51
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Chappell L, Ross P, Orchard L, Russell TJ, Otto TD, Berriman M, Rayner JC, Llinás M. Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq. BMC Genomics 2020; 21:395. [PMID: 32513207 PMCID: PMC7278070 DOI: 10.1186/s12864-020-06787-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Background Plasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90–95%. Results We developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 78% of the genome transcribed into mRNAs. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. These datasets allowed us to refine the 5′ and 3′ untranslated regions (UTRs), which can be variable, long (> 1000 nt), and often overlap those of adjacent transcripts. Conclusions The approaches applied in this study allow a refined description of the transcriptional landscape of P. falciparum and demonstrate that very little of the densely packed P. falciparum genome is inactive or redundant. By capturing the 5′ and 3′ ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle that will be useful in guiding the definition of regulatory regions for use in future experimental gene expression studies.
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Affiliation(s)
- Lia Chappell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Philipp Ross
- Department of Biochemistry & Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA.,Present Address: Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Lindsey Orchard
- Department of Biochemistry & Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Timothy J Russell
- Department of Biochemistry & Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Thomas D Otto
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Present Address: Institute of Infection, Immunity and Inflammation, MVLS, University of Glasgow, Glasgow, G12 8TA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Present Address: Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
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52
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Abstract
Malaria remains a major public health and economic burden. The heterochromatin environment controls the silencing of genes associated with the fate of malaria parasites. Previous studies have demonstrated that a group of GC-rich ncRNAs (RUF6) is associated with the mutually exclusive expression of var genes, but the underlying mechanisms remain elusive. Here, through a series of genetic manipulation and genome-wide multiomics analysis, we have identified the plasmodial orthologue of RNA exosome-associated Rrp6 as an upstream regulator of RUF6 expression and revealed that the dysregulation of RUF6 upon Rrp6 knockdown triggered local chromatin alteration, thereby activating most heterochromatic genes via direct interaction of RUF6 and distal gene loci. This finding not only uncovered the in-depth mechanism of RUF6-mediated regulation of heterochromatic genes but also identified Rrp6 as a novel regulator of gene expression in human malaria parasites, which provides a new target for developing intervention strategies against malaria. The heterochromatin environment plays a central role in silencing genes associated with the malaria parasite’s development, survival in the host, and transmission to the mosquito vector. However, the underlying mechanism regulating the dynamic chromatin structure is not understood yet. Here, we have uncovered that Plasmodium falciparum Rrp6, an orthologue of eukaryotic RNA exosome-associated RNase, controls the silencing of heterochromatic genes. PfRrp6 knockdown disrupted the singular expression of the GC-rich ncRNA RUF6 family, a known critical regulator of virulence gene expression, through the stabilization of the nascent transcripts. Mechanistic investigation showed that the accumulation of the multiple RUF6 ncRNAs triggered local chromatin remodeling in situ, which activated their adjacent var genes. Strikingly, chromatin isolation by RNA purification analysis (ChIRP-seq) revealed that a remarkable RUF6 ncRNA had interacted with distal heterochromatin regions directly and stimulated a global derepression effect on heterochromatic genes, including all variant gene families and the sexual commitment-associated regulator ap2-g gene. Collectively, Rrp6 appears to conduct the epigenetic surveillance of heterochromatic gene expression through controlling RUF6 levels, thereby securing antigenic variation and sexual commitment of malaria parasites during the infection of the host.
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53
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Llorà-Batlle O, Michel-Todó L, Witmer K, Toda H, Fernández-Becerra C, Baum J, Cortés A. Conditional expression of PfAP2-G for controlled massive sexual conversion in Plasmodium falciparum. SCIENCE ADVANCES 2020; 6:eaaz5057. [PMID: 32577509 PMCID: PMC7286680 DOI: 10.1126/sciadv.aaz5057] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 04/15/2020] [Indexed: 05/19/2023]
Abstract
Malaria transmission requires that some asexual parasites convert into sexual forms termed gametocytes. The initial stages of sexual development, including sexually committed schizonts and sexual rings, remain poorly characterized, mainly because they are morphologically identical to their asexual counterparts and only a small subset of parasites undergo sexual development. Here, we describe a system for controlled sexual conversion in the human malaria parasite Plasmodium falciparum, based on conditional expression of the PfAP2-G transcription factor. Using this system, ~90 percent of the parasites converted into sexual forms upon induction, enabling the characterization of committed and early sexual stages without further purification. We characterized sexually committed schizonts and sexual rings at the transcriptomic and phenotypic levels, which revealed down-regulation of genes involved in solute transport upon sexual commitment, among other findings. The new inducible lines will facilitate the study of early sexual stages at additional levels, including multiomic characterization and drug susceptibility assays.
