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Ortiz SFDN, Verdan R, Fortes FDSDA, Benchimol M. Trichomonas vaginalis: Monolayer and Cluster Formation-Ultrastructural Aspects Using High-Resolution Scanning Electron Microscopy. Pathogens 2023; 12:1381. [PMID: 38133266 PMCID: PMC10747464 DOI: 10.3390/pathogens12121381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Trichomonas vaginalis is an extracellular protozoan parasite that causes human trichomoniasis, a sexually transmitted infection (STI) that affects approximately 270 million people worldwide. The phenomenon of T. vaginalis adhesion to inert substrates has been described in several reports. Still, very few studies on cluster formation have been conducted, and more detailed analyses of the contact regions between the parasites' membranes in these aggregate formations have not been carried out. The present study aims to show that T. vaginalis forms a tight monolayer, similar to an epithelium, with parasites firmly adhered to the culture flask bottom by interdigitations and in the absence of host cells. In addition, we analyzed and compared the formation of the clusters, focusing on parasite aggregates that float in the culture flasks. We employed various imaging techniques, including high-resolution scanning electron microscopy, transmission electron microscopy, cytochemistry, TEM tomography, and dye injection. We analyzed whether the monolayer behaves as an epithelium, analyzing cell junctions, cell communication, and ultrastructural aspects, and concluded that monolayer formation differs from cluster formation in many aspects. The monolayers form strong adhesion, whereas the clusters have fragile attachments. We did not find fusion or the passage of molecules between neighbor-attached cells; there is no need for different strains to form filopodia, cytonemes, and extracellular vesicles during cluster and monolayer formation.
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Affiliation(s)
- Sharmila Fiama das Neves Ortiz
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (S.F.d.N.O.); (R.V.)
| | - Raphael Verdan
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; (S.F.d.N.O.); (R.V.)
| | - Fabio da Silva de Azevedo Fortes
- BIOTRANS-CAXIAS Campus, Universidade do Grande Rio, UNIGRANRIO, Rio de Janeiro 96200-000, Brazil;
- Laboratório de Terapia e Fisiologia Celular e Molecular, Departamento de Biologia, Faculdade de Ciências Biológicas e Saúde, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23070-200, Brazil
| | - Marlene Benchimol
- BIOTRANS-CAXIAS Campus, Universidade do Grande Rio, UNIGRANRIO, Rio de Janeiro 96200-000, Brazil;
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
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2
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Padilla‐Mejia NE, Field MC. Evolutionary, structural and functional insights in nuclear organisation and nucleocytoplasmic transport in trypanosomes. FEBS Lett 2023; 597:2501-2518. [PMID: 37789516 PMCID: PMC10953052 DOI: 10.1002/1873-3468.14747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope (NE), a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades, these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently, the critical roles of the lamina, NPC and other NE constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here, we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.
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Affiliation(s)
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeUK
- Institute of Parasitology, Biology CentreCzech Academy of SciencesČeské BudějoviceCzechia
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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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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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5
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Abstract
Malaria remains a significant threat to global health, and despite concerted efforts to curb the disease, malaria-related morbidity and mortality increased in recent years. Malaria is caused by unicellular eukaryotes of the genus Plasmodium, and all clinical manifestations occur during asexual proliferation of the parasite inside host erythrocytes. In the blood stage, Plasmodium proliferates through an unusual cell cycle mode called schizogony. Contrary to most studied eukaryotes, which divide by binary fission, the parasite undergoes several rounds of DNA replication and nuclear division that are not directly followed by cytokinesis, resulting in multinucleated cells. Moreover, despite sharing a common cytoplasm, these nuclei multiply asynchronously. Schizogony challenges our current models of cell cycle regulation and, at the same time, offers targets for therapeutic interventions. Over the recent years, the adaptation of advanced molecular and cell biological techniques have given us deeper insight how DNA replication, nuclear division, and cytokinesis are coordinated. Here, we review our current understanding of the chronological events that characterize the unusual cell division cycle of P. falciparum in the clinically relevant blood stage of infection.
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6
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Epigenetic and Epitranscriptomic Gene Regulation in Plasmodium falciparum and How We Can Use It against Malaria. Genes (Basel) 2022; 13:genes13101734. [PMID: 36292619 PMCID: PMC9601349 DOI: 10.3390/genes13101734] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, is still one of the biggest global health challenges. P. falciparum is the deadliest species to humans. In this review, we discuss how this parasite develops and adapts to the complex and heterogenous environments of its two hosts thanks to varied chromatin-associated and epigenetic mechanisms. First, one small family of transcription factors, the ApiAP2 proteins, functions as master regulators of spatio-temporal patterns of gene expression through the parasite life cycle. In addition, chromatin plasticity determines variable parasite cell phenotypes that link to parasite growth, virulence and transmission, enabling parasite adaptation within host conditions. In recent years, epitranscriptomics is emerging as a new regulatory layer of gene expression. We present evidence of the variety of tRNA and mRNA modifications that are being characterized in Plasmodium spp., and the dynamic changes in their abundance during parasite development and cell fate. We end up outlining that new biological systems, like the mosquito model, to decipher the unknowns about epigenetic mechanisms in vivo; and novel methodologies, to study the function of RNA modifications; are needed to discover the Achilles heel of the parasite. With this new knowledge, future strategies manipulating the epigenetics and epitranscriptomic machinery of the parasite have the potential of providing new weapons against malaria.
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7
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TurboID Identification of Evolutionarily Divergent Components of the Nuclear Pore Complex in the Malaria Model Plasmodium berghei. mBio 2022; 13:e0181522. [PMID: 36040030 PMCID: PMC9601220 DOI: 10.1128/mbio.01815-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty years since the publication of the Plasmodium falciparum and P. berghei genomes one-third of their protein-coding genes still lack functional annotation. In the absence of sequence and structural homology, protein-protein interactions can facilitate functional prediction of such orphan genes by mapping protein complexes in their natural cellular environment. The Plasmodium nuclear pore complex (NPC) is a case in point: it remains poorly defined; its constituents lack conservation with the 30+ proteins described in the NPC of many opisthokonts, a clade of eukaryotes that includes fungi and animals, but not Plasmodium. Here, we developed a labeling methodology based on TurboID fusion proteins, which allows visualization of the P. berghei NPC and facilitates the identification of its components. Following affinity purification and mass spectrometry, we identified 4 known nucleoporins (Nups) (138, 205, 221, and the bait 313), and verify interaction with the putative phenylalanine-glycine (FG) Nup637; we assigned 5 proteins lacking annotation (and therefore meaningful homology with proteins outside the genus) to the NPC, which is confirmed by green fluorescent protein (GFP) tagging. Based on gene deletion attempts, all new Nups — Nup176, 269, 335, 390, and 434 — are essential to parasite survival. They lack primary sequence homology with proteins outside the Plasmodium genus; albeit 2 incorporate short domains with structural homology to human Nup155 and yeast Nup157, and the condensin SMC (Structural Maintenance Of Chromosomes 4). The protocols developed here showcase the power of proximity labeling for elucidating protein complex composition and annotation of taxonomically restricted genes in Plasmodium. It opens the door to exploring the function of the Plasmodium NPC and understanding its evolutionary position.
