1
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Jennison C, Armstrong JM, Dankwa DA, Hertoghs N, Kumar S, Abatiyow BA, Naung M, Minkah NK, Swearingen KE, Moritz R, Barry AE, Kappe SHI, Vaughan AM. Plasmodium GPI-anchored micronemal antigen is essential for parasite transmission through the mosquito host. Mol Microbiol 2024; 121:394-412. [PMID: 37314965 PMCID: PMC11076100 DOI: 10.1111/mmi.15078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
Plasmodium parasites, the eukaryotic pathogens that cause malaria, feature three distinct invasive forms tailored to the host environment they must navigate and invade for life cycle progression. One conserved feature of these invasive forms is the micronemes, apically oriented secretory organelles involved in egress, motility, adhesion, and invasion. Here we investigate the role of GPI-anchored micronemal antigen (GAMA), which shows a micronemal localization in all zoite forms of the rodent-infecting species Plasmodium berghei. ∆GAMA parasites are severely defective for invasion of the mosquito midgut. Once formed, oocysts develop normally, however, sporozoites are unable to egress and exhibit defective motility. Epitope-tagging of GAMA revealed tight temporal expression late during sporogony and showed that GAMA is shed during sporozoite gliding motility in a similar manner to circumsporozoite protein. Complementation of P. berghei knockout parasites with full-length P. falciparum GAMA partially restored infectivity to mosquitoes, indicating conservation of function across Plasmodium species. A suite of parasites with GAMA expressed under the promoters of CTRP, CAP380, and TRAP, further confirmed the involvement of GAMA in midgut infection, motility, and vertebrate infection. These data show GAMA's involvement in sporozoite motility, egress, and invasion, implicating GAMA as a regulator of microneme function.
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Affiliation(s)
- Charlie Jennison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Janna M. Armstrong
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Dorender A. Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Nina Hertoghs
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Biley A. Abatiyow
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Myo Naung
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Victoria, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Victoria, Carlton, Australia
- Department of Global Health, University of Washington, Washington, Seattle, USA
| | - Nana K. Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
| | - Kristian E. Swearingen
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Victoria, Geelong, Australia
| | - Robert Moritz
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Victoria, Geelong, Australia
| | - Alyssa E. Barry
- Department of Global Health, University of Washington, Washington, Seattle, USA
- Institute for Systems Biology, Washington, Seattle, USA
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
- Burnet Institute, Victoria, Melbourne, Australia
- Department of Pediatrics, University of Washington, Washington, Seattle, USA
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington, Seattle, USA
- Burnet Institute, Victoria, Melbourne, Australia
- Department of Pediatrics, University of Washington, Washington, Seattle, USA
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2
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Rosa C, Singh P, Chen P, Sinha A, Claës A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM. Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite. EMBO Rep 2023; 24:e57090. [PMID: 37592911 PMCID: PMC10561359 DOI: 10.15252/embr.202357090] [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: 02/28/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
The complex life cycle of the human malaria parasite, Plasmodium falciparum, is driven by specific transcriptional programs, but it is unclear how most genes are activated or silenced at specific times. There is an association between transcription and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome-organizing proteins found in metazoans, it has all core components of the cohesin complex. To investigate the role of cohesin in P. falciparum, we functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown during early stages of the intraerythrocytic developmental cycle (IDC) upregulates a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq analyses reveal that during the IDC, SMC3 enrichment at the promoter regions of these genes inversely correlates with gene expression and chromatin accessibility. These data suggest that SMC3 binding contributes to the repression of specific genes until their appropriate time of expression, revealing a new mode of stage-specific gene repression in P. falciparum.
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Affiliation(s)
- Catarina Rosa
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
- Sorbonne Université, Collège Doctoral Complexité du Vivant ED515ParisFrance
| | - Parul Singh
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Patty Chen
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | | | - Artur Scherf
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Jessica M Bryant
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
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3
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Elsworth B, Keroack C, Rezvani Y, Paul A, Barazorda K, Tennessen J, Sack S, Moreira C, Gubbels MJ, Meyers M, Zarringhalam K, Duraisingh M. Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases. RESEARCH SQUARE 2023:rs.3.rs-2553721. [PMID: 36909484 PMCID: PMC10002801 DOI: 10.21203/rs.3.rs-2553721/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Apicomplexan egress from host cells is fundamental to the spread of infection and is poorly characterized in Babesia spp., parasites of veterinary importance and emerging zoonoses. Through the use of video microscopy, transcriptomics and chemical genetics, we have implicated signaling, proteases and gliding motility as key drivers of egress by Babesia divergens. We developed reverse genetics to perform a knockdown screen of putative mediators of egress, identifying kinases and proteases involved in distinct steps of egress (ASP3, PKG and CDPK4) and invasion (ASP2, ASP3 and PKG). Inhibition of egress leads to continued intracellular replication, indicating exit from the replication cycle is uncoupled from egress. Chemical genetics validated PKG, ASP2 and ASP3 as druggable targets in Babesia spp. All taken together, egress in B. divergens more closely resembles T. gondii than the more evolutionarily-related Plasmodium spp. We have established a molecular framework for biological and translational studies of B. divergens egress.
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4
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Rezvani Y, Keroack CD, Elsworth B, Arriojas A, Gubbels MJ, Duraisingh MT, Zarringhalam K. Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles. PLoS Biol 2022; 20:e3001816. [PMID: 36137068 PMCID: PMC9531838 DOI: 10.1371/journal.pbio.3001816] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/04/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Babesia is a genus of apicomplexan parasites that infect red blood cells in vertebrate hosts. Pathology occurs during rapid replication cycles in the asexual blood stage of infection. Current knowledge of Babesia replication cycle progression and regulation is limited and relies mostly on comparative studies with related parasites. Due to limitations in synchronizing Babesia parasites, fine-scale time-course transcriptomic resources are not readily available. Single-cell transcriptomics provides a powerful unbiased alternative for profiling asynchronous cell populations. Here, we applied single-cell RNA sequencing to 3 Babesia species (B. divergens, B. bovis, and B. bigemina). We used analytical approaches and algorithms to map the replication cycle and construct pseudo-synchronized time-course gene expression profiles. We identify clusters of co-expressed genes showing "just-in-time" expression profiles, with gradually cascading peaks throughout asexual development. Moreover, clustering analysis of reconstructed gene curves reveals coordinated timing of peak expression in epigenetic markers and transcription factors. Using a regularized Gaussian graphical model, we reconstructed co-expression networks and identified conserved and species-specific nodes. Motif analysis of a co-expression interactome of AP2 transcription factors identified specific motifs previously reported to play a role in DNA replication in Plasmodium species. Finally, we present an interactive web application to visualize and interactively explore the datasets.
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Affiliation(s)
- Yasaman Rezvani
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Department of Physics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
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5
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A single-cell atlas of Plasmodium falciparum transmission through the mosquito. Nat Commun 2021; 12:3196. [PMID: 34045457 PMCID: PMC8159942 DOI: 10.1038/s41467-021-23434-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/28/2021] [Indexed: 01/29/2023] Open
Abstract
Malaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria - Plasmodium falciparum. We reveal developmental trajectories associated with the colonization of the mosquito midgut and salivary glands and elucidate the transcriptional signatures of each transmissible stage. Additionally, we identify both conserved and non-conserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations potentially linked to host tropism. Together, the data presented here, which are made freely available via an interactive website, provide a fine-grained atlas that enables intensive investigation of the P. falciparum transcriptional journey. As well as providing insights into gene function across the transmission cycle, the atlas opens the door for identification of drug and vaccine targets to stop malaria transmission and thereby prevent disease. Here the authors use single-cell RNA-seq to profile the transmission stages of the human malaria parasite Plasmodium falciparum as it progresses through the Anopheles mosquito. They highlight unique patterns of gene usage throughout this development and identify potential pleiotropic genes that function at multiple life cycle stages.
