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Kalamuddin M, Shakri AR, Wang C, Min H, Li X, Cui L, Miao J. MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum. mSphere 2024; 9:e0014024. [PMID: 38564734 PMCID: PMC11036802 DOI: 10.1128/msphere.00140-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Histone lysine acetyltransferase MYST-associated NuA4 complex is conserved from yeast to humans and plays key roles in cell cycle regulation, gene transcription, and DNA replication/repair. Here, we identified a Plasmodium falciparum MYST-associated complex, PfNuA4, which contains 11 of the 13 conserved NuA4 subunits. Reciprocal pulldowns using PfEAF2, a shared component between the NuA4 and SWR1 complexes, not only confirmed the PfNuA4 complex but also identified the PfSWR1 complex, a histone remodeling complex, although their identities are low compared to the homologs in yeast or humans. Notably, both H2A.Z/H2B.Z were associated with the PfSWR1 complex, indicating that this complex is involved in the deposition of H2A.Z/H2B.Z, the variant histone pair that is enriched in the activated promoters. Overexpression of PfMYST resulted in earlier expression of genes involved in cell cycle regulation, DNA replication, and merozoite invasion, and upregulation of the genes related to antigenic variation and DNA repair. Consistently, PfMYST overexpression led to high basal phosphorylated PfH2A (γ-PfH2A), the mark of DNA double-strand breaks, and conferred protection against genotoxic agent methyl methanesulfonate (MMS), X-rays, and artemisinin, the first-line antimalarial drug. In contrast, the knockdown of PfMYST caused a delayed parasite recovery upon MMS treatment. MMS induced the gradual disappearance of PfMYST in the cytoplasm and concomitant accumulation of PfMYST in the nucleus, suggesting cytoplasm-nucleus shuttling of PfMYST. Meanwhile, PfMYST colocalized with the γ-PfH2A, indicating PfMYST was recruited to the DNA damage sites. Collectively, PfMYST plays critical roles in cell cycle regulation, gene transcription, and DNA replication/DNA repair in this low-branching parasitic protist.IMPORTANCEUnderstanding gene regulation and DNA repair in malaria parasites is critical for identifying targets for antimalarials. This study found PfNuA4, a PfMYST-associated, histone modifier complex, and PfSWR1, a chromatin remodeling complex in malaria parasite Plasmodium falciparum. These complexes are divergent due to the low identities compared to their homologs from yeast and humans. Furthermore, overexpression of PfMYST resulted in substantial transcriptomic changes, indicating that PfMYST is involved in regulating the cell cycle, antigenic variation, and DNA replication/repair. Consistently, PfMYST was found to protect against DNA damage caused by the genotoxic agent methyl methanesulfonate, X-rays, and artemisinin, the first-line antimalarial drug. Additionally, DNA damage led to the relocation of cytoplasmic PfMYST to the nucleus and colocalization of PfMYST with γ-PfH2A, the mark of DNA damage. In summary, this study demonstrated that the PfMYST complex has critical functions in regulating cell cycle, antigenic variation, and DNA replication/DNA repair in P. falciparum.
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Affiliation(s)
- Mohammad Kalamuddin
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ahmad Rushdi Shakri
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Hui Min
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Xiaolian Li
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
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Reyser T, Paloque L, Augereau JM, Di Stefano L, Benoit-Vical F. Epigenetic regulation as a therapeutic target in the malaria parasite Plasmodium falciparum. Malar J 2024; 23:44. [PMID: 38347549 PMCID: PMC10863139 DOI: 10.1186/s12936-024-04855-9] [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: 07/28/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Over the past thirty years, epigenetic regulation of gene expression has gained increasing interest as it was shown to be implicated in illnesses ranging from cancers to parasitic diseases. In the malaria parasite, epigenetics was shown to be involved in several key steps of the complex life cycle of Plasmodium, among which asexual development and sexual commitment, but also in major biological processes like immune evasion, response to environmental changes or DNA repair. Because epigenetics plays such paramount roles in the Plasmodium parasite, enzymes involved in these regulating pathways represent a reservoir of potential therapeutic targets. This review focuses on epigenetic regulatory processes and their effectors in the malaria parasite, as well as the inhibitors of epigenetic pathways and their potential as new anti-malarial drugs. Such types of drugs could be formidable tools that may contribute to malaria eradication in a context of widespread resistance to conventional anti-malarials.
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Affiliation(s)
- Thibaud Reyser
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Lucie Paloque
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Jean-Michel Augereau
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Luisa Di Stefano
- MCD, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Françoise Benoit-Vical
- LCC-CNRS, Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, Toulouse, France.
- MAAP, Inserm ERL 1289, Team "New Antiplasmodial Molecules and Pharmacological Approaches", Toulouse, France.
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, UPS, Université de Toulouse, Toulouse, France.
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Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression among Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. PLoS Negl Trop Dis 2024; 18:e0011926. [PMID: 38285730 PMCID: PMC10901308 DOI: 10.1371/journal.pntd.0011926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/28/2024] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
The documentation of Plasmodium vivax malaria across Africa especially in regions where Duffy negatives are dominant suggests possibly alternative erythrocyte invasion mechanisms. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa is unclear. In this study, we examined the expression of 4,404 gene transcripts belong to 12 functional groups and 43 erythrocyte binding gene candidates in Ethiopian isolates and compared them with the Cambodian and Brazilian P. vivax transcriptomes. Overall, there were 10-26% differences in the gene expression profile amongst geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian isolates. Members of the reticulocyte binding protein PvRBP2a and PvRBP3 expressed six-fold higher than Duffy binding protein PvDBP1 and 60-fold higher than PvEBP/DBP2 in the Ethiopian isolates. Other genes including PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression patterns were observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, gametocyte genes including PvAP2-G, PvGAP (female gametocytes), and Pvs47 (male gametocytes) were highly expressed across geographical samples.
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Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, United States of America
- School of Data Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
- Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, United States of America
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Tavares MT, Krüger A, Yan SLR, Waitman KB, Gomes VM, de Oliveira DS, Paz F, Hilscher S, Schutkowski M, Sippl W, Ruiz C, Toledo MFZJ, Hassimotto NMA, Machado-Neto JA, Poso A, Cameron MD, Bannister TD, Palmisano G, Wrenger C, Kronenberger T, Parise-Filho R. 1,3-Diphenylureido hydroxamate as a promising scaffold for generation of potent antimalarial histone deacetylase inhibitors. Sci Rep 2023; 13:21006. [PMID: 38030668 PMCID: PMC10687260 DOI: 10.1038/s41598-023-47959-z] [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: 08/17/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
We report a series of 1,3-diphenylureido hydroxamate HDAC inhibitors evaluated against sensitive and drug-resistant P. falciparum strains. Compounds 8a-d show potent antiplasmodial activity, indicating that a phenyl spacer allows improved potency relative to cinnamyl and di-hydrocinnamyl linkers. In vitro, mechanistic studies demonstrated target activity for PfHDAC1 on a recombinant level, which agreed with cell quantification of the acetylated histone levels. Compounds 6c, 7c, and 8c, identified as the most active in phenotypic assays and PfHDAC1 enzymatic inhibition. Compound 8c stands out as a remarkable inhibitor, displaying an impressive 85% inhibition of PfHDAC1, with an IC50 value of 0.74 µM in the phenotypic screening on Pf3D7 and 0.8 µM against multidrug-resistant PfDd2 parasites. Despite its potent inhibition of PfHDAC1, 8c remains the least active on human HDAC1, displaying remarkable selectivity. In silico studies suggest that the phenyl linker has an ideal length in the series for permitting effective interactions of the hydroxamate with PfHDAC1 and that this compound series could bind as well as in HsHDAC1. Taken together, these results highlight the potential of diphenylurea hydroxamates as a privileged scaffold for the generation of potent antimalarial HDAC inhibitors with improved selectivity over human HDACs.
