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Govindaraju G, Rajavelu A. Reading the epitranscriptome of the human malaria parasite. Biomed J 2024:100703. [PMID: 38316392 DOI: 10.1016/j.bj.2024.100703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
Epigenetic machinery has emerged as a central player in gene regulation and chromatin organization in Plasmodium spp. Epigenetic modifications on histones and their role in antigenic variation in P. falciparum are widely studied. Recent discoveries on nucleic acid methylome are exciting and provide a new dimension to the apicomplexan protozoan parasite's gene regulatory process. Reports have confirmed that N6-methyl adenosine (m6A) methylation plays a crucial role in the translational plasticity of the human malaria parasite during its development in RBC. The YTH domain (YT521-B Homology) protein in P. falciparum binds to m6A epitranscriptome modifications on the mRNA and regulates protein translation. The binding of the PfYTH domain protein to the m6A-modified mRNA is mediated through a binding pocket formed by aromatic amino acids. The P. falciparum genome encodes two members of YTH domain proteins, i.e., YTH1 and YTH2, and both have distinct roles in dictating the epitranscriptome in human malaria parasites. This review highlights recent advancements in the functions and mechanisms of YTH domain protein's role in translational plasticity in the various developmental stages of the parasite.
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Affiliation(s)
- Gayathri Govindaraju
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Chennai, India
| | - Arumugam Rajavelu
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Chennai, India.
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2
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Lodde V, Floris M, Muroni MR, Cucca F, Idda ML. Non-coding RNAs in malaria infection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1697. [PMID: 34651456 PMCID: PMC9286032 DOI: 10.1002/wrna.1697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 12/31/2022]
Abstract
Malaria is one of the most severe infectious diseases affecting humans and it is caused by protozoan pathogens of the species Plasmodium (spp.). The malaria parasite Plasmodium is characterized by a complex, multistage life cycle that requires tight gene regulation which allows for host invasion and defense against host immune responses. Unfortunately, the mechanisms regulating gene expression during Plasmodium infection remain largely elusive, though several lines of evidence implicate a major involvement of non-coding RNAs (ncRNAs). The ncRNAs have been found to play a key role in regulating transcriptional and post-transcriptional events in a broad range of organisms including Plasmodium. In Plasmodium ncRNAs have been shown to regulate key events in the multistage life cycle and virulence ability. Here we review recent progress involving ncRNAs (microRNAs, long non-coding RNAs, and circular RNAs) and their role as regulators of gene expression during Plasmodium infection in human hosts with focus on the possibility of using these molecules as biomarkers for monitoring disease status. We also discuss the surprising function of ncRNAs in mediating the complex interplay between parasite and human host and future perspectives of the field. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Matteo Floris
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Rosaria Muroni
- Department of Medical, Surgical, and Experimental SciencesUniversity of SassariSassariItaly
| | - Francesco Cucca
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Laura Idda
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR)SassariItaly
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3
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Tintó-Font E, Cortés A. Malaria parasites do respond to heat. Trends Parasitol 2022; 38:435-449. [PMID: 35301987 DOI: 10.1016/j.pt.2022.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 01/09/2023]
Abstract
The capacity of malaria parasites to respond to changes in their environment at the transcriptional level has been the subject of debate, but recent evidence has unambiguously demonstrated that Plasmodium spp. can produce adaptive transcriptional responses when exposed to some specific types of stress. These include metabolic conditions and febrile temperature. The Plasmodium falciparum protective response to thermal stress is similar to the response in other organisms, but it is regulated by a transcription factor evolutionarily unrelated to the conserved transcription factor that drives the heat shock (HS) response in most eukaryotes. Of the many genes that change expression during HS, only a subset constitutes an authentic response that contributes to parasite survival.
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Affiliation(s)
- Elisabet Tintó-Font
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Catalonia, Spain; ICREA, Barcelona 08010, Catalonia, Spain.
