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Schwake CJ, Krueger RM, Hanada T, Chishti AH. Plasmodium falciparum Glutamic Acid-Rich Protein-Independent Polyclonal Antibodies Inhibit Malaria Parasite Growth in Human Erythrocytes. J Infect Dis 2024; 229:1565-1573. [PMID: 38298126 PMCID: PMC11095539 DOI: 10.1093/infdis/jiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024] Open
Abstract
Plasmodium falciparum glutamic acid-rich protein (PfGARP) is a recently characterized cell surface antigen encoded by Plasmodium falciparum, the causative agent of severe human malaria pathophysiology. Previously, we reported that the human erythrocyte band 3 (SLC4A1) serves as a host receptor for PfGARP. Antibodies against PfGARP did not affect parasite invasion and growth. We surmised that PfGARP may play a role in the rosetting and adhesion of malaria. Another study reported that antibodies targeting PfGARP exhibit potent inhibition of parasite growth. This inhibition occurred without the presence of any immune or complement components, suggesting the activation of an inherent density-dependent regulatory system. Here, we used polyclonal antibodies against PfGARP and a monoclonal antibody mAb7899 to demonstrate that anti-PfGARP polyclonal antibodies, but not mAb7899, exerted potent inhibition of parasite growth in infected erythrocytes independent of PfGARP. These findings suggest that an unknown malaria protein(s) is the target of growth arrest by polyclonal antibodies raised against PfGARP.
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Affiliation(s)
- Christopher J Schwake
- Program in Cellular, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Rachel M Krueger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Toshihiko Hanada
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Athar H Chishti
- Program in Cellular, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
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2
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Letcher B, Maciuca S, Iqbal Z. Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum. PLoS Biol 2024; 22:e3002507. [PMID: 38451924 PMCID: PMC10919680 DOI: 10.1371/journal.pbio.3002507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/19/2024] [Indexed: 03/09/2024] Open
Abstract
While the malaria parasite Plasmodium falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell-infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical P. falciparum transmission bottleneck.
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Affiliation(s)
- Brice Letcher
- EMBL-EBI, Hinxton, United Kingdom
- Laboratory of Biology and Modelling of the Cell, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
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3
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Su X, Stadler RV, Xu F, Wu J. Malaria Genomics, Vaccine Development, and Microbiome. Pathogens 2023; 12:1061. [PMID: 37624021 PMCID: PMC10459703 DOI: 10.3390/pathogens12081061] [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: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in malaria genetics and genomics have transformed many aspects of malaria research in areas of molecular evolution, epidemiology, transmission, host-parasite interaction, drug resistance, pathogenicity, and vaccine development. Here, in addition to introducing some background information on malaria parasite biology, parasite genetics/genomics, and genotyping methods, we discuss some applications of genetic and genomic approaches in vaccine development and in studying interactions with microbiota. Genetic and genomic data can be used to search for novel vaccine targets, design an effective vaccine strategy, identify protective antigens in a whole-organism vaccine, and evaluate the efficacy of a vaccine. Microbiota has been shown to influence disease outcomes and vaccine efficacy; studying the effects of microbiota in pathogenicity and immunity may provide information for disease control. Malaria genetics and genomics will continue to contribute greatly to many fields of malaria research.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (R.V.S.); (F.X.); (J.W.)
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4
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Wang J, Chen K, Ren Q, Zhang S, Yang J, Wang Y, Nian Y, Li X, Liu G, Luo J, Yin H, Guan G. Comparative genomics reveals unique features of two Babesia motasi subspecies: Babesia motasi lintanensis and Babesia motasi hebeiensis. Int J Parasitol 2023; 53:265-283. [PMID: 37004737 DOI: 10.1016/j.ijpara.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 04/03/2023]
Abstract
Parasites of the Babesia genus are prevalent worldwide and infect a wide diversity of domestic animals and humans. Herein, using Oxford Nanopore Technology and Illumina sequencing technologies, we sequenced two Babesia sub-species, Babesia motasi lintanensis and Babesia motasi hebeiensis. We identified 3,815 one-to-one ortholog genes that are specific to ovine Babesia spp. Phylogenetic analysis reveals that the two B. motasi subspecies form a distinct clade from other Piroplasma spp. Consistent with their phylogenetic position, comparative genomic analysis reveals that these two ovine Babesia spp. share higher colinearity with Babesia bovis than with Babesia microti. Concerning the speciation date, B. m. lintanensis split from B. m. hebeiensis approximately 17 million years ago. Genes correlated to transcription, translation, protein modification and degradation, as well as differential/specialized gene family expansions in these two subspecies may favor adaptation to vertebrate and tick hosts. The close relationship between B. m. lintanensis and B. m. hebeiensis is underlined by a high degree of genomic synteny. Compositions of most invasion, virulence, development, and gene transcript regulation-related multigene families, including spherical body protein, variant erythrocyte surface antigen, glycosylphosphatidylinositol anchored proteins, and transcription factor Apetala 2 genes, is largely conserved, but in contrast to this conserved situation, we observe major differences in species-specific genes that may be involved in multiple functions in parasite biology. For the first time in Babesia spp., we find abundant fragments of long terminal repeat-retrotransposons in these two species. We provide fundamental information to characterize the genomes of B. m. lintanensis and B. m. hebeiensis, providing insights into the evolution of B. motasi group parasites.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Qiaoyun Ren
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Shangdi Zhang
- Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, China.
| | - Jifei Yang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Yanbo Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China; Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, China.
| | - Yueli Nian
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China; Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, China.
| | - Xiaoyun Li
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Guangyuan Liu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Jianxun Luo
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
| | - Hong Yin
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| | - Guiquan Guan
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, China.
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5
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Culleton R, Pain A, Snounou G. Plasmodium malariae: the persisting mysteries of a persistent parasite. Trends Parasitol 2023; 39:113-125. [PMID: 36517330 DOI: 10.1016/j.pt.2022.11.008] [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] [Received: 09/30/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
Plasmodium malariae is a 'neglected malaria parasite' in as much as the amount of research conducted on it pales into insignificance when compared to that pertaining to Plasmodium falciparum and Plasmodium vivax, its more notorious and pathogenic cousins. There has, however, been an increase in interest in this parasite over the past decade. Principally, this is because of the increasing use of sensitive molecular detection techniques that have revealed a wider than previously recorded prevalence in some regions (particularly in Africa), and high numbers of chronic, asymptomatic infections.
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Affiliation(s)
- Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Japan; Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Arnab Pain
- Pathogen Genomics Group, Bioscience Programme, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Georges Snounou
- CEA-Université Paris Sud 11-INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA-HB), IDMIT Department, IBFJ, DRF, Fontenay-aux-Roses, France.
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6
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Highly Variable Expression of Merozoite Surface Protein MSPDBL2 in Diverse Plasmodium falciparum Clinical Isolates and Transcriptome Scans for Correlating Genes. mBio 2022; 13:e0194822. [PMID: 35950755 PMCID: PMC9426457 DOI: 10.1128/mbio.01948-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The merozoite surface protein MSPDBL2 of Plasmodium falciparum is under strong balancing selection and is a target of naturally acquired antibodies. Remarkably, MSPDBL2 is expressed in only a minority of mature schizonts of any cultured parasite line, and mspdbl2 gene transcription increases in response to overexpression of the gametocyte development inducer GDV1, so it is important to understand its natural expression. Here, MSPDBL2 in mature schizonts was analyzed in the first ex vivo culture cycle of 96 clinical isolates from 4 populations with various levels of infection endemicity in different West African countries, by immunofluorescence microscopy with antibodies against a conserved region of the protein. In most isolates, less than 1% of mature schizonts were positive for MSPDBL2, but the frequency distribution was highly skewed, as nine isolates had more than 3% schizonts positive and one had 73% positive. To investigate whether the expression of other gene loci correlated with MSPDBL2 expression, whole-transcriptome sequencing was performed on schizont-enriched material from 17 of the isolates with a wide range of proportions of schizonts positive. Transcripts of particular genes were highly significantly positively correlated with MSPDBL2 positivity in schizonts as well as with mspdbl2 gene transcript levels, showing overrepresentation of genes implicated previously as involved in gametocytogenesis but not including the gametocytogenesis master regulator ap2-g. Single-cell transcriptome analysis of a laboratory-adapted clone showed that most individual parasites expressing mspdbl2 did not express ap2-g, consistent with MSPDBL2 marking a developmental subpopulation that is distinct but likely to co-occur alongside sexual commitment. IMPORTANCE These findings contribute to understanding malaria parasite antigenic and developmental variation, focusing on the merozoite surface protein encoded by the single locus under strongest balancing selection. Analyzing the initial ex vivo generation of parasites grown from a wide sample of clinical infections, we show a unique and highly skewed pattern of natural expression frequencies of MSPDBL2, distinct from that of any other antigen. Bulk transcriptome analysis of a range of clinical isolates showed significant overrepresentation of sexual development genes among those positively correlated with MSPDBL2 protein and mspdbl2 gene expression, indicating the MSPDBL2-positive subpopulation to be often coincident with parasites developing sexually in preparation for transmission. Single-cell transcriptome data confirm the absence of a direct correlation with the ap2-g master regulator of sexual development, indicating that the MSPDBL2-positive subpopulation has a separate function in asexual survival and replication under conditions that promote terminal sexual differentiation.
