1
|
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
Collapse
|
2
|
Predicting Secondary Structure Propensities in IDPs Using Simple Statistics from Three-Residue Fragments. J Mol Biol 2020; 432:5447-5459. [DOI: 10.1016/j.jmb.2020.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023]
|
3
|
Estaña A, Sibille N, Delaforge E, Vaisset M, Cortés J, Bernadó P. Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database. Structure 2019; 27:381-391.e2. [DOI: 10.1016/j.str.2018.10.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/13/2018] [Accepted: 10/19/2018] [Indexed: 11/27/2022]
|
4
|
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. Genes (Basel) 2018; 9:genes9110553. [PMID: 30441862 PMCID: PMC6265720 DOI: 10.3390/genes9110553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement rates are partially driven by a complex interaction among three factors: intrinsic disorder propensity; secondary structure; and functional domain involvement. Here, we use sequence-based predictors to evaluate the effects of these factors on site-specific sequence evolutionary rates within four eukaryotic lineages: Metazoans; Plants; Saccharomycete Fungi; and Alveolate Protists. Our results show broad, consistent trends across all four Eukaryote groups. In all four lineages, there is a significant increase in amino acid replacement rates when comparing: (i) disordered vs. ordered sites; (ii) random coil sites vs. sites in secondary structures; and (iii) inter-domain linker sites vs. sites in functional domains. Additionally, within Metazoans, Plants, and Saccharomycetes, there is a strong confounding interaction between intrinsic disorder and secondary structure-alignment sites exhibiting both high disorder propensity and involvement in secondary structures have very low average rates of sequence evolution. Analysis of gene ontology (GO) terms revealed that in all four lineages, a high fraction of sequences containing these conserved, disordered-structured sites are involved in nucleic acid binding. We also observe notable differences in the statistical trends of Alveolates, where intrinsically disordered sites are more variable than in other Eukaryotes and the statistical interactions between disorder and other factors are less pronounced.
Collapse
|
5
|
Sisquella X, Nebl T, Thompson JK, Whitehead L, Malpede BM, Salinas ND, Rogers K, Tolia NH, Fleig A, O'Neill J, Tham WH, David Horgen F, Cowman AF. Plasmodium falciparum ligand binding to erythrocytes induce alterations in deformability essential for invasion. eLife 2017; 6. [PMID: 28226242 PMCID: PMC5333951 DOI: 10.7554/elife.21083] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/09/2017] [Indexed: 12/31/2022] Open
Abstract
The most lethal form of malaria in humans is caused by Plasmodium falciparum. These parasites invade erythrocytes, a complex process involving multiple ligand-receptor interactions. The parasite makes initial contact with the erythrocyte followed by dramatic deformations linked to the function of the Erythrocyte binding antigen family and P. falciparum reticulocyte binding-like families. We show EBA-175 mediates substantial changes in the deformability of erythrocytes by binding to glycophorin A and activating a phosphorylation cascade that includes erythrocyte cytoskeletal proteins resulting in changes in the viscoelastic properties of the host cell. TRPM7 kinase inhibitors FTY720 and waixenicin A block the changes in the deformability of erythrocytes and inhibit merozoite invasion by directly inhibiting the phosphorylation cascade. Therefore, binding of P. falciparum parasites to the erythrocyte directly activate a signaling pathway through a phosphorylation cascade and this alters the viscoelastic properties of the host membrane conditioning it for successful invasion.
Collapse
Affiliation(s)
- Xavier Sisquella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Thomas Nebl
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jennifer K Thompson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brian M Malpede
- Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, St. Louis, United States.,Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States
| | - Nichole D Salinas
- Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, St. Louis, United States.,Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States
| | - Kelly Rogers
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Niraj H Tolia
- Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, St. Louis, United States.,Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States
| | - Andrea Fleig
- The Queen's Medical Center and John A. Burns School of Medicine, University of Hawaii, Honolulu, United States
| | - Joseph O'Neill
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - F David Horgen
- Department of Natural Sciences, Hawaii Pacific University, Kaneohe, United States
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| |
Collapse
|
6
|
Patarroyo ME, Alba MP, Rojas-Luna R, Bermudez A, Aza-Conde J. Functionally relevant proteins in Plasmodium falciparum host cell invasion. Immunotherapy 2017; 9:131-155. [DOI: 10.2217/imt-2016-0091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A totally effective, antimalarial vaccine must involve sporozoite and merozoite proteins (or their fragments) to ensure complete parasite blocking during critical invasion stages. This Special Report examines proteins involved in critical biological functions for parasite survival and highlights the conserved amino acid sequences of the most important proteins involved in sporozoite invasion of hepatocytes and merozoite invasion of red blood cells. Conserved high activity binding peptides are located in such proteins’ functionally strategic sites, whose functions are related to receptor binding, nutrient and protein transport, enzyme activity and molecule–molecule interactions. They are thus excellent targets for vaccine development as they block proteins binding function involved in invasion and also their biological function.