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Affiliation(s)
- Maurício T Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Sun L Rei Yan
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Karoline B Waitman
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Vinícius M Gomes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Daffiny Sumam de Oliveira
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Franciarli Paz
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Sebastian Hilscher
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Mike Schutkowski
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Wolfgang Sippl
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Claudia Ruiz
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Mônica F Z J Toledo
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Neuza M A Hassimotto
- Food Research Center-(FoRC-CEPID) and Department of Food Science and Nutrition, Faculty of Pharmaceutical Science, University of São Paulo, São Paulo, SP, Brazil
| | - João A Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Michael D Cameron
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Thomas D Bannister
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil.
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany.
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil.
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Reers AB, Bautista R, McLellan J, Morales B, Garza R, Bol S, Hanson KK, Bunnik EM. Histone modification analysis reveals common regulators of gene expression in liver and blood stage merozoites of Plasmodium parasites. Epigenetics Chromatin 2023; 16:25. [PMID: 37322481 DOI: 10.1186/s13072-023-00500-y] [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: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
Gene expression in malaria parasites is subject to various layers of regulation, including histone post-translational modifications (PTMs). Gene regulatory mechanisms have been extensively studied during the main developmental stages of Plasmodium parasites inside erythrocytes, from the ring stage following invasion to the schizont stage leading up to egress. However, gene regulation in merozoites that mediate the transition from one host cell to the next is an understudied area of parasite biology. Here, we sought to characterize gene expression and the corresponding histone PTM landscape during this stage of the parasite lifecycle through RNA-seq and ChIP-seq on P. falciparum blood stage schizonts, merozoites, and rings, as well as P. berghei liver stage merozoites. In both hepatic and erythrocytic merozoites, we identified a subset of genes with a unique histone PTM profile characterized by a region of H3K4me3 depletion in their promoter. These genes were upregulated in hepatic and erythrocytic merozoites and rings, had roles in protein export, translation, and host cell remodeling, and shared a DNA motif. These results indicate that similar regulatory mechanisms may underlie merozoite formation in the liver and blood stages. We also observed that H3K4me2 was deposited in gene bodies of gene families encoding variant surface antigens in erythrocytic merozoites, which may facilitate switching of gene expression between different members of these families. Finally, H3K18me and H2K27me were uncoupled from gene expression and were enriched around the centromeres in erythrocytic schizonts and merozoites, suggesting potential roles in the maintenance of chromosomal organization during schizogony. Together, our results demonstrate that extensive changes in gene expression and histone landscape occur during the schizont-to-ring transition to facilitate productive erythrocyte infection. The dynamic remodeling of the transcriptional program in hepatic and erythrocytic merozoites makes this stage attractive as a target for novel anti-malarial drugs that may have activity against both the liver and blood stages.
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Affiliation(s)
- Ashley B Reers
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Rodriel Bautista
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - James McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Beatriz Morales
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Rolando Garza
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sebastiaan Bol
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
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Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression in Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528793. [PMID: 36824754 PMCID: PMC9949051 DOI: 10.1101/2023.02.16.528793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Plasmodium vivax uses Duffy binding protein (PvDBP1) to bind to the Duffy Antigen-Chemokine Receptor (DARC) to invade human erythrocytes. Individuals who lack DARC expression (Duffy-negative) are thought to be resistance to P. vivax. In recent years, P. vivax malaria is becoming more prevalent in Africa with a portion of these cases detected in Duffy-negatives. Apart from DBP1, members of the reticulocyte binding protein (RBP) and tryptophan-rich antigen (TRAg) families may also play a role in erythrocyte invasion. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa and more specifically the expression level of several erythrocyte binding gene candidates as compared to DBP1 are largely unknown. This paper characterized the first P. vivax transcriptome in Africa and compared with those from the Southeast Asian and South American isolates. The expression of 4,404 gene transcripts belong to 12 functional groups including 43 specific erythrocyte binding gene candidates were examined. Overall, there were 10-26% differences in the gene expression profile amongst the geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian P. vivax. Erythrocyte binding genes including PvRBP2a and PvRBP3 expressed six-fold higher than PvDBP1and 60-fold higher than PvEBP/DBP2. Other genes including PvRBP1a, PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression was observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, the standard biomarker for detecting female gametocytes, PvAP2-G (PVP01_1440800), GAP (PVP01_1403000), and Pvs47 (PVP01_1208000) were highly expressed across geographical samples. These findings provide an important baseline for future comparisons of P. vivax transcriptomes from Duffy-negative infections and highlight potential biomarkers for improved gametocyte detection.
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Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, NC 28223, USA
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
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Merrick CJ. Histone lactylation: a new epigenetic axis for host-parasite signalling in malaria? Trends Parasitol 2023; 39:12-16. [PMID: 36357308 DOI: 10.1016/j.pt.2022.10.004] [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: 09/26/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022]
Abstract
Epigenetic modifications play important roles in the biology of malaria parasites. The new epigenetic mark histone lactylation, discovered only recently in humans, is also present in malaria parasites. It may have important functions as a key player in the epigenetic repertoire of Plasmodium.
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Affiliation(s)
- Catherine J Merrick
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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Shrestha S, Lucky AB, Brashear AM, Li X, Cui L, Miao J. Distinct Histone Post-translational Modifications during Plasmodium falciparum Gametocyte Development. J Proteome Res 2022; 21:1857-1867. [PMID: 35772009 PMCID: PMC9738646 DOI: 10.1021/acs.jproteome.2c00108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histones are the building units of nucleosomes, which constitute chromatin. Histone post-translational modifications (PTMs) play an essential role in epigenetic gene regulation. The Plasmodium falciparum genome encodes canonical and variant histones and a collection of conserved enzymes for histone PTMs and chromatin remodeling. Herein, we profiled the P. falciparum histone PTMs during the development of gametocytes, the obligatory stage for parasite transmission. Mass spectrometric analysis of histones extracted from the early, middle, and late stages of gametocytes identified 457 unique histone peptides with 90 PTMs, of which 50% were novel. The gametocyte histone PTMs display distinct patterns from asexual stages, with many new methylation sites in histones H3 and H3.3 (e.g., K14, K18, and K37). Quantitative analyses revealed a high abundance of acetylation in H3 and H4, mono-methylation of H3/H3.3 K37, and ubiquitination of H3BK112, suggesting that these PTMs play critical roles in gametocytes. Gametocyte histones also showed extensive and unique combinations of PTMs. These data indicate that the parasite harbors distinct transcription regulation mechanisms during gametocyte development and lay the foundation for further characterization of epigenetic regulation in the life cycle of the malaria parasite.