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6
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Peculiarities of Plasmodium falciparum Gene Regulation and Chromatin Structure. Int J Mol Sci 2021; 22:ijms22105168. [PMID: 34068393 PMCID: PMC8153576 DOI: 10.3390/ijms22105168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022] Open
Abstract
The highly complex life cycle of the human malaria parasite, Plasmodium falciparum, is based on an orchestrated and tightly regulated gene expression program. In general, eukaryotic transcription regulation is determined by a combination of sequence-specific transcription factors binding to regulatory DNA elements and the packaging of DNA into chromatin as an additional layer. The accessibility of regulatory DNA elements is controlled by the nucleosome occupancy and changes of their positions by an active process called nucleosome remodeling. These epigenetic mechanisms are poorly explored in P. falciparum. The parasite genome is characterized by an extraordinarily high AT-content and the distinct architecture of functional elements, and chromatin-related proteins also exhibit high sequence divergence compared to other eukaryotes. Together with the distinct biochemical properties of nucleosomes, these features suggest substantial differences in chromatin-dependent regulation. Here, we highlight the peculiarities of epigenetic mechanisms in P. falciparum, addressing chromatin structure and dynamics with respect to their impact on transcriptional control. We focus on the specialized chromatin remodeling enzymes and discuss their essential function in P. falciparum gene regulation.
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7
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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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8
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Markus BM, Waldman BS, Lorenzi HA, Lourido S. High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii. Front Cell Infect Microbiol 2021; 10:617998. [PMID: 33553008 PMCID: PMC7854901 DOI: 10.3389/fcimb.2020.617998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Toxoplasma gondii is a common parasite of humans and animals, causing life-threatening disease in the immunocompromized, fetal abnormalities when contracted during gestation, and recurrent ocular lesions in some patients. Central to the prevalence and pathogenicity of this protozoan is its ability to adapt to a broad range of environments, and to differentiate between acute and chronic stages. These processes are underpinned by a major rewiring of gene expression, yet the mechanisms that regulate transcription in this parasite are only partially characterized. Deciphering these mechanisms requires a precise and comprehensive map of transcription start sites (TSSs); however, Toxoplasma TSSs have remained incompletely defined. To address this challenge, we used 5'-end RNA sequencing to genomically assess transcription initiation in both acute and chronic stages of Toxoplasma. Here, we report an in-depth analysis of transcription initiation at promoters, and provide empirically-defined TSSs for 7603 (91%) protein-coding genes, of which only 1840 concur with existing gene models. Comparing data from acute and chronic stages, we identified instances of stage-specific alternative TSSs that putatively generate mRNA isoforms with distinct 5' termini. Analysis of the nucleotide content and nucleosome occupancy around TSSs allowed us to examine the determinants of TSS choice, and outline features of Toxoplasma promoter architecture. We also found pervasive divergent transcription at Toxoplasma promoters, clustered within the nucleosomes of highly-symmetrical phased arrays, underscoring chromatin contributions to transcription initiation. Corroborating previous observations, we asserted that Toxoplasma 5' leaders are among the longest of any eukaryote studied thus far, displaying a median length of approximately 800 nucleotides. Further highlighting the utility of a precise TSS map, we pinpointed motifs associated with transcription initiation, including the binding sites of the master regulator of chronic-stage differentiation, BFD1, and a novel motif with a similar positional arrangement present at 44% of Toxoplasma promoters. This work provides a critical resource for functional genomics in Toxoplasma, and lays down a foundation to study the interactions between genomic sequences and the regulatory factors that control transcription in this parasite.
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Affiliation(s)
- Benedikt M. Markus
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Benjamin S. Waldman
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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9
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Sultan I, Fromion V, Schbath S, Nicolas P. Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application to Listeria monocytogenes. J R Soc Interface 2020; 17:20200600. [PMID: 33023397 PMCID: PMC7653377 DOI: 10.1098/rsif.2020.0600] [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: 07/26/2020] [Accepted: 09/10/2020] [Indexed: 11/12/2022] Open
Abstract
Automatic de novo identification of the main regulons of a bacterium from genome and transcriptome data remains a challenge. To address this task, we propose a statistical model that can use information on exact positions of the transcription start sites and condition-dependent expression profiles. The central idea of this model is to improve the probabilistic representation of the promoter DNA sequences by incorporating covariates summarizing expression profiles (e.g. coordinates in projection spaces or hierarchical clustering trees). A dedicated trans-dimensional Markov chain Monte Carlo algorithm adjusts the width and palindromic properties of the corresponding position-weight matrices, the number of parameters to describe exact position relative to the transcription start site, and chooses the expression covariates relevant for each motif. All parameters are estimated simultaneously, for many motifs and many expression covariates. The method is applied to a dataset of transcription start sites and expression profiles available for Listeria monocytogenes. The results validate the approach and provide a new global view of the transcription regulatory network of this important pathogen. Remarkably, a previously unreported motif is found in promoter regions of ribosomal protein genes, suggesting a role in the regulation of growth.
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Affiliation(s)
- Ibrahim Sultan
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | | | | | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
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10
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Llorà-Batlle O, Tintó-Font E, Cortés A. Transcriptional variation in malaria parasites: why and how. Brief Funct Genomics 2020; 18:329-341. [PMID: 31114839 DOI: 10.1093/bfgp/elz009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/04/2019] [Accepted: 04/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional differences enable the generation of alternative phenotypes from the same genome. In malaria parasites, transcriptional plasticity plays a major role in the process of adaptation to fluctuations in the environment. Multiple studies with culture-adapted parasites and field isolates are starting to unravel the different transcriptional alternatives available to Plasmodium falciparum and the underlying molecular mechanisms. Here we discuss how epigenetic variation, directed transcriptional responses and also genetic changes that affect transcript levels can all contribute to transcriptional variation and, ultimately, parasite survival. Some transcriptional changes are driven by stochastic events. These changes can occur spontaneously, resulting in heterogeneity within parasite populations that provides the grounds for adaptation by dynamic natural selection. However, transcriptional changes can also occur in response to external cues. A better understanding of the mechanisms that the parasite has evolved to alter its transcriptome may ultimately contribute to the design of strategies to combat malaria to which the parasite cannot adapt.
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Affiliation(s)
- Oriol Llorà-Batlle
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Elisabet Tintó-Font
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036 Barcelona, Catalonia, Spain
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11
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van Biljon R, van Wyk R, Painter HJ, Orchard L, Reader J, Niemand J, Llinás M, Birkholtz LM. Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation. BMC Genomics 2019; 20:920. [PMID: 31795940 PMCID: PMC6889441 DOI: 10.1186/s12864-019-6322-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as it commits to and develops through gametocytogenesis. RESULTS The gametocyte-associated transcriptome is significantly different from that of the asexual parasites, with dynamic gene expression shifts characterizing early, intermediate and late-stage gametocyte development and results in differential timing for sex-specific transcripts. The transcriptional dynamics suggest strict transcriptional control during gametocytogenesis in P. falciparum, which we propose is mediated by putative regulators including epigenetic mechanisms (driving active repression of proliferation-associated processes) and a cascade-like expression of ApiAP2 transcription factors. CONCLUSIONS The gametocyte transcriptome serves as the blueprint for sexual differentiation and will be a rich resource for future functional studies on this critical stage of Plasmodium development, as the intraerythrocytic transcriptome has been for our understanding of the asexual cycle.
