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Mohammed M, Dziedziech A, Macedo D, Huppertz F, Veith Y, Postel Z, Christ E, Scheytt R, Slotte T, Henriksson J, Ankarklev J. Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis. Nat Commun 2024; 15:7177. [PMID: 39187486 PMCID: PMC11347709 DOI: 10.1038/s41467-024-51201-3] [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: 06/02/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
The Plasmodium falciparum life cycle includes obligate transition between a human and mosquito host. Gametocytes are responsible for transmission from the human to the mosquito vector where gamete fusion followed by meiosis occurs. To elucidate how male and female gametocytes differentiate in the absence of sex chromosomes, we perform FACS-based cell enrichment of a P. falciparum gametocyte reporter line followed by single-cell RNA-seq. In our analyses we define the transcriptional programs and predict candidate driver genes underlying male and female development, including genes from the ApiAP2 family of transcription factors. A motif-driven, gene regulatory network analysis indicates that AP2-G5 specifically modulates male development. Additionally, genes linked to the inner membrane complex, involved in morphological changes, are uniquely expressed in the female lineage. The transcriptional programs of male and female development detailed herein allow for further exploration of the evolution of sex in eukaryotes and provide targets for future development of transmission blocking therapies.
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Affiliation(s)
- Mubasher Mohammed
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| | - Alexis Dziedziech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Department of Global Health, Institut Pasteur, 25-28 Rue du Docteur Roux, Paris, France
| | - Diego Macedo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Frederik Huppertz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ylva Veith
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Zoé Postel
- Department of Ecology, Environment and Plant Science, Stockholm University, Stockholm, Sweden
| | - Elena Christ
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Richard Scheytt
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Science, Stockholm University, Stockholm, Sweden
| | - Johan Henriksson
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Integrated Science Lab, Umeå University, Umeå, Sweden
| | - Johan Ankarklev
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
- Microbial Single Cell Genomics Facility, SciLifeLab, Biomedical Center (BMC) Uppsala University, Uppsala, Sweden.
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2
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Nirdosh, Shukla H, Mishra S. An ApiAp2 Transcription Factor with a Dispensable Role in Plasmodium berghei Life Cycle. ACS Infect Dis 2024; 10:1904-1913. [PMID: 38752809 DOI: 10.1021/acsinfecdis.4c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Malaria parasites have a complex life cycle and undergo replication and population expansion within vertebrate hosts and mosquito vectors. These developmental transitions rely on changes in gene expression and chromatin reorganization that result in the activation and silencing of stage-specific genes. The ApiAp2 family of DNA-binding proteins plays an important role in regulating gene expression in malaria parasites. Here, we characterized the ApiAp2 protein in Plasmodium berghei, which we termed Ap2-D. In silico analysis revealed that Ap2-D has three beta-sheets followed by a helix at the C-terminus for DNA binding. Using gene tagging with 3XHA-mCherry, we found that Ap2-D is expressed in Plasmodium blood stages and is present in the parasite cytoplasm and nucleus. Surprisingly, our gene deletion study revealed a completely dispensable role for Ap2-D in the entirety of the P. berghei life cycle. Ap2-D KO parasites were found to grow in the blood successfully and progress through the mosquito midgut and salivary glands. Sporozoites isolated from mosquito salivary glands were infective for hepatocytes and achieved similar patency as WT in mice. We emphasize the importance of genetic validation of antimalarial drug targets before progressing them to drug discovery.