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7
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Wang J, Chen K, Yang J, Zhang S, Li Y, Liu G, Luo J, Yin H, Wang G, Guan G. Comparative genomic analysis of Babesia duncani responsible for human babesiosis. BMC Biol 2022; 20:153. [PMID: 35790982 PMCID: PMC9258201 DOI: 10.1186/s12915-022-01361-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Background Human babesiosis, caused by parasites of the genus Babesia, is an emerging and re-emerging tick-borne disease that is mainly transmitted by tick bites and infected blood transfusion. Babesia duncani has caused majority of human babesiosis in Canada; however, limited data are available to correlate its genomic information and biological features. Results We generated a B. duncani reference genome using Oxford Nanopore Technology (ONT) and Illumina sequencing technology and uncovered its biological features and phylogenetic relationship with other Apicomplexa parasites. Phylogenetic analyses revealed that B. duncani form a clade distinct from B. microti, Babesia spp. infective to bovine and ovine species, and Theileria spp. infective to bovines. We identified the largest species-specific gene family that could be applied as diagnostic markers for this pathogen. In addition, two gene families show signals of significant expansion and several genes that present signatures of positive selection in B. duncani, suggesting their possible roles in the capability of this parasite to infect humans or tick vectors. Conclusions Using ONT sequencing and Illumina sequencing technologies, we provide the first B. duncani reference genome and confirm that B. duncani forms a phylogenetically distinct clade from other Piroplasm parasites. Comparative genomic analyses show that two gene families are significantly expanded in B. duncani and may play important roles in host cell invasion and virulence of B. duncani. Our study provides basic information for further exploring B. duncani features, such as host-parasite and tick-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01361-9.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Shangdi Zhang
- Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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9
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Hou N, Li S, Jiang N, Piao X, Ma Y, Liu S, Chen Q. Merozoite Proteins Discovered by qRT-PCR-Based Transcriptome Screening of Plasmodium falciparum. Front Cell Infect Microbiol 2021; 11:777955. [PMID: 34956931 PMCID: PMC8696357 DOI: 10.3389/fcimb.2021.777955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
The development of malaria vaccines and medicines depends on the discovery of novel malaria protein targets, but the functions of more than 40% of P. falciparum genes remain unknown. Asexual parasites are the critical stage that leads to serious clinical symptoms and that can be modulated by malaria treatments and vaccines. To identify critical genes involved in the development of Plasmodium parasites within erythrocytes, the expression profile of more than 5,000 genes distributed across the 14 chromosomes of the PF3D7 strain during its six critical developmental stages (merozoite, early-ring, late-ring, early trophozoite, late-trophozoite, and middle-schizont) was evaluated. Hence, a qRT-PCR-based transcriptome of the erythrocytic developmental process of P. falciparum was revealed. Weighted gene coexpression network analyses revealed that a large number of genes are upregulated during the merozoite release process. Further gene ontology analysis revealed that a cluster of genes is associated with merozoite and may be apical complex components. Among these genes, 135 were comprised within chromosome 14, and 80% of them were previously unknown in functions. Western blot and immunofluorescence assays using newly developed corresponding antibodies showed that some of these newly discovered proteins are highly expressed in merozoites. Further invasion inhibition assays revealed that specific antibodies against several novel merozoite proteins can interfere with parasite invasion. Taken together, our study provides a developmental transcriptome of the asexual parasites of P. falciparum and identifies a group of previously unknown merozoite proteins that may play important roles in the process of merozoite invasion.
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Affiliation(s)
- Nan Hou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shanshan Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xianyu Piao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Ma
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuai Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
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10
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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11
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de Oliveira LS, Alborghetti MR, Carneiro RG, Bastos IMD, Amino R, Grellier P, Charneau S. Calcium in the Backstage of Malaria Parasite Biology. Front Cell Infect Microbiol 2021; 11:708834. [PMID: 34395314 PMCID: PMC8355824 DOI: 10.3389/fcimb.2021.708834] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 12/26/2022] Open
Abstract
The calcium ion (Ca2+) is a ubiquitous second messenger involved in key biological processes in prokaryotes and eukaryotes. In Plasmodium species, Ca2+ signaling plays a central role in the parasite life cycle. It has been associated with parasite development, fertilization, locomotion, and host cell infection. Despite the lack of a canonical inositol-1,4,5-triphosphate receptor gene in the Plasmodium genome, pharmacological evidence indicates that inositol-1,4,5-triphosphate triggers Ca2+ mobilization from the endoplasmic reticulum. Other structures such as acidocalcisomes, food vacuole and mitochondria are proposed to act as supplementary intracellular Ca2+ reservoirs. Several Ca2+-binding proteins (CaBPs) trigger downstream signaling. Other proteins with no EF-hand motifs, but apparently involved with CaBPs, are depicted as playing an important role in the erythrocyte invasion and egress. It is also proposed that a cross-talk among kinases, which are not members of the family of Ca2+-dependent protein kinases, such as protein kinases G, A and B, play additional roles mediated indirectly by Ca2+ regulation. This statement may be extended for proteins directly related to invasion or egress, such as SUB1, ERC, IMC1I, IMC1g, GAP45 and EBA175. In this review, we update our understanding of aspects of Ca2+-mediated signaling correlated to the developmental stages of the malaria parasite life cycle.
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Affiliation(s)
- Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- UMR 7245 MCAM, Molécules de Communication et Adaptation des Micro-organismes, Muséum National d’Histoire Naturelle, CNRS, Équipe Parasites et Protistes Libres, Paris, France
| | - Marcos Rodrigo Alborghetti
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Renata Garcia Carneiro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Izabela Marques Dourado Bastos
- Laboratory of Host-Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Rogerio Amino
- Unité Infection et Immunité Paludéennes, Institut Pasteur, Paris, France
| | - Philippe Grellier
- UMR 7245 MCAM, Molécules de Communication et Adaptation des Micro-organismes, Muséum National d’Histoire Naturelle, CNRS, Équipe Parasites et Protistes Libres, Paris, France
| | - Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
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12
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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13
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Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biol Evol 2021; 12:1040-1050. [PMID: 32556248 PMCID: PMC7379906 DOI: 10.1093/gbe/evaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface “self-associated molecular patterns” that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2–3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a “hotspot” in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human–Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal–human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.
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Affiliation(s)
- Naazneen Khan
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Stephane Peyregne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raymond Do
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Kay Prufer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Nissi Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Pascal Gagneux
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Ajit Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
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14
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Carrillo Bilbao GA, Navarro JC, Garigliany MM, Martin-Solano S, Minda E, Benítez-Ortiz W, Saegerman C. Molecular Identification of Plasmodium falciparum from Captive Non-Human Primates in the Western Amazon Ecuador. Pathogens 2021; 10:791. [PMID: 34206700 PMCID: PMC8308908 DOI: 10.3390/pathogens10070791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Malaria is a disease caused by hemoparasites of the Plasmodium genus. Non-human primates (NHP) are hosts of Plasmodium sp. around the world. Several studies have demonstrated that Plasmodium sp. emerged from Africa. However, little information is currently available about Plasmodium falciparum in the neotropical NHP and even less in Ecuador. Indeed, the objective of our study was to identify by molecular phylogenetic analyses the Plasmodium species associated with NHP from the Western Amazon region of Ecuador, and to design a molecular taxonomy protocol to use in the NHP disease ecology. Methods: We extracted DNA from faecal samples (n = 26) from nine species of captive (n = 19) and free-ranging (n = 7) NHP, collected from 2011 to 2019 in the Western Amazon region of Ecuador. Results: Using a pan-Plasmodium PCR, we obtained one positive sample from an adult female Leontocebus lagonotus. A maximum likelihood phylogenetic analysis showed that this sequence unequivocally clustered with Plasmodium falciparum. Conclusions: The identification of Plasmodium sp. in NHP of the Ecuadorian Amazon would be essential to identify their role as potential zoonotic reservoirs, and it is also important to identify their origin in wildlife and their transmission in captive NHP.