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Affiliation(s)
- Riëtte van Biljon
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Roelof van Wyk
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Heather J Painter
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Review, U.S. Food & Drug Administration, Silver Spring, MD, 20993, USA
| | - Lindsey Orchard
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Jandeli Niemand
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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12
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Cowell AN, Winzeler EA. Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections. Genome Med 2019; 11:63. [PMID: 31640748 PMCID: PMC6805675 DOI: 10.1186/s13073-019-0673-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/13/2019] [Indexed: 01/23/2023] Open
Abstract
A major advance in antimalarial drug discovery has been the shift towards cell-based phenotypic screening, with notable progress in the screening of compounds against the asexual blood stage, liver stage, and gametocytes. A primary method for drug target deconvolution in Plasmodium falciparum is in vitro evolution of compound-resistant parasites followed by whole-genome scans. Several of the most promising antimalarial drug targets, such as translation elongation factor 2 (eEF2) and phenylalanine tRNA synthetase (PheRS), have been identified or confirmed using this method. One drawback of this method is that if a mutated gene is uncharacterized, a substantial effort may be required to determine whether it is a drug target, a drug resistance gene, or if the mutation is merely a background mutation. Thus, the availability of high-throughput, functional genomic datasets can greatly assist with target deconvolution. Studies mapping genome-wide essentiality in P. falciparum or performing transcriptional profiling of the host and parasite during liver-stage infection with P. berghei have identified potentially druggable pathways. Advances in mapping the epigenomic regulation of the malaria parasite genome have also enabled the identification of key processes involved in parasite development. In addition, the examination of the host genome during infection has identified novel gene candidates associated with susceptibility to severe malaria. Here, we review recent studies that have used omics-based methods to identify novel targets for interventions against protozoan parasites, focusing on malaria, and we highlight the advantages and limitations of the approaches used. These approaches have also been extended to other protozoan pathogens, including Toxoplasma, Trypanosoma, and Leishmania spp., and these studies highlight how drug discovery efforts against these pathogens benefit from the utilization of diverse omics-based methods to identify promising drug targets.
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Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases and Global Health, Department of Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
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13
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Toenhake CG, Bártfai R. What functional genomics has taught us about transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:290-301. [PMID: 31220867 PMCID: PMC6859821 DOI: 10.1093/bfgp/elz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/08/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.
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Affiliation(s)
- Christa G Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
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14
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Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN. The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science 2019; 365:eaaw2619. [PMID: 31439762 PMCID: PMC7056351 DOI: 10.1126/science.aaw2619] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/12/2019] [Indexed: 12/25/2022]
Abstract
Malaria parasites adopt a remarkable variety of morphological life stages as they transition through multiple mammalian host and mosquito vector environments. We profiled the single-cell transcriptomes of thousands of individual parasites, deriving the first high-resolution transcriptional atlas of the entire Plasmodium berghei life cycle. We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals. The Malaria Cell Atlas provides both a comprehensive view of gene usage in a eukaryotic parasite and an open-access reference dataset for the study of malaria parasites.
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Affiliation(s)
- Virginia M Howick
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Andrew J C Russell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tallulah Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Haynes Heaton
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Kedar Natarajan
- Danish Institute of Advanced Study (D-IAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hellen Butungi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Wits Research Institute for Malaria, MRC Collaborating Centre for Multi-disciplinary Research on Malaria, School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Tom Metcalf
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lisa H Verzier
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jeremy K Herren
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Wits Research Institute for Malaria, MRC Collaborating Centre for Multi-disciplinary Research on Malaria, School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Oliver Billker
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Arthur M Talman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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15
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ApiAP2 Transcription Factors in Apicomplexan Parasites. Pathogens 2019; 8:pathogens8020047. [PMID: 30959972 PMCID: PMC6631176 DOI: 10.3390/pathogens8020047] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites.
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16
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Winzeler EA. An improbable journey: Creativity helped me make the transition from art to curing malaria. J Biol Chem 2019; 294:405-409. [PMID: 30401750 DOI: 10.1074/jbc.aw118.005229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
I was recently awarded the Alice and C. C. Wang Award in Molecular Parasitology for my contributions to antimalarial drug development, including laying the groundbreaking work that has led to two new molecular methods for curing malaria. This award means a great deal to me because I have spent much of my scientific career feeling like an imposter-one with the wrong sort of background and poor credentials. I am grateful for the recognition, and I am beginning to recognize that having an atypical background can be an advantage because it gives you a different perspective on a challenge. More generally, diversity in educational and cultural backgrounds is important because it can stimulate new ways of thinking and discovery.
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Affiliation(s)
- Elizabeth A Winzeler
- From the Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California 92093
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17
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Ishino T, Murata E, Tokunaga N, Baba M, Tachibana M, Thongkukiatkul A, Tsuboi T, Torii M. Rhoptry neck protein 2 expressed in Plasmodium sporozoites plays a crucial role during invasion of mosquito salivary glands. Cell Microbiol 2018; 21:e12964. [PMID: 30307699 PMCID: PMC6587811 DOI: 10.1111/cmi.12964] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 01/03/2023]
Abstract
Malaria parasite transmission to humans is initiated by the inoculation of Plasmodium sporozoites into the skin by mosquitoes. Sporozoites develop within mosquito midgut oocysts, first invade the salivary glands of mosquitoes, and finally infect hepatocytes in mammals. The apical structure of sporozoites is conserved with the infective forms of other apicomplexan parasites that have secretory organelles, such as rhoptries and micronemes. Because some rhoptry proteins are crucial for Plasmodium merozoite infection of erythrocytes, we examined the roles of rhoptry proteins in sporozoites. Here, we demonstrate that rhoptry neck protein 2 (RON2) is also localized to rhoptries in sporozoites. To elucidate RON2 function in sporozoites, we applied a promoter swapping strategy to restrict ron2 transcription to the intraerythrocytic stage in the rodent malaria parasite, Plasmodium berghei. Ron2 knockdown sporozoites were severely impaired in their ability to invade salivary glands, via decreasing the attachment capacity to the substrate. This is the first rhoptry protein demonstrated to be involved in salivary gland invasion. In addition, ron2 knockdown sporozoites showed less infectivity to hepatocytes, possibly due to decreased attachment/gliding ability, indicating that parts of the parasite invasion machinery are conserved, but their contribution might differ among infective forms. Our sporozoite stage‐specific knockdown system will help to facilitate understanding the comprehensive molecular mechanisms of parasite invasion of target cells.
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Affiliation(s)
- Tomoko Ishino
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Eri Murata
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan.,Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Naohito Tokunaga
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Minami Baba
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Mayumi Tachibana
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | | | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Motomi Torii
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
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18
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Klug D, Kehrer J, Frischknecht F, Singer M. A synthetic promoter for multi-stage expression to probe complementary functions of Plasmodium adhesins. J Cell Sci 2018; 131:jcs.210971. [PMID: 30237220 DOI: 10.1242/jcs.210971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/10/2018] [Indexed: 11/20/2022] Open
Abstract
Gene expression of malaria parasites is mediated by the apicomplexan Apetala2 (ApiAP2) transcription factor family. Different ApiAP2s control gene expression at distinct stages in the complex life cycle of the parasite, ensuring timely expression of stage-specific genes. ApiAP2s recognize short cis-regulatory elements that are enriched in the upstream/promoter region of their target genes. This should, in principle, allow the generation of 'synthetic' promoters that drive gene expression at desired stages of the Plasmodium life cycle. Here we test this concept by combining cis-regulatory elements of two genes expressed successively within the mosquito part of the life cycle. Our tailored 'synthetic' promoters, named Spooki 1.0 and Spooki 2.0, activate gene expression in early and late mosquito stages, as shown by the expression of a fluorescent reporter. We used these promoters to address the specific functionality of two related adhesins that are exclusively expressed either during the early or late mosquito stage. By modifying the expression profile of both adhesins in absence of their counterpart we were able to test for complementary functions in gliding and invasion. We discuss the possible advantages and drawbacks of our approach.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Dennis Klug
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mirko Singer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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19
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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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20
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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21
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Smith ML, Styczynski MP. Systems Biology-Based Investigation of Host-Plasmodium Interactions. Trends Parasitol 2018; 34:617-632. [PMID: 29779985 DOI: 10.1016/j.pt.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022]
Abstract
Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.
