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Diffendall G, Scherf A. Deciphering the Plasmodium falciparum perinuclear var gene expression site. Trends Parasitol 2024; 40:707-716. [PMID: 38910098 DOI: 10.1016/j.pt.2024.06.002] [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] [Received: 04/15/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
The protozoan parasite Plasmodium falciparum, responsible for the deadliest form of human malaria, employs antigenic variation via monoallelic expression as a key survival strategy. The selective activation of one out of the 60-member var gene family is key to understanding the parasite's ability to cause severe disease and evade the host immune response. var gene activation is initiated by its relocation to a specialized expression site. While the perinuclear expression site (PES) plays a crucial role in enabling the expression of a single allele, the characteristics of this PES remain largely obscure. Recent breakthroughs in genome editing tools and the discovery of regulatory noncoding RNAs have shed light on this intriguing biological feature, offering significant insights into the mechanisms of pathogen virulence.
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Affiliation(s)
- Gretchen Diffendall
- Institut Pasteur, Universite Paris Cité, INSERM U1201, CNRS EMR9195, Paris, France
| | - Artur Scherf
- Institut Pasteur, Universite Paris Cité, INSERM U1201, CNRS EMR9195, Paris, France.
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2
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Zhang C, Yang S, Quansah E, Zhang Z, Da W, Wang B. The dCas9-based genome editing in Plasmodium yoelii. mSphere 2024; 9:e0009524. [PMID: 38411120 DOI: 10.1128/msphere.00095-24] [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: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Genetic editing is a powerful tool for functional characterization of genes in various organisms. With its simplicity and specificity, the CRISPR-Cas9 technology has become a popular editing tool, which introduces site-specific DNA double-strand breaks (DSBs), and then leverages the endogenous repair pathway for DSB repair via homology-directed repair (HDR) or the more error-prone non-homologous end joining (NHEJ) pathways. However, in the Plasmodium parasites, the lack of a typical NHEJ pathway selects for DSB repair through the HDR pathway when a homologous DNA template is available. The AT-rich nature of the Plasmodium genome exacerbates this drawback by making it difficult to clone longer homologous repair DNA templates. To circumvent these challenges, we adopted the hybrid catalytically inactive Cas9 (dCas9)-microbial single-stranded annealing proteins (SSAP) editor to the Plasmodium genome. In Plasmodium yoelii, we demonstrated the use of the dCas9-SSAP, as the cleavage-free gene editor, by targeted gene deletion and gene tagging, even using shorter homologous DNA templates. This dCas9-SSAP method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, would be a great addition to the existing genetic toolbox and could be deployed for the functional characterization of genes in Plasmodium, contributing to improving the ability of the malaria research community in characterizing more than half of genes with unknown functions.IMPORTANCEMalaria caused by Plasmodium parasites infection remains a serious threat to human health, with an estimated 249 million malaria cases and 608,000 deaths worldwide in 2022, according to the latest report from the World Health Organization (WHO). Here, we demonstrated the use of dCas9-single-stranded annealing protein, as the cleavage-free gene editor in Plasmodium yoelii, by targeted deletion and gene tagging, even using shorter homologous DNA templates. This method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, showing the potential significance in greatly improving our ability to elucidate gene functions, would contribute to assisting the malaria research community in deciphering more than half of genes with unknown functions to identify new drug and vaccine targets.
