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Min H, Liang X, Wang C, Qin J, Boonhok R, Muneer A, Brashear AM, Li X, Minns AM, Adapa SR, Jiang RHY, Ning G, Cao Y, Lindner SE, Miao J, Cui L. The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum. Nat Commun 2024; 15:3747. [PMID: 38702310 PMCID: PMC11068891 DOI: 10.1038/s41467-024-48140-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2024] [Indexed: 05/06/2024] Open
Abstract
In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life-stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. We demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.
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Affiliation(s)
- Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Junling Qin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Rachasak Boonhok
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Medical Technology, School of Allied Health Sciences, and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Azhar Muneer
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Awtum M Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Allen M Minns
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Gang Ning
- Electron Microscopy Facility, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
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Nicholas J, De SL, Thawornpan P, Brashear AM, Kolli SK, Subramani PA, Barnes SJ, Cui L, Chootong P, Ntumngia FB, Adams JH. Preliminary characterization of Plasmodium vivax sporozoite antigens as pre-erythrocytic vaccine candidates. PLoS Negl Trop Dis 2023; 17:e0011598. [PMID: 37703302 PMCID: PMC10519608 DOI: 10.1371/journal.pntd.0011598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/25/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023] Open
Abstract
Plasmodium vivax pre-erythrocytic (PE) vaccine research has lagged far behind efforts to develop Plasmodium falciparum vaccines. There is a critical gap in our knowledge of PE antigen targets that can induce functionally inhibitory neutralizing antibody responses. To overcome this gap and guide the selection of potential PE vaccine candidates, we considered key characteristics such as surface exposure, essentiality to infectivity and liver stage development, expression as recombinant proteins, and functional immunogenicity. Selected P. vivax sporozoite antigens were surface sporozoite protein 3 (SSP3), sporozoite microneme protein essential for cell traversal (SPECT1), sporozoite surface protein essential for liver-stage development (SPELD), and M2 domain of MAEBL. Sequence analysis revealed little variation occurred in putative B-cell and T-cell epitopes of the PE candidates. Each antigen was tested for expression as refolded recombinant proteins using an established bacterial expression platform and only SPELD failed. The successfully expressed antigens were immunogenic in vaccinated laboratory mice and were positively reactive with serum antibodies of P. vivax-exposed residents living in an endemic region in Thailand. Vaccine immune antisera were tested for reactivity to native sporozoite proteins and for their potential vaccine efficacy using an in vitro inhibition of liver stage development assay in primary human hepatocytes quantified on day 6 post-infection by high content imaging analysis. The anti-PE sera produced significant inhibition of P. vivax sporozoite invasion and liver stage development. This report provides an initial characterization of potential new PE candidates for a future P. vivax vaccine.
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Affiliation(s)
- Justin Nicholas
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Sai Lata De
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Pongsakorn Thawornpan
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Awtum M. Brashear
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Surendra Kumar Kolli
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Pradeep Annamalai Subramani
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Samantha J. Barnes
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Patchanee Chootong
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Francis Babila Ntumngia
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - John H. Adams
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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Brashear AM, Huckaby AC, Fan Q, Dillard LJ, Hu Y, Li Y, Zhao Y, Wang Z, Cao Y, Miao J, Guler JL, Cui L. New Plasmodium vivax Genomes From the China-Myanmar Border. Front Microbiol 2020; 11:1930. [PMID: 32849480 PMCID: PMC7432439 DOI: 10.3389/fmicb.2020.01930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS.