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CRISPR/Cas9-engineered inducible gametocyte producer lines as a valuable tool for Plasmodium falciparum malaria transmission research. Nat Commun 2021; 12:4806. [PMID: 34376675 PMCID: PMC8355313 DOI: 10.1038/s41467-021-24954-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
The malaria parasite Plasmodium falciparum replicates inside erythrocytes in the blood of infected humans. During each replication cycle, a small proportion of parasites commits to sexual development and differentiates into gametocytes, which are essential for parasite transmission via the mosquito vector. Detailed molecular investigation of gametocyte biology and transmission has been hampered by difficulties in generating large numbers of these highly specialised cells. Here, we engineer P. falciparum NF54 inducible gametocyte producer (iGP) lines for the routine mass production of synchronous gametocytes via conditional overexpression of the sexual commitment factor GDV1. NF54/iGP lines consistently achieve sexual commitment rates of 75% and produce viable gametocytes that are transmissible by mosquitoes. We also demonstrate that further genetic engineering of NF54/iGP parasites is a valuable tool for the targeted exploration of gametocyte biology. In summary, we believe the iGP approach developed here will greatly expedite basic and applied malaria transmission stage research.
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9
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. iScience 2021; 24:102714. [PMID: 34258551 PMCID: PMC8253967 DOI: 10.1016/j.isci.2021.102714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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10
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Gubbels MJ, Coppens I, Zarringhalam K, Duraisingh MT, Engelberg K. The Modular Circuitry of Apicomplexan Cell Division Plasticity. Front Cell Infect Microbiol 2021; 11:670049. [PMID: 33912479 PMCID: PMC8072463 DOI: 10.3389/fcimb.2021.670049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
The close-knit group of apicomplexan parasites displays a wide variety of cell division modes, which differ between parasites as well as between different life stages within a single parasite species. The beginning and endpoint of the asexual replication cycles is a 'zoite' harboring the defining apical organelles required for host cell invasion. However, the number of zoites produced per division round varies dramatically and can unfold in several different ways. This plasticity of the cell division cycle originates from a combination of hard-wired developmental programs modulated by environmental triggers. Although the environmental triggers and sensors differ between species and developmental stages, widely conserved secondary messengers mediate the signal transduction pathways. These environmental and genetic input integrate in division-mode specific chromosome organization and chromatin modifications that set the stage for each division mode. Cell cycle progression is conveyed by a smorgasbord of positively and negatively acting transcription factors, often acting in concert with epigenetic reader complexes, that can vary dramatically between species as well as division modes. A unique set of cell cycle regulators with spatially distinct localization patterns insert discrete check points which permit individual control and can uncouple general cell cycle progression from nuclear amplification. Clusters of expressed genes are grouped into four functional modules seen in all division modes: 1. mother cytoskeleton disassembly; 2. DNA replication and segregation (D&S); 3. karyokinesis; 4. zoite assembly. A plug-and-play strategy results in the variety of extant division modes. The timing of mother cytoskeleton disassembly is hard-wired at the species level for asexual division modes: it is either the first step, or it is the last step. In the former scenario zoite assembly occurs at the plasma membrane (external budding), and in the latter scenario zoites are assembled in the cytoplasm (internal budding). The number of times each other module is repeated can vary regardless of this first decision, and defines the modes of cell division: schizogony, binary fission, endodyogeny, endopolygeny.
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Affiliation(s)
- Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, MA, United States
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, United States
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Klemens Engelberg
- Department of Biology, Boston College, Chestnut Hill, MA, United States
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11
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Machado M, Steinke S, Ganter M. Plasmodium Reproduction, Cell Size, and Transcription: How to Cope With Increasing DNA Content? Front Cell Infect Microbiol 2021; 11:660679. [PMID: 33898332 PMCID: PMC8062723 DOI: 10.3389/fcimb.2021.660679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmodium, the unicellular parasite that causes malaria, evolved a highly unusual mode of reproduction. During its complex life cycle, invasive or transmissive stages alternate with proliferating stages, where a single parasite can produce tens of thousands of progeny. In the clinically relevant blood stage of infection, the parasite replicates its genome up to thirty times and forms a multinucleated cell before daughter cells are assembled. Thus, within a single cell cycle, Plasmodium develops from a haploid to a polypoid cell, harboring multiple copies of its genome. Polyploidy creates several biological challenges, such as imbalances in genome output, and cells can respond to this by changing their size and/or alter the production of RNA species and protein to achieve expression homeostasis. However, the effects and possible adaptations of Plasmodium to the massively increasing DNA content are unknown. Here, we revisit and embed current Plasmodium literature in the context of polyploidy and propose potential mechanisms of the parasite to cope with the increasing gene dosage.
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Affiliation(s)
- Marta Machado
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.,Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Salome Steinke
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ganter
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
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12
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Hollin T, Le Roch KG. From Genes to Transcripts, a Tightly Regulated Journey in Plasmodium. Front Cell Infect Microbiol 2020; 10:618454. [PMID: 33425787 PMCID: PMC7793691 DOI: 10.3389/fcimb.2020.618454] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decade, we have witnessed significant progresses in understanding gene regulation in Apicomplexa including the human malaria parasite, Plasmodium falciparum. This parasite possesses the ability to convert in multiple stages in various hosts, cell types, and environments. Recent findings indicate that P. falciparum is talented at using efficient and complementary molecular mechanisms to ensure a tight control of gene expression at each stage of its life cycle. Here, we review the current understanding on the contribution of the epigenome, atypical transcription factors, and chromatin organization to regulate stage conversion in P. falciparum. The adjustment of these regulatory mechanisms occurring during the progression of the life cycle will be extensively discussed.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
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13
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Weiner A. Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software. Methods Cell Biol 2020; 162:333-351. [PMID: 33707018 DOI: 10.1016/bs.mcb.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissues. These tasks remain challenging and are often rate-limiting to most users. Here we provide a step-by-step guide to image processing and manual correlation using ImageJ and Amira software of a confocal microscopy stack and a focused ion beam/scanning electron microscopy (FIB/SEM) tomogram acquired using a correlative pipeline. These previously published datasets capture a highly transient invasion event by the bacterium Shigella flexneri infecting an epithelial cell grown in culture, and are made available here in their pre-processed form for readers who wish to gain hands-on experience in image processing and correlation using existing data. In this guide we describe a simple protocol for correlation based on internal sample features clearly visible by both fluorescence and electron microscopy, which is normally sufficient when correlating standard fluorescence microscopy stacks with FIB/SEM data. While the guide describes the treatment of specific datasets, it is applicable to a wide variety of samples and different microscopy approaches that require basic correlation and visualization of two or more datasets in a single integrated framework.
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Affiliation(s)
- Allon Weiner
- Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Inserm, Sorbonne Université, Paris, France.
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14
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Abstract
The complex environment of biological cells and tissues has motivated development of three-dimensional (3D) imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper source post facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryoscanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles and then in representative cryotomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.