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4
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Alvarez DR, Ospina A, Barwell T, Zheng B, Dey A, Li C, Basu S, Shi X, Kadri S, Chakrabarti K. The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum. RNA Biol 2021; 18:2480-2497. [PMID: 33960872 DOI: 10.1080/15476286.2021.1926747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and non-coding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5' UTR, CDS and 3' UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA-/RNA-binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
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Affiliation(s)
- Diana Renteria Alvarez
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Alejandra Ospina
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Tiffany Barwell
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Bo Zheng
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Abhishek Dey
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Chong Li
- Temple University, Philadelphia, PA, USA
| | - Shrabani Basu
- Division of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | - Sabah Kadri
- Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine and Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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5
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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van Biljon R, van Wyk R, Painter HJ, Orchard L, Reader J, Niemand J, Llinás M, Birkholtz LM. Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation. BMC Genomics 2019; 20:920. [PMID: 31795940 PMCID: PMC6889441 DOI: 10.1186/s12864-019-6322-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as it commits to and develops through gametocytogenesis. RESULTS The gametocyte-associated transcriptome is significantly different from that of the asexual parasites, with dynamic gene expression shifts characterizing early, intermediate and late-stage gametocyte development and results in differential timing for sex-specific transcripts. The transcriptional dynamics suggest strict transcriptional control during gametocytogenesis in P. falciparum, which we propose is mediated by putative regulators including epigenetic mechanisms (driving active repression of proliferation-associated processes) and a cascade-like expression of ApiAP2 transcription factors. CONCLUSIONS The gametocyte transcriptome serves as the blueprint for sexual differentiation and will be a rich resource for future functional studies on this critical stage of Plasmodium development, as the intraerythrocytic transcriptome has been for our understanding of the asexual cycle.
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Affiliation(s)
- Riëtte van Biljon
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Roelof van Wyk
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Heather J Painter
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Review, U.S. Food & Drug Administration, Silver Spring, MD, 20993, USA
| | - Lindsey Orchard
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Jandeli Niemand
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology, the Huck Center for Malaria Research, University Park, PA, 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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7
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Transcriptome-wide dynamics of extensive m 6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 2019; 4:2246-2259. [PMID: 31384004 DOI: 10.1038/s41564-019-0521-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite's life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
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8
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Ararat-Sarria M, Patarroyo MA, Curtidor H. Parasite-Related Genetic and Epigenetic Aspects and Host Factors Influencing Plasmodium falciparum Invasion of Erythrocytes. Front Cell Infect Microbiol 2019; 8:454. [PMID: 30693273 PMCID: PMC6339890 DOI: 10.3389/fcimb.2018.00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 01/13/2023] Open
Abstract
Malaria, a disease caused by Plasmodium parasites, is widespread throughout tropical and sub-tropical regions worldwide; it mostly affects children and pregnant woman. Eradication has stalled despite effective prevention measures and medication being available for this disease; this has mainly been due to the parasite's resistance to medical treatment and the mosquito vector's resistance to insecticides. Tackling such resistance involves using renewed approaches and techniques for accruing a deep understanding of the parasite's biology, and developing new drugs and vaccines. Studying the parasite's invasion of erythrocytes should shed light on its ability to switch between invasion phenotypes related to the expression of gene sets encoding proteins acting as ligands during target cell invasion, thereby conferring mechanisms for evading a particular host's immune response and adapting to changes in target cell surface receptors. This review considers some factors influencing the expression of such phenotypes, such as Plasmodium's genetic, transcriptional and epigenetic characteristics, and explores some host-related aspects which could affect parasite phenotypes, aiming at integrating knowledge regarding this topic and the possible relationship between the parasite's biology and host factors playing a role in erythrocyte invasion.
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Affiliation(s)
- Monica Ararat-Sarria
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Immunología de Colombia (FIDIC), Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Hernando Curtidor
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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9
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Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR. tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. Mol Syst Biol 2018; 14:e8009. [PMID: 30287681 PMCID: PMC6171970 DOI: 10.15252/msb.20178009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/24/2022] Open
Abstract
Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.