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Affiliation(s)
- Gabriel Alberto Carrillo Bilbao
- Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito 170521, Ecuador; (G.A.C.B.); (S.M.-S.); (E.M.); (W.B.-O.)
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULg), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - Juan-Carlos Navarro
- Grupo de Investigación en Enfermedades Emergentes, Ecoepidemiología y Biodiversidad, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170107, Ecuador;
| | - Mutien-Marie Garigliany
- Department of Pathology, Fundamental and Applied Research for Animal and Health (FARAH) Center, Liège University, B-4000 Liège, Belgium;
- Department of Animal Pathology, Liège University, B-4000 Liège, Belgium
| | - Sarah Martin-Solano
- Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito 170521, Ecuador; (G.A.C.B.); (S.M.-S.); (E.M.); (W.B.-O.)
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, Sangolquí 171103, Ecuador
| | - Elizabeth Minda
- Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito 170521, Ecuador; (G.A.C.B.); (S.M.-S.); (E.M.); (W.B.-O.)
| | - Washington Benítez-Ortiz
- Instituto de Salud Pública y Zoonosis (CIZ), Universidad Central del Ecuador, Quito 170521, Ecuador; (G.A.C.B.); (S.M.-S.); (E.M.); (W.B.-O.)
| | - Claude Saegerman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULg), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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15
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The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii. Parasitology 2021; 148:1277-1287. [PMID: 34099078 PMCID: PMC8383288 DOI: 10.1017/s0031182021000937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During their complex life cycles, the Apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii employ several layers of regulation of their gene expression. One such layer is mediated at the level of translation through upstream open reading frames (uORFs). As uORFs are found in the upstream regions of a majority of transcripts in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant genes, including var2csa in P. falciparum, and ApiAT1 in T. gondii, that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of these genome-wide datasets, taking into account uORFs associated with each gene, will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.
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16
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:843. [PMID: 34070769 PMCID: PMC8228830 DOI: 10.3390/genes12060843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth-the number of Plasmodium species' genomes sequenced-and in depth-massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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Affiliation(s)
| | - Gareth D. Weedall
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
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17
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Isebe TI, Bargul JL, Gichuki BM, Njunge JM, Tuju J, Rono MK. Molecular characterization of Plasmodium falciparum PHISTb proteins as potential targets of naturally-acquired immunity against malaria. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.15919.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Plasmodium falciparum causes the deadliest form of malaria in humans. Upon infection, the host’s infected red blood cells (iRBCs) are remodelled by exported parasite proteins to provide a niche for parasite development and maturation. Methods: Here we analysed the role of three PHISTb proteins Pf3D7_0532400, Pf3D7_1401600, and Pf3D7_1102500 by expressing recombinant proteins and evaluated antibody responses against these proteins using immune sera from malaria-exposed individuals from Kenya and The Gambia in Africa. Results: Children and adults from malaria-endemic regions recognized the three PHISTb proteins. Responses against PHISTb proteins varied with malaria transmission intensity in three different geographical sites in Kenya (Siaya and Takaungu) and The Gambia (Sukuta). Antibody responses against PHISTb antigens Pf3D7_1102500 and Pf3D7_1401600 were higher in Sukuta, a low transmission region in Gambia, compared to Siaya, a high transmission region in western Kenya, unlike Pf3D7_0532400. Anti-PHIST responses indicate negative correlation between antibody levels and malaria transmission intensity for Pf3D7_1102500 and Pf3D7_1401600. We report a correlation in antibody responses between schizont and gametocyte extract, but this is not statistically significant (cor=0.102, p=0.2851, CI=95%) and, Pf3D7_0532400 (cor=0.11, p=0.249, CI=95%) and Pf3D7_1401600 (cor=0.02, p=0.7968, CI=95%). We report a negative correlation in antibody responses between schizont and Pf3D7_1102500 (cor=-0.008, p=0.9348, CI=95%). There is a correlation between gametocyte extract and Pf3D7_1401600 (cor=-0.0402, p=0.6735, CI=95%), Pf3D7_1102500 (cor=0.0758, p=0.4271, CI=95%) and Pf3D7_0532400 (cor=0.155, p=0.1028, CI=95%). Acquisition of anti-PHIST antibodies correlates with exposure to malaria for Pf3D7_0532400 (p=0.009) but not Pf3D7_1102500 and Pf3D7_1401600 (p=0.507 and p=0.15, respectively, CI=95%). Children aged below 2 years had the lowest antibody levels which do not correlate with age differences. Conclusions: Collectively, these findings provide evidence of natural immunity against PHISTb antigens that varies with level of malaria exposure and underscore their potential as possible serological markers to P. falciparum infection aimed at contributing to malaria control through vaccine development.
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18
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Behringer V, Deimel C, Stevens JMG, Kreyer M, Lee SM, Hohmann G, Fruth B, Heistermann M. Cell-Mediated Immune Ontogeny Is Affected by Sex but Not Environmental Context in a Long-Lived Primate Species. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.629094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ecoimmunology conceptualizes the role of immunity in shaping life history in a natural context. Within ecoimmunology, macroimmunology is a framework that explains the effects of habitat and spatial differences on variation in immune phenotypes across populations. Within these frameworks, immune ontogeny—the development of the immune system across an individual life span—has received little attention. Here, we investigated how immune ontogeny from birth until adulthood is affected by age, sex, and developmental environment in a long-lived primate species, the bonobo. We found a progressive, significant decline of urinary neopterin levels, a marker for the cell-mediated immune response, from birth until 5 years of age in both sexes. The overall pattern of age-related neopterin changes was sex-specific, with males having higher urinary neopterin levels than females in the first 3 years of life, and females having higher levels than males between 6 and 8 years. Environmental condition (zoo-housed vs. wild) did not influence neopterin levels, nor did age-related changes in neopterin levels differ between environments. Our data suggest that the post-natal development of cell-mediated immune ontogeny is sex-specific but does not show plasticity in response to environmental conditions in this long-lived primate species. This indicates that cell-mediated immune ontogeny in the bonobo follows a stereotypic and maybe a genetically determined pattern that is not affected by environmental differences in pathogen exposure and energy availability, but that sex is an important, yet often overlooked factor shaping patterns of immune ontogeny. Investigating the causes and consequences of variation in immunity throughout life is critical for our understanding of life-history evolution and strategies, mechanisms of sexual selection, and population dynamics with respect to pathogen susceptibility. A general description of sex-specific immune ontogeny as done here is a crucial step in this direction, particularly when it is considered in the context of a species’ ecology and evolutionary history.
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19
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Structure of the Plasmodium-interspersed repeat proteins of the malaria parasite. Proc Natl Acad Sci U S A 2020; 117:32098-32104. [PMID: 33257570 PMCID: PMC7749308 DOI: 10.1073/pnas.2016775117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Plasmodium parasites that cause malaria replicate within blood cells of an infected host. These parasites send a small number of proteins to infected blood cell surfaces, allowing them to bind host molecules but also risking their detection by the host immune system. These proteins have diversified into large families, allowing the parasite to avoid detection by using antigenic variation. The most ubiquitous of these families is the Plasmodium-interspersed repeat (PIR) protein family. Here we present the structure of a PIR protein, revealing the architecture of its ectodomain and showing how it has diversified. Finally, we use structure-guided methods to understand which small variant surface antigen families are PIRs and to understand their evolution across malaria parasites. The deadly symptoms of malaria occur as Plasmodium parasites replicate within blood cells. Members of several variant surface protein families are expressed on infected blood cell surfaces. Of these, the largest and most ubiquitous are the Plasmodium-interspersed repeat (PIR) proteins, with more than 1,000 variants in some genomes. Their functions are mysterious, but differential pir gene expression associates with acute or chronic infection in a mouse malaria model. The membership of the PIR superfamily, and whether the family includes Plasmodium falciparum variant surface proteins, such as RIFINs and STEVORs, is controversial. Here we reveal the structure of the extracellular domain of a PIR from Plasmodium chabaudi. We use structure-guided sequence analysis and molecular modeling to show that this fold is found across PIR proteins from mouse- and human-infective malaria parasites. Moreover, we show that RIFINs and STEVORs are not PIRs. This study provides a structure-guided definition of the PIRs and a molecular framework to understand their evolution.