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15
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Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites. Trends Genet 2020; 37:73-85. [PMID: 32988634 DOI: 10.1016/j.tig.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Multiple hosts and various life cycle stages prompt the human malaria parasite, Plasmodium falciparum, to acquire sophisticated molecular mechanisms to ensure its survival, spread, and transmission to its next host. To face these environmental challenges, increasing evidence suggests that the parasite has developed complex and complementary layers of regulatory mechanisms controlling gene expression. Here, we discuss the recent developments in the discovery of molecular components that contribute to cell replication and differentiation and highlight the major contributions of epigenetics, transcription factors, and nuclear architecture in controlling gene regulation and life cycle progression in Plasmodium spp.
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16
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mSphere of Influence: the Dynamic Nature of the Nuclear Envelope during Mitosis of Malaria Parasites. mSphere 2020; 5:5/5/e00815-20. [PMID: 32878936 PMCID: PMC7471010 DOI: 10.1128/msphere.00815-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Sabrina Absalon works in the field of cellular and molecular biology of Plasmodium falciparum, the most virulent parasite causing malaria in humans. In this mSphere of Influence article, she reflects on how the paper “3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum” by Allon Weiner et al. (A. Weiner, N. Dahan-Pasternak, E. Shimoni, V. Shinder, et al., Cell Microbiol 13:967–977, 2011, https://doi.org/10.1111/j.1462-5822.2011.01592.x) triggered her aspiration to study the molecular mechanisms governing nuclear envelope assembly and integrity of P. falciparum throughout the intraerythrocytic development cycle. Sabrina Absalon works in the field of cellular and molecular biology of Plasmodium falciparum, the most virulent parasite causing malaria in humans. In this mSphere of Influence article, she reflects on how the paper “3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum” by Allon Weiner et al. (A. Weiner, N. Dahan-Pasternak, E. Shimoni, V. Shinder, et al., Cell Microbiol 13:967–977, 2011, https://doi.org/10.1111/j.1462-5822.2011.01592.x) triggered her aspiration to study the molecular mechanisms governing nuclear envelope assembly and integrity of P. falciparum throughout the intraerythrocytic development cycle.
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17
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Francia ME, Bhavsar S, Ting LM, Croken MM, Kim K, Dubremetz JF, Striepen B. A Homolog of Structural Maintenance of Chromosome 1 Is a Persistent Centromeric Protein Which Associates With Nuclear Pore Components in Toxoplasma gondii. Front Cell Infect Microbiol 2020; 10:295. [PMID: 32714878 PMCID: PMC7343853 DOI: 10.3389/fcimb.2020.00295] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/19/2020] [Indexed: 01/02/2023] Open
Abstract
Apicomplexa are obligate intracellular parasites which cause various animal and human diseases including malaria, toxoplasmosis, and cryptosporidiosis. They proliferate by a unique mechanism that combines physically separated semi-closed mitosis of the nucleus and assembly of daughter cells by internal budding. Mitosis occurs in the presence of a nuclear envelope and with little appreciable chromatin condensation. A long standing question in the field has been how parasites keep track of their uncondensed chromatin chromosomes throughout their development, and hence secure proper chromosome segregation during division. Past work demonstrated that the centromeres, the region of kinetochore assembly at chromosomes, of Toxoplasma gondii remain clustered at a defined region of the nuclear periphery proximal to the main microtubule organizing center of the cell, the centrosome. We have proposed that this mechanism is likely involved in the process. Here we set out to identify underlying molecular players involved in centromere clustering. Through pharmacological treatment and structural analysis we show that centromere clustering is not mediated by persistent microtubules of the mitotic spindle. We identify the chromatin binding factor a homolog of structural maintenance of chromosomes 1 (SMC1). Additionally, we show that both TgSMC1, and a centromeric histone, interact with TgExportin1, a predicted soluble component of the nuclear pore complex. Our results suggest that the nuclear envelope, and in particular the nuclear pore complex may play a role in positioning centromeres in T. gondii.
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Affiliation(s)
- Maria E Francia
- Department of Cellular Biology, University of Georgia, Athens, GA, United States
| | - Sheila Bhavsar
- Department of Cellular Biology, University of Georgia, Athens, GA, United States
| | - Li-Min Ting
- Morsani College of Medicine, University of South Florida Health, Tampa, FL, United States
| | - Matthew M Croken
- Pathology, Molecular and Cell Based Medicine, Mount Sinai Medical Center, New York, NY, United States
| | - Kami Kim
- Morsani College of Medicine, University of South Florida Health, Tampa, FL, United States
| | | | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, United States.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
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18
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Three-dimensional ultrastructure of Plasmodium falciparum throughout cytokinesis. PLoS Pathog 2020; 16:e1008587. [PMID: 32511279 PMCID: PMC7302870 DOI: 10.1371/journal.ppat.1008587] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/18/2020] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
New techniques for obtaining electron microscopy data through the cell volume are being increasingly utilized to answer cell biologic questions. Here, we present a three-dimensional atlas of Plasmodium falciparum ultrastructure throughout parasite cell division. Multiple wild type schizonts at different stages of segmentation, or budding, were imaged and rendered, and the 3D structure of their organelles and daughter cells are shown. Our high-resolution volume electron microscopy both confirms previously described features in 3D and adds new layers to our understanding of Plasmodium nuclear division. Interestingly, we demonstrate asynchrony of the final nuclear division, a process that had previously been reported as synchronous. Use of volume electron microscopy techniques for biological imaging is gaining prominence, and there is much we can learn from applying them to answer questions about Plasmodium cell biology. We provide this resource to encourage readers to consider adding these techniques to their cell biology toolbox.
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19
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Hammam E, Ananda G, Sinha A, Scheidig-Benatar C, Bohec M, Preiser PR, Dedon PC, Scherf A, Vembar SS. Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites. Nucleic Acids Res 2020; 48:184-199. [PMID: 31777939 PMCID: PMC6943133 DOI: 10.1093/nar/gkz1093] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/09/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
DNA cytosine modifications are key epigenetic regulators of cellular processes in mammalian cells, with their misregulation leading to varied disease states. In the human malaria parasite Plasmodium falciparum, a unicellular eukaryotic pathogen, little is known about the predominant cytosine modifications, cytosine methylation (5mC) and hydroxymethylation (5hmC). Here, we report the first identification of a hydroxymethylcytosine-like (5hmC-like) modification in P. falciparum asexual blood stages using a suite of biochemical methods. In contrast to mammalian cells, we report 5hmC-like levels in the P. falciparum genome of 0.2–0.4%, which are significantly higher than the methylated cytosine (mC) levels of 0.01–0.05%. Immunoprecipitation of hydroxymethylated DNA followed by next generation sequencing (hmeDIP-seq) revealed that 5hmC-like modifications are enriched in gene bodies with minimal dynamic changes during asexual development. Moreover, levels of the 5hmC-like base in gene bodies positively correlated to transcript levels, with more than 2000 genes stably marked with this modification throughout asexual development. Our work highlights the existence of a new predominant cytosine DNA modification pathway in P. falciparum and opens up exciting avenues for gene regulation research and the development of antimalarials.