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Affiliation(s)
- Awtum M. Brashear
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Adam C. Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Qi Fan
- Dalian Institute of Science and Technology, Dalian, China
| | - Luke J. Dillard
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Zenglei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
| | - Jennifer L. Guler
- Department of Biology, University of Virginia, Charlottesville, VA, United States
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, Tampa, FL, United States
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Brashear AM, Fan Q, Hu Y, Li Y, Zhao Y, Wang Z, Cao Y, Miao J, Barry A, Cui L. Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. PLoS Negl Trop Dis 2020; 14:e0008506. [PMID: 32745103 PMCID: PMC7425983 DOI: 10.1371/journal.pntd.0008506] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/13/2020] [Accepted: 06/22/2020] [Indexed: 01/31/2023] Open
Abstract
Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from the China-Myanmar border (CMB) and used 21 high-coverage samples to compare to over 200 samples from the rest of the GMS. Using genome-wide single nucleotide polymorphisms (SNPs), we analyzed population differentiation, genetic structure, migration and potential selection using an array of methods. The CMB parasites displayed a higher proportion of monoclonal infections, and 52% shared over 90% of their genomes in identity-by-descent segments with at least one other sample from the CMB, suggesting preferential expansion of certain parasite strains in this region, likely resulting from the P. vivax outbreaks occurring during this study period. Principal component, admixture, fixation index and phylogenetic analyses all identified that parasites from the CMB were genetically distinct from parasites from eastern parts of the GMS (Cambodia, Laos, Vietnam, and Thailand), whereas the eastern GMS parasite populations were largely undifferentiated. Such a genetic differentiation pattern of the P. vivax populations from the GMS parasite was largely explainable through geographic distance. Using the genome-wide SNPs, we narrowed down to a set of 36 SNPs for differentiating parasites from different areas of the GMS. Genome-wide scans to determine selection in the genome with two statistical methods identified genes potentially under drug selection, including genes associated with antifolate resistance and genes linked to chloroquine resistance in Plasmodium falciparum.
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Affiliation(s)
- Awtum M. Brashear
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
- Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Qi Fan
- Dalian Institute of Technology, Dalian, Liaoning Province, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Zenglei Wang
- MHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Alyssa Barry
- Infection Systems Epidemiology, School of Medicine, Faculty of Health, Deakin University, Geelong, VIC, Australia
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
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Brashear AM, Roobsoong W, Siddiqui FA, Nguitragool W, Sattabongkot J, López-Uribe MM, Miao J, Cui L. A glance of the blood stage transcriptome of a Southeast Asian Plasmodium ovale isolate. PLoS Negl Trop Dis 2019; 13:e0007850. [PMID: 31730621 PMCID: PMC6881071 DOI: 10.1371/journal.pntd.0007850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/27/2019] [Accepted: 10/16/2019] [Indexed: 11/24/2022] Open
Abstract
Plasmodium ovale accounts for a disproportionate number of travel-related malaria cases. This parasite is understudied since there is a reliance on clinical samples. We collected a P. ovale curtisi parasite isolate from a clinical case in western Thailand and performed RNA-seq analysis on the blood stage transcriptomes. Using both de novo assembly and alignment-based methods, we detected the transcripts for 6628 out of 7280 annotated genes. For those lacking evidence of expression, the vast majority belonged to the PIR and STP1 gene families. We identified new splicing patterns for over 2500 genes, and mapped at least one untranslated region for over half of all annotated genes. Our analysis also detected a notable presence of anti-sense transcripts for over 10% of P. ovale curtisi genes. This transcriptomic analysis provides new insights into the blood-stage biology of this neglected parasite. Ovale malaria can be caused by one of two Plasmodium parasites, P. ovale curtisi and P. ovale wallikeri. P. ovale parasites are especially adept at evading prophylactic antimalarial drugs and traveling internationally, which makes them interesting from a global health perspective. Due to the lack of a continuous culture system for these parasites, research on P. ovale parasites has lagged behind and relies on clinical samples. Recent genome sequencing of a few P. ovale clinical isolates provides the blueprint of the parasite genome and in silico prediction of parasite genes. However, confirmation of the annotated genes and proof of their expression are needed. Here we obtained a P. ovale curtisi clinical isolate from western Thailand and performed RNA-seq analysis on the blood-stage parasites. High-quality RNA-seq data has enabled us to identify transcripts for 6628 of the 7280 annotated genes. Consistent with the blood stage development, housekeeping genes such as those involved in translation and metabolism are highly expressed. Prediction of the UTRs as well as detection of anti-sense transcripts and potential splicing patterns suggests the presence of complex gene regulation mechanisms for this parasite. This transcriptome dataset will serve as a useful resource for future studies of P. ovale.
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Affiliation(s)
- Awtum M Brashear
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America.,Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Faiza A Siddiqui
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Margarita M López-Uribe
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America.,Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
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