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Affiliation(s)
- Oriol Llorà-Batlle
- ISGlobal, Hospital Clinic–Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
| | - Lucas Michel-Todó
- ISGlobal, Hospital Clinic–Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
| | - Kathrin Witmer
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Haruka Toda
- ISGlobal, Hospital Clinic–Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
| | - Carmen Fernández-Becerra
- ISGlobal, Hospital Clinic–Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
- IGTP Institut d’Investigació Germans Trias i Pujol, Badalona 08916, Catalonia, Spain
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alfred Cortés
- ISGlobal, Hospital Clinic–Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
- ICREA, Barcelona 08010, Catalonia, Spain
- Corresponding author.
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54
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Hoeijmakers WAM, Miao J, Schmidt S, Toenhake CG, Shrestha S, Venhuizen J, Henderson R, Birnbaum J, Ghidelli-Disse S, Drewes G, Cui L, Stunnenberg HG, Spielmann T, Bártfai R. Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum. Nucleic Acids Res 2020; 47:11574-11588. [PMID: 31728527 PMCID: PMC7145593 DOI: 10.1093/nar/gkz1044] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/09/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulatory mechanisms are central to the development and survival of all eukaryotic organisms. These mechanisms critically depend on the marking of chromatin domains with distinctive histone tail modifications (PTMs) and their recognition by effector protein complexes. Here we used quantitative proteomic approaches to unveil interactions between PTMs and associated reader protein complexes of Plasmodium falciparum, a unicellular parasite causing malaria. Histone peptide pull-downs with the most prominent and/or parasite-specific PTMs revealed the binding preference for 14 putative and novel reader proteins. Amongst others, they highlighted the acetylation-level-dependent recruitment of the BDP1/BDP2 complex and identified an PhD-finger protein (PHD 1, PF3D7_1008100) that could mediate a cross-talk between H3K4me2/3 and H3K9ac marks. Tagging and interaction proteomics of 12 identified proteins unveiled the composition of 5 major epigenetic complexes, including the elusive TBP-associated-factor complex as well as two distinct GCN5/ADA2 complexes. Furthermore, it has highlighted a remarkable degree of interaction between these five (sub)complexes. Collectively, this study provides an extensive inventory of PTM-reader interactions and composition of epigenetic complexes. It will not only fuel further explorations of gene regulation amongst ancient eukaryotes, but also provides a stepping stone for exploration of PTM-reader interactions for antimalarial drug development.
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Affiliation(s)
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sabine Schmidt
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg D-20359, Germany
| | | | - Sony Shrestha
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jeron Venhuizen
- Department of Molecular Biology, Radboud University, Nijmegen 6525 GA, the Netherlands
| | - Rob Henderson
- Department of Molecular Biology, Radboud University, Nijmegen 6525 GA, the Netherlands.,TropIQ Health Sciences, Nijmegen 6534 AT, the Netherlands
| | - Jakob Birnbaum
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg D-20359, Germany
| | | | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Heidelberg 69117, Germany
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hendrik Gerard Stunnenberg
- Department of Molecular Biology, Radboud University, Nijmegen 6525 GA, the Netherlands.,Princess Maxima Center for Pediatric Oncology, Utrecht 3584CS, the Netherlands
| | - Tobias Spielmann
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg D-20359, Germany
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, Nijmegen 6525 GA, the Netherlands
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55
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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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56
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Galinski MR. Functional genomics of simian malaria parasites and host-parasite interactions. Brief Funct Genomics 2020; 18:270-280. [PMID: 31241151 PMCID: PMC6859816 DOI: 10.1093/bfgp/elz013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/21/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Two simian malaria parasite species, Plasmodium knowlesi and Plasmodium cynomolgi, cause zoonotic infections in Southeast Asia, and they have therefore gained recognition among scientists and public health officials. Notwithstanding, these species and others including Plasmodium coatneyi have served for decades as sources of knowledge on the biology, genetics and evolution of Plasmodium, and the diverse ramifications and outcomes of malaria in their monkey hosts. Experimental analysis of these species can help to fill gaps in knowledge beyond what may be possible studying the human malaria parasites or rodent parasite species. The genome sequences for these simian malaria parasite species were reported during the last decade, and functional genomics research has since been pursued. Here research on the functional genomics analysis involving these species is summarized and their importance is stressed, particularly for understanding host–parasite interactions, and potentially testing novel interventions. Importantly, while Plasmodium falciparum and Plasmodium vivax can be studied in small New World monkeys, the simian malaria parasites can be studied more effectively in the larger Old World monkey macaque hosts, which are more closely related to humans. In addition to ex vivo analyses, experimental scenarios can include passage through Anopheline mosquito hosts and longitudinal infections in monkeys to study acute and chronic infections, as well as relapses, all in the context of the in vivo host environment. Such experiments provide opportunities for understanding functional genomic elements that govern host–parasite interactions, immunity and pathogenesis in-depth, addressing hypotheses not possible from in vitro cultures or cross-sectional clinical studies with humans.