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Affiliation(s)
- Maren L Smith
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA.
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22
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Toenhake CG, Fraschka SAK, Vijayabaskar MS, Westhead DR, van Heeringen SJ, Bártfai R. Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development. Cell Host Microbe 2018; 23:557-569.e9. [PMID: 29649445 PMCID: PMC5899830 DOI: 10.1016/j.chom.2018.03.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/05/2018] [Accepted: 03/05/2018] [Indexed: 02/07/2023]
Abstract
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript. Importantly, these regions are sufficient to drive stage-specific reporter gene expression and DNA motifs enriched in stage-specific sets of regulatory regions interact with members of the P. falciparum AP2 transcription factor family. Collectively, this study provides initial insights into the in vivo gene regulatory network of P. falciparum intraerythrocytic stages and should serve as a valuable resource for future studies.
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Affiliation(s)
- Christa Geeke Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, 6525 GA, the Netherlands
| | | | | | - David Robert Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Simon Jan van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, 6525 GA, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, 6525 GA, the Netherlands.
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23
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A Knockout Screen of ApiAP2 Genes Reveals Networks of Interacting Transcriptional Regulators Controlling the Plasmodium Life Cycle. Cell Host Microbe 2017; 21:11-22. [PMID: 28081440 PMCID: PMC5241200 DOI: 10.1016/j.chom.2016.12.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 08/17/2016] [Accepted: 11/17/2016] [Indexed: 01/17/2023]
Abstract
A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This family includes sequence-specific transcription factors that are key regulators of development. However, functions for the majority of ApiAP2 genes remain unknown. Here, a systematic knockout screen in Plasmodium berghei identified ten ApiAP2 genes that were essential for mosquito transmission: four were critical for the formation of infectious ookinetes, and three were required for sporogony. We describe non-essential functions for AP2-O and AP2-SP proteins in blood stages, and identify AP2-G2 as a repressor active in both asexual and sexual stages. Comparative transcriptomics across mutants and developmental stages revealed clusters of co-regulated genes with shared cis promoter elements, whose expression can be controlled positively or negatively by different ApiAP2 factors. We propose that stage-specific interactions between ApiAP2 proteins on partly overlapping sets of target genes generate the complex transcriptional network that controls the Plasmodium life cycle. Mutants in 11 of 26 apiAP2 genes reveal gene functions in mosquito transmission Co-expression clustering across mutants and stages reveals molecular phenotypes Multifunctional apiAP2 genes create complex regulatory networks in Plasmodium Ap2-g2 is a transcriptional repressor in both asexual and sexual blood stages
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24
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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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25
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Santos JM, Josling G, Ross P, Joshi P, Orchard L, Campbell T, Schieler A, Cristea IM, Llinás M. Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor. Cell Host Microbe 2017; 21:731-741.e10. [PMID: 28618269 PMCID: PMC5855115 DOI: 10.1016/j.chom.2017.05.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 02/16/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Obligate intracellular parasites must efficiently invade host cells in order to mature and be transmitted. For the malaria parasite Plasmodium falciparum, invasion of host red blood cells (RBCs) is essential. Here we describe a parasite-specific transcription factor PfAP2-I, belonging to the Apicomplexan AP2 (ApiAP2) family, that is responsible for regulating the expression of genes involved in RBC invasion. Our genome-wide analysis by ChIP-seq shows that PfAP2-I interacts with a specific DNA motif in the promoters of target genes. Although PfAP2-I contains three AP2 DNA-binding domains, only one is required for binding of the target genes during blood stage development. Furthermore, we find that PfAP2-I associates with several chromatin-associated proteins, including the Plasmodium bromodomain protein PfBDP1 and that complex formation is associated with transcriptional regulation. As a key regulator of red blood cell invasion, PfAP2-I represents a potential new antimalarial therapeutic target.
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Affiliation(s)
- Joana Mendonca Santos
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, State College, PA 16802, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Gabrielle Josling
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, State College, PA 16802, USA
| | - Philipp Ross
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, State College, PA 16802, USA
| | - Preeti Joshi
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lindsey Orchard
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, State College, PA 16802, USA
| | - Tracey Campbell
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ariel Schieler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, State College, PA 16802, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry and Huck Center for Infectious Disease Dynamics, Pennsylvania State University, State College, PA 16802, USA.
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26
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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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27
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Painter HJ, Carrasquilla M, Llinás M. Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum. Genome Res 2017; 27:1074-1086. [PMID: 28416533 PMCID: PMC5453321 DOI: 10.1101/gr.217356.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
To capture the transcriptional dynamics within proliferating cells, methods to differentiate nascent transcription from preexisting mRNAs are desired. One approach is to label newly synthesized mRNA transcripts in vivo through the incorporation of modified pyrimidines. However, the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine deaminase/uracil phosphoribosyltransferase (FCU). We show that expression of FCU allows for the direct incorporation of thiol-modified pyrimidines into nascent mRNAs. Using developmental stage-specific promoters to express FCU-GFP enables the biosynthetic capture and in-depth analysis of mRNA dynamics from subpopulations of cells undergoing differentiation. We demonstrate the utility of this method by examining the transcriptional dynamics of the sexual gametocyte stage transition, a process that is essential to malaria transmission between hosts. Using the pfs16 gametocyte-specific promoter to express FCU-GFP in 3D7 parasites, we found that sexual stage commitment is governed by transcriptional reprogramming and stabilization of a subset of essential gametocyte transcripts. We also measured mRNA dynamics in F12 gametocyte-deficient parasites and demonstrate that the transcriptional program required for sexual commitment and maturation is initiated but likely aborted due to the absence of the PfAP2-G transcriptional regulator and a lack of gametocyte-specific mRNA stabilization. Biosynthetic labeling of Plasmodium mRNAs is incredibly versatile, can be used to measure transcriptional dynamics at any stage of parasite development, and will allow for future applications to comprehensively measure RNA-protein interactions in the malaria parasite.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuela Carrasquilla
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Ashano E, Isewon I, Oyelade J, Adebiyi E. Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements. F1000Res 2016; 5. [PMID: 27990252 PMCID: PMC5155496 DOI: 10.12688/f1000research.9093.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2016] [Indexed: 12/26/2022] Open
Abstract
In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control. Five cluster groups showed upregulated profile patterns of biological interest. This included two clusters from the Intraerythrocytic Developmental Cycle (cluster 4 = 16 genes, and cluster 9 = 32 genes), one from the sexual development stage (cluster 2 = 851 genes), and two from the gamete-fertilization stage in the mosquito host (cluster 4 = 153 genes, and cluster 9 = 258 genes). The IDC expressed the least numbers of genes with only 1448 genes showing any significant activity of the 5020 genes (~29%) in the experiment. Gene ontology (GO) enrichment analysis of these clusters revealed a total of 671 uncharacterized genes implicated in 14 biological processes and components associated with these stages, some of which are currently being investigated as drug targets in on-going research. Five putative transcription regulatory binding motifs shared by members of each cluster were also identified, one of which was also identified in a previous study by separate researchers. Our study shows stage-specific genes and biological processes that may be important in antimalarial drug research efforts. In addition, timed-coordinated control of separate processes may explain the paucity of factors in parasites.