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Affiliation(s)
- Sony Shrestha
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Awtum Marie Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States; Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States; Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
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Plasmodium falciparum S-Adenosylmethionine Synthetase Is Essential for Parasite Survival through a Complex Interaction Network with Cytoplasmic and Nuclear Proteins. Microorganisms 2022; 10:microorganisms10071419. [PMID: 35889137 PMCID: PMC9320499 DOI: 10.3390/microorganisms10071419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
S-adenosylmethionine synthetase (SAMS) is a key enzyme for the synthesis of the lone methyl donor S-adenosyl methionine (SAM), which is involved in transmethylation reactions and hence required for cellular processes such as DNA, RNA, and histone methylation, but also polyamine biosynthesis and proteostasis. In the human malaria parasite Plasmodium falciparum, PfSAMS is encoded by a single gene and has been suggested to be crucial for malaria pathogenesis and transmission; however, to date, PfSAMS has not been fully characterized. To gain deeper insight into the function of PfSAMS, we generated a conditional gene knockdown (KD) using the glmS ribozyme system. We show that PfSAMS localizes to the cytoplasm and the nucleus of blood-stage parasites. PfSAMS-KD results in reduced histone methylation and leads to impaired intraerythrocytic growth and gametocyte development. To further determine the interaction network of PfSAMS, we performed a proximity-dependent biotin identification analysis. We identified a complex network of 1114 proteins involved in biological processes such as cell cycle control and DNA replication, or transcription, but also in phosphatidylcholine and polyamine biosynthesis and proteasome regulation. Our findings highlight the diverse roles of PfSAMS during intraerythrocytic growth and sexual stage development and emphasize that PfSAMS is a potential drug target.
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Abstract
In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput “omic” studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action.
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Affiliation(s)
- Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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Sethumadhavan DV, Tiburcio M, Kanyal A, Jabeena CA, Govindaraju G, Karmodiya K, Rajavelu A. Chromodomain Protein Interacts with H3K9me3 and Controls RBC Rosette Formation by Regulating the Expression of a Subset of RIFINs in the Malaria Parasite. J Mol Biol 2022; 434:167601. [PMID: 35460670 DOI: 10.1016/j.jmb.2022.167601] [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: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/17/2022] [Indexed: 11/27/2022]
Abstract
Plasmodium falciparum expresses clonally variant proteins on the surface of infected erythrocytes to evade the host immune system. The clonally variant multigene families include var, rifin, and stevor, which express Erythrocyte Membrane Protein 1 (EMP1), Repetitive Interspersed Families of polypeptides (RIFINs), and Sub-telomeric Variable Open Reading frame (STEVOR) proteins, respectively. The rifins are the largest multigene family and are essentially involved in the RBC rosetting, the hallmark of severe malaria. The molecular regulators that control the RIFINs expression in Plasmodium spp. have not been reported so far. This study reports a chromodomain-containing protein (PfCDP) that binds to H3K9me3 modification on P. falciparum chromatin. Conditional deletion of the chromodomain (CD) gene in P. falciparum using an inducible DiCre-LoxP system leads to selective up-regulation of a subset of virulence genes, including rifins, a few var, and stevor genes. Further, we show that PfCDP conditional knockout (PfΔCDP) promotes RBC rosette formation. This study provides the first evidence of an epigenetic regulator mediated control on a subset of RIFINs expression and RBC rosetting by P. falciparum.
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Affiliation(s)
- Devadathan Valiyamangalath Sethumadhavan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu 600 036, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576 104, India
| | - Marta Tiburcio
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, Maharashtra, India. https://twitter.com/AbhishekKanyal7
| | - C A Jabeena
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu 600 036, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576 104, India
| | - Gayathri Govindaraju
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu 600 036, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka 576 104, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411 008, Maharashtra, India. https://twitter.com/Krishanpal_K
| | - Arumugam Rajavelu
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu 600 036, India; Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram 695 014, Kerala, India.
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Connacher J, von Grüning H, Birkholtz L. Histone Modification Landscapes as a Roadmap for Malaria Parasite Development. Front Cell Dev Biol 2022; 10:848797. [PMID: 35433676 PMCID: PMC9010790 DOI: 10.3389/fcell.2022.848797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum remains the deadliest parasite species in the world, responsible for 229 million cases of human malaria in 2019. The ability of the P. falciparum parasite to progress through multiple life cycle stages and thrive in diverse host and vector species hinges on sophisticated mechanisms of epigenetic regulation of gene expression. Emerging evidence indicates such epigenetic control exists in concentric layers, revolving around core histone post-translational modification (PTM) landscapes. Here, we provide a necessary update of recent epigenome research in malaria parasites, focusing specifically on the ability of dynamic histone PTM landscapes to orchestrate the divergent development and differentiation pathways in P. falciparum parasites. In addition to individual histone PTMs, we discuss recent findings that imply functional importance for combinatorial PTMs in P. falciparum parasites, representing an operational histone code. Finally, this review highlights the remaining gaps and provides strategies to address these to obtain a more thorough understanding of the histone modification landscapes that are at the center of epigenetic regulation in human malaria parasites.
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von Grüning H, Coradin M, Mendoza MR, Reader J, Sidoli S, Garcia BA, Birkholtz LM. A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development. Mol Cell Proteomics 2022; 21:100199. [PMID: 35051657 PMCID: PMC8941266 DOI: 10.1016/j.mcpro.2022.100199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
Histone posttranslational modifications (PTMs) frequently co-occur on the same chromatin domains or even in the same molecule. It is now established that these “histone codes” are the result of cross talk between enzymes that catalyze multiple PTMs with univocal readout as compared with these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 77 PTMs on H3 and H3.3, of which 34 are newly identified in P. falciparum. Coexisting PTMs with unique stage distinctions were identified, indicating that many of these combinatorial PTMs are associated with specific stages of the parasite life cycle. We focused on the code H3R17me2K18acK23ac for its unique presence in mature gametocytes; chromatin proteomics identified a gametocyte-specific SAGA-like effector complex including the transcription factor AP2-G2, which we tied to this specific histone code, as involved in regulating gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with coexisting partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher-order gene regulation for distinct proliferation and differentiation processes. First middle-down chromatin proteomics compendium of the malaria parasite, Plasmodium falciparum. Novel histone PTMs (including arginine methylation) in both asexual parasites and transmissible gametocytes. Histone PTM cross talk is dynamic life cycle stage stratified. Gametocytes rely on histone PTM connectivity to allow onward transmission. AP2-G2 is an important effector of H3K18acK23ac in mature gametocytes.
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Affiliation(s)
- Hilde von Grüning
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariel R Mendoza
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa.
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Miao J, Wang C, Lucky AB, Liang X, Min H, Adapa SR, Jiang R, Kim K, Cui L. A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum. PLoS Pathog 2021; 17:e1009351. [PMID: 34403450 PMCID: PMC8396726 DOI: 10.1371/journal.ppat.1009351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/27/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasite lines with either the bromodomain in PfGCN5 or the PHD domain in PfPHD1 deleted. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific down-regulation of merozoite genes involved in erythrocyte invasion, many of which contain the AP2-LT binding motif and are also regulated by AP2-I and BDP1, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silent and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including an AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist. Epigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. To better understand the epigenetic mechanisms in this parasite, we characterized the histone acetyltransferase GCN5-mediated transcription regulation during intraerythrocytic development of the parasite. Using tandem affinity purification and proteomic characterization, we identified that the PfGCN5-associated complex contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and an AP2-domain transcription factor, which is divergent from the canonical GCN5 complexes evolutionarily conserved from yeast to human. To understand the functions of the PfGCN5 complex, we performed domain deletions in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Consistent with the phenotypes, genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.
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Affiliation(s)
- Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Rays Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
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How much epigenetics and quantitative trait loci (QTL) mapping tell us about parasitism maintenance and resistance/susceptibility to hosts. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166214. [PMID: 34271118 DOI: 10.1016/j.bbadis.2021.166214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/07/2021] [Indexed: 01/20/2023]
Abstract
Interactions between the environment, parasites, vectors, and/or intermediate hosts are complex and involve several factors that define the success or failure of an infection. Among these interactions that can affect infections by a parasite, it is possible to highlight the genetic and epigenetic mechanisms in hosts and parasites. The interaction between genetics, epigenetics, infection, and the host's internal and external environment is decisive and dictates the outcome of a parasitic infection and the resistance, susceptibility, and transmission of this parasite. Epigenetic changes become important mediators in the regulation of gene expression, allowing the evasion of the parasite to immune host barriers, its transmission to new hosts, and the end of its development cycle. Epigenetics is a new frontier in the understanding of the interaction mechanisms between parasite and host that, along with information from the gene regions associated with complex phenotypic variations, the Quantitative Trait Loci, brings new possibilities to investigate more modern and efficient approaches to the treatment, control, and eradication of parasitic diseases. In this brief review, a general overview of the use of epigenetic information and mapping of Quantitative Trait Loci was summarized, both in genes of parasites and hosts, for understanding the mechanisms of resistance and/or susceptibility in parasitic relationships; also, the main search platforms were quantitatively compared, aiming to facilitate access data produced over a period of twenty years.