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Affiliation(s)
- Chee Sheng Ng
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ameya Sinha
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yaw Aniweh
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Qianhui Nah
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
| | - Indrakanti Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Microbiology and Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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10
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Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun 2018; 9:2656. [PMID: 29985403 PMCID: PMC6037754 DOI: 10.1038/s41467-018-04966-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/31/2018] [Indexed: 01/12/2023] Open
Abstract
Genome-wide analysis of transcription in the malaria parasite Plasmodium falciparum has revealed robust variation in steady-state mRNA abundance throughout the 48-h intraerythrocytic developmental cycle (IDC), suggesting that this process is highly dynamic and tightly regulated. Here, we utilize rapid 4-thiouracil (4-TU) incorporation via pyrimidine salvage to specifically label, capture, and quantify newly-synthesized RNA transcripts at every hour throughout the IDC. This high-resolution global analysis of the transcriptome captures the timing and rate of transcription for each newly synthesized mRNA in vivo, revealing active transcription throughout all IDC stages. Using a statistical model to predict the mRNA dynamics contributing to the total mRNA abundance at each timepoint, we find varying degrees of transcription and stabilization for each mRNA corresponding to developmental transitions. Finally, our results provide new insight into co-regulation of mRNAs throughout the IDC through regulatory DNA sequence motifs, thereby expanding our understanding of P. falciparum mRNA dynamics. Transcriptomic analysis often doesn’t differentiate between newly synthesized and stabilized mRNAs. Using rapid 4-thiouracil incorporation, Painter et al. here define genome-wide active transcription throughout Plasmodium blood-stage developmental stages and identify associated regulatory DNA sequence motifs.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Neo Christopher Chung
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08544, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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11
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Jiang N, Yu S, Yang N, Feng Y, Sang X, Wang Y, Wahlgren M, Chen Q. Characterization of the Catalytic Subunits of the RNA Exosome-like Complex in Plasmodium falciparum. J Eukaryot Microbiol 2018; 65:843-853. [PMID: 29664138 PMCID: PMC6282785 DOI: 10.1111/jeu.12625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 12/21/2022]
Abstract
The eukaryotic ribonucleic acid (RNA) exosome is a versatile multiribonuclease complex that mediates the processing, surveillance, and degradation of virtually all classes of RNA in both the nucleus and cytoplasm. The complex, composed of 10 to 11 subunits, has been widely described in many organisms. Bioinformatic analyses revealed that there may be also an exosome‐like complex in Plasmodium falciparum, a parasite of great importance in public health, with eight predicted subunits having high sequence similarity to their counterparts in yeast and human. In this work, the putative RNA catalytic components, designated as PfRrp4, PfRrp41, PfDis3, and PfRrp6, were identified and systematically analyzed. Quantitative polymerase chain reaction (QPCR) analyses suggested that all of them were transcribed steadily throughout the asexual stage. The expression of these proteins was determined by Western blot, and their localization narrowed to the cytoplasm of the parasite by indirect immunofluorescence. The recombinant proteins of PfRrp41, PfDis3, and PfRrp6 exhibited catalytic activity for single‐stranded RNA (ssRNA), whereas PfRrp4 showed no processing activity of both ssRNA and dsRNA. The identification of these putative components of the RNA exosome complex opens up new perspectives for a deep understanding of RNA metabolism in the malarial parasite P. falciparum.
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Affiliation(s)
- Ning Jiang
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China
| | - Shengchao Yu
- Key Laboratory of Zoonosis, Jilin University, 53333 Xi An Da Lu, Changchun, 130062, China
| | - Na Yang
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China
| | - Ying Feng
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China
| | - Xiaoyu Sang
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China
| | - Yao Wang
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China
| | - Mats Wahlgren
- Department of Microbiology, Tumour and Cellular Biology, Karolinska Institutet, Nobels väg 16, Stockholm, Sweden
| | - Qijun Chen
- Key Laboratory of Zoonosis, Shenyang Agricultural University, 120 Dongling Road, Shenyang, China.,Department of Microbiology, Tumour and Cellular Biology, Karolinska Institutet, Nobels väg 16, Stockholm, Sweden
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12
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Kim A, Popovici J, Vantaux A, Samreth R, Bin S, Kim S, Roesch C, Liang L, Davies H, Felgner P, Herrera S, Arévalo-Herrera M, Ménard D, Serre D. Characterization of P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms. Sci Rep 2017; 7:7761. [PMID: 28798400 PMCID: PMC5552866 DOI: 10.1038/s41598-017-07275-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/23/2017] [Indexed: 01/19/2023] Open
Abstract
Our understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures. Most P. vivax studies must therefore rely on patient samples, which typically display a low proportion of parasites and asynchronous parasites. Here, we present stranded RNA-seq data generated directly from a small volume of blood from three Cambodian vivax malaria patients collected before treatment. Our analyses show surprising similarities of the parasite gene expression patterns across infections, despite extensive variations in parasite stage proportion. These similarities contrast with the unique gene expression patterns observed in sporozoites isolated from salivary glands of infected Colombian mosquitoes. Our analyses also indicate that more than 10% of P. vivax genes encode multiple, often undescribed, protein-coding sequences, potentially increasing the diversity of proteins synthesized by blood stage parasites. These data also greatly improve the annotations of P. vivax gene untranslated regions, providing an important resource for future studies of specific genes.