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Affiliation(s)
- Efejiro Ashano
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 110001, Nigeria
| | - Itunuoluwa Isewon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 110001, Nigeria.,Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, 110001, Nigeria
| | - Jelili Oyelade
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 110001, Nigeria.,Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, 110001, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, 110001, Nigeria.,Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, 110001, Nigeria.,Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg,, 69120, Germany
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Kensche PR, Hoeijmakers WAM, Toenhake CG, Bras M, Chappell L, Berriman M, Bártfai R. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res 2015; 44:2110-24. [PMID: 26578577 PMCID: PMC4797266 DOI: 10.1093/nar/gkv1214] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/28/2015] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen.
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Affiliation(s)
- Philip Reiner Kensche
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | | | | | - Maaike Bras
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Lia Chappell
- Parasite Genomics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Matthew Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
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Isewon I, Oyelade J, Brors B, Adebiyi E. In Silico Gene Regulatory Network of the Maurer's Cleft Pathway in Plasmodium falciparum. Evol Bioinform Online 2015; 11:231-8. [PMID: 26526876 PMCID: PMC4620995 DOI: 10.4137/ebo.s25585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 07/28/2015] [Accepted: 08/03/2015] [Indexed: 11/15/2022] Open
Abstract
The Maurer's clefts (MCs) are very important for the survival of Plasmodium falciparum within an infected cell as they are induced by the parasite itself in the erythrocyte for protein trafficking. The MCs form an interesting part of the parasite's biology as they shed more light on how the parasite remodels the erythrocyte leading to host pathogenesis and death. Here, we predicted and analyzed the genetic regulatory network of genes identified to belong to the MCs using regularized graphical Gaussian model. Our network shows four major activators, their corresponding target genes, and predicted binding sites. One of these master activators is the serine repeat antigen 5 (SERA5), predominantly expressed among the SERA multigene family of P. falciparum, which is one of the blood-stage malaria vaccine candidates. Our results provide more details about functional interactions and the regulation of the genes in the MCs’ pathway of P. falciparum.
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Affiliation(s)
- Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Jelili Oyelade
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Benedikt Brors
- Department of Applied Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Applied Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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31
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Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:381-400. [PMID: 26306749 PMCID: PMC4679367 DOI: 10.1002/wsbm.1311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug‐resistant parasites necessitates that the research community take an active role in understanding host–parasite infection biology in order to develop improved therapeutics. Recent advances in next‐generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host–parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high‐throughput ‐omic data will undoubtedly generate extraordinary insight into host–parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host–parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies. WIREs Syst Biol Med 2015, 7:381–400. doi: 10.1002/wsbm.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Justine Swann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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Pieszko M, Weir W, Goodhead I, Kinnaird J, Shiels B. ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata. PLoS Negl Trop Dis 2015; 9:e0003933. [PMID: 26273826 PMCID: PMC4537280 DOI: 10.1371/journal.pntd.0003933] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/25/2015] [Indexed: 02/05/2023] Open
Abstract
Background Differentiation of one life-cycle stage to the next is critical for survival and transmission of apicomplexan parasites. A number of studies have shown that stage differentiation is a stochastic process and is associated with a point that commits the cell to a change over in the pattern of gene expression. Studies on differentiation to merozoite production (merogony) in T. annulata postulated that commitment involves a concentration threshold of DNA binding proteins and an auto-regulatory loop. Principal Findings In this study ApiAP2 DNA binding proteins that show changes in expression level during merogony of T. annulata have been identified. DNA motifs bound by orthologous domains in Plasmodium were found to be enriched in upstream regions of stage-regulated T. annulata genes and validated as targets for the T. annulata AP2 domains by electrophoretic mobility shift assay (EMSA). Two findings were of particular note: the gene in T. annulata encoding the orthologue of the ApiAP2 domain in the AP2-G factor that commits Plasmodium to gametocyte production, has an expression profile indicating involvement in transmission of T. annulata to the tick vector; genes encoding related domains that bind, or are predicted to bind, sequence motifs of the type 5'-(A)CACAC(A) are implicated in differential regulation of gene expression, with one gene (TA11145) likely to be preferentially up-regulated via auto-regulation as the cell progresses to merogony. Conclusions We postulate that the Theileria factor possessing the AP2 domain orthologous to that of Plasmodium AP2-G may regulate gametocytogenesis in a similar manner to AP2-G. In addition, paralogous ApiAP2 factors that recognise 5'-(A)CACAC(A) type motifs could operate in a competitive manner to promote reversible progression towards the point that commits the cell to undergo merogony. Factors possessing AP2 domains that bind (or are predicted to bind) this motif are present in the vector-borne genera Theileria, Babesia and Plasmodium, and other Apicomplexa; leading to the proposal that the mechanisms that control stage differentiation will show a degree of conservation. The ability of vector-borne Apicomplexan parasites (Babesia, Plasmodium and Theileria) to change from one life-cycle stage to the next is critical for establishment of infection and transmission to new hosts. Stage differentiation steps of both Plasmodium and Theileria are known to involve stochastic transition through an intermediate form to a point that commits the cell to generate the next stage in the life-cycle. In this study we have identified genes encoding ApiAP2 DNA binding proteins in Theileria annulata that are differentially expressed during differentiation from the macroschizont stage, through merozoite production (merogony) to the piroplasm stage. The results provide evidence that the ApiAp2 factor in Theileria that possesses the orthologue of the Plasmodium AP2-G domain may also operate to regulate gametocytogenesis, and that progression to merogony is promoted by the ability of a merozoite DNA binding protein to preferentially up-regulate its own production. In addition, identification of multiple ApiAP2 DNA binding domains that bind related motifs within and across vector-borne Apicomplexan genera lead to the proposal that the mechanisms that promote the transition from asexual to sexual replication will show a degree of conservation.
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Affiliation(s)
- Marta Pieszko
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, United Kingdom
| | - William Weir
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, United Kingdom
| | - Ian Goodhead
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, United Kingdom
| | - Jane Kinnaird
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, United Kingdom
| | - Brian Shiels
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, United Kingdom
- * E-mail:
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Josling G, Petter M, Oehring S, Gupta A, Dietz O, Wilson D, Schubert T, Längst G, Gilson P, Crabb B, Moes S, Jenoe P, Lim S, Brown G, Bozdech Z, Voss T, Duffy M. A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression. Cell Host Microbe 2015; 17:741-51. [DOI: 10.1016/j.chom.2015.05.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/30/2015] [Accepted: 05/14/2015] [Indexed: 11/27/2022]
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De Niz M, Helm S, Horstmann S, Annoura T, del Portillo HA, Khan SM, Heussler VT. In vivo and in vitro characterization of a Plasmodium liver stage-specific promoter. PLoS One 2015; 10:e0123473. [PMID: 25874388 PMCID: PMC4398466 DOI: 10.1371/journal.pone.0123473] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 03/03/2015] [Indexed: 12/28/2022] Open
Abstract
Little is known about stage-specific gene regulation in Plasmodium parasites, in particular the liver stage of development. We have previously described in the Plasmodium berghei rodent model, a liver stage-specific (lisp2) gene promoter region, in vitro. Using a dual luminescence system, we now confirm the stage specificity of this promoter region also in vivo. Furthermore, by substitution and deletion analyses we have extended our in vitro characterization of important elements within the promoter region. Importantly, the dual luminescence system allows analyzing promoter constructs avoiding mouse-consuming cloning procedures of transgenic parasites. This makes extensive mutation and deletion studies a reasonable approach also in the malaria mouse model. Stage-specific expression constructs and parasite lines are extremely valuable tools for research on Plasmodium liver stage biology. Such reporter lines offer a promising opportunity for assessment of liver stage drugs, characterization of genetically attenuated parasites and liver stage-specific vaccines both in vivo and in vitro, and may be key for the generation of inducible systems.
