite their critical roles, the mechanisms behind their biogenesis are still poorly defined. Our earlier work had suggested that the interaction between the glycosylphosphatidylinositol (GPI)-anchored rhoptry-associated membrane antigen (RAMA) and the soluble rhoptry-associated protein 1 was involved in the transport of the latter from the Golgi apparatus to the rhoptry. However, how this protein complex could interact with the intracellular trafficking machinery was unknown at this stage. Here we show that the P. falciparum homologue of the transmembrane protein sortilin-VPS10 interacts with regions of RAMA that are sufficient to target a fluorescent reporter to the rhoptries. These results suggest that P. falciparum sortilin (PfSortilin) could potentially act as the escorter for the transport of rhoptry-destined cargo. IMPORTANCE The malaria parasite is a massive burden in several parts of the world. Worryingly, the parasite has become resistant to several of the drugs commonly used to treat the disease, and at this time, there is no commercial vaccine. It is therefore critical to identify new targets for the development of antimalarials. To survive in the human body, the malaria parasite needs to invade red blood cells. For this, it uses a variety of effectors stored in organelles forming a structure called the apical complex. The mechanisms behind how the parasite generates the apical complex are poorly understood. In this study, we present evidence that a transmembrane protein called sortilin potentially acts as an escorter to transport proteins from the Golgi apparatus to the rhoptries, a component of the apical complex. Our study provides new insight into the biogenesis of a critical structure of the malaria parasite.
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