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      Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites

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          Abstract

          Plasmodium falciparum and Plasmodium vivax cause the majority of human malaria cases. Research efforts predominantly focus on P. falciparum because of the clinical severity of infection and associated mortality rates. However, P. vivax malaria affects more people in a wider global range. Furthermore, unlike P. falciparum, P. vivax can persist in the liver as dormant hypnozoites that can be activated weeks to years after primary infection, causing relapse of symptomatic blood stages. This feature makes P. vivax unique and difficult to eliminate with the standard tools of vector control and treatment of symptomatic blood stage infection with antimalarial drugs. Infection by Plasmodium is initiated by the mosquito-transmitted sporozoite stage, a highly motile invasive cell that targets hepatocytes in the liver. The most advanced malaria vaccine for P. falciparum (RTS,S, a subunit vaccine containing of a portion of the major sporozoite surface protein) conferred limited protection in Phase III trials, falling short of WHO-established vaccine efficacy goals. However, blocking the sporozoite stage of infection in P. vivax, before the establishment of the chronic liver infection, might be an effective malaria vaccine strategy to reduce the occurrence of relapsing blood stages. It is also thought that a multivalent vaccine comprising multiple sporozoite surface antigens will provide better protection, but a comprehensive analysis of proteins in P. vivax sporozoites is not available. To inform sporozoite-based vaccine development, we employed mass spectrometry-based proteomics to identify nearly 2,000 proteins present in P. vivax salivary gland sporozoites. Analysis of protein post-translational modifications revealed extensive phosphorylation of glideosome proteins as well as regulators of transcription and translation. Additionally, the sporozoite surface proteins CSP and TRAP, which were recently discovered to be glycosylated in P. falciparum salivary gland sporozoites, were also observed to be similarly modified in P. vivax sporozoites. Quantitative comparison of the P. vivax and P. falciparum salivary gland sporozoite proteomes revealed a high degree of similarity in protein expression levels, including among invasion-related proteins. Nevertheless, orthologs with significantly different expression levels between the two species could be identified, as well as highly abundant, species-specific proteins with no known orthologs. Finally, we employed chemical labeling of live sporozoites to isolate and identify 36 proteins that are putatively surface-exposed on P. vivax salivary gland sporozoites. In addition to identifying conserved sporozoite surface proteins identified by similar analyses of other Plasmodium species, our analysis identified several as-yet uncharacterized proteins, including a putative 6-Cys protein with no known ortholog in P. falciparum.

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          Malaria is one of the most important infectious diseases in the world with hundreds of millions of new cases every year. Malaria is caused by parasites of the genus Plasmodium which have a complex life cycle, alternating between mosquito and mammalian hosts. Human infections are initiated with a sporozoite inoculum deposited into the skin by parasite-infected mosquitoes as they probe for blood. Sporozoites must locate blood vessels and enter the circulation to reach the liver where they invade and grow in hepatocytes. In the case of Plasmodium vivax, one of the two Plasmodium species responsible for the majority of the disease burden in the world, the parasite has the ability to persist for months in the liver after the initial infection and its activation causes the recurring appearance of the parasite in the blood. Though all clinical symptoms are attributable to the blood stages, it is only by attacking the transmission stages before the formation of hypnozoites (the persisting parasites in the liver) that an impact on the burden of vivax malaria can be achieved. We used state-of-the-art mass spectrometry-based proteomics tools to identify the total protein make-up of P. vivax sporozoites. By analyzing which proteins are exposed to the parasite surface and determining the degree of protein’s post-translational modifications, our investigation will aid the understanding of the novel biology of sporozoites and importantly, advise the development of potential vaccine candidates targeting this parasite stage.

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          Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

          We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic termini of peptides. Using SEQUEST search results for spectra generated from a sample of known protein components, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared.
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            Discovery of gene function by expression profiling of the malaria parasite life cycle.

            The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes.
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              Epidemiology and infectivity of Plasmodium falciparum and Plasmodium vivax gametocytes in relation to malaria control and elimination.