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Affiliation(s)
- Nirdosh
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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3
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Hollin T, Abel S, Banks C, Hristov B, Prudhomme J, Hales K, Florens L, Stafford Noble W, Le Roch KG. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat Commun 2024; 15:1365. [PMID: 38355719 PMCID: PMC10866993 DOI: 10.1038/s41467-024-45519-1] [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: 04/11/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Charles Banks
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Kianna Hales
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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4
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Li B. Telomere maintenance in African trypanosomes. Front Mol Biosci 2023; 10:1302557. [PMID: 38074093 PMCID: PMC10704157 DOI: 10.3389/fmolb.2023.1302557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the "end replication problem" is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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5
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Abstract
Plasmodium falciparum, the human malaria parasite, infects two hosts and various cell types, inducing distinct morphological and physiological changes in the parasite in response to different environmental conditions. These variations required the parasite to adapt and develop elaborate molecular mechanisms to ensure its spread and transmission. Recent findings have significantly improved our understanding of the regulation of gene expression in P. falciparum. Here, we provide an up-to-date overview of technologies used to highlight the transcriptomic adjustments occurring in the parasite throughout its life cycle. We also emphasize the complementary and complex epigenetic mechanisms regulating gene expression in malaria parasites. This review concludes with an outlook on the chromatin architecture, the remodeling systems, and how this 3D genome organization is critical in various biological processes.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
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6
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Ouologuem DT, Dara A, Kone A, Ouattara A, Djimde AA. Plasmodium falciparum Development from Gametocyte to Oocyst: Insight from Functional Studies. Microorganisms 2023; 11:1966. [PMID: 37630530 PMCID: PMC10460021 DOI: 10.3390/microorganisms11081966] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Malaria elimination may never succeed without the implementation of transmission-blocking strategies. The transmission of Plasmodium spp. parasites from the human host to the mosquito vector depends on circulating gametocytes in the peripheral blood of the vertebrate host. Once ingested by the mosquito during blood meals, these sexual forms undergo a series of radical morphological and metabolic changes to survive and progress from the gut to the salivary glands, where they will be waiting to be injected into the vertebrate host. The design of effective transmission-blocking strategies requires a thorough understanding of all the mechanisms that drive the development of gametocytes, gametes, sexual reproduction, and subsequent differentiation within the mosquito. The drastic changes in Plasmodium falciparum shape and function throughout its life cycle rely on the tight regulation of stage-specific gene expression. This review outlines the mechanisms involved in Plasmodium falciparum sexual stage development in both the human and mosquito vector, and zygote to oocyst differentiation. Functional studies unravel mechanisms employed by P. falciparum to orchestrate the expression of stage-specific functional products required to succeed in its complex life cycle, thus providing us with potential targets for developing new therapeutics. These mechanisms are based on studies conducted with various Plasmodium species, including predominantly P. falciparum and the rodent malaria parasites P. berghei. However, the great potential of epigenetics, genomics, transcriptomics, proteomics, and functional genetic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in studies using human malaria parasites and field isolates.
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Affiliation(s)
- Dinkorma T. Ouologuem
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Antoine Dara
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Aminatou Kone
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Abdoulaye A. Djimde
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
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7
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Mohammed M, Dziedziech A, Sekar V, Ernest M, Alves E Silva TL, Balan B, Emami SN, Biryukova I, Friedländer MR, Jex A, Jacobs-Lorena M, Henriksson J, Vega-Rodriguez J, Ankarklev J. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut. Microbiol Spectr 2023; 11:e0367122. [PMID: 36847501 PMCID: PMC10100735 DOI: 10.1128/spectrum.03671-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 h after blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses, we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation, and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody- or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early to late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives. IMPORTANCE The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host. However, recent incentives in the field call for novel interventions to block parasite transmission from humans to the mosquito vector. Therefore, we need to better understand the parasite biology during its development inside the mosquito, including a deeper understanding of the expression of genes controlling parasite progression during these stages. Here, we have generated single-cell transcriptome data, covering P. falciparum's development, from gamete to ookinete inside the mosquito midgut, uncovering previously untapped parasite biology, including a repertoire of novel biomarkers to be explored in future transmission-blocking efforts. We anticipate that our study provides an important resource, which can be further explored to improve our understanding of the parasite biology as well as aid in guiding future malaria intervention strategies.
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Affiliation(s)
- Mubasher Mohammed
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexis Dziedziech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Medard Ernest
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Thiago Luiz Alves E Silva
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - S. Noushin Emami
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aaron Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Johan Henriksson
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Joel Vega-Rodriguez
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Johan Ankarklev
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Microbial Single Cell Genomics, Department of Cell and Molecular Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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8
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Russell TJ, De Silva EK, Crowley VM, Shaw-Saliba K, Dube N, Josling G, Pasaje CFA, Kouskoumvekaki I, Panagiotou G, Niles JC, Jacobs-Lorena M, Denise Okafor C, Gamo FJ, Llinás M. Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites. PLoS Pathog 2022; 18:e1010887. [PMID: 36223427 PMCID: PMC9591056 DOI: 10.1371/journal.ppat.1010887] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/24/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified putative AP2-EXP interacting compounds. Four compounds were found to block DNA binding by AP2-EXP and at least one additional ApiAP2 protein. Our top ApiAP2 competitor compound perturbs the transcriptome of P. falciparum trophozoites and results in a decrease in abundance of log2 fold change > 2 for 50% (46/93) of AP2-EXP target genes. Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that interact with AP2 DNA binding domains. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics.