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Connacher J, Josling GA, Orchard LM, Reader J, Llinás M, Birkholtz LM. H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum. Epigenetics Chromatin 2021; 14:19. [PMID: 33794978 PMCID: PMC8017609 DOI: 10.1186/s13072-021-00393-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program. However, the processes that drive the differentiation and development of the gametocyte post-commitment, remain largely unexplored. A previous study reported enrichment of H3K36 di- and tri-methylated (H3K36me2&3) histones in early-stage gametocytes. Using chromatin immunoprecipitation followed by high-throughput sequencing, we identify a stage-specific association between these repressive histone modifications and transcriptional reprogramming that define a stage II gametocyte transition point. Results Here, we show that H3K36me2 and H3K36me3 from stage II gametocytes are associated with repression of genes involved in asexual proliferation and sexual commitment, indicating that H3K36me2&3-mediated repression of such genes is essential to the transition from early gametocyte differentiation to intermediate development. Importantly, we show that the gene encoding the transcription factor AP2-G as commitment master regulator is enriched with H3K36me2&3 and actively repressed in stage II gametocytes, providing the first evidence of ap2-g gene repression in post-commitment gametocytes. Lastly, we associate the enhanced potency of the pan-selective Jumonji inhibitor JIB-04 in gametocytes with the inhibition of histone demethylation including H3K36me2&3 and a disruption of normal transcriptional programs. Conclusions Taken together, our results provide the first description of an association between global gene expression reprogramming and histone post-translational modifications during P. falciparum early sexual development. The stage II gametocyte-specific abundance of H3K36me2&3 manifests predominantly as an independent regulatory mechanism targeted towards genes that are repressed post-commitment. H3K36me2&3-associated repression of genes is therefore involved in key transcriptional shifts that accompany the transition from early gametocyte differentiation to intermediate development. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00393-9.
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Affiliation(s)
- Jessica Connacher
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Gabrielle A Josling
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lindsey M Orchard
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, 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
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marié 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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Inhibition of PfMYST Histone Acetyltransferase Activity Blocks Plasmodium falciparum Growth and Survival. Antimicrob Agents Chemother 2020; 65:AAC.00953-20. [PMID: 33046499 DOI: 10.1128/aac.00953-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/01/2020] [Indexed: 12/25/2022] Open
Abstract
One of the major barriers in the prevention and control of malaria programs worldwide is the growing emergence of multidrug resistance in Plasmodium parasites, and this necessitates continued efforts to discover and develop effective drug molecules targeting novel proteins essential for parasite survival. In recent years, epigenetic regulators have evolved as an attractive drug target option owing to their crucial role in survival and development of Plasmodium at different stages of its life cycle. PfMYST, a histone acetyltransferase protein, is known to regulate key cellular processes, such as cell cycle progression, DNA damage repair, and antigenic variation, that facilitate parasite growth, adaptation, and survival inside its host. With the aim of assessing the therapeutic potential of PfMYST as a novel drug target, we examined the effect of NU9056 (an HsTIP60 inhibitor) on the rate of parasite growth and survival. In the present study, by using a yeast complementation assay, we established that PfMYST is a true homolog of TIP60 and showed that NU9056 can inhibit PfMYST catalytic activity and kill P. falciparum parasites in culture. Inhibiting the catalytic activity of PfMYST arrests the parasite in the trophozoite stage and inhibits its further transition to the schizont stage, eventually leading to its death. Overall, our study provides proof of concept that PfMYST catalytic activity is essential for parasite growth and survival and that PfMYST can be a potential target for antimalarial therapy.
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Wang C, Gibbons J, Adapa SR, Oberstaller J, Liao X, Zhang M, Adams JH, Jiang RHY. The human malaria parasite genome is configured into thousands of coexpressed linear regulatory units. J Genet Genomics 2020; 47:513-521. [PMID: 33272860 DOI: 10.1016/j.jgg.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/07/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
The human malaria parasite Plasmodium falciparum thrives in radically different host environments in mosquitoes and humans, with only a limited set of transcription factors. The nature of regulatory elements or their target genes in the P. falciparum genome remains elusive. Here, we found that this eukaryotic parasite uses an efficient way to maximally use genetic and epigenetic regulation to form regulatory units (RUs) during blood infections. Genes located in the same RU tend to have the same pattern of expression over time and are associated with open chromatin along regulatory elements. To precisely define and quantify these RUs, a novel hidden Markov model was developed to capture the regulatory structure in a genome-wide fashion by integrating expression and epigenetic evidence. We successfully identified thousands of RUs and cross-validated with previous findings. We found more genes involved in red blood cell (RBC) invasion located in the same RU as the PfAP2-I (AP2-I) transcription factor, demonstrating that AP2-I is responsible for regulating RBC invasion. Our study has provided a regulatory mechanism for a compact eukaryotic genome and offers new insights into the in vivo transcriptional regulation of the P. falciparum intraerythrocytic stage.
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Affiliation(s)
- Chengqi Wang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Justin Gibbons
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Min Zhang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - John H Adams
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Rays H Y Jiang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
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Wang WF, Zhang YL. PfSWIB, a potential chromatin regulator for var gene regulation and parasite development in Plasmodium falciparum. Parasit Vectors 2020; 13:48. [PMID: 32019597 PMCID: PMC7001229 DOI: 10.1186/s13071-020-3918-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/29/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Various transcription factors are involved in the process of mutually exclusive expression and clonal variation of the Plasmodium multigene (var) family. Recent studies revealed that a P. falciparum SWI/SNF-related matrix-associated actin-dependent regulator of chromatin (PfSWIB) might trigger stage-specific programmed cell death (PCD), and was not only crucial for the survival and development of parasite, but also had profound effects on the parasite by interacting with other unknown proteins. However, it remains unclear whether PfSIWB is involved in transcriptional regulation of this virulence gene and its functional properties. METHODS A conditional knockdown system "PfSWIB-FKBP-LID" was introduced to the parasite clone 3D7, and an integrated parasite line "PfSWIB-HA-FKBP-LID" was obtained by drug cycling and clone screening. Growth curve analysis (GCA) was performed to investigate the growth and development of different parasite lines during 96 h in vitro culturing, by assessing parasitemia. Finally, we performed qPCR assays to detect var gene expression profiling in various comparison groups, as well as the mutually exclusive expression pattern of the var genes within a single 48 h life-cycle of P. falciparum in different parasite lines. In addition, RNA-seq was applied to analyze the var gene expression in different lines. RESULTS GCA revealed that conditional knockdown of PfSWIB could interfere with the growth and development of P. falciparum. The parasitemia of PfSWIB∆ showed a significant decline at 96 h during in vitro culture compared with the PfSWIB and 3D7 lines (P < 0.0001). qPCR and RNA-seq analysis confirmed that depletion of PfSWIB not only silences upsA, upsC and partial upsB var genes, as well as removes the silencing of partial upsB var genes at the ring stage in PfSWIB∆ line, but also leads to aberrant expression of upsA and partial upsB/upsC var genes at the mature stage of P. falciparum, during a single 48-h life-cycle. CONCLUSIONS We demonstrated that PfSWIB was involved in the process of clonal variation in var gene expression, and crucial for the survival and development of Plasmodium parasite. These findings could provide better understanding of the mechanism and function of PfSWIB contributing to the pathogenesis in malaria parasites.