Collapse
Affiliation(s)
- Manuel E Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26–20 Bogotá, Colombia
- Universidad Nacional de Colombia, Bogotá DC, Colombia
| | - Martha P Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26–20 Bogotá, Colombia
- Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Rocío Rojas-Luna
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26–20 Bogotá, Colombia
| | - Adriana Bermudez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26–20 Bogotá, Colombia
- Universidad del Rosario, Bogotá DC, Colombia
| | - Jorge Aza-Conde
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26–20 Bogotá, Colombia
| |
Collapse
|
7
|
Chiu CY, White MT, Healer J, Thompson JK, Siba PM, Mueller I, Cowman AF, Hansen DS. Different Regions of Plasmodium falciparum Erythrocyte-Binding Antigen 175 Induce Antibody Responses to Infection of Varied Efficacy. J Infect Dis 2016; 214:96-104. [PMID: 27020092 DOI: 10.1093/infdis/jiw119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/18/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Increasing evidence suggests that antibodies against merozoite proteins involved in Plasmodium falciparum invasion into the red blood cell play an important role in clinical immunity to malaria. Erythrocyte-binding antigen 175 (EBA-175) is the best-characterized P. falciparum invasion ligand, reported to recognize glycophorin A on the surface of erythrocytes. Its protein structure comprises 6 extracellular regions. Whereas region II contains Duffy binding-like domains involved in the binding to glycophorin A, the functional role of regions III-V is less clear. METHODS We developed a novel cytometric bead array for assessment of antigen-specific antibody concentration in plasma to evaluate the efficacy of immune responses to different regions of EBA-175 and associations between antibody levels with protection from symptomatic malaria in a treatment-reinfection cohort study. RESULTS We found that while antibodies to region II are highly abundant, circulating levels as low as 5-10 µg/mL of antibodies specific for region III or the highly conserved regions IV-V predict strong protection from clinical malaria. CONCLUSIONS These results lend support for the development of conserved regions of EBA-175 as components in a combination of a malaria vaccine.
Collapse
Affiliation(s)
- Chris Y Chiu
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael T White
- The Walter and Eliza Hall Institute of Medical Research MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | - Julie Healer
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jenny K Thompson
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter M Siba
- Vector Borne Disease Unit, Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands Province
| | - Ivo Mueller
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Diana S Hansen
- The Walter and Eliza Hall Institute of Medical Research Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
8
|
Guy AJ, Irani V, MacRaild CA, Anders RF, Norton RS, Beeson JG, Richards JS, Ramsland PA. Insights into the Immunological Properties of Intrinsically Disordered Malaria Proteins Using Proteome Scale Predictions. PLoS One 2015; 10:e0141729. [PMID: 26513658 PMCID: PMC4626106 DOI: 10.1371/journal.pone.0141729] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/12/2015] [Indexed: 12/31/2022] Open
Abstract
Malaria remains a significant global health burden. The development of an effective malaria vaccine remains as a major challenge with the potential to significantly reduce morbidity and mortality. While Plasmodium spp. have been shown to contain a large number of intrinsically disordered proteins (IDPs) or disordered protein regions, the relationship of protein structure to subcellular localisation and adaptive immune responses remains unclear. In this study, we employed several computational prediction algorithms to identify IDPs at the proteome level of six Plasmodium spp. and to investigate the potential impact of protein disorder on adaptive immunity against P. falciparum parasites. IDPs were shown to be particularly enriched within nuclear proteins, apical proteins, exported proteins and proteins localised to the parasitophorous vacuole. Furthermore, several leading vaccine candidates, and proteins with known roles in host-cell invasion, have extensive regions of disorder. Presentation of peptides by MHC molecules plays an important role in adaptive immune responses, and we show that IDP regions are predicted to contain relatively few MHC class I and II binding peptides owing to inherent differences in amino acid composition compared to structured domains. In contrast, linear B-cell epitopes were predicted to be enriched in IDPs. Tandem repeat regions and non-synonymous single nucleotide polymorphisms were found to be strongly associated with regions of disorder. In summary, immune responses against IDPs appear to have characteristics distinct from those against structured protein domains, with increased antibody recognition of linear epitopes but some constraints for MHC presentation and issues of polymorphisms. These findings have major implications for vaccine design, and understanding immunity to malaria.
Collapse
Affiliation(s)
- Andrew J. Guy
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
| | - Vashti Irani
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Christopher A. MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Robin F. Anders
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - James G. Beeson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
| | - Jack S. Richards
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia
- * E-mail: (JSR); (PAR)
| | - Paul A. Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
- * E-mail: (JSR); (PAR)
| |
Collapse
|