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Affiliation(s)
- Timothy James Russell
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Eukaryotic Gene Regulation (CEGR), Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Malaria Research (CMaR), Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Erandi K. De Silva
- Lewis-Singler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Valerie M. Crowley
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Kathryn Shaw-Saliba
- Department of Molecular Biology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Namita Dube
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Gabrielle Josling
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Malaria Research (CMaR), Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Charisse Flerida A. Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Irene Kouskoumvekaki
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Products Research and Infection Biology, Hans Knöll Institute, Jena, Germany
- Department of Medicine, the University of Hong Kong, Hong Kong SAR, China
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Marcelo Jacobs-Lorena
- Department of Molecular Biology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - C. Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Chemistry, Pennsylvania State University, State College, Pennsylvania, United States of America
| | | | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Eukaryotic Gene Regulation (CEGR), Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Malaria Research (CMaR), Pennsylvania State University, State College, Pennsylvania, United States of America
- Huck Institutes Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Chemistry, Pennsylvania State University, State College, Pennsylvania, United States of America
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9
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ApiAP2 Gene-Network Regulates Gametocytogenesis in Plasmodium Parasites. Cell Microbiol 2022. [DOI: 10.1155/2022/5796578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Malaria is a mosquito-borne infectious disease, caused by unicellular Apicomplexan protozoa of the genus Plasmodium. The sexual stage of Plasmodium is one of the most fascinating aspects of the Plasmodium life cycle, yet relatively less explored until now. The production of sexually fit gametocytes through gametocytogenesis is essential to the transmission of the Plasmodium parasite into an anopheline mosquito vector. Understanding how gametocytogenesis is regulated promotes the identification of novel drug targets and also the development of transmission-blocking vaccines that would help reduce the disease burden in endemic areas. Transcriptional regulation in Plasmodium parasites is primarily controlled by a family of twenty-seven Apicomplexan Apetela 2 (ApiAP2) genes which act in a cascade to enable the parasite to progress through its asexual replication as well as gametocytogenesis. Here, we review the latest progress made on members of the ApiAP2 family characterized as key players of the transcriptional machinery of gametocytes. Further, we will highlight the transcriptional regulation network of ApiAP2 genes at each stage of gametocytogenesis.
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10
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Quinn JE, Jeninga MD, Limm K, Pareek K, Meißgeier T, Bachmann A, Duffy MF, Petter M. The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression. Front Cell Dev Biol 2022; 10:816558. [PMID: 35493110 PMCID: PMC9039026 DOI: 10.3389/fcell.2022.816558] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulation is a critical mechanism in controlling virulence, differentiation, and survival of the human malaria parasite Plasmodium (P.) falciparum. Bromodomain proteins contribute to this process by binding to acetylated lysine residues of histones and thereby targeting the gene regulatory machinery to gene promoters. A protein complex containing the P. falciparum bromodomain proteins (PfBDP) 1 and PfBDP2 (BDP1/BDP2 core complex) was previously shown to play an essential role for the correct transcription of invasion related genes. Here, we performed a functional characterization of a third component of this complex, which we dubbed PfBDP7, because structural modelling predicted a typical bromodomain fold. We confirmed that PfBDP7 is a nuclear protein that interacts with PfBDP1 at invasion gene promoters in mature schizont stage parasites and contributes to their transcription. Although partial depletion of PfBDP7 showed no significant effect on parasite viability, conditional knock down of either PfBDP7 or PfBDP1 resulted in the de-repression of variant surface antigens (VSA), which are important pathogenicity factors. This de-repression was evident both on mRNA and protein level. To understand the underlying mechanism, we mapped the genome wide binding sites of PfBDP7 by ChIPseq and showed that in early schizonts, PfBDP7 and PfBDP1 are commonly enriched in heterochromatic regions across the gene body of all VSA families, including genes coding for PfEMP1, RIFIN, STEVOR, and PfMC-2TM. This suggests that PfBDP7 and PfBDP1 contribute to the silencing of VSAs by associating with heterochromatin. In conclusion, we identified PfBDP7 as a chromatin binding protein that is a constitutive part of the P. falciparum BDP1/BDP2 core complex and established PfBDP1 and PfBDP7 as novel players in the silencing of heterochromatin regulated virulence gene families of the malaria parasite P. falciparum.