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Affiliation(s)
- Chao Zhang
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Shijie Yang
- The Second Clinical Medical College, Anhui Medical University, Hefei, China
| | - Elvis Quansah
- Department of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Ziyu Zhang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Weiran Da
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Bingjie Wang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
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3
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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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4
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Wichers-Misterek JS, Krumkamp R, Held J, von Thien H, Wittmann I, Höppner YD, Ruge JM, Moser K, Dara A, Strauss J, Esen M, Fendel R, Sulyok Z, Jeninga MD, Kremsner PG, Sim BKL, Hoffman SL, Duffy MF, Otto TD, Gilberger TW, Silva JC, Mordmüller B, Petter M, Bachmann A. The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections. PLoS Pathog 2023; 19:e1011468. [PMID: 37384799 DOI: 10.1371/journal.ppat.1011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Controlled human malaria infections (CHMI) are a valuable tool to study parasite gene expression in vivo under defined conditions. In previous studies, virulence gene expression was analyzed in samples from volunteers infected with the Plasmodium falciparum (Pf) NF54 isolate, which is of African origin. Here, we provide an in-depth investigation of parasite virulence gene expression in malaria-naïve European volunteers undergoing CHMI with the genetically distinct Pf 7G8 clone, originating in Brazil. Differential expression of var genes, encoding major virulence factors of Pf, PfEMP1s, was assessed in ex vivo parasite samples as well as in parasites from the in vitro cell bank culture that was used to generate the sporozoites (SPZ) for CHMI (Sanaria PfSPZ Challenge (7G8)). We report broad activation of mainly B-type subtelomeric located var genes at the onset of a 7G8 blood stage infection in naïve volunteers, mirroring the NF54 expression study and suggesting that the expression of virulence-associated genes is generally reset during transmission from the mosquito to the human host. However, in 7G8 parasites, we additionally detected a continuously expressed single C-type variant, Pf7G8_040025600, that was most highly expressed in both pre-mosquito cell bank and volunteer samples, suggesting that 7G8, unlike NF54, maintains expression of some previously expressed var variants during transmission. This suggests that in a new host, the parasite may preferentially express the variants that previously allowed successful infection and transmission. Trial registration: ClinicalTrials.gov - NCT02704533; 2018-004523-36.
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Affiliation(s)
- Jan Stephan Wichers-Misterek
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Heidrun von Thien
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Irene Wittmann
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Yannick Daniel Höppner
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Julia M Ruge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Kara Moser
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Antoine Dara
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Jan Strauss
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Meral Esen
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Zita Sulyok
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Myriam D Jeninga
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - B Kim Lee Sim
- Sanaria Inc., Rockville, Maryland, United States of America
| | | | - Michael F Duffy
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas D Otto
- School of Infection & Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Tim-Wolf Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Michaela Petter
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
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5
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Real E, Nardella F, Scherf A, Mancio-Silva L. Repurposing of Plasmodium falciparum var genes beyond the blood stage. Curr Opin Microbiol 2022; 70:102207. [PMID: 36183663 DOI: 10.1016/j.mib.2022.102207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/03/2022] [Indexed: 01/25/2023]
Abstract
A commonly observed survival strategy in protozoan parasites is the sequential expression of clonally variant-surface antigens to avoid elimination by the host's immune response. In malaria-causing P. falciparum, the immunovariant erythrocyte-membrane protein-1 (PfEMP1) adhesin family, encoded by var genes, is responsible for both antigenic variation and cytoadherence of infected erythrocytes to the microvasculature. Until recently, the biological function of these variant genes was believed to be restricted to intraerythrocytic developmental stages. With the advent of new technologies, var gene expression has been confirmed in transmission and pre-erythrocytic stages. Here, we discuss how repurposing of var gene expression beyond chronic blood-stage infection may be critical for successful transmission.
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Affiliation(s)
- Eliana Real
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France
| | - Flore Nardella
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France
| | - Artur Scherf
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France.
| | - Liliana Mancio-Silva
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France.
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6
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Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS. A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics 2022; 23:780. [PMID: 36451097 PMCID: PMC9710153 DOI: 10.1186/s12864-022-09017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. RESULTS We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. CONCLUSIONS The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
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Affiliation(s)
- Johanna Hoshizaki
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie H. Adjalley
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,Micrographia Bio, London, W12 0BZ UK
| | - Vandana Thathy
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS UK ,grid.239585.00000 0001 2285 2675Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY10032 USA
| | - Kim Judge
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew Berriman
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.8756.c0000 0001 2193 314XWellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA UK
| | - Adam J. Reid
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.5335.00000000121885934Present address: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN UK
| | - Marcus C. S. Lee
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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7
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Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion. Life Sci Alliance 2022; 6:6/1/e202201577. [PMID: 36379669 PMCID: PMC9670795 DOI: 10.26508/lsa.202201577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of Plasmodium falciparum RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique's robustness for identifying ncRNA interactomes in P. falciparum Inducible displacement of nuclear Pf-DDX5 resulted in significant down-regulation of the active var gene. Our work identifies a RUF6 ncRNA-protein complex that interacts with RNA Pol II to sustain the var gene expression, including a helicase that may resolve G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
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Affiliation(s)
- Gretchen M Diffendall
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France
| | - Anna Barcons-Simon
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Artur Scherf
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France
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8
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Adjalley S, Lee MCS. CRISPR/Cas9 Editing of the Plasmodium falciparum Genome. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2470:221-239. [PMID: 35881349 DOI: 10.1007/978-1-0716-2189-9_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability to interrogate gene function in Plasmodium parasites has been greatly enhanced by the advent of CRISPR/Cas9 systems. The breadth of genome manipulations ranges from single point mutations to large multigene deletions, however many of the technical considerations for designing CRISPR-based experiments are common to any editing approach. This review will discuss protocols for vector construction and donor design for genome editing P. falciparum, including pitfalls, variables, and validation methods.