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Affiliation(s)
- Mariana De Niz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
| | - Susanne Helm
- Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Horstmann
- Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Takeshi Annoura
- Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Department of Parasitology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Hernando A. del Portillo
- Barcelona Centre for International Health Research (CRESIB), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Shahid M. Khan
- Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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Russell K, Emes R, Horrocks P. Triaging informative cis-regulatory elements for the combinatorial control of temporal gene expression during Plasmodium falciparum intraerythrocytic development. Parasit Vectors 2015; 8:81. [PMID: 25652008 PMCID: PMC4322800 DOI: 10.1186/s13071-015-0701-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/27/2015] [Indexed: 01/18/2023] Open
Abstract
Background Over 2700 genes are subject to stage-specific regulation during the intraerythrocytic development of the human malaria parasite Plasmodium falciparum. Bioinformatic analyses have identified a large number of over-represented motifs in the 5′ flanking regions of these genes that may act as cis-acting factors in the promoter-based control of temporal expression. Triaging these lists to provide candidates most likely to play a role in regulating temporal expression is challenging, but important if we are to effectively design in vitro studies to validate this role. Methods We report here the application of a repeated search of variations of 5′ flanking sequences from P. falciparum using the Finding Informative Regulatory Elements (FIRE) algorithm. Results Our approach repeatedly found a short-list of high scoring DNA motifs, for which cognate specific transcription factors were available, that appear to be typically associated with upregulation of mRNA accumulation during the first half of intraerythrocytic development. Conclusions We propose these cis-trans interactions may provide a combinatorial promoter-based control of gene expression to complement more global mechanisms of gene regulation that can account for temporal control during the second half of intraerythrocytic development. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0701-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karen Russell
- Institute for Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK.
| | - Richard Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, UK. .,Advanced Data Analysis Centre, University of Nottingham, Leicestershire, LE12 5RD, UK.
| | - Paul Horrocks
- Institute for Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, UK.
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Yamagishi J, Wakaguri H, Yokoyama N, Yamashita R, Suzuki Y, Xuan X, Igarashi I. The Babesia bovis gene and promoter model: an update from full-length EST analysis. BMC Genomics 2014; 15:678. [PMID: 25124460 PMCID: PMC4148916 DOI: 10.1186/1471-2164-15-678] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/08/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. Although the genome of B. bovis is publically available, annotated gene models are not highly reliable prior to experimental validation. Therefore, we validated a preproposed gene model of B. bovis and extended the associated annotations on the basis of experimentally obtained full-length expressed sequence tags (ESTs). RESULTS From in vitro cultured merozoites, 12,286 clones harboring full-length cDNAs were sequenced from both ends using the Sanger method, and 6,787 full-length cDNAs were assembled. These were then clustered, and a nonredundant referential data set of 2,115 full-length cDNA sequences was constructed. The comparison of the preproposed gene model with our data set identified 310 identical genes, 342 almost identical genes, 1,054 genes with potential structural inconsistencies, and 409 novel genes. The median length of 5' untranslated regions (UTRs) was 152 nt. Subsequently, we identified 4,086 transcription start sites (TSSs) and 2,023 transcriptionally active regions (TARs) by examining 5' ESTs. We identified ATGGGG and CCCCAT sites as consensus motifs in TARs that were distributed around -50 bp from TSSs. In addition, we found ACACA, TGTGT, and TATAT sites, which were distributed periodically around TSSs in cycles of approximately 150 bp. Moreover, related periodical distributions were not observed in mammalian promoter regions. CONCLUSIONS The observations in this study indicate the utility of integrated bioinformatics and experimental data for improving genome annotations. In particular, full-length cDNAs with one-base resolution for TSSs enabled the identification of consensus motifs in promoter sequences and demonstrated clear distributions of identified motifs. These observations allowed the illustration of a model promoter composition, which supports the differences in transcriptional regulation frameworks between apicomplexan parasites and mammals.
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Affiliation(s)
- Junya Yamagishi
- />Tohoku Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Sendai, Miyagi 980-8579 Japan
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Hiroyuki Wakaguri
- />Department of Medical Genome Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Naoaki Yokoyama
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Riu Yamashita
- />Tohoku Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Sendai, Miyagi 980-8579 Japan
| | - Yutaka Suzuki
- />Department of Medical Genome Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Xuenan Xuan
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Ikuo Igarashi
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
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Oberstaller J, Joseph SJ, Kissinger JC. Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile. BMC Genomics 2013; 14:516. [PMID: 23895416 PMCID: PMC3734150 DOI: 10.1186/1471-2164-14-516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/09/2013] [Indexed: 11/16/2022] Open
Abstract
Background There are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in C. parvum. Results We have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of in vitro epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinant C. parvum DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters. Conclusion Several DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential cis-regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a global C. parvum gene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.
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Affiliation(s)
- Jenna Oberstaller
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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38
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Cai H, Hong C, Gu J, Lilburn TG, Kuang R, Wang Y. Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 3:S5. [PMID: 23282319 PMCID: PMC3524314 DOI: 10.1186/1752-0509-6-s3-s5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Malaria causes over one million deaths annually, posing an enormous health and economic burden in endemic regions. The completion of genome sequencing of the causative agents, a group of parasites in the genus Plasmodium, revealed potential drug and vaccine candidates. However, genomics-driven target discovery has been significantly hampered by our limited knowledge of the cellular networks associated with parasite development and pathogenesis. In this paper, we propose an approach based on aligning neighborhood PPI subnetworks across species to identify network components in the malaria parasite P. falciparum. Results Instead of only relying on sequence similarities to detect functional orthologs, our approach measures the conservation between the neighborhood subnetworks in protein-protein interaction (PPI) networks in two species, P. falciparum and E. coli. 1,082 P. falciparum proteins were predicted as functional orthologs of known transcriptional regulators in the E. coli network, including general transcriptional regulators, parasite-specific transcriptional regulators in the ApiAP2 protein family, and other potential regulatory proteins. They are implicated in a variety of cellular processes involving chromatin remodeling, genome integrity, secretion, invasion, protein processing, and metabolism. Conclusions In this proof-of-concept study, we demonstrate that a subnetwork alignment approach can reveal previously uncharacterized members of the subnetworks, which opens new opportunities to identify potential therapeutic targets and provide new insights into parasite biology, pathogenesis and virulence. This approach can be extended to other systems, especially those with poor genome annotation and a paucity of knowledge about cellular networks.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Lajoie M, Gascuel O, Lefort V, Bréhélin L. Computational discovery of regulatory elements in a continuous expression space. Genome Biol 2012. [PMID: 23186104 PMCID: PMC4053739 DOI: 10.1186/gb-2012-13-11-r109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Approaches for regulatory element discovery from gene expression data usually rely on clustering algorithms to partition the data into clusters of co-expressed genes. Gene regulatory sequences are then mined to find overrepresented motifs in each cluster. However, this ad hoc partition rarely fits the biological reality. We propose a novel method called RED2 that avoids data clustering by estimating motif densities locally around each gene. We show that RED2 detects numerous motifs not detected by clustering-based approaches, and that most of these correspond to characterized motifs. RED2 can be accessed online through a user-friendly interface.