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Affiliation(s)
- Jennifer E. Quinn
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Myriam D. Jeninga
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina Limm
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Kapil Pareek
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tina Meißgeier
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Bachmann
- Department of Cellular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Michael F. Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Parkville, VIC, Australia
| | - Michaela Petter
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
- *Correspondence: Michaela Petter,
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11
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Edwards-Smallbone J, Jensen AL, Roberts LE, Totañes FIG, Hart SR, Merrick CJ. Plasmodium falciparum GBP2 Is a Telomere-Associated Protein That Binds to G-Quadruplex DNA and RNA. Front Cell Infect Microbiol 2022; 12:782537. [PMID: 35273922 PMCID: PMC8902816 DOI: 10.3389/fcimb.2022.782537] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023] Open
Abstract
In the early-diverging protozoan parasite Plasmodium, few telomere-binding proteins have been identified and several are unique. Plasmodium telomeres, like those of most eukaryotes, contain guanine-rich repeats that can form G-quadruplex structures. In model systems, quadruplex-binding drugs can disrupt telomere maintenance and some quadruplex-binding drugs are potent anti-plasmodial agents. Therefore, telomere-interacting and quadruplex-interacting proteins may offer new targets for anti-malarial therapy. Here, we report that P. falciparum GBP2 is such a protein. It was identified via 'Proteomics of Isolated Chromatin fragments', applied here for the first time in Plasmodium. In vitro, PfGBP2 binds specifically to G-rich telomere repeats in quadruplex form and it can also bind to G-rich RNA. In vivo, PfGBP2 partially colocalises with the known telomeric protein HP1 but is also found in the cytoplasm, probably due to its affinity for RNA. Consistently, its interactome includes numerous RNA-associated proteins. PfGBP2 is evidently a multifunctional DNA/RNA-binding factor in Plasmodium.
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Affiliation(s)
- James Edwards-Smallbone
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, United Kingdom
| | - Anders L. Jensen
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Lydia E. Roberts
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | | | - Sarah R. Hart
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Staffordshire, United Kingdom
| | - Catherine J. Merrick
- Department of Pathology, Cambridge University, Cambridge, United Kingdom,*Correspondence: Catherine J. Merrick,
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12
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Shang X, Wang C, Shen L, Sheng F, He X, Wang F, Fan Y, He X, Jiang M. PfAP2-EXP2, an Essential Transcription Factor for the Intraerythrocytic Development of Plasmodium falciparum. Front Cell Dev Biol 2022; 9:782293. [PMID: 35083215 PMCID: PMC8785209 DOI: 10.3389/fcell.2021.782293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum undergoes a series of asexual replications in human erythrocytes after infection, which are effective targets for combatting malaria. Here, we report roles of an ApiAP2 transcription factor PfAP2-EXP2 (PF3D7_0611200) in the intraerythrocytic developmental cycle of P. falciparum. PfAP2-EXP2 conditional knockdown resulted in an asexual growth defect but without an appreciable effect on parasite morphology. Further ChIP-seq analysis revealed that PfAP2-EXP2 targeted genes related to virulence and interaction between erythrocytes and parasites. Especially, PfAP2-EXP2 regulation of euchromatic genes does not depend on recognizing specific DNA sequences, while a CCCTAAACCC motif is found in its heterochromatic binding sites. Combined with transcriptome profiling, we suggest that PfAP2-EXP2 is participated in the intraerythrocytic development by affecting the expression of genes related to cell remodeling at the schizont stage. In summary, this study explores an ApiAP2 member plays an important role for the P. falciparum blood-stage replication, which suggests a new perspective for malaria elimination.
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Affiliation(s)
- Xiaomin Shang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Changhong Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Sheng
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Fei Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanting Fan
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Mei Jiang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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13
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Shang X, Wang C, Fan Y, Guo G, Wang F, Zhao Y, Sheng F, Tang J, He X, Yu X, Zhang M, Zhu G, Yin S, Mu J, Culleton R, Cao J, Jiang M, Zhang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3413-3431. [PMID: 35288749 PMCID: PMC8989538 DOI: 10.1093/nar/gkac176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Heterochromatin-associated gene silencing controls multiple physiological processes in malaria parasites, however, little is known concerning the regulatory network and cis-acting sequences involved in the organization of heterochromatin and how they modulate heterochromatic gene expression. Based on systematic profiling of genome-wide occupancy of eighteen Apicomplexan AP2 transcription factors by ChIP-seq analysis, we identify and characterize eight heterochromatin-associated factors (PfAP2-HFs), which exhibit preferential enrichment within heterochromatic regions but with differential coverage profiles. Although these ApiAP2s target euchromatic gene loci via specific DNA motifs, they are likely integral components of heterochromatin independent of DNA motif recognition. Systematic knockout screenings of ApiAP2 factors coupled with RNA-seq transcriptomic profiling revealed three activators and three repressors of heterochromatic gene expression including four PfAP2-HFs. Notably, expression of virulence genes is either completely silenced or significantly reduced upon the depletion of PfAP2-HC. Integrated multi-omics analyses reveal autoregulation and feed-forward loops to be common features of the ApiAP2 regulatory network, in addition to the occurrence of dynamic interplay between local chromatin structure and ApiAP2s in transcriptional control. Collectively, this study provides a valuable resource describing the genome-wide landscape of the ApiAP2 family and insights into functional divergence and cooperation within this family during the blood-stage development of malaria parasites.