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20
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Derilus D, Rahman MZ, Serrano AE, Massey SE. Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. INFECTION GENETICS AND EVOLUTION 2020; 87:104642. [PMID: 33296723 DOI: 10.1016/j.meegid.2020.104642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico-Rio Piedras, United States of America
| | - M Z Rahman
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America
| | - A E Serrano
- Department of Microbiology, University of Puerto Rico-School of Medicine, Medical Sciences, United States of America
| | - S E Massey
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America.
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21
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020; 10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is the most deadly parasitic disease, affecting hundreds of millions of people worldwide. Malaria parasites have been associated with their hosts for millions of years. During the long history of host-parasite co-evolution, both parasites and hosts have applied pressure on each other through complex host-parasite molecular interactions. Whereas the hosts activate various immune mechanisms to remove parasites during an infection, the parasites attempt to evade host immunity by diversifying their genome and switching expression of targets of the host immune system. Human intervention to control the disease such as antimalarial drugs and vaccination can greatly alter parasite population dynamics and evolution, particularly the massive applications of antimalarial drugs in recent human history. Vaccination is likely the best method to prevent the disease; however, a partially protective vaccine may have unwanted consequences that require further investigation. Studies of host-parasite interactions and co-evolution will provide important information for designing safe and effective vaccines and for preventing drug resistance. In this essay, we will discuss some interesting molecules involved in host-parasite interactions, including important parasite antigens. We also discuss subjects relevant to drug and vaccine development and some approaches for studying host-parasite interactions.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cui Zhang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Deirdre A Joy
- Parasitology and International Programs Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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22
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Andrade CM, Fleckenstein H, Thomson-Luque R, Doumbo S, Lima NF, Anderson C, Hibbert J, Hopp CS, Tran TM, Li S, Niangaly M, Cisse H, Doumtabe D, Skinner J, Sturdevant D, Ricklefs S, Virtaneva K, Asghar M, Homann MV, Turner L, Martins J, Allman EL, N'Dri ME, Winkler V, Llinás M, Lavazec C, Martens C, Färnert A, Kayentao K, Ongoiba A, Lavstsen T, Osório NS, Otto TD, Recker M, Traore B, Crompton PD, Portugal S. Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season. Nat Med 2020; 26:1929-1940. [PMID: 33106664 DOI: 10.1038/s41591-020-1084-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022]
Abstract
The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquito vectors to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the human host or compromising host survival, is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of individuals with febrile malaria in the transmission season, coinciding with longer circulation within each replicative cycle of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication but rather to increased splenic clearance of longer-circulating infected erythrocytes, which likely maintain parasitemias below clinical and immunological radar. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence.
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Affiliation(s)
- Carolina M Andrade
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hannah Fleckenstein
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Richard Thomson-Luque
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nathalia F Lima
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carrie Anderson
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Hibbert
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christine S Hopp
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Tuan M Tran
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shanping Li
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Moussa Niangaly
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Hamidou Cisse
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Dan Sturdevant
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stacy Ricklefs
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kimmo Virtaneva
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Muhammad Asghar
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Manijeh Vafa Homann
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Louise Turner
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, København N, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Joana Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal and ICVS/3B's -PT Government Associate Laboratory, Braga, Portugal
| | - Erik L Allman
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, State College, PA, USA
| | | | - Volker Winkler
- Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, State College, PA, USA.,Department of Chemistry, The Pennsylvania State University, State College, PA, USA
| | | | - Craig Martens
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Anna Färnert
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Thomas Lavstsen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, København N, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal and ICVS/3B's -PT Government Associate Laboratory, Braga, Portugal
| | - Thomas D Otto
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Mario Recker
- Centre for Mathematics & the Environment, University of Exeter, Penryn Campus, Penryn, UK
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Silvia Portugal
- Center for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany. .,German Center for Infection Research (DZIF), Heidelberg, Heidelberg, Germany. .,Max Planck Institute for Infection Biology, Berlin, Germany.
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23
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Aunin E, Böhme U, Sanderson T, Simons ND, Goldberg TL, Ting N, Chapman CA, Newbold CI, Berriman M, Reid AJ. Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PLoS Pathog 2020; 16:e1008717. [PMID: 32745123 PMCID: PMC7425995 DOI: 10.1371/journal.ppat.1008717] [Citation(s) in RCA: 12] [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: 12/13/2019] [Revised: 08/13/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatocystis is a genus of single-celled parasites infecting, amongst other hosts, monkeys, bats and squirrels. Although thought to have descended from malaria parasites (Plasmodium spp.), Hepatocystis spp. are thought not to undergo replication in the blood-the part of the Plasmodium life cycle which causes the symptoms of malaria. Furthermore, Hepatocystis is transmitted by biting midges, not mosquitoes. Comparative genomics of Hepatocystis and Plasmodium species therefore presents an opportunity to better understand some of the most important aspects of malaria parasite biology. We were able to generate a draft genome for Hepatocystis sp. using DNA sequencing reads from the blood of a naturally infected red colobus monkey. We provide robust phylogenetic support for Hepatocystis sp. as a sister group to Plasmodium parasites infecting rodents. We show transcriptomic support for a lack of replication in the blood and genomic support for a complete loss of a family of genes involved in red blood cell invasion. Our analyses highlight the rapid evolution of genes involved in parasite vector stages, revealing genes that may be critical for interactions between malaria parasites and mosquitoes.
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Affiliation(s)
- Eerik Aunin
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ulrike Böhme
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Theo Sanderson
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Noah D. Simons
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nelson Ting
- Department of Anthropology and Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Colin A. Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington DC, United States of America
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an, China
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Chris I. Newbold
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Matthew Berriman
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Adam J. Reid
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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24
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Davies H, Belda H, Broncel M, Ye X, Bisson C, Introini V, Dorin-Semblat D, Semblat JP, Tibúrcio M, Gamain B, Kaforou M, Treeck M. An exported kinase family mediates species-specific erythrocyte remodelling and virulence in human malaria. Nat Microbiol 2020; 5:848-863. [PMID: 32284562 PMCID: PMC7116245 DOI: 10.1038/s41564-020-0702-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/05/2020] [Indexed: 01/31/2023]
Abstract
The most severe form of human malaria is caused by Plasmodium falciparum. Its virulence is closely linked to the increase in rigidity of infected erythrocytes and their adhesion to endothelial receptors, obstructing blood flow to vital organs. Unlike other human-infecting Plasmodium species, P. falciparum exports a family of 18 FIKK serine/threonine kinases into the host cell, suggesting that phosphorylation may modulate erythrocyte modifications. We reveal substantial species-specific phosphorylation of erythrocyte proteins by P. falciparum but not by Plasmodium knowlesi, which does not export FIKK kinases. By conditionally deleting all FIKK kinases combined with large-scale quantitative phosphoproteomics we identified unique phosphorylation fingerprints for each kinase, including phosphosites on parasite virulence factors and host erythrocyte proteins. Despite their non-overlapping target sites, a network analysis revealed that some FIKKs may act in the same pathways. Only the deletion of the non-exported kinase FIKK8 resulted in reduced parasite growth, suggesting the exported FIKKs may instead support functions important for survival in the host. We show that one kinase, FIKK4.1, mediates both rigidification of the erythrocyte cytoskeleton and trafficking of the adhesin and key virulence factor PfEMP1 to the host cell surface. This establishes the FIKK family as important drivers of parasite evolution and malaria pathology.
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Affiliation(s)
- Heledd Davies
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Hugo Belda
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Malgorzata Broncel
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Xingda Ye
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Claudine Bisson
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Viola Introini
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Dominique Dorin-Semblat
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France
- Institut National de la Transfusion Sanguine, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Jean-Philippe Semblat
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France
- Institut National de la Transfusion Sanguine, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Marta Tibúrcio
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK
| | - Benoit Gamain
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France
- Institut National de la Transfusion Sanguine, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Myrsini Kaforou
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK.