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Affiliation(s)
- Elie Hammam
- Institut Pasteur, 75015 Paris, France.,CNRS ERL9195, 75015 Paris, France.,INSERM U1201, 75015 Paris, France.,Sorbonne Université, Ecole doctorale Complexité du Vivant ED515, F-75005 Paris, France
| | - Guruprasad Ananda
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ameya Sinha
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Christine Scheidig-Benatar
- Institut Pasteur, 75015 Paris, France.,CNRS ERL9195, 75015 Paris, France.,INSERM U1201, 75015 Paris, France
| | - Mylene Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Artur Scherf
- Institut Pasteur, 75015 Paris, France.,CNRS ERL9195, 75015 Paris, France.,INSERM U1201, 75015 Paris, France
| | - Shruthi S Vembar
- Institut Pasteur, 75015 Paris, France.,CNRS ERL9195, 75015 Paris, France.,INSERM U1201, 75015 Paris, France
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20
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Araki T, Kawai S, Kakuta S, Kobayashi H, Umeki Y, Saito-Nakano Y, Sasaki T, Nagamune K, Yasutomi Y, Nozaki T, Franke-Fayard B, Khan SM, Hisaeda H, Annoura T. Three-dimensional electron microscopy analysis reveals endopolygeny-like nuclear architecture segregation in Plasmodium oocyst development. Parasitol Int 2019; 76:102034. [PMID: 31805442 DOI: 10.1016/j.parint.2019.102034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
Abstract
The genus Plasmodium is a unicellular eukaryotic parasite that is the causative agent of malaria, which is transmitted by Anopheline mosquito. There are a total of three developmental stages in the production of haploid parasites in the Plasmodium life cycle: the oocyst stage in mosquitoes and the liver and blood stages in mammalian hosts. The Plasmodium oocyst stage plays an important role in the production of the first generation of haploid parasites. Nuclear division is the most important event that occurs during the proliferation of all eukaryotes. However, obtaining the details of nuclear division at the oocyst stage is challenging owing to difficulties in preparation. In this study, we used focused-ion-beam-milling combined with scanning-electron-microscopy to report the 3D architecture during nuclear segregations in oocyst stage. This advanced technology allowed us to analyse the 3D details of organelle segregation inside the oocyst during sporogony formation. It was revealed that multiple nuclei were involved with several centrosomes in one germ nucleus during sporozoite budding (endopolygeny). Our high-resolution 3D analysis uncovered the endopolygeny-like nuclear architecture of Plasmodium in the definitive host. This nuclear segregation was different from that in the blood stage, and its similarity to other apicomplexan parasite nuclear divisions such as Sarcocystis is discussed.
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Affiliation(s)
- Tamasa Araki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Satoru Kawai
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Research Support Center, Juntendo University Graduate School of Medicine, Bunkyo, Tokyo 113-8421, Japan
| | - Hirotaka Kobayashi
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yuko Umeki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Toshinori Sasaki
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kisaburo Nagamune
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Yasuhiro Yasutomi
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Blandine Franke-Fayard
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), 2333 ZA Leiden, the Netherlands
| | - Shahid M Khan
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), 2333 ZA Leiden, the Netherlands
| | - Hajime Hisaeda
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takeshi Annoura
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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21
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Suzuki M, Kubota K, Nishimura R, Negishi L, Komatsu K, Kagi H, Rehav K, Cohen S, Weiner S. A unique methionine-rich protein-aragonite crystal complex: Structure and mechanical functions of the Pinctada fucata bivalve hinge ligament. Acta Biomater 2019; 100:1-9. [PMID: 31604125 DOI: 10.1016/j.actbio.2019.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 11/28/2022]
Abstract
The bivalve hinge ligament holds the two shells together. The ligament functions as a spring to open the shells after they were closed by the adductor muscle. The ligament is a mineralized tissue that bears no resemblance to any other known tissue. About half the ligament is composed of a protein-rich matrix, and half of long and extremely thin segmented aragonite crystals. Here we study the hinge ligament of the pearl oyster Pinctada fucata. FIB SEM shows that the 3D organization is remarkably ordered. The full sequence of the major protein component contains a continuous segment of 30 repeats of MMMLPD. There is no known homologous protein. Knockdown of this protein prevents crystal formation, demonstrating that the integrity of the matrix is necessary for crystals to form. X-ray diffraction shows that the aragonite crystals are more aligned in the compressed ligament, indicating that the crystals may be actively contributing to the elastic properties. The fusion interphase that joins the ligament to the shell nacre is composed of a prismatic mineralized tissue with a thin organic-rich layer at its center. Nanoindentation of the dry interphase shows that the elastic modulus of the nacre adjacent to the interphase gradually decreases until it approximates that of the interphase. The interphase modulus slightly increases until it matches the ligament. All these observations demonstrate that the ligament shell complex is a remarkable biological tissue that has evolved unique properties that enable bivalves to open their shell effectively innumerable times during the lifetime of the animal. STATEMENT OF SIGNIFICANCE: The hinge ligament shell complex is a unique functioning structural tissue whose elastic properties enable the shell to open without expending energy. Methionine-rich proteins are not known elsewhere raising fundamental questions about secondary and tertiary structures contributing to its elastic properties. The segmented and extremely thin aragonite crystals embedded in this matrix may also have unexpected elastic materials properties as they flex during compression. The structure of the interphase comprises a fascinating biological joint that connects two very different materials. The interphase materials, including the nacre, are graded with respect to elastic modulus so as to approximately match the connecting components. The interphase incorporates a thin organic rich layer that presumably functions as a gasket. This study raises many fundamental questions relevant to the diverse fields of protein chemistry, biomineralization and biological materials.
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Affiliation(s)
- Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Kazuki Kubota
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Nishimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuki Komatsu
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hioryuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Katya Rehav
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sidney Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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22
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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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23
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Weiner A, Enninga J. The Pathogen–Host Interface in Three Dimensions: Correlative FIB/SEM Applications. Trends Microbiol 2019; 27:426-439. [DOI: 10.1016/j.tim.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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24
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Mehnert AK, Simon CS, Guizetti J. Immunofluorescence staining protocol for STED nanoscopy of Plasmodium-infected red blood cells. Mol Biochem Parasitol 2019; 229:47-52. [PMID: 30831155 DOI: 10.1016/j.molbiopara.2019.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022]
Abstract
Immunofluorescence staining is the key technique for visualizing organization of endogenous cellular structures in single cells. Labeling and imaging of blood stage Plasmodium falciparum has always been challenging since it is a small intracellular parasite. A widely-used standard for parasite immunofluorescence is fixation in suspension with addition of minute amounts of glutaraldehyde to the paraformaldehyde-based solution. While this maintains red blood cell integrity, it has been postulated that antigenicity of the parasite proteins was, if at all, only slightly reduced. Here we show the deleterious effect that even these small quantities of glutaraldehyde can have on immunofluorescence staining quality and present an alternative cell seeding protocol that allows fixation with only paraformaldehyde. The highly improved signal intensity and staining efficiency enabled us to carry out RescueSTED nanoscopy on microtubules and nuclear pores and describe their organization in greater detail throughout the blood stage cycle.