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Affiliation(s)
| | | | | | | | - Fei Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fei Sheng
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132, USA
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Cao
- Correspondence may also be addressed to Jun Cao. Tel: +05 10 6878 1007;
| | - Mei Jiang
- Correspondence may also be addressed to Mei Jiang. Tel: +86 21 6598 5138;
| | - Qingfeng Zhang
- To whom correspondence should be addressed. Tel: +86 21 6598 5138;
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14
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Shang X, Shen S, Tang J, He X, Zhao Y, Wang C, He X, Guo G, Liu M, Wang L, Zhu Q, Yang G, Jiang C, Zhang M, Yu X, Han J, Culleton R, Jiang L, Cao J, Gu L, Zhang Q. A cascade of transcriptional repression determines sexual commitment and development in Plasmodium falciparum. Nucleic Acids Res 2021; 49:9264-9279. [PMID: 34365503 PMCID: PMC8450074 DOI: 10.1093/nar/gkab683] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gametocytogenesis, the process by which malaria parasites produce sexual forms that can infect mosquitoes, is essential for the transmission of malaria. A transcriptional switch of the pfap2-g gene triggers sexual commitment, but how the complex multi-step process is precisely programed remains largely unknown. Here, by systematic functional screening of a panel of ApiAP2 transcription factors, we identify six new ApiAP2 members associated with gametocytogenesis in Plasmodium falciparum. Among these, PfAP2-G5 (PF3D7_1139300) was found to be indispensable for gametocytogenesis. This factor suppresses the transcriptional activity of the pfap2-g gene via binding to both the upstream region and exonic gene body, the latter is linked to the maintenance of local heterochromatin structure, thereby preventing initiation of sexual commitment. Removal of this repressive effect through pfap2-g5 knockout disrupts the asexual replication cycle and promotes sexual commitment accompanied by upregulation of pfap2-g expression. However, the gametocytes produced fail to mature fully. Further analyses show that PfAP2-G5 is essential for gametocyte maturation, and causes the down-regulation of pfap2-g and a set of early gametocyte genes activated by PfAP2-G prior to gametocyte development. Collectively, our findings reveal a regulation cascade of gametocyte production in malaria parasites, and provide a new target for transmission blocking interventions.
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Affiliation(s)
- Xiaomin Shang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China.,Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Xiaohui He
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Gangqiang Guo
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Jiping Han
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan.,Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Lubin Jiang
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Public Health Research Center, Jiangnan University, Wuxi 214122, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
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15
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Walters HA, Temesvari LA. Target acquired: transcriptional regulators as drug targets for protozoan parasites. Int J Parasitol 2021; 51:599-611. [PMID: 33722681 PMCID: PMC8169582 DOI: 10.1016/j.ijpara.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022]
Abstract
Protozoan parasites are single-celled eukaryotic organisms that cause significant human disease and pose a substantial health and socioeconomic burden worldwide. They are responsible for at least 1 million deaths annually. The treatment of such diseases is hindered by the ability of parasites to form latent cysts, develop drug resistance, or be transmitted by insect vectors. Additionally, these pathogens have developed complex mechanisms to alter host gene expression. The prevalence of these diseases is predicted to increase as climate change leads to the augmentation of ambient temperatures, insect ranges, and warm water reservoirs. Therefore, the discovery of novel treatments is necessary. Transcription factors lie at the junction of multiple signalling pathways in eukaryotes and aberrant transcription factor function contributes to the progression of numerous human diseases including cancer, diabetes, inflammatory disorders and cardiovascular disease. Transcription factors were previously thought to be undruggable. However, due to recent advances, transcription factors now represent appealing drug targets. It is conceivable that transcription factors, and the pathways they regulate, may also serve as targets for anti-parasitic drug design. Here, we review transcription factors and transcriptional modulators of protozoan parasites, and discuss how they may be useful in drug discovery. We also provide information on transcription factors that play a role in stage conversion of parasites, TATA box-binding proteins, and transcription factors and cofactors that participate with RNA polymerases I, II and III. We also highlight a significant gap in knowledge in that the transcription factors of some of parasites have been under-investigated. Understanding parasite transcriptional pathways and how parasites alter host gene expression will be essential in discovering innovative drug targets.