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25
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Smith EC, Limbach KJ, Rangel N, Oda K, Bolton JS, Du M, Gowda K, Wang J, Moch JK, Sonawane S, Velasco R, Belmonte A, Danner R, Lumsden JM, Patterson NB, Sedegah M, Hollingdale MR, Richie TL, Sacci JB, Villasante ED, Aguiar JC. Novel malaria antigen Plasmodium yoelii E140 induces antibody-mediated sterile protection in mice against malaria challenge. PLoS One 2020; 15:e0232234. [PMID: 32407410 PMCID: PMC7224506 DOI: 10.1371/journal.pone.0232234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
Only a small fraction of the antigens expressed by malaria parasites have been evaluated as vaccine candidates. A successful malaria subunit vaccine will likely require multiple antigenic targets to achieve broad protection with high protective efficacy. Here we describe protective efficacy of a novel antigen, Plasmodium yoelii (Py) E140 (PyE140), evaluated against P. yoelii challenge of mice. Vaccines targeting PyE140 reproducibly induced up to 100% sterile protection in both inbred and outbred murine challenge models. Although PyE140 immunization induced high frequency and multifunctional CD8+ T cell responses, as well as CD4+ T cell responses, protection was mediated by PyE140 antibodies acting against blood stage parasites. Protection in mice was long-lasting with up to 100% sterile protection at twelve weeks post-immunization and durable high titer anti-PyE140 antibodies. The E140 antigen is expressed in all Plasmodium species, is highly conserved in both P. falciparum lab-adapted strains and endemic circulating parasites, and is thus a promising lead vaccine candidate for future evaluation against human malaria parasite species.
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Affiliation(s)
- Emily C. Smith
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Keith J. Limbach
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Nonenipha Rangel
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- CAMRIS International, Bethesda, Maryland, United States of America
| | - Kyosuke Oda
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- CAMRIS International, Bethesda, Maryland, United States of America
| | - Jessica S. Bolton
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Mengyan Du
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Kalpana Gowda
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Jianyang Wang
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- CAMRIS International, Bethesda, Maryland, United States of America
| | - J. Kathleen Moch
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sharvari Sonawane
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Rachel Velasco
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Arnel Belmonte
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Rebecca Danner
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Joanne M. Lumsden
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Noelle B. Patterson
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Martha Sedegah
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Michael R. Hollingdale
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Thomas L. Richie
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - John B. Sacci
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Eileen D. Villasante
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Joao C. Aguiar
- Malaria Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- CAMRIS International, Bethesda, Maryland, United States of America
- * E-mail:
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26
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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27
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Morgan AP, Brazeau NF, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Mårtensson A, Bjorkman A, Juliano JJ. Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago. Malar J 2020; 19:47. [PMID: 31992305 PMCID: PMC6988337 DOI: 10.1186/s12936-020-3137-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tanzania's Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria's persistence, but this paradigm has not been studied using modern genetic tools. METHODS Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. RESULTS Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation. CONCLUSIONS These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
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Affiliation(s)
- Andrew P Morgan
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Lwidiko E Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Madeline Denton
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mwinyi Msellem
- Training and Research, Mnazi Mmoja Hospital, Zanzibar, Tanzania
| | - Ulrika Morris
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Dayne L Filer
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ozkan Aydemir
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, 02912, USA
| | - Jeffrey A Bailey
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, 02912, USA
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Anders Bjorkman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599, USA.
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28
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Otto TD, Assefa SA, Böhme U, Sanders MJ, Kwiatkowski D, Berriman M, Newbold C. Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome Open Res 2019; 4:193. [PMID: 32055709 PMCID: PMC7001760 DOI: 10.12688/wellcomeopenres.15590.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
The var gene family of the human malaria parasite Plasmodium falciparum encode proteins that are crucial determinants of both pathogenesis and immune evasion and are highly polymorphic. Here we have assembled nearly complete var gene repertoires from 2398 field isolates and analysed a normalised set of 714 from across 12 countries. This therefore represents the first large scale attempt to catalogue the worldwide distribution of var gene sequences We confirm the extreme polymorphism of this gene family but also demonstrate an unexpected level of sequence sharing both within and between continents. We show that this is likely due to both the remnants of selective sweeps as well as a worrying degree of recent gene flow across continents with implications for the spread of drug resistance. We also address the evolution of the var repertoire with respect to the ancestral genes within the Laverania and show that diversity generated by recombination is concentrated in a number of hotspots. An analysis of the subdomain structure indicates that some existing definitions may need to be revised From the analysis of this data, we can now understand the way in which the family has evolved and how the diversity is continuously being generated. Finally, we demonstrate that because the genes are distributed across the genome, sequence sharing between genotypes acts as a useful population genetic marker.
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Affiliation(s)
- Thomas D. Otto
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
| | - Sammy A. Assefa
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ulrike Böhme
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Dominic Kwiatkowski
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pf3k consortium
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Infection, Immunity & Inflammation, MVLS, University of Glasgow, Glasgow, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Matt Berriman
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Chris Newbold
- Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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29
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Gangnard S, Chêne A, Dechavanne S, Srivastava A, Avril M, Smith JD, Gamain B. VAR2CSA binding phenotype has ancient origin and arose before Plasmodium falciparum crossed to humans: implications in placental malaria vaccine design. Sci Rep 2019; 9:16978. [PMID: 31740695 PMCID: PMC6861233 DOI: 10.1038/s41598-019-53334-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/24/2019] [Indexed: 11/09/2022] Open
Abstract
VAR2CSA is a leading candidate for developing a placental malaria (PM) vaccine that would protect pregnant women living in malaria endemic areas against placental infections and improve birth outcomes. Two VAR2CSA-based PM vaccines are currently under clinical trials, but it is still unclear if the use of a single VAR2CSA variant will be sufficient to induce a broad enough humoral response in humans to cross-react with genetically diverse parasite populations. Additional immuno-focusing vaccine strategies may therefore be required to identify functionally conserved antibody epitopes in VAR2CSA. We explored the possibility that conserved epitopes could exist between VAR2CSA from the chimpanzee parasite Plasmodium reichenowi and Plasmodium falciparum sequences. Making use of VAR2CSA recombinant proteins originating from both species, we showed that VAR2CSA from P. reichenowi (Pr-VAR2CSA) binds to the placental receptor CSA with high specificity and affinity. Antibodies raised against Pr-VAR2CSA were able to recognize native VAR2CSA from different P. falciparum genotypes and to inhibit the interaction between CSA and P. falciparum-infected erythrocytes expressing different VAR2CSA variants. Our work revealed the existence of cross-species inhibitory epitopes in VAR2CSA and calls for pre-clinical studies assessing the efficacy of novel VAR2CSA-based cross-species boosting regimens.
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Affiliation(s)
- Stéphane Gangnard
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Arnaud Chêne
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Sébastien Dechavanne
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Anand Srivastava
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France.,Institut National de la Transfusion Sanguine, F-75015, Paris, France.,Laboratory of excellence GR-Ex, F-75015, Paris, France
| | - Marion Avril
- Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Joseph D Smith
- Seattle Children's Research Institute, Seattle, WA, 98109, USA.,Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Benoît Gamain
- Université de Paris, UMR_S1134, BIGR, INSERM, F-75015, Paris, France. .,Institut National de la Transfusion Sanguine, F-75015, Paris, France. .,Laboratory of excellence GR-Ex, F-75015, Paris, France.
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30
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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31
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Wichers JS, Scholz JAM, Strauss J, Witt S, Lill A, Ehnold LI, Neupert N, Liffner B, Lühken R, Petter M, Lorenzen S, Wilson DW, Löw C, Lavazec C, Bruchhaus I, Tannich E, Gilberger TW, Bachmann A. Dissecting the Gene Expression, Localization, Membrane Topology, and Function of the Plasmodium falciparum STEVOR Protein Family. mBio 2019; 10:e01500-19. [PMID: 31363031 PMCID: PMC6667621 DOI: 10.1128/mbio.01500-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
During its intraerythrocytic development, the malaria parasite Plasmodium falciparum exposes variant surface antigens (VSAs) on infected erythrocytes to establish and maintain an infection. One family of small VSAs is the polymorphic STEVOR proteins, which are marked for export to the host cell surface through their PEXEL signal peptide. Interestingly, some STEVORs have also been reported to localize to the parasite plasma membrane and apical organelles, pointing toward a putative function in host cell egress or invasion. Using deep RNA sequencing analysis, we characterized P. falciparumstevor gene expression across the intraerythrocytic development cycle, including free merozoites, in detail and used the resulting stevor expression profiles for hierarchical clustering. We found that most stevor genes show biphasic expression oscillation, with maximum expression during trophozoite stages and a second peak in late schizonts. We selected four STEVOR variants, confirmed the expected export of these proteins to the host cell membrane, and tracked them to a secondary location, either to the parasite plasma membrane or the secretory organelles of merozoites in late schizont stages. We investigated the function of a particular STEVOR that showed rhoptry localization and demonstrated its role at the parasite-host interface during host cell invasion by specific antisera and targeted gene disruption. Experimentally determined membrane topology of this STEVOR revealed a single transmembrane domain exposing the semiconserved as well as variable protein regions to the cell surface.IMPORTANCE Malaria claims about half a million lives each year. Plasmodium falciparum, the causative agent of the most severe form of the disease, uses proteins that are translocated to the surface of infected erythrocytes for immune evasion. To circumvent the detection of these gene products by the immune system, the parasite evolved a complex strategy that includes gene duplications and elaborate sequence polymorphism. STEVORs are one family of these variant surface antigens and are encoded by about 40 genes. Using deep RNA sequencing of blood-stage parasites, including free merozoites, we first established stevor expression of the cultured isolate and compared it with published transcriptomes. We reveal a biphasic expression of most stevor genes and confirm this for individual STEVORs at the protein level. The membrane topology of a rhoptry-associated variant was experimentally elucidated and linked to host cell invasion, underlining the importance of this multifunctional protein family for parasite proliferation.