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Affiliation(s)
- Adam Kim
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Jean Popovici
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Reingsey Samreth
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Sophalai Bin
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Camille Roesch
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Li Liang
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | - Huw Davies
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | - Philip Felgner
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | | | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia.,School of Health, University of Valle, Cali, Colombia
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia. .,Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France. .,Inserm U1016, CNRS UMR8104, Institut Cochin, Paris, France.
| | - David Serre
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA.
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13
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Abstract
Malaria is caused in humans by five species of single-celled eukaryotic Plasmodium parasites (mainly Plasmodium falciparum and Plasmodium vivax) that are transmitted by the bite of Anopheles spp. mosquitoes. Malaria remains one of the most serious infectious diseases; it threatens nearly half of the world's population and led to hundreds of thousands of deaths in 2015, predominantly among children in Africa. Malaria is managed through a combination of vector control approaches (such as insecticide spraying and the use of insecticide-treated bed nets) and drugs for both treatment and prevention. The widespread use of artemisinin-based combination therapies has contributed to substantial declines in the number of malaria-related deaths; however, the emergence of drug resistance threatens to reverse this progress. Advances in our understanding of the underlying molecular basis of pathogenesis have fuelled the development of new diagnostics, drugs and insecticides. Several new combination therapies are in clinical development that have efficacy against drug-resistant parasites and the potential to be used in single-dose regimens to improve compliance. This ambitious programme to eliminate malaria also includes new approaches that could yield malaria vaccines or novel vector control strategies. However, despite these achievements, a well-coordinated global effort on multiple fronts is needed if malaria elimination is to be achieved.
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Affiliation(s)
- Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
| | | | | | | | - Wesley C Van Voorhis
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Seattle, Washington, USA
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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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15
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Vembar SS, Droll D, Scherf A. Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems-wide studies pave the way. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:772-792. [PMID: 27230797 PMCID: PMC5111744 DOI: 10.1002/wrna.1365] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 11/10/2022]
Abstract
The malaria parasite Plasmodium spp. varies the expression profile of its genes depending on the host it resides in and its developmental stage. Virtually all messenger RNA (mRNA) is expressed in a monocistronic manner, with transcriptional activation regulated at the epigenetic level and by specialized transcription factors. Furthermore, recent systems-wide studies have identified distinct mechanisms of post-transcriptional and translational control at various points of the parasite lifecycle. Taken together, it is evident that 'just-in-time' transcription and translation strategies coexist and coordinate protein expression during Plasmodium development, some of which we review here. In particular, we discuss global and specific mechanisms that control protein translation in blood stages of the human malaria parasite Plasmodium falciparum, once a cytoplasmic mRNA has been generated, and its crosstalk with mRNA decay and storage. We also focus on the widespread translational delay observed during the 48-hour blood stage lifecycle of P. falciparum-for over 30% of transcribed genes, including virulence factors required to invade erythrocytes-and its regulation by cis-elements in the mRNA, RNA-processing enzymes and RNA-binding proteins; the first-characterized amongst these are the DNA- and RNA-binding Alba proteins. More generally, we conclude that translational regulation is an emerging research field in malaria parasites and propose that its elucidation will not only shed light on the complex developmental program of this parasite, but may also reveal mechanisms contributing to drug resistance and define new targets for malaria intervention strategies. WIREs RNA 2016, 7:772-792. doi: 10.1002/wrna.1365 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.
| | - Dorothea Droll
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
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16
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Guttery DS, Roques M, Holder AA, Tewari R. Commit and Transmit: Molecular Players in Plasmodium Sexual Development and Zygote Differentiation. Trends Parasitol 2015; 31:676-685. [PMID: 26440790 DOI: 10.1016/j.pt.2015.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 11/27/2022]
Abstract
During each cycle of asexual endomitotic division in erythrocytes, the malaria parasite makes a fundamental and crucial decision: to continue to invade and proliferate or to differentiate into gametocytes ready for continuation of sexual development. The proteins and regulatory pathways involved in Plasmodium sexual development have been of great interest in recent years as targets for blocking malaria transmission. However, the 'Holy Grail', the master switch orchestrating asexual-to-sexual commitment and further differentiation, has remained elusive - until now. Here we highlight the recent studies identifying the epigenetic and transcriptional master regulators of sexual commitment and discuss the key players in reversible phosphorylation pathways involved in sexual and zygote differentiation.