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Affiliation(s)
- Wei-Feng Wang
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, China.,Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China
| | - Yi-Long Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Second Military Medical University, Shanghai, 200433, China. .,Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China.
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Nawaz M, Malik I, Hameed M, Hussain Kuthu Z, Zhou J. Modifications of histones in parasites as drug targets. Vet Parasitol 2020; 278:109029. [PMID: 31978703 DOI: 10.1016/j.vetpar.2020.109029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
Post-translational modifications of histones and histone modifying enzymes play important roles in gene regulations and other physiological processes in parasites. Inhibitors of such modifying enzymes could be useful as novel therapeutics against parasitic diseases or as chemical probes for investigation of epigenetics. Development of parasitic histone modulators has got rapid expansion in the last few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Some of these compounds have been widely used in humans targeting cancer and are found non-toxic. This review summarizes the antiparasitic activities of histone and histone modifying enzymes inhibitors evaluated in last few years. As the current chemotherapy against parasites is still not satisfactory, therefore, such compounds represents good starting points for the discovery of effective antiparasitic drugs.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Irfan Malik
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Mudassar Hameed
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zulfiqar Hussain Kuthu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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22
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Nguyen HHT, Yeoh LM, Chisholm SA, Duffy MF. Developments in drug design strategies for bromodomain protein inhibitors to target Plasmodium falciparum parasites. Expert Opin Drug Discov 2019; 15:415-425. [PMID: 31870185 DOI: 10.1080/17460441.2020.1704251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Bromodomains (BRDs) bind to acetylated lysine residues, often on histones. The BRD proteins can contribute to gene regulation either directly through enzymatic activity or indirectly through recruitment of chromatin-modifying complexes or transcription factors. There is no evidence of direct orthologues of the Plasmodium falciparum BRD proteins (PfBDPs) outside the apicomplexans. PfBDPs are expressed during the parasite's life cycle in both the human host's blood and in the mosquito. PfBDPs could also prove to be promising targets for novel antimalarials, which are urgently required to address increasing drug resistance.Areas covered: This review discusses recent studies of the biology of PfBDPs, current target-based strategies for PfBDP inhibitor discovery, and different approaches to the important step of validating the specificity of hit compounds for PfBDPs.Expert opinion: The novelty of Plasmodium BRDs suggests that they could be targeted by selective compounds. Chemical series that showed promise in screens against human BRDs could be leveraged to create targeted compound libraries, as could hits from P. falciparum phenotypic screens. These targeted libraries and hits could be screened in target-based strategies aimed at discovery and optimization of novel inhibitors of PfBDPs. A key task for the field is to generate parasite assays to validate the hit compounds' specificity for PfBDPs.
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Affiliation(s)
- Hanh H T Nguyen
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Lee M Yeoh
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Scott A Chisholm
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Michael F Duffy
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
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23
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Ngwa CJ, Kiesow MJ, Orchard LM, Farrukh A, Llinás M, Pradel G. The G9a Histone Methyltransferase Inhibitor BIX-01294 Modulates Gene Expression during Plasmodium falciparum Gametocyte Development and Transmission. Int J Mol Sci 2019; 20:ijms20205087. [PMID: 31615031 PMCID: PMC6829282 DOI: 10.3390/ijms20205087] [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: 08/29/2019] [Revised: 10/01/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is initiated by specialized sexual cells, the gametocytes. In the human, gametocytes are formed in response to stress signals and following uptake by a blood-feeding Anopheles mosquito initiate sexual reproduction. Gametocytes need to fine-tune their gene expression in order to develop inside the mosquito to continue life-cycle progression. Previously, we showed that post-translational histone acetylation controls gene expression during gametocyte development and transmission. However, the role of histone methylation remains poorly understood. We here use the histone G9a methyltransferase inhibitor BIX-01294 to investigate the role of histone methylation in regulating gene expression in gametocytes. In vitro assays demonstrated that BIX-01294 inhibits intraerythrocytic replication with a half maximal inhibitory concentration (IC50) of 13.0 nM. Furthermore, BIX-01294 significantly impairs gametocyte maturation and reduces the formation of gametes and zygotes. Comparative transcriptomics between BIX-01294-treated and untreated immature, mature and activated gametocytes demonstrated greater than 1.5-fold deregulation of approximately 359 genes. The majority of these genes are transcriptionally downregulated in the activated gametocytes and could be assigned to transcription, translation, and signaling, indicating a contribution of histone methylations in mediating gametogenesis. Our combined data show that inhibitors of histone methylation may serve as a multi-stage antimalarial.
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Affiliation(s)
- Che Julius Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Meike Jutta Kiesow
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Lindsey Marie Orchard
- Department of Biochemistry and Molecular Biology & Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Afia Farrukh
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology & Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
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24
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Jabeena CA, Rajavelu A. Epigenetic Players of Chromatin Structure Regulation in Plasmodium falciparum. Chembiochem 2019; 20:1225-1230. [PMID: 30632244 DOI: 10.1002/cbic.201800718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Indexed: 12/16/2022]
Abstract
The protozoan parasite Plasmodium has evolved to survive in different hosts and environments. The diverse strategies of adaptation to different niches involve differential gene expression mechanisms mediated by chromatin plasticity that are poorly characterized in Plasmodium. The parasite employs a wide variety of regulatory mechanisms to complete their life cycle and survive inside hosts. Among them, epigenetic-mediated mechanisms have been implicated for controlling chromatin organization, gene regulation, morphological differentiation, and antigenic variation. The differential gene expression in parasite is largely dependent on the nature of the chromatin structure. The histone core methylation marks and methyl mark readers contribute to chromatin dynamics. Here, we review the recent developments on various epigenetic marks and its enzymes in the Plasmodium falciparum, how these marks play a key role in the regulation of transcriptional activity of variable genes and coordinate the differential gene expression. We also discuss the possible roles of these epigenetic marks in chromatin structure regulation and plasticity at various stages of its development.
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Affiliation(s)
- C A Jabeena
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Arumugam Rajavelu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India
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25
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Herrera-Solorio AM, Vembar SS, MacPherson CR, Lozano-Amado D, Meza GR, Xoconostle-Cazares B, Martins RM, Chen P, Vargas M, Scherf A, Hernández-Rivas R. Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum. EMBO Rep 2019; 20:embr.201846331. [PMID: 30833341 PMCID: PMC6446197 DOI: 10.15252/embr.201846331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 01/15/2023] Open
Abstract
Post-translational modifications of histone H3 N-terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum Here, we identify proteolytic clipping of the N-terminal tail of nucleosome-associated histone H3 at amino acid position 21 as a new chromatin modification. A cathepsin C-like proteolytic clipping activity is observed in nuclear parasite extracts. Notably, an ectopically expressed version of clipped histone H3, PfH3p-HA, is targeted to the nucleus and integrates into mononucleosomes. Furthermore, chromatin immunoprecipitation and next-generation sequencing analysis identified PfH3p-HA as being highly enriched in the upstream region of six genes that play a key role in DNA replication and repair: In these genes, PfH3p-HA demarcates a specific 1.5 kb chromatin island adjacent to the open reading frame. Our results indicate that, in P. falciparum, the process of histone clipping may precede chromatin integration hinting at preferential targeting of pre-assembled PfH3p-containing nucleosomes to specific genomic regions. The discovery of a protease-directed mode of chromatin organization in P. falciparum opens up new avenues to develop new anti-malarials.