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Affiliation(s)
- Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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57
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Llorà-Batlle O, Tintó-Font E, Cortés A. Transcriptional variation in malaria parasites: why and how. Brief Funct Genomics 2020; 18:329-341. [PMID: 31114839 DOI: 10.1093/bfgp/elz009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/04/2019] [Accepted: 04/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional differences enable the generation of alternative phenotypes from the same genome. In malaria parasites, transcriptional plasticity plays a major role in the process of adaptation to fluctuations in the environment. Multiple studies with culture-adapted parasites and field isolates are starting to unravel the different transcriptional alternatives available to Plasmodium falciparum and the underlying molecular mechanisms. Here we discuss how epigenetic variation, directed transcriptional responses and also genetic changes that affect transcript levels can all contribute to transcriptional variation and, ultimately, parasite survival. Some transcriptional changes are driven by stochastic events. These changes can occur spontaneously, resulting in heterogeneity within parasite populations that provides the grounds for adaptation by dynamic natural selection. However, transcriptional changes can also occur in response to external cues. A better understanding of the mechanisms that the parasite has evolved to alter its transcriptome may ultimately contribute to the design of strategies to combat malaria to which the parasite cannot adapt.
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Affiliation(s)
- Oriol Llorà-Batlle
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Elisabet Tintó-Font
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
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58
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Witmer K, Fraschka SA, Vlachou D, Bártfai R, Christophides GK. An epigenetic map of malaria parasite development from host to vector. Sci Rep 2020; 10:6354. [PMID: 32286373 PMCID: PMC7156373 DOI: 10.1038/s41598-020-63121-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/24/2020] [Indexed: 12/23/2022] Open
Abstract
The malaria parasite replicates asexually in the red blood cells of its vertebrate host employing epigenetic mechanisms to regulate gene expression in response to changes in its environment. We used chromatin immunoprecipitation followed by sequencing in conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental transition from asexual blood stages to male and female gametocytes and to ookinetes in the rodent malaria parasite Plasmodium berghei. Across the developmental stages examined, heterochromatin protein 1 associates with variantly expressed gene families localised at subtelomeric regions and variant gene expression based on heterochromatic silencing is observed only in some genes. Conversely, the euchromatin mark histone 3 lysine 9 acetylation (H3K9ac) is abundant in non-heterochromatic regions across all developmental stages. H3K9ac presents a distinct pattern of enrichment around the start codon of ribosomal protein genes in all stages but male gametocytes. Additionally, H3K9ac occupancy positively correlates with transcript abundance in all stages but female gametocytes suggesting that transcription in this stage is independent of H3K9ac levels. This finding together with known mRNA repression in female gametocytes suggests a multilayered mechanism operating in female gametocytes in preparation for fertilization and zygote development, coinciding with parasite transition from host to vector.
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Affiliation(s)
- Kathrin Witmer
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
| | - Sabine A Fraschka
- Department of Molecular Biology, Radboud University, 6525, GA, Nijmegen, The Netherlands.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076, Tübingen, Germany
| | - Dina Vlachou
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525, GA, Nijmegen, The Netherlands
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59
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Dissecting the role of PfAP2-G in malaria gametocytogenesis. Nat Commun 2020; 11:1503. [PMID: 32198457 PMCID: PMC7083873 DOI: 10.1038/s41467-020-15026-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/15/2020] [Indexed: 12/20/2022] Open
Abstract
In the malaria parasite Plasmodium falciparum, the switch from asexual multiplication to sexual differentiation into gametocytes is essential for transmission to mosquitos. The transcription factor PfAP2-G is a key determinant of sexual commitment that orchestrates this crucial cell fate decision. Here we identify the direct targets of PfAP2-G and demonstrate that it dynamically binds hundreds of sites across the genome. We find that PfAP2-G is a transcriptional activator of early gametocyte genes, and identify differences in PfAP2-G occupancy between gametocytes derived via next-cycle and same-cycle conversion. Our data implicate PfAP2-G not only as a transcriptional activator of gametocyte genes, but also as a potential regulator of genes important for red blood cell invasion. We also find that regulation by PfAP2-G requires interaction with a second transcription factor, PfAP2-I. These results clarify the functional role of PfAP2-G during sexual commitment and early gametocytogenesis. The transcription factor PfAP2-G is a key determinant of sexual commitment in Plasmodium falciparum. Here, Josling et al. define the transcriptional regulatory network of PfAP2-G by identifying its DNA binding sites genome-wide, which vary depending on the route of sexual conversion and rely on interactions with the PfAP2-I transcription factor.