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Affiliation(s)
- David S Guttery
- Cell and Developmental Biology Group, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG2 7UH, UK; Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Magali Roques
- Cell and Developmental Biology Group, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG2 7UH, UK
| | - Anthony A Holder
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Rita Tewari
- Cell and Developmental Biology Group, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG2 7UH, UK.
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17
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Vembar SS, Macpherson CR, Sismeiro O, Coppée JY, Scherf A. The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages. Genome Biol 2015; 16:212. [PMID: 26415947 PMCID: PMC4587749 DOI: 10.1186/s13059-015-0771-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Transcriptome-wide ribosome occupancy studies have suggested that during the intra-erythrocytic lifecycle of Plasmodium falciparum, select mRNAs are post-transcriptionally regulated. A subset of these encodes parasite virulence factors required for invading host erythrocytes, and are currently being developed as vaccine candidates. However, the molecular mechanisms that govern post-transcriptional regulation are currently unknown. Results We explore the previously identified DNA/RNA-binding protein PfAlba1, which localizes to multiple foci in the cytoplasm of P. falciparum trophozoites. We establish that PfAlba1 is essential for asexual proliferation, and subsequently investigate parasites overexpressing epitope-tagged PfAlba1 to identify its RNA targets and effects on mRNA homeostasis and translational regulation. Using deep sequencing of affinity-purified PfAlba1-associated RNAs, we identify 1193 transcripts that directly bind to PfAlba1 in trophozoites. For 105 such transcripts, 43 % of which are uncharacterized and 13 % of which encode erythrocyte invasion components, the steady state levels significantly change at this stage, evidencing a role for PfAlba1 in maintaining mRNA homeostasis. Additionally, we discover that binding of PfAlba1 to four erythrocyte invasion mRNAs, Rap1, RhopH3, CDPK1, and AMA1, is linked to translation repression in trophozoites whereas release of these mRNAs from a PfAlba1 complex in mature stages correlates with protein synthesis. Conclusions We show that PfAlba1 binds to a sub-population of asexual stage mRNAs and fine-tunes the timing of translation. This mode of post-transcriptional regulation may be especially important for P. falciparum erythrocyte invasion components that have to be assembled into apical secretory organelles in a highly time-dependent manner towards the end of the parasite’s asexual lifecycle. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0771-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, UMR 1201, Paris, 75015, France.
| | - Cameron Ross Macpherson
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, UMR 1201, Paris, 75015, France
| | - Odile Sismeiro
- Plate-forme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Jean-Yves Coppée
- Plate-forme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, UMR 1201, Paris, 75015, France.
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18
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Josling GA, Llinás M. Sexual development in Plasmodium parasites: knowing when it's time to commit. Nat Rev Microbiol 2015; 13:573-87. [DOI: 10.1038/nrmicro3519] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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19
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Caro F, Ahyong V, Betegon M, DeRisi JL. Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages. eLife 2014; 3. [PMID: 25493618 PMCID: PMC4371882 DOI: 10.7554/elife.04106] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022] Open
Abstract
The characterization of the transcriptome and proteome of Plasmodium
falciparum has been a tremendous resource for the understanding of the
molecular physiology of this parasite. However, the translational dynamics that link
steady-state mRNA with protein levels are not well understood. In this study, we
bridge this disconnect by measuring genome-wide translation using ribosome profiling,
through five stages of the P. falciparum blood phase developmental
cycle. Our findings show that transcription and translation are tightly coupled, with
overt translational control occurring for less than 10% of the transcriptome.