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Affiliation(s)
- J Stephan Wichers
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Jan Strauss
- Centre for Structural Systems Biology (CSSB), DESY, and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Susanne Witt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andrés Lill
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | | | - Benjamin Liffner
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Renke Lühken
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Michaela Petter
- Institute of Microbiology, University Hospital Erlangen, Erlangen, Germany
| | - Stephan Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Burnet Institute, Melbourne, Victoria, Australia
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY, and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | | | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Tim W Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
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32
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Ngotho P, Soares AB, Hentzschel F, Achcar F, Bertuccini L, Marti M. Revisiting gametocyte biology in malaria parasites. FEMS Microbiol Rev 2019; 43:401-414. [PMID: 31220244 PMCID: PMC6606849 DOI: 10.1093/femsre/fuz010] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/05/2019] [Indexed: 12/21/2022] Open
Abstract
Gametocytes are the only form of the malaria parasite that is transmissible to the mosquito vector. They are present at low levels in blood circulation and significant knowledge gaps exist in their biology. Recent reductions in the global malaria burden have brought the possibility of elimination and eradication, with renewed focus on malaria transmission biology as a basis for interventions. This review discusses recent insights into gametocyte biology in the major human malaria parasite, Plasmodium falciparum and related species.
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Affiliation(s)
- Priscilla Ngotho
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Alexandra Blancke Soares
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Franziska Hentzschel
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Lucia Bertuccini
- Core Facilities, Microscopy Area, Instituto Superiore di Sanita, Via Regina Elena 299, 00161 Rome, Italy
| | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA
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33
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Böhme U, Otto TD, Sanders M, Newbold CI, Berriman M. Progression of the canonical reference malaria parasite genome from 2002-2019. Wellcome Open Res 2019; 4:58. [PMID: 31080894 PMCID: PMC6484455 DOI: 10.12688/wellcomeopenres.15194.2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 01/15/2023] Open
Abstract
Here we describe the ways in which the sequence and annotation of the
Plasmodium falciparum reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the richness of annotation and accuracy of the sequence are important resources for the
P. falciparum research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpreting intra-species sequence diversity. We therefore describe in this publication a population reference genome of
P. falciparum, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly.
P. falciparum 3D7 will continue to be maintained, with ongoing curation ensuring continual improvements in annotation quality.
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Affiliation(s)
- Ulrike Böhme
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas D Otto
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Institute of Infection, Immunity and Inflammation, MVLS, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mandy Sanders
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Chris I Newbold
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthew Berriman
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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34
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Böhme U, Otto TD, Sanders M, Newbold CI, Berriman M. Progression of the canonical reference malaria parasite genome from 2002-2019. Wellcome Open Res 2019; 4:58. [PMID: 31080894 DOI: 10.12688/wellcomeopenres.15194.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2019] [Indexed: 11/20/2022] Open
Abstract
Here we describe the ways in which the sequence and annotation of the Plasmodium falciparum reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the richness of annotation and accuracy of the sequence are important resources for the P. falciparum research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpreting intra-species sequence diversity. We therefore describe in this publication a population reference genome of P. falciparum, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly. P. falciparum 3D7 will continue to be maintained, with ongoing curation ensuring continual improvements in annotation quality.
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Affiliation(s)
- Ulrike Böhme
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas D Otto
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Institute of Infection, Immunity and Inflammation, MVLS, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mandy Sanders
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Chris I Newbold
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Matthew Berriman
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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35
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Garcia-Longoria L, Marzal A, de Lope F, Garamszegi L. Host-parasite interaction explains variation in the prevalence of avian haemosporidians at the community level. PLoS One 2019; 14:e0205624. [PMID: 30840636 PMCID: PMC6402683 DOI: 10.1371/journal.pone.0205624] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/15/2019] [Indexed: 11/25/2022] Open
Abstract
Parasites are a selective force that shape host community structure and dynamics, but host communities can also influence parasitism. Understanding the dual nature from host-parasite interactions can be facilitated by quantifying the variation in parasite prevalence among host species and then comparing that variation to other ecological factors that are known to also shape host communities. Avian haemosporidian parasites (e.g. Plasmodium and Haemoproteus) are abundant and widespread representing an excellent model for the study of host-parasite interactions. Several geographic and environmental factors have been suggested to determine prevalence of avian haemosporidians in bird communities. However, it remains unknown whether host and parasite traits, represented by phylogenetic distances among species and degree of specialization in host-parasite relationships, can influence infection status. The aims of this study were to analyze factors affecting infection status in a bird community and to test whether the degree of parasite specialization on their hosts is determined by host traits. Our statistical analyses suggest that infection status is mainly determined by the interaction between host species and parasite lineages where tolerance and/or susceptibility to parasites plays an essential role. Additionally, we found that although some of the parasite lineages infected a low number of bird individuals, the species they infected were distantly related and therefore the parasites themselves should not be considered typical host specialists. Infection status was higher for generalist than for specialist parasites in some, but not all, host species. These results suggest that detected prevalence in a species mainly results from the interaction between host immune defences and parasite exploitation strategies wherein the result of an association between particular parasite lineages and particular host species is idiosyncratic.
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Affiliation(s)
- Luz Garcia-Longoria
- Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, Badajoz (Spain)
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, Lund, Sweden
- * E-mail:
| | - Alfonso Marzal
- Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, Badajoz (Spain)
| | - Florentino de Lope
- Departamento de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, Badajoz (Spain)
| | - Laszlo Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain
- MTA-ELTE, Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
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36
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Origin of the New World Plasmodium vivax: Facts and New Approaches. Int Microbiol 2019; 22:337-342. [PMID: 30810995 DOI: 10.1007/s10123-018-00053-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Abstract
Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA) expansion, having a higher genetic diversity in African populations and a low genetic diversity in South American populations. Modeling the evolutionary rate of conserved genes for both P. falciparum and P. vivax determined the approximate arrival of human malaria in South America. Bayesian computational methods suggest that P. falciparum originated in Africa and arrived in South America through multiple independent introductions by the transatlantic African slave trade; however, in South America, P. vivax could have been introduced through an alternate migratory route. Alignments of P. vivax mitogenomes have revealed low genetic variation between the South American and Southeast Asian populations suggesting introduction through either pre-Columbian human migration or post-colonization events. To confirm the findings of these phylogeographical analyses, molecular methods were used to diagnose malaria infection in archeological remains of pre-Columbian ethnic groups. Immunohistochemistry tests were used and identified P. vivax but not P. falciparum in histologically prepared tissues from pre-Columbian Peruvian mummies, whereas shotgun metagenomics sequencing of DNA isolated from pre-Columbian Caribbean coprolites revealed Plasmodium-homologous reads; current evidence suggests that only P. vivax might have been present in pre-Columbian South America.
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37
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Human erythrocyte band 3 is a host receptor for Plasmodium falciparum glutamic acid-rich protein. Blood 2018; 133:470-480. [PMID: 30545833 DOI: 10.1182/blood-2018-07-865451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Malaria remains a major global threat to human health and economic development. Microvascular lesions caused by Plasmodium falciparum-infected human erythrocytes/red blood cells are hallmarks of severe pathogenesis contributing to high mortality, particularly in children from sub-Saharan Africa. In this study, we used a phage display complementary DNA library screening strategy to identify P falciparum glutamic acid-rich protein (PfGARP) as a secreted ligand that recognizes an ectodomain of human erythrocyte anion-exchanger, band 3/AE1, as a host receptor. Domain mapping of PfGARP revealed distinct nonoverlapping repeats encoding the immune response epitopes and core erythrocyte-binding activity. Synthetic peptides derived from the erythrocyte-binding repeats of PfGARP induced erythrocyte aggregation reminiscent of the rosetting phenomenon. Using peptides derived from the immunogenic repeats, a quantitative immunoassay was developed to detect a selective immune response against PfGARP in human plasma samples obtained from patients in rural Mali, suggesting the feasibility of PfGARP as a potential biomarker of disease progression. Collectively, our results suggest that PfGARP may play a functional role in enhancing the adhesive properties of human erythrocytes by engaging band 3 as a host receptor. We propose that immunological and pharmacological inhibition of PfGARP may unveil new therapeutic options for mitigating lesions in cerebral and pregnancy-associated malaria.