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Affiliation(s)
- Abril Marcela Herrera-Solorio
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Cameron Ross MacPherson
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Daniela Lozano-Amado
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Gabriela Romero Meza
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Beatriz Xoconostle-Cazares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de México, México
| | - Rafael Miyazawa Martins
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Patty Chen
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France .,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
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26
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Kumar A, Dhar SK, Subbarao N. In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1). J Mol Model 2018; 24:232. [PMID: 30109440 DOI: 10.1007/s00894-018-3761-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
In erythrocytes, actively multiplying Plasmodium falciparum parasites exhibit a unique signature of virulence associated histone modifications, thereby epigenetically regulating the expression of the majority of genes. Histone acetylation is one such modification, effectuated and maintained by the dynamic interplay of two functionally antagonist enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). Their inhibition leads to hypo/hyperacetylation and is known to be deleterious for P. falciparum, and hence they have become attractive molecular targets to design novel antimalarials. Many compounds, including four Food and Drug Administration (FDA) approved drugs, have been developed so far to inhibit HDAC activity but are not suitable to treat malaria as they lack selectivity and cause cytotoxicity in mammalian cells. In this study, we used comparative modeling and molecular docking to establish different binding modes of nonselective and selective compounds in the PfHDAC-1 (a class I HDAC protein in P. falciparum) active site and identified the involvement of active site nonidentical residues in binding of selective compounds. Further, we have applied virtual screening with precise selection criteria and molecular dynamics simulation to identify novel potential inhibitors against PfHDAC-1. We report 20 compounds (10 from ChEMBL and 10 from analogues compound library) bearing seven scaffolds having better affinity toward PfHDAC-1. Sixteen of these compounds are known antimalarials with 14 having activity in the nanomolar range against various drug resistant and sensitive strains of P. falciparum. The cytotoxicity of these compounds against various human cell lines are reported at relatively higher concentration and hence can be used as potential PfHDAC-1 inhibitors in P. falciparum. These findings indeed show great potential for using the above molecules as prospective antimalarials.
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Affiliation(s)
- Amarjeet Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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27
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Varoquaux N. Unfolding the Genome: The Case Study of P. falciparum. Int J Biostat 2018; 15:ijb-2017-0061. [PMID: 29878883 DOI: 10.1515/ijb-2017-0061] [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: 08/01/2017] [Accepted: 05/10/2018] [Indexed: 11/15/2022]
Abstract
The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions between pairs of loci in a genome-wide fashion, thus enabling the creation of genome-by-genome contact maps. The spreading of such protocols creates many new opportunities for methodological development: how can we infer 3D models from these contact maps? Can such models help us gain insights into biological processes? Several recent studies applied such protocols to P. falciparum (the deadliest of the five human malaria parasites), assessing its genome organization at different moments of its life cycle. With its small genomic size, fairly simple (yet changing) genomic organization during its lifecyle and strong correlation between chromatin folding and gene expression, this parasite is the ideal case study for applying and developing methods to infer 3D models and use them for downstream analysis. Here, I review a set of methods used to build and analyse three-dimensional models from contact maps data with a special highlight on P. falciparum's genome organization.
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Affiliation(s)
- Nelle Varoquaux
- Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California, USA
- Berkeley Institute for Data Science, 190, Doe libraryBerkeley, United States of America
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28
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Evolution of genome organization and epigenetic machineries. J Biosci 2018. [DOI: 10.1007/s12038-018-9742-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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Kundu TK, Sikder S. Evolution of genome organization and epigenetic machineries. J Biosci 2018; 43:239-242. [PMID: 29872012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur,Bengaluru 560 064, India,
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30
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Kanyal A, Rawat M, Gurung P, Choubey D, Anamika K, Karmodiya K. Genome‐wide survey and phylogenetic analysis of histone acetyltransferases and histone deacetylases of
Plasmodium falciparum. FEBS J 2018; 285:1767-1782. [DOI: 10.1111/febs.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Abhishek Kanyal
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Mukul Rawat
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Pratima Gurung
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | | | | | - Krishanpal Karmodiya
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
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31
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Martins RM, Macpherson CR, Claes A, Scheidig-Benatar C, Sakamoto H, Yam XY, Preiser P, Goel S, Wahlgren M, Sismeiro O, Coppée JY, Scherf A. An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum. Sci Rep 2017; 7:14042. [PMID: 29070841 PMCID: PMC5656681 DOI: 10.1038/s41598-017-12578-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/09/2017] [Indexed: 02/02/2023] Open
Abstract
Variegated surface antigen expression is key to chronic infection and pathogenesis of the human malaria parasite Plasmodium falciparum. This protozoan parasite expresses distinct surface molecules that are encoded by clonally variant gene families such as var, rif and stevor. The molecular mechanisms governing activation of individual members remain ill-defined. To investigate the molecular events of the initial transcriptional activation process we focused on a member of the apicomplexan ApiAP2 transcription factor family predicted to bind to the 5′ upstream regions of the var gene family, AP2-exp (PF3D7_1466400). Viable AP2-exp mutant parasites rely on expressing no less than a short truncated protein including the N-terminal AP2 DNA-binding domain. RNA-seq analysis in mutant parasites revealed transcriptional changes in a subset of exported proteins encoded by clonally variant gene families. Upregulation of RIFINs and STEVORs was validated at the protein levels. In addition, morphological alterations were observed on the surface of the host cells infected by the mutants. This work points to a complex regulatory network of clonally variant gene families in which transcription of a subset of members is regulated by the same transcription factor. In addition, we highlight the importance of the non-DNA binding AP2 domain in functional gene regulation.
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Affiliation(s)
- Rafael M Martins
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, Unit U1201, Paris, 75015, France. .,CNRS 5290/IRD 224/University of Montpellier ("MiVEGEC"), Montpellier, France.
| | - Cameron R Macpherson
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Aurélie Claes
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Christine Scheidig-Benatar
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Hiroshi Sakamoto
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Xue Yan Yam
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Peter Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Suchi Goel
- MTC, Nobels väg 16, KI Solna Campus Karolinska Institutet, Box 280, SE-171 77, Stockholm, Sweden.,Institute of Science Education and Research (IISER), Tirupati Rami Reddy Nagar, 517507, Mangalam, Tirupati Andhra Pradhesh, India
| | - Mats Wahlgren
- MTC, Nobels väg 16, KI Solna Campus Karolinska Institutet, Box 280, SE-171 77, Stockholm, Sweden
| | - Odile Sismeiro
- Plateforme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Jean-Yves Coppée
- Plateforme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, Unit U1201, Paris, 75015, France.