Translationally regulated genes are predominantly associated with merozoite egress
functions. We systematically define mRNA 5′ leader sequences, and 3′
UTRs, as well as antisense transcripts, along with ribosome occupancy for each, and
establish that accumulation of ribosomes on 5′ leaders is a common transcript
feature. This work represents the highest resolution and broadest portrait of gene
expression and translation to date for this medically important parasite. DOI:http://dx.doi.org/10.7554/eLife.04106.001 The genome of an organism includes all of the genes or information necessary to
build, maintain, and replicate that organism. However, cells with the same
genome—such as a skin cell and a liver cell from the same person—can
look and behave very differently depending on which of the genes in their genomes
they express, and to what extent. For a gene to be expressed, its DNA is ‘transcribed’ to make an RNA
molecule, which is then ‘translated’ to make a protein. Efforts to
measure the transcription and translation processes in diseased cells, or in the
microorganisms that cause infections, may lead to new treatments and preventative
medicines. Such work is currently ongoing in the global effort to treat and prevent
malaria. Malaria is both preventable and curable, yet over 600,000 people are estimated to die
from this disease each year. The disease is caused by a single-celled parasite called
Plasmodium. Mosquitoes carry the parasites in their salivary
glands, and when a mosquito bites a human, these parasites are injected into the
bloodstream with the mosquito's saliva. Plasmodium parasites then
travel to and infect the liver, before bursting out of this tissue into the
bloodstream. Here, the parasites infect red blood cells and undergo rounds of
replication during which the symptoms of the disease are manifested. It is also
during this bloodstream phase that parasites can develop into forms capable of
infecting another mosquito and continuing the transmission cycle. The genes, RNA molecules, and proteins of the Plasmodium falciparum
parasite—which causes the most serious cases of malaria in humans—have
been cataloged to better understand the biology of this parasite. However, the
processes that control how, and when, an RNA transcript is translated into a protein
are not well understood. Now Caro et al. have uncovered which RNA molecules are being translated, and by how
much, during Plasmodium development within the blood. The
transcription and translation of genes in this parasite were found to be tightly
linked processes; the expression of only a few genes was controlled more by the
translation process than by transcription. These translationally regulated genes were
found mainly to be those that encode proteins involved in the parasite's exit from
the red blood cells and spread throughout the bloodstream. Caro et al. discovered that genetic regulation of the malaria parasite resembles a
preset genetic program, rather than a system that responds to changes and external
signals. As such, these findings suggest that targeting such a genetic program within
Plasmodium and preventing its implementation could prove an
effective strategy to curb the spread of malaria. DOI:http://dx.doi.org/10.7554/eLife.04106.002
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Affiliation(s)
- Florence Caro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Vida Ahyong
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Miguel Betegon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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20
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Abstract
SUMMARYEimeriais a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic loss. Like all apicomplexans, eimerians have a complex life cycle characterized by asexual divisions that amplify the parasite population in preparation for sexual reproduction. This can be divided into three events: gametocytogenesis, producing gametocytes from merozoites; gametogenesis, producing microgametes and macrogametes from gametocytes; and fertilization of macrogametes by microgametes, producing diploid zygotes with ensuing meiosis completing the sexual phase. Sexual development inEimeriadepends on the differential expression of stage-specific genes, rather than presence or absence of sex chromosomes. Thus, it involves the generation of specific structures and, implicitly, storage of proteins and regulation of protein expression in macrogametes, in preparation for fertilization. InEimeria, the formation of a unique, resilient structure, the oocyst wall, is essential for completion of the sexual phase and parasite transmission. In this review, we piece together the molecular events that underpin sexual reproduction inEimeriaand use additional details from analogous events inPlasmodiumto fill current knowledge gaps. The mechanisms governing sexual stage formation and subsequent fertilization may represent targets for counteracting parasite transmission.
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21
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Russell K, Hasenkamp S, Emes R, Horrocks P. Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum. BMC Genomics 2013; 14:267. [PMID: 23601558 PMCID: PMC3681616 DOI: 10.1186/1471-2164-14-267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/06/2013] [Indexed: 11/25/2022] Open
Abstract
Background The ability of the human malarial parasite Plasmodium falciparum to invade, colonise and multiply within diverse host environments, as well as to manifest its virulence within the human host, are activities tightly linked to the temporal and spatial control of gene expression. Yet, despite the wealth of high throughput transcriptomic data available for this organism there is very little information regarding the location of key transcriptional landmarks or their associated cis-acting regulatory elements. Here we provide a systematic exploration of the size and organisation of transcripts within intergenic regions to yield surrogate information regarding transcriptional landmarks, and to also explore the spatial and temporal organisation of transcripts over these poorly characterised genomic regions. Results Utilising the transcript data for a cohort of 105 genes we demonstrate that the untranscribed regions of mRNA are large and apportioned predominantly to the 5′ end of the open reading frame. Given the relatively compact size of the P. falciparum genome, we suggest that whilst transcriptional units are likely to spatially overlap, temporal co-transcription of adjacent transcriptional units is actually limited. Critically, the size of intergenic regions is directly dependent on the orientation of the two transcriptional units arrayed over them, an observation we extend to an analysis of the complete sequences of twelve additional organisms that share moderately compact genomes. Conclusions Our study provides a theoretical framework that extends our current understanding of the transcriptional landscape across the P. falciparum genome. Demonstration of a consensus gene-spacing rule that is shared between P. falciparum and ten other moderately compact genomes of apicomplexan parasites reveals the potential for our findings to have a wider impact across a phylum that contains many organisms important to human and veterinary health.