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Affiliation(s)
- H A Walters
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States
| | - L A Temesvari
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States.
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16
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A single-cell atlas of Plasmodium falciparum transmission through the mosquito. Nat Commun 2021; 12:3196. [PMID: 34045457 PMCID: PMC8159942 DOI: 10.1038/s41467-021-23434-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/28/2021] [Indexed: 01/29/2023] Open
Abstract
Malaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria - Plasmodium falciparum. We reveal developmental trajectories associated with the colonization of the mosquito midgut and salivary glands and elucidate the transcriptional signatures of each transmissible stage. Additionally, we identify both conserved and non-conserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations potentially linked to host tropism. Together, the data presented here, which are made freely available via an interactive website, provide a fine-grained atlas that enables intensive investigation of the P. falciparum transcriptional journey. As well as providing insights into gene function across the transmission cycle, the atlas opens the door for identification of drug and vaccine targets to stop malaria transmission and thereby prevent disease. Here the authors use single-cell RNA-seq to profile the transmission stages of the human malaria parasite Plasmodium falciparum as it progresses through the Anopheles mosquito. They highlight unique patterns of gene usage throughout this development and identify potential pleiotropic genes that function at multiple life cycle stages.
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17
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Carrington E, Cooijmans RHM, Keller D, Toenhake CG, Bártfai R, Voss TS. The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum. iScience 2021; 24:102444. [PMID: 33997710 PMCID: PMC8105651 DOI: 10.1016/j.isci.2021.102444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/10/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria parasites undergo a complex life cycle in the human host and the mosquito vector. The ApiAP2 family of DNA-binding proteins plays a dominant role in parasite development and life cycle progression. Most ApiAP2 factors studied to date act as transcription factors regulating stage-specific gene expression. Here, we characterized an ApiAP2 factor in Plasmodium falciparum that we termed PfAP2-HC. We demonstrate that PfAP2-HC specifically binds to heterochromatin throughout the genome. Intriguingly, PfAP2-HC does not bind DNA in vivo and recruitment of PfAP2-HC to heterochromatin is independent of its DNA-binding domain but strictly dependent on heterochromatin protein 1. Furthermore, our results suggest that PfAP2-HC functions neither in the regulation of gene expression nor in heterochromatin formation or maintenance. In summary, our findings reveal PfAP2-HC as a core component of heterochromatin in malaria parasites and identify unexpected properties and substantial functional divergence among the members of the ApiAP2 family of regulatory proteins. The ApiAP2 factor AP2-HC is a core component of heterochromatin in malaria parasites Binding of AP2-HC to heterochromatin strictly depends on heterochromatin protein 1 The AP2 DNA-binding domain of AP2-HC is dispensable for heterochromatin association
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Affiliation(s)
- Eilidh Carrington
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Dominique Keller
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Till Steffen Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
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18
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Xu Y, Qiao D, Wen Y, Bi Y, Chen Y, Huang Z, Cui L, Guo J, Cao Y. PfAP2-G2 Is Associated to Production and Maturation of Gametocytes in Plasmodium falciparum via Regulating the Expression of PfMDV-1. Front Microbiol 2021; 11:631444. [PMID: 33537025 PMCID: PMC7848025 DOI: 10.3389/fmicb.2020.631444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Gametocyte is the sole form of the Plasmodium falciparum which is transmissible to the mosquito vector. Here, we report that an Apicomplexan Apetala2 (ApiAP2) family transcription factor, PfAP2-G2 (Pf3D7_1408200), plays a role in the development of gametocytes in P. falciparum by regulating the expression of PfMDV-1 (Pf3D7_1216500). Reverse transcriptase-quantitative PCR (RT-qPCR) analysis showed that PfAP2-G2 was highly expressed in the ring stage. Indirect immunofluorescence assay showed nuclear localization of PfAP2-G2 in asexual stages. The knockout of PfAP2-G2 led to a ~95% decrease in the number of mature gametocytes with a more substantial influence on the production and maturation of the male gametocytes, resulting in a higher female/male gametocyte ratio. To test the mechanism of this phenotype, RNA-seq and RT-qPCR showed that disruption of PfAP2-G2 led to the down-regulation of male development gene-1 (PfMDV-1) in asexual stages. We further found that PfAP2-G2 was enriched at the transcriptional start site (TSS) of PfMDV-1 by chromatin immunoprecipitation and qPCR assay in both ring stage and schizont stage, which demonstrated that PfMDV-1 is one of the targets of PfAP2-G2. In addition, RT-qPCR also showed that PfAP2-G (Pf3D7_1222600), the master regulator for sexual commitment, was also down-regulated in the PfAP2-G2 knockout parasites in the schizont stage, but no change in the ring stage. This phenomenon suggested that PfAP2-G2 played a role at the asexual stage for the development of parasite gametocytes and warrants further investigations in regulatory pathways of PfAP2-G2.