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32
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Gupta AP, Zhu L, Tripathi J, Kucharski M, Patra A, Bozdech Z. Histone 4 lysine 8 acetylation regulates proliferation and host-pathogen interaction in Plasmodium falciparum. Epigenetics Chromatin 2017; 10:40. [PMID: 28830512 PMCID: PMC5568195 DOI: 10.1186/s13072-017-0147-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023] Open
Abstract
Background The dynamics of histone modifications in Plasmodium falciparum indicates the existence of unique mechanisms that link epigenetic factors with transcription. Here, we studied the impact of acetylated histone code on transcriptional regulation during the intraerythrocytic developmental cycle (IDC) of P. falciparum. Results Using a dominant-negative transgenic approach, we showed that acetylations of histone H4 play a direct role in transcription. Specifically, these histone modifications mediate an inverse transcriptional relationship between the factors of cell proliferation and host–parasite interaction. Out of the four H4 acetylations, H4K8ac is likely the rate-limiting, regulatory step, which modulates the overall dynamics of H4 posttranslational modifications. H4K8ac exhibits maximum responsiveness to HDAC inhibitors and has a highly dynamic distribution pattern along the genome of P. falciparum during the IDC. Moreover, H4K8ac functions mainly in the euchromatin where its occupancy shifts from intergenic regions located upstream of 5′ end of open reading frame into the protein coding regions. This shift is directly or indirectly associated with transcriptional activities at the corresponding genes. H4K8ac is also active in the heterochromatin where it stimulates expression of the main antigenic gene family (var) by its presence in the promoter region. Conclusions Overall, we demonstrate that H4K8ac is a potential major regulator of chromatin-linked transcriptional changes during P. falciparum life cycle which is associated not only with euchromatin but also with heterochromatin environment. This is potentially a highly significant finding that suggests a regulatory connection between growth and parasite–host interaction both of which play a major role in malaria parasite virulence. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0147-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Archana P Gupta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Alok Patra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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33
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Ngwa CJ, Kiesow MJ, Papst O, Orchard LM, Filarsky M, Rosinski AN, Voss TS, Llinás M, Pradel G. Transcriptional Profiling Defines Histone Acetylation as a Regulator of Gene Expression during Human-to-Mosquito Transmission of the Malaria Parasite Plasmodium falciparum. Front Cell Infect Microbiol 2017; 7:320. [PMID: 28791254 PMCID: PMC5522858 DOI: 10.3389/fcimb.2017.00320] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022] Open
Abstract
Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is mediated by the intraerythrocytic gametocytes, which, once taken up during a blood meal, become activated to initiate sexual reproduction. Because gametocytes are the only parasite stages able to establish an infection in the mosquito, they are crucial for spreading the tropical disease. During gametocyte maturation, different repertoires of genes are switched on and off in a well-coordinated sequence, pointing to regulatory mechanisms of gene expression. While epigenetic gene control has been studied during erythrocytic schizogony of P. falciparum, little is known about this process during human-to-mosquito transmission of the parasite. To unveil the potential role of histone acetylation during gene expression in gametocytes, we carried out a microarray-based transcriptome analysis on gametocytes treated with the histone deacetylase inhibitor trichostatin A (TSA). TSA-treatment impaired gametocyte maturation and lead to histone hyper-acetylation in these stages. Comparative transcriptomics identified 294 transcripts, which were more than 2-fold up-regulated during gametocytogenesis following TSA-treatment. In activated gametocytes, which were less sensitive to TSA, the transcript levels of 48 genes were increased. TSA-treatment further led to repression of ~145 genes in immature and mature gametocytes and 7 genes in activated gametocytes. Up-regulated genes are mainly associated with functions in invasion, cytoadherence, and protein export, while down-regulated genes could particularly be assigned to transcription and translation. Chromatin immunoprecipitation demonstrated a link between gene activation and histone acetylation for selected genes. Among the genes up-regulated in TSA-treated mature gametocytes was a gene encoding the ring finger (RING)-domain protein PfRNF1, a putative E3 ligase of the ubiquitin-mediated signaling pathway. Immunochemistry demonstrated PfRNF1 expression mainly in the sexual stages of P. falciparum with peak expression in stage II gametocytes, where the protein localized to the nucleus and cytoplasm. Pfrnf1 promoter and coding regions associated with acetylated histones, and TSA-treatment resulted in increased PfRNF1 levels. Our combined data point to an essential role of histone acetylation for gene regulation in gametocytes, which can be exploited for malaria transmission-blocking interventions.
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Affiliation(s)
- Che J Ngwa
- Division of Cellular and Applied Infection Biology, RWTH Aachen UniversityAachen, Germany
| | - Meike J Kiesow
- Division of Cellular and Applied Infection Biology, RWTH Aachen UniversityAachen, Germany
| | - Olga Papst
- Division of Cellular and Applied Infection Biology, RWTH Aachen UniversityAachen, Germany
| | - Lindsey M Orchard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, United States
| | - Michael Filarsky
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteBasel, Switzerland
| | - Alina N Rosinski
- Division of Cellular and Applied Infection Biology, RWTH Aachen UniversityAachen, Germany
| | - Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteBasel, Switzerland
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, United States.,Department of Chemistry and Huck Center for Malaria Research, The Pennsylvania State UniversityUniversity Park, PA, United States
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, RWTH Aachen UniversityAachen, Germany
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Bechtsi D, Waters A. Genomics and epigenetics of sexual commitment in Plasmodium. Int J Parasitol 2017; 47:425-434. [DOI: 10.1016/j.ijpara.2017.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/01/2017] [Accepted: 03/11/2017] [Indexed: 11/27/2022]
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Gupta AP, Bozdech Z. Epigenetic landscapes underlining global patterns of gene expression in the human malaria parasite, Plasmodium falciparum. Int J Parasitol 2017; 47:399-407. [PMID: 28414071 DOI: 10.1016/j.ijpara.2016.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022]
Abstract
The dynamic chromatin landscape displaying combinatorial complexity of the epigenome impacts gene expression that underlies many events of differentiation and cell cycle progression. In the past few years, epigenetic mechanisms have emerged as important processes involved in the tight gene regulation in malaria parasites, Plasmodium spp. Focusing predominantly on Plasmodium falciparum, the species associated with the most severe form of the disease, many advances have been made in our understanding of the interaction between transcriptional regulation and epigenetic mechanisms as the pivotal processes in regulating life cycle progression, host parasite interactions and parasite adaptation to the host environment. This review focuses on the epigenome and its effect on transcriptional regulation in P. falciparum, highlighting its unique, evolutionary diverse features.
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Affiliation(s)
- Archana P Gupta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Sci Rep 2017; 7:607. [PMID: 28377601 PMCID: PMC5428830 DOI: 10.1038/s41598-017-00687-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/08/2017] [Indexed: 01/24/2023] Open
Abstract
Gene expression in Plasmodia integrates post-transcriptional regulation with epigenetic marking of active genomic regions through histone post-translational modifications (PTMs). To generate insights into the importance of histone PTMs to the entire asexual and sexual developmental cycles of the parasite, we used complementary and comparative quantitative chromatin proteomics to identify and functionally characterise histone PTMs in 8 distinct life cycle stages of P. falciparum parasites. ~500 individual histone PTMs were identified of which 106 could be stringently validated. 46 individual histone PTMs and 30 co-existing PTMs were fully quantified with high confidence. Importantly, 15 of these histone PTMs are novel for Plasmodia (e.g. H3K122ac, H3K27me3, H3K56me3). The comparative nature of the data revealed a highly dynamic histone PTM landscape during life cycle development, with a set of histone PTMs (H3K4ac, H3K9me1 and H3K36me2) displaying a unique and conserved abundance profile exclusively during gametocytogenesis (P < 0.001). Euchromatic histone PTMs are abundant during schizogony and late gametocytes; heterochromatic PTMs mark early gametocytes. Collectively, this data provides the most accurate, complete and comparative chromatin proteomic analyses of the entire life cycle development of malaria parasites. A substantial association between histone PTMs and stage-specific transition provides insights into the intricacies characterising Plasmodial developmental biology.