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38
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Frimpong A, Kusi KA, Ofori MF, Ndifon W. Novel Strategies for Malaria Vaccine Design. Front Immunol 2018; 9:2769. [PMID: 30555463 PMCID: PMC6281765 DOI: 10.3389/fimmu.2018.02769] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022] Open
Abstract
The quest for a licensed effective vaccine against malaria remains a global priority. Even though classical vaccine design strategies have been successful for some viral and bacterial pathogens, little success has been achieved for Plasmodium falciparum, which causes the deadliest form of malaria due to its diversity and ability to evade host immune responses. Nevertheless, recent advances in vaccinology through high throughput discovery of immune correlates of protection, lymphocyte repertoire sequencing and structural design of immunogens, provide a comprehensive approach to identifying and designing a highly efficacious vaccine for malaria. In this review, we discuss novel vaccine approaches that can be employed in malaria vaccine design.
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Affiliation(s)
- Augustina Frimpong
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana.,Immunology Department, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.,African Institute for Mathematical Sciences, Cape Coast, Ghana
| | - Kwadwo Asamoah Kusi
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana.,Immunology Department, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michael Fokuo Ofori
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana.,Immunology Department, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Wilfred Ndifon
- African Institute for Mathematical Sciences, Cape Coast, Ghana.,African Institute for Mathematical Sciences, University of Stellenbosch, Cape Town, South Africa
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39
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Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence. Sci Rep 2018; 8:17336. [PMID: 30478412 PMCID: PMC6255768 DOI: 10.1038/s41598-018-35778-6] [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: 05/22/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022] Open
Abstract
The establishment of Leishmania infection in mammalian hosts and the subsequent manifestation of clinical symptoms require internalization into macrophages, immune evasion and parasite survival and replication. Although many of the genes involved in these processes have been described, the genetic and genomic variability associated to differences in virulence is largely unknown. Here we present the genomic variation of four Leishmania (Viannia) panamensis strains exhibiting different levels of virulence in BALB/c mice and its application to predict novel genes related to virulence. De novo DNA sequencing and assembly of the most virulent strain allowed comparative genomics analysis with sequenced L. (Viannia) panamensis and L. (Viannia) braziliensis strains, and showed important variations at intra and interspecific levels. Moreover, the mutation detection and a CNV search revealed both base and structural genomic variation within the species. Interestingly, we found differences in the copy number and protein diversity of some genes previously related to virulence. Several machine-learning approaches were applied to combine previous knowledge with features derived from genomic variation and predict a curated set of 66 novel genes related to virulence. These genes can be prioritized for validation experiments and could potentially become promising drug and immune targets for the development of novel prophylactic and therapeutic interventions.
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40
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Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray L, Stewart LB, D'Alessandro U, Otto TD, Kwiatkowski DP, Conway DJ. Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Sci Rep 2018; 8:15763. [PMID: 30361631 PMCID: PMC6202401 DOI: 10.1038/s41598-018-34078-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3'-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
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Affiliation(s)
- Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | | | | | - Mahamadou Diakite
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) and Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherches en Santé Publique (INRSP), Nouakchott, Mauritania
| | - Sarah J Tarr
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lee Murray
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Lindsay B Stewart
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Umberto D'Alessandro
- MRC Gambia Unit, Fajara, The Gambia
- Disease Control Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel St, London, UK.
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Gilabert A, Otto TD, Rutledge GG, Franzon B, Ollomo B, Arnathau C, Durand P, Moukodoum ND, Okouga AP, Ngoubangoye B, Makanga B, Boundenga L, Paupy C, Renaud F, Prugnolle F, Rougeron V. Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biol 2018; 16:e2006035. [PMID: 30142149 PMCID: PMC6130868 DOI: 10.1371/journal.pbio.2006035] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 09/10/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022] Open
Abstract
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P. vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long- and short-read sequence technologies 2 new P. vivax-like reference genomes and 9 additional P. vivax-like genotypes. Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and colinear within the core regions. Phylogenetic analyses clearly show that P. vivax-like parasites form a genetically distinct clade from P. vivax. Concerning the relative divergence dating, we show that the evolution of P. vivax in humans did not occur at the same time as the other agents of human malaria, thus suggesting that the transfer of Plasmodium parasites to humans happened several times independently over the history of the Homo genus. We further identify several key genes that exhibit signatures of positive selection exclusively in the human P. vivax parasites. Two of these genes have been identified to also be under positive selection in the other main human malaria agent, P. falciparum, thus suggesting their key role in the evolution of the ability of these parasites to infect humans or their anthropophilic vectors. Finally, we demonstrate that some gene families important for red blood cell (RBC) invasion (a key step of the life cycle of these parasites) have undergone lineage-specific evolution in the human parasite (e.g., reticulocyte-binding proteins [RBPs]).
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Affiliation(s)
- Aude Gilabert
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Thomas D. Otto
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, College of Medical, Veterinary and Life Sciences, Glasgow, United Kingdom
| | - Gavin G. Rutledge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Blaise Franzon
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Benjamin Ollomo
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Patrick Durand
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Nancy D. Moukodoum
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Alain-Prince Okouga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Boris Makanga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - François Renaud
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Franck Prugnolle
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Virginie Rougeron
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
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42
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Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications. Biotechnol Adv 2018; 36:894-904. [DOI: 10.1016/j.biotechadv.2018.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 12/27/2022]
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43
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Otto TD, Gilabert A, Crellen T, Böhme U, Arnathau C, Sanders M, Oyola SO, Okouga AP, Boundenga L, Willaume E, Ngoubangoye B, Moukodoum ND, Paupy C, Durand P, Rougeron V, Ollomo B, Renaud F, Newbold C, Berriman M, Prugnolle F. Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nat Microbiol 2018; 3:687-697. [PMID: 29784978 PMCID: PMC5985962 DOI: 10.1038/s41564-018-0162-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/16/2018] [Indexed: 11/08/2022]
Abstract
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers, as well as convergent evolution, were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor, shows a host-specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate the timing of the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans.
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Affiliation(s)
- Thomas D. Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Aude Gilabert
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
| | - Thomas Crellen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary’s Campus, Norfolk Place, London W2 1PG, United Kingdom
| | - Ulrike Böhme
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Céline Arnathau
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Samuel O. Oyola
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Alain Prince Okouga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | | | | | | | - Christophe Paupy
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Benjamin Ollomo
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - François Renaud
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
| | - Chris Newbold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Franck Prugnolle
- Laboratoire MIVEGEC, UMR 5290-224 CNRS 5290-IRD 224-UM, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
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44
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Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S, Stewart LB, Campino S, Kekre M, Hamilton WL, Claessens A, Volkman SK, Ndiaye D, Amambua-Ngwa A, Diakite M, Fairhurst RM, Conway DJ, Franck M, Newbold CI, Berriman M. Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Res 2018; 3:52. [PMID: 29862326 PMCID: PMC5964635 DOI: 10.12688/wellcomeopenres.14571.1] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2018] [Indexed: 12/30/2022] Open
Abstract
Background: Although thousands of clinical isolates of
Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15
P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal
var genes clusters.
Results: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates. We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa. Conclusions: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.
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Affiliation(s)
- Thomas D Otto
- Wellcome Sanger Institute, Hinxton, UK.,Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Adam Reid
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen I Bruske
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Craig W Duffy
- London School of Hygiene and Tropical Medicine, London, UK
| | - Pete C Bull
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | | | - Sandra Dimonte
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Susana Campino
- Wellcome Sanger Institute, Hinxton, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | - Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Simmons College, Boston, MA, USA
| | - Daouda Ndiaye
- Faculty of Medicine and Pharmacy, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Mahamadou Diakite
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Matthias Franck
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Chris I Newbold
- Wellcome Sanger Institute, Hinxton, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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45
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Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, Newbold CI, Berriman M. Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. Genome Res 2018; 28:547-560. [PMID: 29500236 PMCID: PMC5880244 DOI: 10.1101/gr.218123.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/28/2018] [Indexed: 01/08/2023]
Abstract
Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report the sequencing and analysis of high-quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species, and using amino acid divergence between species, we estimate the avian- and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion-related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum, and within these proteins, we detect distinct regions that are specific to nonhuman primate, humans, rodent, and avian hosts. For the first time in the Plasmodium lineage, we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum.