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60
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Venugopal K, Hentzschel F, Valkiūnas G, Marti M. Plasmodium asexual growth and sexual development in the haematopoietic niche of the host. Nat Rev Microbiol 2020; 18:177-189. [PMID: 31919479 PMCID: PMC7223625 DOI: 10.1038/s41579-019-0306-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/28/2022]
Abstract
Plasmodium spp. parasites are the causative agents of malaria in humans and animals, and they are exceptionally diverse in their morphology and life cycles. They grow and develop in a wide range of host environments, both within blood-feeding mosquitoes, their definitive hosts, and in vertebrates, which are intermediate hosts. This diversity is testament to their exceptional adaptability and poses a major challenge for developing effective strategies to reduce the disease burden and transmission. Following one asexual amplification cycle in the liver, parasites reach high burdens by rounds of asexual replication within red blood cells. A few of these blood-stage parasites make a developmental switch into the sexual stage (or gametocyte), which is essential for transmission. The bone marrow, in particular the haematopoietic niche (in rodents, also the spleen), is a major site of parasite growth and sexual development. This Review focuses on our current understanding of blood-stage parasite development and vascular and tissue sequestration, which is responsible for disease symptoms and complications, and when involving the bone marrow, provides a niche for asexual replication and gametocyte development. Understanding these processes provides an opportunity for novel therapies and interventions.
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Affiliation(s)
- Kannan Venugopal
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Franziska Hentzschel
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | | | - Matthias Marti
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
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61
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Brancucci NMB, Heussler VT, Grüring C. Targeting Plasmodium Plasmepsin V: Hitting Two Birds with One Stone. Trends Parasitol 2019; 36:85-87. [PMID: 31883707 DOI: 10.1016/j.pt.2019.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 11/16/2022]
Abstract
A recent report by Jennison et al. reveals an important role for plasmepsin V (PMV), an aspartyl protease, in the development of malaria transmission stages. The authors showed that PMV activity is critical for protein export in these stages and that specific PMV inhibitors block parasite transmission to mosquitoes.
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Affiliation(s)
- Nicolas M B Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | | | - Christof Grüring
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
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62
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van Biljon R, van Wyk R, Painter HJ, Orchard L, Reader J, Niemand J, Llinás M, Birkholtz LM. Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation. BMC Genomics 2019; 20:920. [PMID: 31795940 PMCID: PMC6889441 DOI: 10.1186/s12864-019-6322-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as it commits to and develops through gametocytogenesis. RESULTS The gametocyte-associated transcriptome is significantly different from that of the asexual parasites, with dynamic gene expression shifts characterizing early, intermediate and late-stage gametocyte development and results in differential timing for sex-specific transcripts. The transcriptional dynamics suggest strict transcriptional control during gametocytogenesis in P. falciparum, which we propose is mediated by putative regulators including epigenetic mechanisms (driving active repression of proliferation-associated processes) and a cascade-like expression of ApiAP2 transcription factors. CONCLUSIONS The gametocyte transcriptome serves as the blueprint for sexual differentiation and will be a rich resource for future functional studies on this critical stage of Plasmodium development, as the intraerythrocytic transcriptome has been for our understanding of the asexual cycle.