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Affiliation(s)
- Karen Russell
- Institute for Science and Technology in Medicine, Keele University, Huxley Building, Staffordshire ST5 5BG, United Kingdom
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22
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Schlarman MS, Roberts RN, Kariuki MM, LaCrue AN, Ou R, Beerntsen BT. PFE0565w, a Plasmodium falciparum protein expressed in salivary gland sporozoites. Am J Trop Med Hyg 2012; 86:943-54. [PMID: 22665598 DOI: 10.4269/ajtmh.2012.11-0797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Because malaria is still a significant problem worldwide, additional control methods need to be developed. The Plasmodium sporozoite is a good target for control measures because it displays dual infectivity for both mosquito and vertebrate host tissues. The Plasmodium falciparum gene, PFE0565w, was chosen as a candidate for study based on data from PlasmoDB, the Plasmodium database, indicating that it is expressed both at the transcriptional and protein levels in sporozoites, likely encodes a putative surface protein, and may have a potential role in the invasion of host tissues. Additional sequence analysis shows that the PFE0565w protein has orthologs in other Plasmodium species, but none outside of the genus Plasmodium. PFE0565w expresses transcript during both the sporozoite and erythrocytic stages of the parasite life cycle, where an alternative transcript was discovered during the erythrocytic stages. Data show that transcript is not present during axenic exoerythrocytic stages. Despite transcript being present in several life cycle stages, the PFE0565w protein is present only during the salivary gland sporozoite stage. Because the PFE0565w protein is present in salivary gland sporozoites, it could be a novel candidate for a pre-erythrocytic stage vaccine.
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Affiliation(s)
- Maggie S Schlarman
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
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23
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Schlarman MS, Roberts RN, Kariuki MM, LaCrue AN, Ou R, Beerntsen BT. Transcript and protein expression profile of PF11_0394, a Plasmodium falciparum protein expressed in salivary gland sporozoites. Malar J 2012; 11:80. [PMID: 22443220 PMCID: PMC3355004 DOI: 10.1186/1475-2875-11-80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/23/2012] [Indexed: 11/12/2022] Open
Abstract
Background Plasmodium falciparum malaria is a significant problem around the world today, thus there is still a need for new control methods to be developed. Because the sporozoite displays dual infectivity for both the mosquito salivary glands and vertebrate host tissue, it is a good target for vaccine development. Methods The P. falciparum gene, PF11_0394, was chosen as a candidate for study due to its potential role in the invasion of host tissues. This gene, which was selected using a data mining approach from PlasmoDB, is expressed both at the transcriptional and protein levels in sporozoites and likely encodes a putative surface protein. Using reverse transcription-polymerase chain reaction (RT-PCR) and green fluorescent protein (GFP)-trafficking studies, a transcript and protein expression profile of PF11_0394 was determined. Results The PF11_0394 protein has orthologs in other Plasmodium species and Apicomplexans, but none outside of the group Apicomplexa. PF11_0394 transcript was found to be present during both the sporozoite and erythrocytic stages of the parasite life cycle, but no transcript was detected during axenic exoerythrocytic stages. Despite the presence of transcript throughout several life cycle stages, the PF11_0394 protein was only detected in salivary gland sporozoites. Conclusions PF11_0394 appears to be a protein uniquely detected in salivary gland sporozoites. Even though a specific function of PF11_0394 has not been determined in P. falciparum biology, it could be another candidate for a new vaccine.
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Affiliation(s)
- Maggie S Schlarman
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
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