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Cai H, Zhou Z, Gu J, Wang Y. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium.. Curr Bioinform 2012; 7. [PMID: 24298232 DOI: 10.2174/157489312803900965] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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41
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Xia X. Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction. SCIENTIFICA 2012; 2012:917540. [PMID: 24278755 PMCID: PMC3820676 DOI: 10.6064/2012/917540] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/11/2012] [Indexed: 05/31/2023]
Abstract
Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods, but also a key component in more advanced computational algorithms (e.g., Gibbs sampler) for characterizing and discovering motifs in nucleotide or amino acid sequences. However, few generally applicable statistical tests are available for evaluating the significance of site patterns, PWM, and PWM scores (PWMS) of putative motifs. Statistical significance tests of the PWM output, that is, site-specific frequencies, PWM itself, and PWMS, are in disparate sources and have never been collected in a single paper, with the consequence that many implementations of PWM do not include any significance test. Here I review PWM-based methods used in motif characterization and prediction (including a detailed illustration of the Gibbs sampler for de novo motif discovery), present statistical and probabilistic rationales behind statistical significance tests relevant to PWM, and illustrate their application with real data. The multiple comparison problem associated with the test of site-specific frequencies is best handled by false discovery rate methods. The test of PWM, due to the use of pseudocounts, is best done by resampling methods. The test of individual PWMS for each sequence segment should be based on the extreme value distribution.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5
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42
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Milner DA, Pochet N, Krupka M, Williams C, Seydel K, Taylor TE, Van de Peer Y, Regev A, Wirth D, Daily JP, Mesirov JP. Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. PLoS One 2012; 7:e40739. [PMID: 22815802 PMCID: PMC3399889 DOI: 10.1371/journal.pone.0040739] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/12/2012] [Indexed: 01/30/2023] Open
Abstract
Background In the past decade, estimates of malaria infections have dropped from 500 million to 225 million per year; likewise, mortality rates have dropped from 3 million to 791,000 per year. However, approximately 90% of these deaths continue to occur in sub-Saharan Africa, and 85% involve children less than 5 years of age. Malaria mortality in children generally results from one or more of the following clinical syndromes: severe anemia, acidosis, and cerebral malaria. Although much is known about the clinical and pathological manifestations of CM, insights into the biology of the malaria parasite, specifically transcription during this manifestation of severe infection, are lacking. Methods and Findings We collected peripheral blood from children meeting the clinical case definition of cerebral malaria from a cohort in Malawi, examined the patients for the presence or absence of malaria retinopathy, and performed whole genome transcriptional profiling for Plasmodium falciparum using a custom designed Affymetrix array. We identified two distinct physiological states that showed highly significant association with the level of parasitemia. We compared both groups of Malawi expression profiles with our previously acquired ex vivo expression profiles of parasites derived from infected patients with mild disease; a large collection of in vitro Plasmodium falciparum life cycle gene expression profiles; and an extensively annotated compendium of expression data from Saccharomyces cerevisiae. The high parasitemia patient group demonstrated a unique biology with elevated expression of Hrd1, a member of endoplasmic reticulum-associated protein degradation system. Conclusions The presence of a unique high parasitemia state may be indicative of the parasite biology of the clinically recognized hyperparasitemic severe disease syndrome.
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Affiliation(s)
- Danny A Milner
- The Brigham and Women's Hospital, Department of Pathology, Boston, Massachusetts, United States of America.
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Rovira-Graells N, Gupta AP, Planet E, Crowley VM, Mok S, Ribas de Pouplana L, Preiser PR, Bozdech Z, Cortés A. Transcriptional variation in the malaria parasite Plasmodium falciparum. Genome Res 2012; 22:925-38. [PMID: 22415456 PMCID: PMC3337437 DOI: 10.1101/gr.129692.111] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional analysis of isogenic parasite lines grown under homogeneous conditions. This analysis revealed extensive transcriptional heterogeneity within genetically homogeneous clonal parasite populations. We show that clonally variant expression controlled at the epigenetic level is an intrinsic property of specific genes and gene families, the majority of which participate in host–parasite interactions. Intrinsic transcriptional variability is not restricted to genes involved in immune evasion, but also affects genes linked to lipid metabolism, protein folding, erythrocyte remodeling, or transcriptional regulation, among others, indicating that epigenetic variation results in both antigenic and functional variation. We observed a general association between heterochromatin marks and clonally variant expression, extending previous observations for specific genes to essentially all variantly expressed gene families. These results suggest that phenotypic variation of functionally unrelated P. falciparum gene families is mediated by a common mechanism based on reversible formation of H3K9me3-based heterochromatin. In changing environments, diversity confers fitness to a population. Our results support the idea that P. falciparum uses a bet-hedging strategy, as an alternative to directed transcriptional responses, to adapt to common fluctuations in its environment. Consistent with this idea, we found that transcriptionally different isogenic parasite lines markedly differed in their survival to heat-shock mimicking febrile episodes and adapted to periodic heat-shock with a pattern consistent with natural selection of pre-existing parasites.
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Liu Z, Miao J, Cui L. Gametocytogenesis in malaria parasite: commitment, development and regulation. Future Microbiol 2012; 6:1351-69. [PMID: 22082293 DOI: 10.2217/fmb.11.108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Malaria parasites have evolved a complicated life cycle alternating between two hosts. Gametocytes are produced in the vertebrate hosts and are obligatory for natural transmission of the parasites through mosquito vectors. The mechanism of sexual development in Plasmodium has been the focus of extensive studies. In the postgenomic era, the advent of genome-wide analytical tools and genetic manipulation technology has enabled rapid advancement of our knowledge in this area. Patterns of gene expression during sexual development, molecular distinction of the two sexes, and mechanisms underlying subsequent formation of gametes and their fertilization have been progressively elucidated. However, the triggers and mechanism of sexual development remain largely unknown. This article provides an update of our understanding of the molecular and cellular events associated with the decision for commitment to sexual development and regulation of gene expression during gametocytogenesis. Insights into the molecular mechanisms of gametocyte development are essential for designing proper control strategies for interruption of malaria transmission and ultimate elimination.
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Affiliation(s)
- Zhenyu Liu
- Department of Entomology, The Pennsylvania State University, 537 ASI Building University Park, PA 16802, USA
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Harris EY, Ponts N, Le Roch KG, Lonardi S. Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite. BMC Genomics 2011; 12:601. [PMID: 22165844 PMCID: PMC3282892 DOI: 10.1186/1471-2164-12-601] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 12/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background Despite extensive efforts to discover transcription factors and their binding sites in the human malaria parasite Plasmodium falciparum, only a few transcription factor binding motifs have been experimentally validated to date. As a consequence, gene regulation in P. falciparum is still poorly understood. There is now evidence that the chromatin architecture plays an important role in transcriptional control in malaria. Results We propose a methodology for discovering cis-regulatory elements that uses for the first time exclusively dynamic chromatin remodeling data. Our method employs nucleosome positioning data collected at seven time points during the erythrocytic cycle of P. falciparum to discover putative DNA binding motifs and their transcription factor binding sites along with their associated clusters of target genes. Our approach results in 129 putative binding motifs within the promoter region of known genes. About 75% of those are novel, the remaining being highly similar to experimentally validated binding motifs. About half of the binding motifs reported show statistically significant enrichment in functional gene sets and strong positional bias in the promoter region. Conclusion Experimental results establish the principle that dynamic chromatin remodeling data can be used in lieu of gene expression data to discover binding motifs and their transcription factor binding sites. Our approach can be applied using only dynamic nucleosome positioning data, independent from any knowledge of gene function or expression.