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Affiliation(s)
- Riëtte van Biljon
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Roelof van Wyk
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Heather J Painter
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Review, U.S. Food & Drug Administration, Silver Spring, MD, 20993, USA
| | - Lindsey Orchard
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Jandeli Niemand
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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63
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Mapping and functional analysis of heterochromatin protein 1 phosphorylation in the malaria parasite Plasmodium falciparum. Sci Rep 2019; 9:16720. [PMID: 31723180 PMCID: PMC6853920 DOI: 10.1038/s41598-019-53325-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Previous studies in model eukaryotes have demonstrated that phosphorylation of heterochromatin protein 1 (HP1) is important for dynamically regulating its various functions. However, in the malaria parasite Plasmodium falciparum both the function of HP1 phosphorylation and the identity of the protein kinases targeting HP1 are still elusive. In order to functionally analyze phosphorylation of P. falciparum HP1 (PfHP1), we first mapped PfHP1 phosphorylation sites by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of native PfHP1, which identified motifs from which potential kinases could be predicted; in particular, several phosphorylated residues were embedded in motifs rich in acidic residues, reminiscent of targets for P. falciparum casein kinase 2 (PfCK2). Secondly, we tested recombinant PfCK2 and a number of additional protein kinases for their ability to phosphorylate PfHP1 in in vitro kinase assays. These experiments validated our prediction that PfHP1 acts as a substrate for PfCK2. Furthermore, LC-MS/MS analysis showed that PfCK2 phosphorylates three clustered serine residues in an acidic motif within the central hinge region of PfHP1. To study the role of PfHP1 phosphorylation in live parasites we used CRISPR/Cas9-mediated genome editing to generate a number of conditional PfHP1 phosphomutants based on the DiCre/LoxP system. Our studies revealed that neither PfCK2-dependent phosphorylation of PfHP1, nor phosphorylation of the hinge domain in general, affect PfHP1's ability to localize to heterochromatin, and that PfHP1 phosphorylation in this region is dispensable for the proliferation of P. falciparum blood stage parasites.
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64
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Cowell AN, Winzeler EA. Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections. Genome Med 2019; 11:63. [PMID: 31640748 PMCID: PMC6805675 DOI: 10.1186/s13073-019-0673-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/13/2019] [Indexed: 01/23/2023] Open
Abstract
A major advance in antimalarial drug discovery has been the shift towards cell-based phenotypic screening, with notable progress in the screening of compounds against the asexual blood stage, liver stage, and gametocytes. A primary method for drug target deconvolution in Plasmodium falciparum is in vitro evolution of compound-resistant parasites followed by whole-genome scans. Several of the most promising antimalarial drug targets, such as translation elongation factor 2 (eEF2) and phenylalanine tRNA synthetase (PheRS), have been identified or confirmed using this method. One drawback of this method is that if a mutated gene is uncharacterized, a substantial effort may be required to determine whether it is a drug target, a drug resistance gene, or if the mutation is merely a background mutation. Thus, the availability of high-throughput, functional genomic datasets can greatly assist with target deconvolution. Studies mapping genome-wide essentiality in P. falciparum or performing transcriptional profiling of the host and parasite during liver-stage infection with P. berghei have identified potentially druggable pathways. Advances in mapping the epigenomic regulation of the malaria parasite genome have also enabled the identification of key processes involved in parasite development. In addition, the examination of the host genome during infection has identified novel gene candidates associated with susceptibility to severe malaria. Here, we review recent studies that have used omics-based methods to identify novel targets for interventions against protozoan parasites, focusing on malaria, and we highlight the advantages and limitations of the approaches used. These approaches have also been extended to other protozoan pathogens, including Toxoplasma, Trypanosoma, and Leishmania spp., and these studies highlight how drug discovery efforts against these pathogens benefit from the utilization of diverse omics-based methods to identify promising drug targets.
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Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases and Global Health, Department of Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
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65
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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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66
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Abel S, Le Roch KG. The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:302-313. [PMID: 31220857 PMCID: PMC6859822 DOI: 10.1093/bfgp/elz005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/25/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
Due to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.
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Affiliation(s)
- Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
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67
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Ngotho P, Soares AB, Hentzschel F, Achcar F, Bertuccini L, Marti M. Revisiting gametocyte biology in malaria parasites. FEMS Microbiol Rev 2019; 43:401-414. [PMID: 31220244 PMCID: PMC6606849 DOI: 10.1093/femsre/fuz010] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/05/2019] [Indexed: 12/21/2022] Open
Abstract
Gametocytes are the only form of the malaria parasite that is transmissible to the mosquito vector. They are present at low levels in blood circulation and significant knowledge gaps exist in their biology. Recent reductions in the global malaria burden have brought the possibility of elimination and eradication, with renewed focus on malaria transmission biology as a basis for interventions. This review discusses recent insights into gametocyte biology in the major human malaria parasite, Plasmodium falciparum and related species.