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Affiliation(s)
- Sophie Adjalley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
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9
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Gross MR, Hsu R, Deitsch KW. Evolution of transcriptional control of antigenic variation and virulence in human and ape malaria parasites. BMC Ecol Evol 2021; 21:139. [PMID: 34238209 PMCID: PMC8265125 DOI: 10.1186/s12862-021-01872-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Background The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. This unicellular organism is a member of a subgenus of Plasmodium called the Laverania that infects apes, with P. falciparum being the only member that infects humans. The exceptional virulence of this species to humans can be largely attributed to a family of variant surface antigens placed by the parasites onto the surface of infected red blood cells that mediate adherence to the vascular endothelium. These proteins are encoded by a large, multicopy gene family called var, with each var gene encoding a different form of the protein. By changing which var gene is expressed, parasites avoid immune recognition, a process called antigenic variation that underlies the chronic nature of malaria infections. Results Here we show that the common ancestor of the branch of the Laverania lineage that includes the human parasite underwent a remarkable change in the organization and structure of elements linked to the complex transcriptional regulation displayed by the var gene family. Unlike the other members of the Laverania, the clade that gave rise to P. falciparum evolved distinct subsets of var genes distinguishable by different upstream transcriptional regulatory regions that have been associated with different expression profiles and virulence properties. In addition, two uniquely conserved var genes that have been proposed to play a role in coordinating transcriptional switching similarly arose uniquely within this clade. We hypothesize that these changes originated at a time of dramatic climatic change on the African continent that is predicted to have led to significant changes in transmission dynamics, thus selecting for patterns of antigenic variation that enabled lengthier, more chronic infections. Conclusions These observations suggest that changes in transmission dynamics selected for significant alterations in the transcriptional regulatory mechanisms that mediate antigenic variation in the parasite lineage that includes P. falciparum. These changes likely underlie the chronic nature of these infections as well as their exceptional virulence. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01872-z.
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Affiliation(s)
- Mackensie R Gross
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Rosie Hsu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
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10
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Li Y, Baptista RP, Kissinger JC. Noncoding RNAs in Apicomplexan Parasites: An Update. Trends Parasitol 2020; 36:835-849. [DOI: 10.1016/j.pt.2020.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/26/2020] [Accepted: 07/18/2020] [Indexed: 12/16/2022]
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11
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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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CRISPR Interference of a Clonally Variant GC-Rich Noncoding RNA Family Leads to General Repression of var Genes in Plasmodium falciparum. mBio 2020; 11:mBio.03054-19. [PMID: 31964736 PMCID: PMC6974570 DOI: 10.1128/mbio.03054-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Plasmodium falciparum is the deadliest malaria parasite species, accounting for the vast majority of disease cases and deaths. The virulence of this parasite is reliant upon the mutually exclusive expression of cytoadherence proteins encoded by the 60-member var gene family. Antigenic variation of this multigene family serves as an immune evasion mechanism, ultimately leading to chronic infection and pathogenesis. Understanding the regulation mechanism of antigenic variation is key to developing new therapeutic and control strategies. Our study uncovers a novel layer in the epigenetic regulation of transcription of this family of virulence genes by means of a multigene-targeting CRISPR interference approach. The human malaria parasite Plasmodium falciparum uses mutually exclusive expression of the PfEMP1-encoding var gene family to evade the host immune system. Despite progress in the molecular understanding of the default silencing mechanism, the activation mechanism of the uniquely expressed var member remains elusive. A GC-rich noncoding RNA (ncRNA) gene family has coevolved with Plasmodium species that express var genes. Here, we show that this ncRNA family is transcribed in a clonally variant manner, with predominant transcription of a single member occurring when the ncRNA is located adjacent to and upstream of an active var gene. We developed a specific CRISPR interference (CRISPRi) strategy that allowed for the transcriptional repression of all GC-rich members. A lack of GC-rich ncRNA transcription led to the downregulation of the entire var gene family in ring-stage parasites. Strikingly, in mature blood-stage parasites, the GC-rich ncRNA CRISPRi affected the transcription patterns of other clonally variant gene families, including the downregulation of all Pfmc-2TM members. We provide evidence for the key role of GC-rich ncRNA transcription in var gene activation and discovered a molecular link between the transcriptional control of various clonally variant multigene families involved in parasite virulence. This work opens new avenues for elucidating the molecular processes that control immune evasion and pathogenesis in P. falciparum.