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Affiliation(s)
- Ann-Kathrin Mehnert
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Caroline Sophie Simon
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Julien Guizetti
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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25
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Weiner A, Orange F, Lacas‐Gervais S, Rechav K, Ghugtyal V, Bassilana M, Arkowitz RA. On‐site secretory vesicle delivery drives filamentous growth in the fungal pathogenCandida albicans. Cell Microbiol 2018; 21:e12963. [DOI: 10.1111/cmi.12963] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Allon Weiner
- Université Côte d'AzurCNRS, Inserm, Institute of Biology Valrose Parc Valrose Nice France
| | | | | | - Katya Rechav
- Chemical Research SupportWeizmann Institute of Science Rehovot Israel
| | - Vikram Ghugtyal
- Université Côte d'AzurCNRS, Inserm, Institute of Biology Valrose Parc Valrose Nice France
| | - Martine Bassilana
- Université Côte d'AzurCNRS, Inserm, Institute of Biology Valrose Parc Valrose Nice France
| | - Robert A. Arkowitz
- Université Côte d'AzurCNRS, Inserm, Institute of Biology Valrose Parc Valrose Nice France
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26
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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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27
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Kehrer J, Kuss C, Andres-Pons A, Reustle A, Dahan N, Devos D, Kudryashev M, Beck M, Mair GR, Frischknecht F. Nuclear Pore Complex Components in the Malaria Parasite Plasmodium berghei. Sci Rep 2018; 8:11249. [PMID: 30050042 PMCID: PMC6062611 DOI: 10.1038/s41598-018-29590-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The nuclear pore complex (NPC) is a large macromolecular assembly of around 30 different proteins, so-called nucleoporins (Nups). Embedded in the nuclear envelope the NPC mediates bi-directional exchange between the cytoplasm and the nucleus and plays a role in transcriptional regulation that is poorly understood. NPCs display modular arrangements with an overall structure that is generally conserved among many eukaryotic phyla. However, Nups of yeast or human origin show little primary sequence conservation with those from early-branching protozoans leaving those of the malaria parasite unrecognized. Here we have combined bioinformatic and genetic methods to identify and spatially characterize Nup components in the rodent infecting parasite Plasmodium berghei and identified orthologs from the human malaria parasite P. falciparum, as well as the related apicomplexan parasite Toxoplasma gondii. For the first time we show the localization of selected Nups throughout the P. berghei life cycle. Largely restricted to apicomplexans we identify an extended C-terminal poly-proline extension in SEC13 that is essential for parasite survival and provide high-resolution images of Plasmodium NPCs obtained by cryo electron tomography. Our data provide the basis for full characterization of NPCs in malaria parasites, early branching unicellular eukaryotes with significant impact on human health.
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Affiliation(s)
- Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Claudia Kuss
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Amparo Andres-Pons
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Anna Reustle
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Noa Dahan
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany
| | - Damien Devos
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Centro Andaluz de Biología del Desarrollo CABD, Universidad Pablo de Olavide-CSIC, Carretera de Utrera, 41013, Sevilla, Spain
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Str. 17, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Gunnar R Mair
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany. .,Iowa State University, Biomedical Sciences, College of Veterinary Medicine, 1800 Christensen Drive, Ames, IA, 50011, USA.
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.
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28
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Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun 2018; 9:1910. [PMID: 29765020 PMCID: PMC5954139 DOI: 10.1038/s41467-018-04295-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
The development of malaria parasites throughout their various life cycle stages is coordinated by changes in gene expression. We previously showed that the three-dimensional organization of the Plasmodium falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyze genome organization in the P. falciparum and P. vivax transmission stages. Major changes occur in the localization and interactions of genes involved in pathogenesis and immune evasion, host cell invasion, sexual differentiation, and master regulation of gene expression. Furthermore, we observe reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Our results suggest that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycle.
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Affiliation(s)
- Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Kate B Cook
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Nelle Varoquaux
- Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA, 94720, USA
- Berkeley Institute for Data Science, 190 Doe Library, Berkeley, CA, 94720, USA
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Lirong Shi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Chiara Andolina
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Leila S Ross
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy & Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Jean-Philippe Vert
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
- Département de mathématiques et applications, École normale supérieure, CNRS, PSL Research University, Paris, 75005, France
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA.
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA.
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29
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Lu X, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch K. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2017; 45:7825-7840. [PMID: 28531310 PMCID: PMC5737683 DOI: 10.1093/nar/gkx464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
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MESH Headings
- Animals
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Genes, Protozoan
- Humans
- Malaria, Falciparum/blood
- Malaria, Falciparum/parasitology
- Plasmodium falciparum/genetics
- Plasmodium falciparum/growth & development
- Plasmodium falciparum/pathogenicity
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Xueqing Maggie Lu
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Michael Lee
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Evelien M. Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Karine G. Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
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30
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Single-molecule analysis reveals that DNA replication dynamics vary across the course of schizogony in the malaria parasite Plasmodium falciparum. Sci Rep 2017. [PMID: 28638076 PMCID: PMC5479783 DOI: 10.1038/s41598-017-04407-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mechanics of DNA replication and cell cycling are well-characterized in model organisms, but less is known about these basic aspects of cell biology in early-diverging Apicomplexan parasites, which do not divide by canonical binary fission but undergo unconventional cycles. Schizogony in the malaria parasite, Plasmodium, generates ~16–24 new nuclei via independent, asynchronous rounds of genome replication prior to cytokinesis and little is known about the control of DNA replication that facilitates this. We have characterised replication dynamics in P. falciparum throughout schizogony, using DNA fibre labelling and combing to visualise replication forks at a single-molecule level. We show that origins are very closely spaced in Plasmodium compared to most model systems, and that replication dynamics vary across the course of schizogony, from faster synthesis rates and more widely-spaced origins through to slower synthesis rates and closer-spaced origins. This is the opposite of the pattern usually seen across S-phase in human cells, when a single genome is replicated. Replication forks also appear to stall at an unusually high rate throughout schizogony. Our work explores Plasmodium DNA replication in unprecedented detail and opens up tremendous scope for analysing cell cycle dynamics and developing interventions targetting this unique aspect of malaria biology.