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Affiliation(s)
- Priscilla Ngotho
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Alexandra Blancke Soares
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Franziska Hentzschel
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Lucia Bertuccini
- Core Facilities, Microscopy Area, Instituto Superiore di Sanita, Via Regina Elena 299, 00161 Rome, Italy
| | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA
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68
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Jabeena CA, Rajavelu A. Epigenetic Players of Chromatin Structure Regulation in Plasmodium falciparum. Chembiochem 2019; 20:1225-1230. [PMID: 30632244 DOI: 10.1002/cbic.201800718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Indexed: 12/16/2022]
Abstract
The protozoan parasite Plasmodium has evolved to survive in different hosts and environments. The diverse strategies of adaptation to different niches involve differential gene expression mechanisms mediated by chromatin plasticity that are poorly characterized in Plasmodium. The parasite employs a wide variety of regulatory mechanisms to complete their life cycle and survive inside hosts. Among them, epigenetic-mediated mechanisms have been implicated for controlling chromatin organization, gene regulation, morphological differentiation, and antigenic variation. The differential gene expression in parasite is largely dependent on the nature of the chromatin structure. The histone core methylation marks and methyl mark readers contribute to chromatin dynamics. Here, we review the recent developments on various epigenetic marks and its enzymes in the Plasmodium falciparum, how these marks play a key role in the regulation of transcriptional activity of variable genes and coordinate the differential gene expression. We also discuss the possible roles of these epigenetic marks in chromatin structure regulation and plasticity at various stages of its development.
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Affiliation(s)
- C A Jabeena
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Arumugam Rajavelu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India
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69
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Ararat-Sarria M, Patarroyo MA, Curtidor H. Parasite-Related Genetic and Epigenetic Aspects and Host Factors Influencing Plasmodium falciparum Invasion of Erythrocytes. Front Cell Infect Microbiol 2019; 8:454. [PMID: 30693273 PMCID: PMC6339890 DOI: 10.3389/fcimb.2018.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 01/13/2023] Open
Abstract
Malaria, a disease caused by Plasmodium parasites, is widespread throughout tropical and sub-tropical regions worldwide; it mostly affects children and pregnant woman. Eradication has stalled despite effective prevention measures and medication being available for this disease; this has mainly been due to the parasite's resistance to medical treatment and the mosquito vector's resistance to insecticides. Tackling such resistance involves using renewed approaches and techniques for accruing a deep understanding of the parasite's biology, and developing new drugs and vaccines. Studying the parasite's invasion of erythrocytes should shed light on its ability to switch between invasion phenotypes related to the expression of gene sets encoding proteins acting as ligands during target cell invasion, thereby conferring mechanisms for evading a particular host's immune response and adapting to changes in target cell surface receptors. This review considers some factors influencing the expression of such phenotypes, such as Plasmodium's genetic, transcriptional and epigenetic characteristics, and explores some host-related aspects which could affect parasite phenotypes, aiming at integrating knowledge regarding this topic and the possible relationship between the parasite's biology and host factors playing a role in erythrocyte invasion.
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Affiliation(s)
- Monica Ararat-Sarria
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Immunología de Colombia (FIDIC), Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Hernando Curtidor
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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70
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Bancells C, Llorà-Batlle O, Poran A, Nötzel C, Rovira-Graells N, Elemento O, Kafsack BFC, Cortés A. Revisiting the initial steps of sexual development in the malaria parasite Plasmodium falciparum. Nat Microbiol 2019; 4:144-154. [PMID: 30478286 PMCID: PMC6294672 DOI: 10.1038/s41564-018-0291-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/11/2018] [Indexed: 01/01/2023]
Abstract
Human to vector transmission of malaria requires that some blood-stage parasites abandon asexual growth and convert into non-replicating sexual forms called gametocytes. The initial steps of gametocytogenesis remain largely uncharacterized. Here, we study this part of the malaria life cycle in Plasmodium falciparum using PfAP2-G, the master regulator of sexual conversion, as a marker of commitment. We demonstrate the existence of PfAP2-G-positive sexually committed parasite stages that precede the previously known committed schizont stage. We also found that sexual conversion can occur by two different routes: the previously described route in which PfAP2-G-expressing parasites complete a replicative cycle as committed forms before converting into gametocytes upon re-invasion, or a direct route with conversion within the same cycle as initial PfAP2-G expression. The latter route is linked to early PfAP2-G expression in ring stages. Reanalysis of published single-cell RNA-sequencing (RNA-seq) data confirmed the presence of both routes. Consistent with these results, using plaque assays we observed that, in contrast to the prevailing model, many schizonts produced mixed plaques containing both asexual parasites and gametocytes. Altogether, our results reveal unexpected features of the initial steps of sexual development and extend the current view of this part of the malaria life cycle.