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Affiliation(s)
- Ulrike Böhme
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sascha Steinbiss
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Samuel O Oyola
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Antoine Nicot
- CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 34293 Montpellier Cedex 5, France
| | - Sylvain Gandon
- CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 34293 Montpellier Cedex 5, France
| | - Kailash P Patra
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Colin Herd
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ellen Bushell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Katarzyna K Modrzynska
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Joseph M Vinetz
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Ana Rivero
- MIVEGEC (CNRS UMR 5290), 34394 Montpellier Cedex 5, France
| | - Chris I Newbold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Abstract
The genomic architecture of organisms, including nucleotide composition, can be highly variable, even among closely-related species. To better understand the causes leading to structural variation in genomes, information on distinct and diverse genomic features is needed. Malaria parasites are known for encompassing a wide range of genomic GC-content and it has long been thought that Plasmodium falciparum, the virulent malaria parasite of humans, has the most AT-biased eukaryotic genome. Here, I perform comparative genomic analyses of the most AT-rich eukaryotes sequenced to date, and show that the avian malaria parasites Plasmodium gallinaceum, P. ashfordi, and P. relictum have the most extreme coding sequences in terms of AT-bias. Their mean GC-content is 21.21, 21.22 and 21.60 %, respectively, which is considerably lower than the transcriptome of P. falciparum (23.79 %) and other eukaryotes. This information enables a better understanding of genome evolution and raises the question of how certain organisms are able to prosper despite severe compositional constraints.
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Plenderleith LJ, Liu W, MacLean OA, Li Y, Loy DE, Sundararaman SA, Bibollet-Ruche F, Learn GH, Hahn BH, Sharp PM. Adaptive Evolution of RH5 in Ape Plasmodium species of the Laverania Subgenus. mBio 2018; 9:e02237-17. [PMID: 29362238 PMCID: PMC5784257 DOI: 10.1128/mbio.02237-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 01/03/2023] Open
Abstract
Plasmodium falciparum, the major cause of malaria morbidity and mortality in humans, has been shown to have emerged after cross-species transmission of one of six host-specific parasites (subgenus Laverania) infecting wild chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla). Binding of the parasite-encoded ligand RH5 to the host protein basigin is essential for erythrocyte invasion and has been implicated in host specificity. A recent study claimed to have found two amino acid changes in RH5 that "drove the host shift leading to the emergence of P. falciparum as a human pathogen." However, the ape Laverania data available at that time, which included only a single distantly related chimpanzee parasite sequence, were inadequate to justify any such conclusion. Here, we have investigated Laverania Rh5 gene evolution using sequences from all six ape parasite species. Searching for gene-wide episodic selection across the entire Laverania phylogeny, we found eight codons to be under positive selection, including three that correspond to contact residues known to form hydrogen bonds between P. falciparum RH5 and human basigin. One of these sites (residue 197) has changed subsequent to the transmission from apes to humans that gave rise to P. falciparum, suggesting a possible role in the adaptation of the gorilla parasite to the human host. We also found evidence that the patterns of nucleotide polymorphisms in P. falciparum are not typical of Laverania species and likely reflect the recent demographic history of the human parasite.IMPORTANCE A number of closely related, host-specific malaria parasites infecting wild chimpanzees and gorillas have recently been described. The most important cause of human malaria, Plasmodium falciparum, is now known to have resulted from a cross-species transmission of one of the gorilla parasites. Overcoming species-specific interactions between a parasite ligand, RH5, and its receptor on host cells, basigin, was likely an important step in the origin of the human parasite. We have investigated the evolution of the Rh5 gene and found evidence of adaptive changes during the diversification of the ape parasite species at sites that are known to form bonds with human basigin. One of these changes occurred at the origin of P. falciparum, implicating it as an important adaptation to the human host.
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Affiliation(s)
- Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Oscar A MacLean
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sesh A Sundararaman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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Simpalipan P, Pattaradilokrat S, Harnyuttanakorn P. Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum. Malar J 2018; 17:16. [PMID: 29316927 PMCID: PMC5761093 DOI: 10.1186/s12936-017-2157-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P. falciparum ldh gene in Thailand and to construct the map of LDH sequence diversity in P. falciparum populations worldwide. METHODS The ldh gene was sequenced for 50 P. falciparum isolates in Thailand and compared with hundreds of sequences from P. falciparum populations worldwide. Several indices of molecular variation were calculated, including the proportion of polymorphic sites, the average nucleotide diversity index (π), and the haplotype diversity index (H). Tests of positive selection and neutrality tests were performed to determine signatures of natural selection on the gene. Mean genetic distance within and between species of Plasmodium ldh was analysed to infer evolutionary relationships. RESULTS Nucleotide sequences of P. falciparum ldh could be classified into 9 alleles, encoding 5 isoforms of LDH. L1a was the most common allelic type and was distributed in P. falciparum populations worldwide. Plasmodium falciparum ldh sequences were highly conserved, with haplotype and nucleotide diversity values of 0.203 and 0.0004, respectively. The extremely low genetic diversity was maintained by purifying selection, likely due to functional constraints. Phylogenetic analysis inferred the close genetic relationship of P. falciparum to malaria parasites of great apes, rather than to other human malaria parasites. CONCLUSIONS This study revealed the global genetic variation of the ldh gene in P. falciparum, providing knowledge for improving detection of LDH-based RDTs and supporting the candidacy of LDH as a therapeutic drug target.
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Affiliation(s)
- Phumin Simpalipan
- Zoology Ph.D. Programme, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Sittiporn Pattaradilokrat
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
- Veterinary Parasitology Research Group, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330 Thailand
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49
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Plasmodium falciparum. Emerg Top Life Sci 2017; 1:517-523. [PMID: 33525841 DOI: 10.1042/etls20170099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/17/2022]
Abstract
Plasmodium falciparum is a protozoan parasite that causes the most severe form of human malaria. Five other Plasmodium species can also infect humans - P. vivax, P. malariae, P. ovale curtisi, P. ovale wallikeri and P. knowlesi - but P. falciparum is the most prevalent Plasmodium species in the African region, where 90% of all malaria occurs, and it is this species that causes the great majority of malaria deaths. These were reported by the WHO at 438 000 in 2015 from an estimated 214 million cases; importantly, however, figures for the global burden of malaria tend to have wide margins of error due to poor and inaccurate reporting. In this Perspective, features of P. falciparum that are unique among human malaria parasites are highlighted, and current issues surrounding the control and treatment of this major human pathogen are discussed.
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50
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Liu W, Sherrill-Mix S, Learn GH, Scully EJ, Li Y, Avitto AN, Loy DE, Lauder AP, Sundararaman SA, Plenderleith LJ, Ndjango JBN, Georgiev AV, Ahuka-Mundeke S, Peeters M, Bertolani P, Dupain J, Garai C, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species. Nat Commun 2017; 8:1635. [PMID: 29158512 PMCID: PMC5696340 DOI: 10.1038/s41467-017-01798-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/16/2017] [Indexed: 02/01/2023] Open
Abstract
Malaria parasites, though widespread among wild chimpanzees and gorillas, have not been detected in bonobos. Here, we show that wild-living bonobos are endemically Plasmodium infected in the eastern-most part of their range. Testing 1556 faecal samples from 11 field sites, we identify high prevalence Laverania infections in the Tshuapa-Lomami-Lualaba (TL2) area, but not at other locations across the Congo. TL2 bonobos harbour P. gaboni, formerly only found in chimpanzees, as well as a potential new species, Plasmodium lomamiensis sp. nov. Rare co-infections with non-Laverania parasites were also observed. Phylogenetic relationships among Laverania species are consistent with co-divergence with their gorilla, chimpanzee and bonobo hosts, suggesting a timescale for their evolution. The absence of Plasmodium from most field sites could not be explained by parasite seasonality, nor by bonobo population structure, diet or gut microbiota. Thus, the geographic restriction of bonobo Plasmodium reflects still unidentified factors that likely influence parasite transmission.
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Affiliation(s)
- Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abigail P Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sesh A Sundararaman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012, Kisangani, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomedicale, University of Kinshasa, BP 1197, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier 1, BP 5045, Montpellier, 34394, France
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, CB2 1QH, UK
| | - Jef Dupain
- African Wildlife Foundation Conservation Centre, P.O. Box 310, 00502, Nairobi, Kenya
| | - Cintia Garai
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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