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Affiliation(s)
- Elena Y Harris
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
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Boisson B, Lacroix C, Bischoff E, Gueirard P, Bargieri DY, Franke-Fayard B, Janse CJ, Ménard R, Baldacci P. The novel putative transporter NPT1 plays a critical role in early stages of Plasmodium berghei sexual development. Mol Microbiol 2011; 81:1343-57. [PMID: 21752110 DOI: 10.1111/j.1365-2958.2011.07767.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transmission of Plasmodium species from a mammalian host to the mosquito vector requires the uptake, during an infected blood meal, of gametocytes, the precursor cells of the gametes. Relatively little is known about the molecular mechanisms involved in the developmental switch from asexual development to sexual differentiation or the maturation and survival of gametocytes. Here, we show that a gene coding for a novel putative transporter, NPT1, plays a crucial role in the development of Plasmodium berghei gametocytes. Parasites lacking NPT1 are severely compromised in the production of gametocytes and the rare gametocytes produced are unable to differentiate into fertile gametes. This is the earliest block in gametocytogenesis obtained by reverse genetics and the first to demonstrate the role of a protein with a putative transport function in sexual development. These results and the high degree of conservation of NPT1 in Plasmodium species suggest that this protein could be an attractive target for the development of novel drugs to block the spread of malaria.
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Affiliation(s)
- Bertrand Boisson
- Institut Pasteur, Biologie et Génétique du Paludisme, 75724 Paris, France.
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Mu J, Seydel KB, Bates A, Su XZ. Recent Progress in Functional Genomic Research in Plasmodium falciparum. Curr Genomics 2011; 11:279-86. [PMID: 21119892 PMCID: PMC2930667 DOI: 10.2174/138920210791233081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/22/2010] [Accepted: 03/09/2010] [Indexed: 02/02/2023] Open
Abstract
With the completion and near completion of many malaria parasite genome-sequencing projects, efforts are now being directed to a better understanding of gene functions and to the discovery of vaccine and drug targets. Inter- and intraspecies comparisons of the parasite genomes will provide invaluable insights into parasite evolution, virulence, drug resistance, and immune invasion. Genome-wide searches for loci under various selection pressures may lead to discovery of genes conferring drug resistance or encoding for protective antigens. In addition, the Plasmodium falciparum genome sequence provides the basis for the development of various microarrays to monitor gene expression and to detect nucleotide substitution and deletion/amplification. Genome-wide profiling of the parasite proteome, chromatin modification, and nucleosome position also depend on availability of the parasite genome. In this brief review, we will highlight some recent advances and studies in characterizing gene function and related phenotype in P. falciparum that were made possible by the genome sequence, particularly the development of a genome-wide diversity map and various high-throughput genotyping methods for genome-wide association studies (GWAS).
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Affiliation(s)
- Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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48
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Wong EH, Hasenkamp S, Horrocks P. Analysis of the molecular mechanisms governing the stage-specific expression of a prototypical housekeeping gene during intraerythrocytic development of P. falciparum. J Mol Biol 2011; 408:205-21. [PMID: 21354176 PMCID: PMC3081073 DOI: 10.1016/j.jmb.2011.02.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 02/10/2011] [Accepted: 02/17/2011] [Indexed: 01/22/2023]
Abstract
Gene expression during the intraerythrocytic development cycle of the human malarial parasite Plasmodium falciparum is subject to tight temporal control, resulting in a cascade of gene expression to meet the physiological demands of growth, replication, and reinvasion. The roles of the different molecular mechanisms that drive this temporal program of gene expression are poorly understood. Here we report the use of the bxb1 integrase system to reconstitute all aspects of the absolute and temporal control of the prototypical housekeeping gene encoding the proliferating cell nuclear antigen (Pfpcna) around an integrated luciferase reporter cassette. A quantitative analysis of the effect of the serial deletion of 5′ and 3′ genetic elements and sublethal doses of histone deacetylase inhibitors demonstrates that while the absolute control of gene expression could be perturbed, no effect on the temporal control of gene expression was observed. These data provide support for a novel model for the temporal control of potentially hundreds of genes during the intraerythrocytic development of this important human pathogen.
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Affiliation(s)
- Eleanor H. Wong
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Sandra Hasenkamp
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Paul Horrocks
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
- Corresponding author. Institute for Science and Technology in Medicine, Keele University, Huxley Building, Staffordshire ST5 5BG, UK.
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Cai H, Gu J, Wang Y. Core genome components and lineage specific expansions in malaria parasites plasmodium. BMC Genomics 2010; 11 Suppl 3:S13. [PMID: 21143780 PMCID: PMC2999343 DOI: 10.1186/1471-2164-11-s3-s13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, which can lead us to a better understanding of how the parasites develop the genetic variability that is associated with their response to environmental challenges and other adaptive phenotypes. Results We present the results of a comprehensive analysis of the genomes of six Plasmodium species, including two species that infect humans, one that infects monkeys, and three that infect rodents. The core genome shared by all six species is composed of 3,351 genes, which make up about 22%-65% of the genome repertoire. These components play important roles in fundamental functions as well as in parasite-specific activities. We further investigated the distribution and features of genes that have been expanded in specific Plasmodium lineage(s). Abundant duplicate genes are present in the six species, with 5%-9% of the whole genomes composed lineage specific radiations. The majority of these gene families are hypothetical proteins with unknown functions; a few may have predicted roles such as antigenic variation. Conclusions The core genome components in the malaria parasites have functions ranging from fundamental biological processes to roles in the complex networks that sustain the parasite-specific lifestyles appropriate to different hosts. They represent the minimum requirement to maintain a successful life cycle that spans vertebrate hosts and mosquito vectors. Lineage specific expansions (LSEs) have given rise to abundant gene families in Plasmodium. Although the functions of most families remain unknown, these LSEs could reveal components in parasite networks that, by their enhanced genetic variability, can contribute to pathogenesis, virulence, responses to environmental challenges, or interesting phenotypes.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, TX 78249, USA.
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Painter HJ, Campbell TL, Llinás M. The Apicomplexan AP2 family: integral factors regulating Plasmodium development. Mol Biochem Parasitol 2010; 176:1-7. [PMID: 21126543 DOI: 10.1016/j.molbiopara.2010.11.014] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/20/2010] [Accepted: 11/23/2010] [Indexed: 12/01/2022]
Abstract
Malaria is caused by protozoan parasites of the genus Plasmodium and involves infection of multiple hosts and cell types during the course of an infection. To complete its complex life cycle the parasite requires strict control of gene regulation for survival and successful propagation. Thus far, the Apicomplexan AP2 (ApiAP2) family of DNA-binding proteins is the sole family of proteins to have surfaced as candidate transcription factors in all apicomplexan species. Work from several laboratories is beginning to shed light on how the ApiAP2 proteins from Plasmodium spp. contribute to the regulation of gene expression at various stages of parasite development. Here we highlight recent progress toward understanding the role of Plasmodium ApiAP2 proteins in DNA related regulatory processes including transcriptional regulation and gene silencing.
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Affiliation(s)
- Heather J Painter
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544,, USA
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