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Affiliation(s)
- Cristina Bancells
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Asaf Poran
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Nötzel
- Biochemistry, Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, USA
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Björn F C Kafsack
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Alfred Cortés
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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71
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Tarr SJ, Díaz-Ingelmo O, Stewart LB, Hocking SE, Murray L, Duffy CW, Otto TD, Chappell L, Rayner JC, Awandare GA, Conway DJ. Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum. BMC Genomics 2018; 19:894. [PMID: 30526479 PMCID: PMC6288915 DOI: 10.1186/s12864-018-5257-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria parasites are genetically polymorphic and phenotypically plastic. In studying transcriptome variation among parasites from different infections, it is challenging to overcome potentially confounding technical and biological variation between samples. We investigate variation in the major human parasite Plasmodium falciparum, generating RNA-seq data on multiple independent replicate sample preparations of merozoite-containing intra-erythrocytic schizonts from a panel of clinical isolates and from long-term laboratory-adapted clones, with a goal of robustly identifying differentially expressed genes. RESULTS Analysis of biological sample replicates shows that increased numbers improve the true discovery rate of differentially expressed genes, and that six independent replicates of each parasite line allowed identification of most differences that could be detected with larger numbers. For highly expressed genes, focusing on the top quartile at schizont stages, there was more power to detect differences. Comparing cultured clinical isolates and laboratory-adapted clones, genes more highly expressed in the laboratory-adapted clones include those encoding an AP2 transcription factor (PF3D7_0420300), a ubiquitin-binding protein and two putative methyl transferases. In contrast, higher expression in clinical isolates was seen for the merozoite surface protein gene dblmsp2, proposed to be a marker of schizonts forming merozoites committed to sexual differentiation. Variable expression was extremely strongly, but not exclusively, associated with genes known to be targeted by Heterochromatin Protein 1. Clinical isolates show variable expression of several known merozoite invasion ligands, as well as other genes for which new RT-qPCR assays validate the quantitation and allow characterisation in samples with more limited material. Expression levels of these genes vary among schizont preparations of different clinical isolates in the first ex vivo cycle in patient erythrocytes, but mean levels are similar to those in continuously cultured clinical isolates. CONCLUSIONS Analysis of multiple biological sample replicates greatly improves identification of genes variably expressed between different cultured parasite lines. Clinical isolates recently established in culture show differences from long-term adapted clones in transcript levels of particular genes, and are suitable for analyses requiring biological replicates to understand parasite phenotypes and variable expression likely to be relevant in nature.
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Affiliation(s)
- Sarah J Tarr
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK.
| | - Ofelia Díaz-Ingelmo
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Lindsay B Stewart
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Suzanne E Hocking
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Lee Murray
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Craig W Duffy
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas D Otto
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Scotland, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Lia Chappell
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - David J Conway
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK.
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72
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Zhu L, Tripathi J, Rocamora FM, Miotto O, van der Pluijm R, Voss TS, Mok S, Kwiatkowski DP, Nosten F, Day NPJ, White NJ, Dondorp AM, Bozdech Z. The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background. Nat Commun 2018; 9:5158. [PMID: 30514877 PMCID: PMC6279830 DOI: 10.1038/s41467-018-07588-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
The predisposition of parasites acquiring artemisinin resistance still remains unclear beyond the mutations in Pfk13 gene and modulation of the unfolded protein response pathway. To explore the chain of casualty underlying artemisinin resistance, we reanalyze 773 P. falciparum isolates from TRACI-study integrating TWAS, GWAS, and eQTL analyses. We find the majority of P. falciparum parasites are transcriptomically converged within each geographic site with two broader physiological profiles across the Greater Mekong Subregion (GMS). We report 8720 SNP-expression linkages in the eastern GMS parasites and 4537 in the western. The minimal overlap between them suggests differential gene regulatory networks facilitating parasite adaptations to their unique host environments. Finally, we identify two genetic and physiological backgrounds associating with artemisinin resistance in the GMS, together with a farnesyltransferase protein and a thioredoxin-like protein which may act as vital intermediators linking the Pfk13 C580Y mutation to the prolonged parasite clearance time.