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31
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Courjol F, Mouveaux T, Lesage K, Saliou JM, Werkmeister E, Bonabaud M, Rohmer M, Slomianny C, Lafont F, Gissot M. Characterization of a nuclear pore protein sheds light on the roles and composition of the Toxoplasma gondii nuclear pore complex. Cell Mol Life Sci 2017; 74:2107-2125. [PMID: 28138739 PMCID: PMC11107709 DOI: 10.1007/s00018-017-2459-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/21/2016] [Accepted: 01/05/2017] [Indexed: 01/19/2023]
Abstract
The nuclear pore is a key structure in eukaryotes regulating nuclear-cytoplasmic transport as well as a wide range of cellular processes. Here, we report the characterization of the first Toxoplasma gondii nuclear pore protein, named TgNup302, which appears to be the orthologue of the mammalian Nup98-96 protein. We produced a conditional knock-down mutant that expresses TgNup302 under the control of an inducible tetracycline-regulated promoter. Under ATc treatment, a substantial decrease of TgNup302 protein in inducible knock-down (iKD) parasites was observed, causing a delay in parasite proliferation. Moreover, the nuclear protein TgENO2 was trapped in the cytoplasm of ATc-treated mutants, suggesting that TgNup302 is involved in nuclear transport. Fluorescence in situ hybridization revealed that TgNup302 is essential for 18S RNA export from the nucleus to the cytoplasm, while global mRNA export remains unchanged. Using an affinity tag purification combined with mass spectrometry, we identified additional components of the nuclear pore complex, including proteins potentially interacting with chromatin. Furthermore, reverse immunoprecipitation confirmed their interaction with TgNup302, and structured illuminated microscopy confirmed the NPC localization of some of the TgNup302-interacting proteins. Intriguingly, facilitates chromatin transcription complex (FACT) components were identified, suggesting the existence of an NPC-chromatin interaction in T. gondii. Identification of TgNup302-interacting proteins also provides the first glimpse at the NPC structure in Apicomplexa, suggesting a structural conservation of the NPC components between distant eukaryotes.
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Affiliation(s)
- Flavie Courjol
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Thomas Mouveaux
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Kevin Lesage
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Jean-Michel Saliou
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Elisabeth Werkmeister
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Maurine Bonabaud
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094, Montpellier Cedex 5, France
| | - Marine Rohmer
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094, Montpellier Cedex 5, France
| | - Christian Slomianny
- Laboratory of Cell Physiology, INSERM U 1003, Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Franck Lafont
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Mathieu Gissot
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, CIIL-Centre d'Infection et d'Immunité de Lille, 59000, Lille, France.
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32
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Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 2017; 33:364-377. [PMID: 28065669 PMCID: PMC5410391 DOI: 10.1016/j.pt.2016.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022]
Abstract
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined. Finally, we address the use of epigenetic processes as targets for novel antimalarial therapies. Collectively, these topics highlight the unique biology of P. falciparum, and contribute to our understanding of mechanisms regulating gene expression in this deadly parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M Lu
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
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33
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Rout MP, Obado SO, Schenkman S, Field MC. Specialising the parasite nucleus: Pores, lamins, chromatin, and diversity. PLoS Pathog 2017; 13:e1006170. [PMID: 28253370 PMCID: PMC5333908 DOI: 10.1371/journal.ppat.1006170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael P. Rout
- The Rockefeller University, New York, New York, United States of America
| | - Samson O. Obado
- The Rockefeller University, New York, New York, United States of America
| | | | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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34
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Hoang TV, Kizilyaprak C, Spehner D, Humbel BM, Schultz P. Automatic segmentation of high pressure frozen and freeze-substituted mouse retina nuclei from FIB-SEM tomograms. J Struct Biol 2017; 197:123-134. [DOI: 10.1016/j.jsb.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
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35
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Duffy MF, Tang J, Sumardy F, Nguyen HHT, Selvarajah SA, Josling GA, Day KP, Petter M, Brown GV. Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences. FEBS J 2016; 284:237-257. [PMID: 27860263 DOI: 10.1111/febs.13967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/12/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Jingyi Tang
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Hanh H T Nguyen
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Shamista A Selvarajah
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Gabrielle A Josling
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA
| | - Karen P Day
- The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Michaela Petter
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Graham V Brown
- The Nossal Institute for Global Health, The University of Melbourne, Victoria, Australia
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36
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Abstract
Over the past decade, major advances in imaging techniques have enhanced our understanding of Plasmodium spp. parasites and their interplay with mammalian hosts and mosquito vectors. Cryoelectron tomography, cryo-X-ray tomography and super-resolution microscopy have shifted paradigms of sporozoite and gametocyte structure, the process of erythrocyte invasion by merozoites, and the architecture of Maurer's clefts. Intravital time-lapse imaging has been revolutionary for our understanding of pre-erythrocytic stages of rodent Plasmodium parasites. Furthermore, high-speed imaging has revealed the link between sporozoite structure and motility, and improvements in time-lapse microscopy have enabled imaging of the entire Plasmodium falciparum erythrocytic cycle and the complete Plasmodium berghei pre-erythrocytic stages for the first time. In this Review, we discuss the contribution of key imaging tools to these and other discoveries in the malaria field over the past 10 years.
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37
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Vidavsky N, Akiva A, Kaplan-Ashiri I, Rechav K, Addadi L, Weiner S, Schertel A. Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state. J Struct Biol 2016; 196:487-495. [PMID: 27693309 DOI: 10.1016/j.jsb.2016.09.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
Many important biological questions can be addressed by studying in 3D large volumes of intact, cryo fixed hydrated tissues (⩾10,000μm3) at high resolution (5-20nm). This can be achieved using serial FIB milling and block face surface imaging under cryo conditions. Here we demonstrate the unique potential of the cryo-FIB-SEM approach using two extensively studied model systems; sea urchin embryos and the tail fin of zebrafish larvae. We focus in particular on the environment of mineral deposition sites. The cellular organelles, including mitochondria, Golgi, ER, nuclei and nuclear pores are made visible by the image contrast created by differences in surface potential of different biochemical components. Auto segmentation and/or volume rendering of the image stacks and 3D reconstruction of the skeleton and the cellular environment, provides a detailed view of the relative distribution in space of the tissue/cellular components, and thus of their interactions. Simultaneous acquisition of secondary and back-scattered electron images adds additional information. For example, a serial view of the zebrafish tail reveals the presence of electron dense mineral particles inside mitochondrial networks extending more than 20μm in depth in the block. Large volume imaging using cryo FIB SEM, as demonstrated here, can contribute significantly to the understanding of the structures and functions of diverse biological tissues.
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Affiliation(s)
- Netta Vidavsky
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Anat Akiva
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ifat Kaplan-Ashiri
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lia Addadi
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Steve Weiner
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Global Applications Support, Oberkochen, Germany
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38
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The nuclear envelope and gene organization in parasitic protozoa: Specializations associated with disease. Mol Biochem Parasitol 2016; 209:104-113. [PMID: 27475118 DOI: 10.1016/j.molbiopara.2016.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/12/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The parasitic protozoa Trypanosoma brucei and Plasmodium falciparum are lethal human parasites that have developed elegant strategies of immune evasion by antigenic variation. Despite the vast evolutionary distance between the two taxa, both parasites employ strict monoallelic expression of their membrane proteins, variant surface glycoproteins in Trypanosomes and the var, rif and stevor genes in Plasmodium, in order to evade their host's immune system. Additionally, both telomeric location and epigenetic controls are prominent features of these membrane proteins. As such, telomeres, chromatin structure and nuclear organization all contribute to control of gene expression and immune evasion. Here, we discuss the importance of epigenetics and sub-nuclear context for the survival of these disease-causing parasites.