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13
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Lee MCS, Lindner SE, Lopez-Rubio JJ, Llinás M. Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium. Brief Funct Genomics 2019; 18:281-289. [PMID: 31365053 PMCID: PMC6859820 DOI: 10.1093/bfgp/elz012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/15/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas9 approaches are revolutionizing our ability to perform functional genomics across a wide range of organisms, including the Plasmodium parasites that cause malaria. The ability to deliver single point mutations, epitope tags and gene deletions at increased speed and scale is enabling our understanding of the biology of these complex parasites, and pointing to potential new therapeutic targets. In this review, we describe some of the biological and technical considerations for designing CRISPR-based experiments, and discuss potential future developments that broaden the applications for CRISPR/Cas9 interrogation of the malaria parasite genome.
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Affiliation(s)
- Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
| | - Jose-Juan Lopez-Rubio
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, INSERM, Université Montpellier, Montpellier, France
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
- Department of Chemistry, The Pennsylvania State University, Pennsylvania, USA
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14
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Bryant JM, Baumgarten S, Glover L, Hutchinson S, Rachidi N. CRISPR in Parasitology: Not Exactly Cut and Dried! Trends Parasitol 2019; 35:409-422. [DOI: 10.1016/j.pt.2019.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022]
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15
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Moormann AM, Nixon CE, Forconi CS. Immune effector mechanisms in malaria: An update focusing on human immunity. Parasite Immunol 2019; 41:e12628. [PMID: 30972776 DOI: 10.1111/pim.12628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed dramatic decreases in malaria-associated mortality and morbidity around the world. This progress has largely been due to intensified malaria control measures, implementation of rapid diagnostics and establishing a network to anticipate and mitigate antimalarial drug resistance. However, the ultimate tool for malaria prevention is the development and implementation of an effective vaccine. To date, malaria vaccine efforts have focused on determining which of the thousands of antigens expressed by Plasmodium falciparum are instrumental targets of protective immunity. The antigenic variation and antigenic polymorphisms arising in parasite genes under immune selection present a daunting challenge for target antigen selection and prioritization, and is a given caveat when interpreting immune recall responses or results from monovalent vaccine trials. Other immune evasion strategies executed by the parasite highlight the myriad of ways in which it can become a recurrent infection. This review provides an update on immune effector mechanisms in malaria and focuses on our improved ability to interrogate the complexity of human immune system, accelerated by recent methodological advances. Appreciating how the human immune landscape influences the effectiveness and longevity of antimalarial immunity will help explain which conditions are necessary for immune effector mechanisms to prevail.
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Affiliation(s)
- Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Christina E Nixon
- Department of Pathology and Lab Medicine, Brown University, Providence, Rhode Island
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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16
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Ng CL, Fidock DA. Plasmodium falciparum In Vitro Drug Resistance Selections and Gene Editing. Methods Mol Biol 2019; 2013:123-140. [PMID: 31267498 DOI: 10.1007/978-1-4939-9550-9_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Malaria continues to be a global health burden, threatening over 40% of the world's population. Drug resistance in Plasmodium falciparum, the etiological agent of the majority of human malaria cases, is compromising elimination efforts. New approaches to treating drug-resistant malaria benefit from defining resistance liabilities of known antimalarial agents and compounds in development and defining genetic changes that mediate loss of parasite susceptibility. Here, we present protocols for in vitro selection of drug-resistant parasites and for site-directed gene editing of candidate resistance mediators to test for causality.