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Affiliation(s)
- Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
- Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Rob van der Pluijm
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
| | - Till S Voss
- Swiss Tropical and Public Health Institute, Basel, 4051, Switzerland
- University of Basel, Basel, 4001, Switzerland
| | - Sachel Mok
- Columbia University Medical Center, Columbia University, New York, 10027, USA
| | - Dominic P Kwiatkowski
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
- Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - François Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, 63110, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research, University of Oxford, Oxford, OX3 7LF, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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73
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Batugedara G, Le Roch KG. Unraveling the 3D genome of human malaria parasites. Semin Cell Dev Biol 2018; 90:144-153. [PMID: 30009946 DOI: 10.1016/j.semcdb.2018.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/31/2023]
Abstract
The chromosomes within the eukaryotic cell nucleus are highly dynamic and adopt complex hierarchical structures. Understanding how this three-dimensional (3D) nuclear architectureaffects gene regulation, cell cycle progression and disease pathogenesis are important biological questions in development and disease. Recently, many genome-wide technologies including chromosome conformation capture (3C) and 3C-based methodologies (4C, 5C, and Hi-C) have been developed to investigate 3D chromatin structure. In this review, we introduce 3D genome methodologies, with a focus on their application for understanding the nuclear architecture of the human malaria parasite, Plasmodium falciparum. An increasing amount of evidence now suggests that gene regulation in the parasite is largely regulated by epigenetic mechanisms and nuclear reorganization. Here, we explore the 3D genome architecture of P. falciparum, including local and global chromatin structure. In addition, molecular components important for maintaining 3D chromatin organization including architectural proteins and long non-coding RNAs are discussed. Collectively, these studies contribute to our understanding of how the plasticity of 3D genome architecture regulates gene expression and cell cycle progression in this deadly parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA.
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74
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Josling GA, Williamson KC, Llinás M. Regulation of Sexual Commitment and Gametocytogenesis in Malaria Parasites. Annu Rev Microbiol 2018; 72:501-519. [PMID: 29975590 DOI: 10.1146/annurev-micro-090817-062712] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sexual differentiation of malaria parasites from the asexual blood stage into gametocytes is an essential part of the life cycle, as gametocytes are the form that is taken up by the mosquito host. Because of the essentiality of this process for transmission to the mosquito, gametocytogenesis is an extremely attractive target for therapeutic interventions. The subject of this review is the considerable progress that has been made in recent years in elucidating the molecular mechanisms governing this important differentiation process. In particular, a number of critical transcription factors and epigenetic regulators have emerged as crucial elements in the regulation of commitment. The identification of these factors has allowed us to understand better than ever before the events occurring prior to and during commitment to sexual development and offers potential for new therapeutic interventions.
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Affiliation(s)
- Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; .,Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kim C Williamson
- Microbiology and Immunology Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; .,Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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75
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Rea E, Le Roch KG, Tewari R. Sex in Plasmodium falciparum: Silence Play between GDV1 and HP1. Trends Parasitol 2018; 34:450-452. [PMID: 29752147 DOI: 10.1016/j.pt.2018.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/26/2018] [Indexed: 02/01/2023]
Abstract
Understanding how malaria parasites commit to sexual development is key to the development of transmission-blocking strategies. Recent work by Filarsky and colleagues extends our understanding of the molecular mechanisms driving this process by characterizing an early factor in gametocytogenesis, and showing how this fits neatly into our current knowledge of sexual commitment.
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Affiliation(s)
- Edward Rea
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK.
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76
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Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S, Stewart LB, Campino S, Kekre M, Hamilton WL, Claessens A, Volkman SK, Ndiaye D, Amambua-Ngwa A, Diakite M, Fairhurst RM, Conway DJ, Franck M, Newbold CI, Berriman M. Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Res 2018; 3:52. [PMID: 29862326 PMCID: PMC5964635 DOI: 10.12688/wellcomeopenres.14571.1] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2018] [Indexed: 12/30/2022] Open
Abstract
Background: Although thousands of clinical isolates of
Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15
P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal
var genes clusters.
Results: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates. We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa. Conclusions: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.
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Affiliation(s)
- Thomas D Otto
- Wellcome Sanger Institute, Hinxton, UK.,Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Adam Reid
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen I Bruske
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Craig W Duffy
- London School of Hygiene and Tropical Medicine, London, UK
| | - Pete C Bull
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | | | - Sandra Dimonte
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Susana Campino
- Wellcome Sanger Institute, Hinxton, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | - Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Simmons College, Boston, MA, USA
| | - Daouda Ndiaye
- Faculty of Medicine and Pharmacy, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Mahamadou Diakite
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Matthias Franck
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Chris I Newbold
- Wellcome Sanger Institute, Hinxton, UK.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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