              Malaria remains a major cause of morbidity and mortality in the tropics, with Plasmodium falciparum responsible for the majority of the disease burden and P. vivax being the geographically most widely distributed cause of malaria. Gametocytes are the sexual-stage parasites that infect Anopheles mosquitoes and mediate the onward transmission of the disease. Gametocytes are poorly studied despite this crucial role, but with a recent resurgence of interest in malaria elimination, the study of gametocytes is in vogue. This review highlights the current state of knowledge with regard to the development and longevity of P. falciparum and P. vivax gametocytes in the human host and the factors influencing their distribution within endemic populations. The evidence for immune responses, antimalarial drugs, and drug resistance influencing infectiousness to mosquitoes is reviewed. We discuss how the application of molecular techniques has led to the identification of submicroscopic gametocyte carriage and to a reassessment of the human infectious reservoir. These components are drawn together to show how control measures that aim to reduce malaria transmission, such as mass drug administration and a transmission-blocking vaccine, might better be deployed.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: Writing – review & editing
                Role: Investigation
                Role: Formal analysis
                Role: InvestigationRole: MethodologyRole: Resources
                Role: Formal analysisRole: Investigation
                Role: Funding acquisitionRole: Resources
                Role: Funding acquisitionRole: MethodologyRole: Resources
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: MethodologyRole: Resources
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                31 July 2017
                July 2017
                : 11
                : 7
                : e0005791
                Affiliations
                [1 ] Institute for Systems Biology, Seattle, Washington, United States of America
                [2 ] Center for Infectious Disease Research, Seattle, Washington, United States of America
                [3 ] Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
                [4 ] Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
                [5 ] Population Health and Immunity Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
                [6 ] Malaria: Parasites & Hosts Unit, Institut Pasteur, Paris, France
                [7 ] Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
                [8 ] Department of Global Health, University of Washington, Seattle, Washington, United States of America
                National Institute of Allergy and Infectious Diseases, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-1996-9703
                Article
                PNTD-D-17-00343
                10.1371/journal.pntd.0005791
                5552340
                28759593
                6627703b-0c6f-4cd9-8880-e28daaa7f934
                © 2017 Swearingen et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 March 2017
                : 10 July 2017
                Page count
                Figures: 4, Tables: 4, Pages: 36
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000005, U.S. Department of Defense;
                Award ID: PR141672
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: K25AI119229
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: P50GM076547
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: R01GM087221
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 0923536
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000925, National Health and Medical Research Council;
                Award ID: 1021544
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000925, National Health and Medical Research Council;
                Award ID: 1043345
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000925, National Health and Medical Research Council;
                Award ID: 1126395
                Award Recipient :
                Research reported in this publication was supported by the Department of Defense under award number PR141672 (SAM, ELF, RP, JS), by the National Institutes of Health National Institute of Allergy and Infectious Disease ( http://www.niaid.nih.gov/) under award numbers K25AI119229 (KES), 1K22AI101039 (SEL) and 1R01AI123341 (SEL), by the National Institutes of Health National Institute of General Medical Sciences ( www.nigms.nih.gov) under award number P50GM076547 (RLM) and R01GM087221 (RLM), by the National Institutes of Health National Center for Research Resources under award number S10RR027584 (RLM), by the National Science Foundation ( www.nsf.gov) under award number 0923536 (RLM, KES), by the National Health and Medical Research Council ( https://www.nhmrc.gov.au/) under award numbers 1021544, 1043345, 1092789 (CK, IM, AJ) and 1126395 (AJ) and the Victorian State Government Operational Infrastructure Support and Australian Government National Health and Medical Research Council Independent Research Institute Infrastructure Support Scheme (CK, IM, AJ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the Department of Defense, National Institutes of Health, the National Science Foundation, or the National Health and Medical Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Parasitology
                Parasite Groups
                Apicomplexa
                Plasmodium
                Biology and Life Sciences
                Parasitology
                Parasite Groups
                Apicomplexa
                Sporozoites
                Biology and Life Sciences
                Anatomy
                Digestive System
                Salivary Glands
                Medicine and Health Sciences
                Anatomy
                Digestive System
                Salivary Glands
                Biology and Life Sciences
                Anatomy
                Exocrine Glands
                Salivary Glands
                Medicine and Health Sciences
                Anatomy
                Exocrine Glands
                Salivary Glands
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Biology and Life Sciences
                Biochemistry
                Peptides
                Biology and Life Sciences
                Biochemistry
                Proteins
                Post-Translational Modification
                Phosphorylation
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Cell Membranes
                Membrane Proteins
                Biology and Life Sciences
                Biochemistry
                Proteins
                Proteomes
                Custom metadata
                vor-update-to-uncorrected-proof
                2017-08-10
                The mass spectrometry data generated for this manuscript, along with the search parameters, analysis parameters and protein databases can be downloaded from PeptideAtlas ( www.peptideatlas.org) using the identifiers PASS00976 (whole proteome) and PASS00977 (surface-labeled).

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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