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Affiliation(s)
- Yaozheng Xu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Dan Qiao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhao Wen
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yifei Bi
- Philosophy, Politics and Economics Department, University College London, London, United Kingdom
| | - Yuxi Chen
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Zhenghui Huang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
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19
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Bryant JM, Baumgarten S, Dingli F, Loew D, Sinha A, Claës A, Preiser PR, Dedon PC, Scherf A. Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite. Mol Syst Biol 2020; 16:e9569. [PMID: 32816370 PMCID: PMC7440042 DOI: 10.15252/msb.20209569] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Mutually exclusive expression of the var multigene family is key to immune evasion and pathogenesis in Plasmodium falciparum, but few factors have been shown to play a direct role. We adapted a CRISPR-based proteomics approach to identify novel factors associated with var genes in their natural chromatin context. Catalytically inactive Cas9 ("dCas9") was targeted to var gene regulatory elements, immunoprecipitated, and analyzed with mass spectrometry. Known and novel factors were enriched including structural proteins, DNA helicases, and chromatin remodelers. Functional characterization of PfISWI, an evolutionarily divergent putative chromatin remodeler enriched at the var gene promoter, revealed a role in transcriptional activation. Proteomics of PfISWI identified several proteins enriched at the var gene promoter such as acetyl-CoA synthetase, a putative MORC protein, and an ApiAP2 transcription factor. These findings validate the CRISPR/dCas9 proteomics method and define a new var gene-associated chromatin complex. This study establishes a tool for targeted chromatin purification of unaltered genomic loci and identifies novel chromatin-associated factors potentially involved in transcriptional control and/or chromatin organization of virulence genes in the human malaria parasite.
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Affiliation(s)
- Jessica M Bryant
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Sebastian Baumgarten
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Florent Dingli
- Institut CuriePSL Research UniversityCentre de RechercheMass Spectrometry and Proteomics FacilityParisFrance
| | - Damarys Loew
- Institut CuriePSL Research UniversityCentre de RechercheMass Spectrometry and Proteomics FacilityParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Artur Scherf
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
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20
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Ruiz JL, Gómez-Díaz E. The second life of Plasmodium in the mosquito host: gene regulation on the move. Brief Funct Genomics 2020; 18:313-357. [PMID: 31058281 DOI: 10.1093/bfgp/elz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites face dynamically changing environments and strong selective constraints within human and mosquito hosts. To survive such hostile and shifting conditions, Plasmodium switches transcriptional programs during development and has evolved mechanisms to adjust its phenotype through heterogeneous patterns of gene expression. In vitro studies on culture-adapted isolates have served to set the link between chromatin structure and functional gene expression. Yet, experimental evidence is limited to certain stages of the parasite in the vertebrate, i.e. blood, while the precise mechanisms underlying the dynamic regulatory landscapes during development and in the adaptation to within-host conditions remain poorly understood. In this review, we discuss available data on transcriptional and epigenetic regulation in Plasmodium mosquito stages in the context of sporogonic development and phenotypic variation, including both bet-hedging and environmentally triggered direct transcriptional responses. With this, we advocate the mosquito offers an in vivo biological model to investigate the regulatory networks, transcription factors and chromatin-modifying enzymes and their modes of interaction with regulatory sequences, which might be responsible for the plasticity of the Plasmodium genome that dictates stage- and cell type-specific blueprints of gene expression.
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Affiliation(s)
- José L Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
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21
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Toenhake CG, Bártfai R. What functional genomics has taught us about transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:290-301. [PMID: 31220867 PMCID: PMC6859821 DOI: 10.1093/bfgp/elz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/08/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.
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Affiliation(s)
- Christa G Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
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22
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Ruiz JL, Tena JJ, Bancells C, Cortés A, Gómez-Skarmeta JL, Gómez-Díaz E. Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2019; 46:9414-9431. [PMID: 30016465 PMCID: PMC6182165 DOI: 10.1093/nar/gky643] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022] Open
Abstract
Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a differential ATAC-seq signal at their promoters. Altogether, this study identifies genome-wide regulatory regions likely to play an essential function in the developmental transitions and in CVG expression in P. falciparum.