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Affiliation(s)
- Caroline L Ng
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA. .,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
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17
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Jing Q, Cao L, Zhang L, Cheng X, Gilbert N, Dai X, Sun M, Liang S, Jiang L. Plasmodium falciparum var Gene Is Activated by Its Antisense Long Noncoding RNA. Front Microbiol 2018; 9:3117. [PMID: 30619191 PMCID: PMC6305453 DOI: 10.3389/fmicb.2018.03117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/03/2018] [Indexed: 12/21/2022] Open
Abstract
Plasmodium falciparum erythrocyte membrane protein 1, encoded by var gene, is an immunodominant antigen mediating immune evasion in humans. At a given time, only a single var gene is commonly expressed in one parasite. However, the regulation mechanism of var transcription remains largely unknown. In this study, we identified the antisense long non-coding RNA (aslncRNA) derived from var intron as an activation factor for the corresponding var gene. The exogenous artificial var aslncRNA transcribed by T7 RNA polymerase from episome can specifically activate the homologous var gene, and the exogenous aslncRNA activates transcription of both var mRNA and endogenous aslncRNA in a manner independent of the conserved intron sequence within the var gene family. Interestingly, the newly activated var gene and the previously dominant var gene then could be co-expressed in the same parasite nuclei, which suggests that the aslncRNA-mediated var gene activation could escape from the control of mutually exclusively expression of the var gene family. Together, our work shows that var aslncRNA is the activator responsible for var gene transcriptional regulation.
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Affiliation(s)
- Qingqing Jing
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Long Cao
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Liangliang Zhang
- Clinical Laboratory Medicine, Changzhi People's Hospital, Changzhi, China.,Department of Parasitology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Xiu Cheng
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nicolas Gilbert
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France
| | - Xueyu Dai
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Maoxin Sun
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,ShanghaiTech University, Shanghai, China
| | - Shaohui Liang
- Department of Parasitology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Lubin Jiang
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,ShanghaiTech University, Shanghai, China
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18
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Silva Pereira S, Casas-Sánchez A, Haines LR, Ogugo M, Absolomon K, Sanders M, Kemp S, Acosta-Serrano Á, Noyes H, Berriman M, Jackson AP. Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs. Genome Res 2018; 28:1383-1394. [PMID: 30006414 PMCID: PMC6120623 DOI: 10.1101/gr.234146.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/12/2018] [Indexed: 11/25/2022]
Abstract
African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distinct parasite clones. Trypanosome genomes contain many hundreds of VSG genes, subject to rapid changes in nucleotide sequence, copy number, and chromosomal position. Thus, analyzing, or even quantifying, VSG diversity over space and time presents an enormous challenge to conventional techniques. Indeed, previous population genomic studies have overlooked this vital aspect of pathogen biology for lack of analytical tools. Here we present a method for analyzing population-scale VSG diversity in Trypanosoma congolense from deep sequencing data. Previously, we suggested that T. congolense VSGs segregate into defined “phylotypes” that do not recombine. In our data set comprising 41 T. congolense genome sequences from across Africa, these phylotypes are universal and exhaustive. Screening sequence contigs with diagnostic protein motifs accurately quantifies relative phylotype frequencies, providing a metric of VSG diversity, called the “variant antigen profile.” We applied our metric to VSG expression in the tsetse fly, showing that certain, rare VSG phylotypes may be preferentially expressed in infective, metacyclic-stage parasites. Hence, variant antigen profiling accurately and rapidly determines the T. congolense VSG gene and transcript repertoire from sequence data, without need for manual curation or highly contiguous sequences. It offers a tractable approach to measuring VSG diversity across strains and during infections, which is imperative to understanding the host–parasite interaction at population and individual scales.
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Affiliation(s)
- Sara Silva Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Aitor Casas-Sánchez
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Lee R Haines
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Moses Ogugo
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Kihara Absolomon
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Steve Kemp
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Álvaro Acosta-Serrano
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
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19
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Abstract
Although the application of CRISPR/Cas9 genome engineering approaches was first reported in apicomplexan parasites only 3 years ago, this technology has rapidly become an essential component of research on apicomplexan parasites. This review briefly describes the history of CRISPR/Cas9 and the principles behind its use along with documenting its implementation in apicomplexan parasites, especially Plasmodium spp. and Toxoplasma gondii. We also discuss the recent use of CRISPR/Cas9 for whole genome screening of gene knockout mutants in T. gondii and highlight its use for seminal genetic manipulations of Cryptosporidium spp. Finally, we consider new variations of CRISPR/Cas9 that have yet to be implemented in apicomplexans. Whereas CRISPR/Cas9 has already accelerated rapid interrogation of gene function in apicomplexans, the full potential of this technology is yet to be realized as new variations and innovations are integrated into the field.
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