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39
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Ben-Yishay R, Ashkenazy AJ, Shav-Tal Y. Dynamic Encounters of Genes and Transcripts with the Nuclear Pore. Trends Genet 2016; 32:419-431. [DOI: 10.1016/j.tig.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/04/2023]
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40
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McCulloch R, Navarro M. The protozoan nucleus. Mol Biochem Parasitol 2016; 209:76-87. [PMID: 27181562 DOI: 10.1016/j.molbiopara.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022]
Abstract
The nucleus is arguably the defining characteristic of eukaryotes, distinguishing their cell organisation from both bacteria and archaea. Though the evolutionary history of the nucleus remains the subject of debate, its emergence differs from several other eukaryotic organelles in that it appears not to have evolved through symbiosis, but by cell membrane elaboration from an archaeal ancestor. Evolution of the nucleus has been accompanied by elaboration of nuclear structures that are intimately linked with most aspects of nuclear genome function, including chromosome organisation, DNA maintenance, replication and segregation, and gene expression controls. Here we discuss the complexity of the nucleus and its substructures in protozoan eukaryotes, with a particular emphasis on divergent aspects in eukaryotic parasites, which shed light on nuclear function throughout eukaryotes and reveal specialisations that underpin pathogen biology.
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Affiliation(s)
- Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Avda. del Conocimiento s/n, 18100 Granada, Spain.
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41
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Dhanyasi N, Segal D, Shimoni E, Shinder V, Shilo BZ, VijayRaghavan K, Schejter ED. Surface apposition and multiple cell contacts promote myoblast fusion in Drosophila flight muscles. J Cell Biol 2016; 211:191-203. [PMID: 26459604 PMCID: PMC4602036 DOI: 10.1083/jcb.201503005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transmission EM methods reveal that cell–cell fusion of individual myoblasts with growing Drosophila flight muscles is a stepwise process in which the cell adhesion and branched actin machineries mediate tight apposition and formation of multiple contacts and pores between the surfaces of the fusing cells. Fusion of individual myoblasts to form multinucleated myofibers constitutes a widely conserved program for growth of the somatic musculature. We have used electron microscopy methods to study this key form of cell–cell fusion during development of the indirect flight muscles (IFMs) of Drosophila melanogaster. We find that IFM myoblast–myotube fusion proceeds in a stepwise fashion and is governed by apparent cross talk between transmembrane and cytoskeletal elements. Our analysis suggests that cell adhesion is necessary for bringing myoblasts to within a minimal distance from the myotubes. The branched actin polymerization machinery acts subsequently to promote tight apposition between the surfaces of the two cell types and formation of multiple sites of cell–cell contact, giving rise to nascent fusion pores whose expansion establishes full cytoplasmic continuity. Given the conserved features of IFM myogenesis, this sequence of cell interactions and membrane events and the mechanistic significance of cell adhesion elements and the actin-based cytoskeleton are likely to represent general principles of the myoblast fusion process.
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Affiliation(s)
- Nagaraju Dhanyasi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India Manipal University, Manipal, Karnataka 576104, India
| | - Dagan Segal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Vera Shinder
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ben-Zion Shilo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - K VijayRaghavan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Eyal D Schejter
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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42
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Three-dimensional analysis of morphological changes in the malaria parasite infected red blood cell by serial block-face scanning electron microscopy. J Struct Biol 2016; 193:162-171. [PMID: 26772147 DOI: 10.1016/j.jsb.2016.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/16/2015] [Accepted: 01/05/2016] [Indexed: 01/22/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, exhibits morphological changes during the blood stage cycle in vertebrate hosts. Here, we used serial block-face scanning electron microscopy (SBF-SEM) to visualize the entire structures of P. falciparum-infected red blood cells (iRBCs) and to examine their morphological and volumetric changes at different stages. During developmental stages, the parasite forms Maurer's clefts and vesicles in the iRBC cytoplasm and knobs on the iRBC surface, and extensively remodels the iRBC structure for proliferation of the parasite. In our observations, the Maurer's clefts and vesicles in the P. falciparum-iRBCs, resembling the so-called tubovesicular network (TVN), were not connected to each other, and continuous membrane networks were not observed between the parasitophorous vacuole membrane (PVM) and the iRBC cytoplasmic membrane. In the volumetric analysis, the iRBC volume initially increased and then decreased to the end of the blood stage cycle. This suggests that it is necessary to absorb a substantial amount of nutrients from outside the iRBC during the initial stage, but to release waste materials from inside the iRBC at the multinucleate stage. Transportation of the materials may be through the iRBC membrane, rather than a special structure formed by the parasite, because there is no direct connection between the iRBC membrane and the parasite. These results provide new insights as to how the malaria parasite grows in the iRBC and remodels iRBC structure during developmental stages; these observation can serve as a baseline for further experiments on the effects of therapeutic agents on malaria.
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43
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Life without a Host Cell: What is Cryptosporidium ? Trends Parasitol 2015; 31:614-624. [DOI: 10.1016/j.pt.2015.08.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 01/13/2023]
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Mellouk N, Weiner A, Aulner N, Schmitt C, Elbaum M, Shorte SL, Danckaert A, Enninga J. Shigella subverts the host recycling compartment to rupture its vacuole. Cell Host Microbe 2015; 16:517-30. [PMID: 25299335 DOI: 10.1016/j.chom.2014.09.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/21/2014] [Accepted: 08/12/2014] [Indexed: 01/01/2023]
Abstract
Shigella enters epithlial cells via internalization into a vacuole. Subsequent vacuolar membrane rupture allows bacterial escape into the cytosol for replication and cell-to-cell spread. Bacterial effectors such as IpgD, a PI(4,5)P2 phosphatase that generates PI(5)P and alters host actin, facilitate this internalization. Here, we identify host proteins involved in Shigella uptake and vacuolar membrane rupture by high-content siRNA screening and subsequently focus on Rab11, a constituent of the recycling compartment. Rab11-positive vesicles are recruited to the invasion site before vacuolar rupture, and Rab11 knockdown dramatically decreases vacuolar membrane rupture. Additionally, Rab11 recruitment is absent and vacuolar rupture is delayed in the ipgD mutant that does not dephosphorylate PI(4,5)P₂ into PI(5)P. Ultrastructural analyses of Rab11-positive vesicles further reveal that ipgD mutant-containing vacuoles become confined in actin structures that likely contribute to delayed vacular rupture. These findings provide insight into the underlying molecular mechanism of vacuole progression and rupture during Shigella invasion.
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Affiliation(s)
- Nora Mellouk
- Institut Pasteur, Dynamics of Host-Pathogen interactions Unit, 25 Rue du Dr. Roux, 75724 Paris, France
| | - Allon Weiner
- Institut Pasteur, Dynamics of Host-Pathogen interactions Unit, 25 Rue du Dr. Roux, 75724 Paris, France
| | - Nathalie Aulner
- Institut Pasteur, Imagopole, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Christine Schmitt
- Institut Pasteur, Imagopole, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Michael Elbaum
- Department of Materials and Interfaces, Weizmann Institute of Sciences, 234 Herzl Street, Rehovot 76100, Israel
| | - Spencer L Shorte
- Institut Pasteur, Imagopole, 28 Rue du Dr. Roux, 75724 Paris, France
| | - Anne Danckaert
- Institut Pasteur, Imagopole, 28 Rue du Dr. Roux, 75724 Paris, France.
| | - Jost Enninga
- Institut Pasteur, Dynamics of Host-Pathogen interactions Unit, 25 Rue du Dr. Roux, 75724 Paris, France.