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Affiliation(s)
- José Luis Ruiz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Cristina Bancells
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Elena Gómez-Díaz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain.,Instituto de Parasitología y Biomedicina 'López-Neyra' (IPBLN), Consejo Superior de Investigaciones Científicas, Granada 18016, Spain
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23
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ApiAP2 Transcription Factors in Apicomplexan Parasites. Pathogens 2019; 8:pathogens8020047. [PMID: 30959972 PMCID: PMC6631176 DOI: 10.3390/pathogens8020047] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites.
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24
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Fraschka SA, Filarsky M, Hoo R, Niederwieser I, Yam XY, Brancucci NMB, Mohring F, Mushunje AT, Huang X, Christensen PR, Nosten F, Bozdech Z, Russell B, Moon RW, Marti M, Preiser PR, Bártfai R, Voss TS. Comparative Heterochromatin Profiling Reveals Conserved and Unique Epigenome Signatures Linked to Adaptation and Development of Malaria Parasites. Cell Host Microbe 2018; 23:407-420.e8. [PMID: 29503181 PMCID: PMC5853956 DOI: 10.1016/j.chom.2018.01.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/22/2017] [Accepted: 01/16/2018] [Indexed: 01/23/2023]
Abstract
Heterochromatin-dependent gene silencing is central to the adaptation and survival of Plasmodium falciparum malaria parasites, allowing clonally variant gene expression during blood infection in humans. By assessing genome-wide heterochromatin protein 1 (HP1) occupancy, we present a comprehensive analysis of heterochromatin landscapes across different Plasmodium species, strains, and life cycle stages. Common targets of epigenetic silencing include fast-evolving multi-gene families encoding surface antigens and a small set of conserved HP1-associated genes with regulatory potential. Many P. falciparum heterochromatic genes are marked in a strain-specific manner, increasing the parasite's adaptive capacity. Whereas heterochromatin is strictly maintained during mitotic proliferation of asexual blood stage parasites, substantial heterochromatin reorganization occurs in differentiating gametocytes and appears crucial for the activation of key gametocyte-specific genes and adaptation of erythrocyte remodeling machinery. Collectively, these findings provide a catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control across the genus Plasmodium.
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Affiliation(s)
- Sabine A Fraschka
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Michael Filarsky
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Regina Hoo
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Xue Yan Yam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Nicolas M B Brancucci
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK; Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA 02155, USA
| | - Franziska Mohring
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Annals T Mushunje
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ximei Huang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Peter R Christensen
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford OX3 7FZ, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Robert W Moon
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Matthias Marti
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK; Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA 02155, USA
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Richárd Bártfai
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands.
| | - Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland.
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25
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Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development. mBio 2017; 8:mBio.01986-17. [PMID: 29233900 PMCID: PMC5727417 DOI: 10.1128/mbio.01986-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites have a complex life cycle with multiple developmental stages in mosquito and vertebrate hosts, and different developmental stages express unique sets of genes. Unexpectedly, many transcription factors (TFs) commonly found in eukaryotic organisms are absent in malaria parasites; instead, a family of genes encoding proteins similar to the plant Apetala2 (ApiAP2) transcription factors is expanded in the parasites. Several malaria ApiAP2 genes have been shown to play a critical role in parasite development; however, the functions of the majority of the ApiAP2 genes remain to be elucidated. In particular, no study on the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family has been reported so far. This study systematically investigated the functional roles of PyApiAP2 genes in parasite development. Twenty-four of the 26 PyApiAP2 genes were selected for disruption, and 12 were successfully knocked out using the clustered regularly interspaced short palindromic repeat–CRISPR-associated protein 9 (CRISPR-Cas9) method. The effects of gene knockout (KO) on parasite development in mouse and mosquito stages were evaluated. Ten of 12 successfully disrupted genes, including two genes that have not been functionally characterized in any Plasmodium species previously, were shown to be critical for P. yoelii development of sexual and mosquito stages. Additionally, seven of the genes were labeled for protein expression analysis, revealing important information supporting their functions. This study represents the first systematic functional characterization of the P. yoelii ApiAP2 gene family and discovers important insights on the roles of the ApiAP2 genes in parasite development. Malaria is a parasitic disease that infects hundreds of millions of people, leading to an estimated 0.35 million deaths in 2015. A better understanding of the mechanism of gene expression regulation during parasite development may provide important clues for disease control and prevention. In this study, systematic gene disruption experiments were performed to study the functional roles of members of the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family in parasite development. Genes that are critical for the development of male and female gametocytes, oocysts, and sporozoites were characterized. The protein expression profiles for seven of the PyApiAP2 gene products were also analyzed, revealing important information on their functions. This study provides expression and functional information for many PyApiAP2 genes, which can be explored for disease management.
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