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Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R. PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs. Mol Microbiol 2015; 96:1283-97. [PMID: 25807998 DOI: 10.1111/mmi.13007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 11/28/2022]
Abstract
Plasmodium species have evolved complex biology to adapt to different hosts and changing environments throughout their life cycle. Remarkably, these adaptations are achieved by a relatively small genome. One way by which the parasite expands its proteome is through alternative splicing (AS). We recently identified PfSR1 as a bona fide Ser/Arg-rich (SR) protein that shuttles between the nucleus and cytoplasm and regulates AS in Plasmodium falciparum. Here we show that PfSR1 is localized adjacent to the Nuclear Pore Complex (NPC) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of PfSR1, we adapted an inducible overexpression system for tagged PfSR1 and performed RNA immunoprecipitation followed by microarray analysis (RIP-chip) to recover and identify the endogenous RNA targets that bind PfSR1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by PfSR1. RNA-EMSAs show that PfSR1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that PfSR1 not only regulates AS but also the steady-state levels of mRNAs containing these motifs in vivo.
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Affiliation(s)
- Shiri Eshar
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Lindsey Altenhofen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Alona Rabner
- Department of Biology, Israel Institute of Technology-Technion, Haifa, Israel
| | - Phil Ross
- Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Yair Fastman
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | | | - Rotem Karni
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
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46
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Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays 2014; 37:182-94. [PMID: 25394267 DOI: 10.1002/bies.201400145] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plasmodium falciparum is the most deadly human malarial parasite, responsible for an estimated 207 million cases of disease and 627,000 deaths in 2012. Recent studies reveal that the parasite actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells and that epigenetics plays an important role in this precise gene regulation. Here, we discuss recent advances in our understanding of three aspects of epigenetic regulation in P. falciparum: changes in histone modifications, nucleosome occupancy and the three-dimensional genome structure. We compare these three aspects of the P. falciparum epigenome to those of other eukaryotes, and show that large-scale compartmentalization is particularly important in determining histone decomposition and gene regulation in P. falciparum. We conclude by presenting a gene regulation model for P. falciparum that combines the described epigenetic factors, and by discussing the implications of this model for the future of malaria research.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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47
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Reznikov N, Shahar R, Weiner S. Bone hierarchical structure in three dimensions. Acta Biomater 2014; 10:3815-26. [PMID: 24914825 DOI: 10.1016/j.actbio.2014.05.024] [Citation(s) in RCA: 344] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/24/2022]
Abstract
Bone is a complex hierarchically structured family of materials that includes a network of cells and their interconnected cell processes. New insights into the 3-D structure of various bone materials (mainly rat and human lamellar bone and minipig fibrolamellar bone) were obtained using a focused ion beam electron microscope and the serial surface view method. These studies revealed the presence of two different materials, the major material being the well-known ordered arrays of mineralized collagen fibrils and associated macromolecules, and the minor component being a relatively disordered material composed of individual collagen fibrils with no preferred orientation, with crystals inside and possibly between fibrils, and extensive ground mass. Significantly, the canaliculi and their cell processes are confined within the disordered material. Here we present a new hierarchical scheme for several bone tissue types that incorporates these two materials. The new scheme updates the hierarchical scheme presented by Weiner and Wagner (1998). We discuss the structures at different hierarchical levels with the aim of obtaining further insights into structure-function-related questions, as well as defining some remaining unanswered questions.
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48
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Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res 2014; 24:974-88. [PMID: 24671853 PMCID: PMC4032861 DOI: 10.1101/gr.169417.113] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of the human malaria parasite Plasmodium falciparum is controlled by coordinated changes in gene expression throughout its complex life cycle, but the corresponding regulatory mechanisms are incompletely understood. To study the relationship between genome architecture and gene regulation in Plasmodium, we assayed the genome architecture of P. falciparum at three time points during its erythrocytic (asexual) cycle. Using chromosome conformation capture coupled with next-generation sequencing technology (Hi-C), we obtained high-resolution chromosomal contact maps, which we then used to construct a consensus three-dimensional genome structure for each time point. We observed strong clustering of centromeres, telomeres, ribosomal DNA, and virulence genes, resulting in a complex architecture that cannot be explained by a simple volume exclusion model. Internal virulence gene clusters exhibit domain-like structures in contact maps, suggesting that they play an important role in the genome architecture. Midway during the erythrocytic cycle, at the highly transcriptionally active trophozoite stage, the genome adopts a more open chromatin structure with increased chromosomal intermingling. In addition, we observed reduced expression of genes located in spatial proximity to the repressive subtelomeric center, and colocalization of distinct groups of parasite-specific genes with coordinated expression profiles. Overall, our results are indicative of a strong association between the P. falciparum spatial genome organization and gene expression. Understanding the molecular processes involved in genome conformation dynamics could contribute to the discovery of novel antimalarial strategies.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA
| | - Nelle Varoquaux
- Centre for Computational Biology, Mines ParisTech, Fontainebleau F-77300, France; Institut Curie, Paris F-75248, France; U900, INSERM, Paris F-75248, France
| | - Sebastiaan M Bol
- Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA
| | - Jean-Philippe Vert
- Centre for Computational Biology, Mines ParisTech, Fontainebleau F-77300, France; Institut Curie, Paris F-75248, France; U900, INSERM, Paris F-75248, France
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA
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49
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Lusk CP, Colombi P. Toward a consensus on the mechanism of nuclear pore complex inheritance. Nucleus 2014; 5:97-102. [PMID: 24637838 DOI: 10.4161/nucl.28314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear compartmentalization is achieved through the enclosure of the genome by the nuclear envelope; the nuclear envelope is perforated by nuclear pore complexes (NPCs), which form portals that control molecular exchange between the nucleus and cytoplasm. The number of NPCs per nucleus establishes a limit to the flux of molecules across the nuclear envelope and might directly impact genome organization and gene expression in a cell type specific manner. Mechanisms that control NPC number remain ill defined. Our recent study implicates a cytoplasmic pool of the nucleoporin Nsp1 as a factor that controls NPC number during the asymmetric division of budding yeast; Nsp1 acts to ensure that daughters inherit NPCs. We place our data within an emerging model of NPC inheritance in yeast and consider potential analogous mechanisms in multicellular eukaryotes, including the functional conservation of a cytoplasmic pool of Nsp1.
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50
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Abstract
Toxoplasma gondii and Plasmodium falciparum are important human pathogens. These parasites and many of their apicomplexan relatives undergo a complex developmental process in the cells of their hosts, which includes genome replication, cell division and the assembly of new invasive stages. Apicomplexan cell cycle progression is both globally and locally regulated. Global regulation is carried out throughout the cytoplasm by diffusible factors that include cell cycle-specific kinases, cyclins and transcription factors. Local regulation acts on individual nuclei and daughter cells that are developing inside the mother cell. We propose that the centrosome is a master regulator that physically tethers cellular components and that provides spatial and temporal control of apicomplexan cell division.
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Affiliation(s)
- Maria E Francia
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Boris Striepen
- 1] Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA. [2] Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
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