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Chen Z, Li W, Choi G, Yang X, Miao J, Cui L, Guan W. Arbitrarily Accessible 3D Microfluidic Device for Combinatorial High-Throughput Drug Screening. SENSORS 2016; 16:s16101616. [PMID: 27690055 PMCID: PMC5087404 DOI: 10.3390/s16101616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 12/30/2022]
Abstract
Microfluidics-based drug-screening systems have enabled efficient and high-throughput drug screening, but their routine uses in ordinary labs are limited due to the complexity involved in device fabrication and system setup. In this work, we report an easy-to-use and low-cost arbitrarily accessible 3D microfluidic device that can be easily adopted by various labs to perform combinatorial assays for high-throughput drug screening. The device is capable of precisely performing automatic and simultaneous reagent loading and aliquoting tasks and performing multistep assays with arbitrary sequences. The device is not intended to compete with other microfluidic technologies regarding ultra-low reaction volume. Instead, its freedom from tubing or pumping systems and easy operation makes it an ideal platform for routine high-throughput drug screening outside traditional microfluidic labs. The functionality and quantitative reliability of the 3D microfluidic device were demonstrated with a histone acetyltransferase-based drug-screening assay using the recombinant Plasmodium falciparum GCN5 enzyme, benchmarked with a traditional microtiter plate-based method. This arbitrarily accessible, multistep capable, low-cost, and easy-to-use device can be widely adopted in various combinatorial assays beyond high-throughput drug screening.
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Affiliation(s)
- Zhuofa Chen
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Weizhi Li
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Xiaonan Yang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Jun Miao
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.
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Affiliation(s)
- Sebastian Kirchner
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - B Joanne Power
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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Saraf A, Cervantes S, Bunnik EM, Ponts N, Sardiu ME, Chung DWD, Prudhomme J, Varberg JM, Wen Z, Washburn MP, Florens L, Le Roch KG. Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite. J Proteome Res 2016; 15:2787-801. [PMID: 27291344 DOI: 10.1021/acs.jproteome.6b00366] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major obstacle in understanding the complex biology of the malaria parasite remains to discover how gene transcription is controlled during its life cycle. Accumulating evidence indicates that the parasite's epigenetic state plays a fundamental role in gene expression and virulence. Using a comprehensive and quantitative mass spectrometry approach, we determined the global and dynamic abundance of histones and their covalent post-transcriptional modifications throughout the intraerythrocytic developmental cycle of Plasmodium falciparum. We detected a total of 232 distinct modifications, of which 160 had never been detected in Plasmodium and 88 had never been identified in any other species. We further validated over 10% of the detected modifications and their expression patterns by multiple reaction monitoring assays. In addition, we uncovered an unusual chromatin organization with parasite-specific histone modifications and combinatorial dynamics that may be directly related to transcriptional activity, DNA replication, and cell cycle progression. Overall, our data suggest that the malaria parasite has a unique histone modification signature that correlates with parasite virulence.
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Affiliation(s)
- Anita Saraf
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Serena Cervantes
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Nadia Ponts
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Duk-Won D Chung
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Joseph M Varberg
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Zhihui Wen
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center , 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
| | - Laurence Florens
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
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40
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Arnot DE, Jensen ATR. Antigenic Variation and the Genetics and Epigenetics of the PfEMP1 Erythrocyte Surface Antigens in Plasmodium falciparum Malaria. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:77-96. [PMID: 21459194 DOI: 10.1016/b978-0-12-387022-3.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
How immunity to malaria develops remains one of the great unresolved issues in bio-medicine and resolution of its various paradoxes is likely to be the key to developing effective malaria vaccines. The basic epidemiological observations are; under conditions of intense natural transmission, humans do become immune to P. falciparum malaria, but this is a slow process requiring multiple disease episodes which many, particularly young children, do not survive. Adult survivors are immune to the symptoms of malaria, and unless pregnant, can control the growth of most or all new inoculations. Sterile immunity is not achieved and chronic parasitization of apparently healthy adults is the norm. In this article, we analyse the best understood malaria "antigenic variation" system, that based on Plasmodium falciparum's PfEMP1-type cytoadhesion antigens, and critically review recent literature on the function and control of this multi-gene family of parasite variable surface antigens.
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Affiliation(s)
- David E Arnot
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Institute of Immunology and Infection Research, School of Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Cobbold SA, Santos JM, Ochoa A, Perlman DH, Llinás M. Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. Sci Rep 2016; 6:19722. [PMID: 26813983 PMCID: PMC4728587 DOI: 10.1038/srep19722] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/16/2015] [Indexed: 01/18/2023] Open
Abstract
Lysine acetylation is a ubiquitous post-translational modification in many organisms including the malaria parasite Plasmodium falciparum, yet the full extent of acetylation across the parasite proteome remains unresolved. Moreover, the functional significance of acetylation or how specific acetyl-lysine sites are regulated is largely unknown. Here we report a seven-fold expansion of the known parasite ‘acetylome’, characterizing 2,876 acetylation sites on 1,146 proteins. We observe that lysine acetylation targets a diverse range of protein complexes and is particularly enriched within the Apicomplexan AP2 (ApiAP2) DNA-binding protein family. Using quantitative proteomics we determined that artificial perturbation of the acetate/acetyl-CoA balance alters the acetyl-lysine occupancy of several ApiAP2 DNA-binding proteins and related transcriptional proteins. This metabolic signaling could mediate significant downstream transcriptional responses, as we show that acetylation of an ApiAP2 DNA-binding domain ablates its DNA-binding propensity. Lastly, we investigated the acetyl-lysine targets of each class of lysine deacetylase in order to begin to explore how each class of enzyme contributes to regulating the P. falciparum acetylome.
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Affiliation(s)
- Simon A Cobbold
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Joana M Santos
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Biochemistry and Molecular Biology, Department of Chemistry, Center for Malaria Research and Center for Infectious Disease Dynamics, W126 Millennium Science Complex, Pennsylvania State University, State College, PA 16802, USA
| | - Alejandro Ochoa
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Center for Statistics and Machine Learning, Princeton University, Princeton, NJ 08544
| | - David H Perlman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544.,Department of Chemistry Princeton University, Princeton, NJ 08544.,Collaborative Proteomics and Mass Spectrometry Center, Princeton University, Princeton, NJ 08544
| | - Manuel Llinás
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544.,Department of Biochemistry and Molecular Biology, Department of Chemistry, Center for Malaria Research and Center for Infectious Disease Dynamics, W126 Millennium Science Complex, Pennsylvania State University, State College, PA 16802, USA
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Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 2015; 16:454. [PMID: 26070627 PMCID: PMC4465157 DOI: 10.1186/s12864-015-1603-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 11/21/2022] Open
Abstract
Background The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs (lncRNAs) could represent a missing regulatory layer across a broad range of organisms. Results To investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs, six of which we validated experimentally. Conclusions We found that a subset of lncRNAs, including all subtelomeric lncRNAs, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mRNAs, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circRNAs, which is notable given the lack of RNA interference in the organism, and discovered that a highly expressed, five-exon antisense RNA is poised to regulate P. falciparum gametocyte development 1 (PfGDV1), a gene required for early sexual commitment events. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1603-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kate M Broadbent
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA.
| | - Jill C Broadbent
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA. .,Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden.
| | - Dyann Wirth
- Broad Institute, Cambridge, Massachusetts, USA. .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.
| | - John L Rinn
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Pardis C Sabeti
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
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Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. BMC SYSTEMS BIOLOGY 2015; 9 Suppl 4:S1. [PMID: 26100579 PMCID: PMC4474416 DOI: 10.1186/1752-0509-9-s4-s1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627,000 deaths in 2012 alone. During the past decade, new therapeutic targets have been identified and are at various stages of characterization, thanks to the emerging omics-based technologies. However, the mechanism of malaria pathogenesis remains largely unknown. In this paper, we employ a novel neighborhood subnetwork alignment approach to identify network components that are potentially involved in pathogenesis. RESULTS Our module-based subnetwork alignment approach identified 24 functional homologs of pathogenesis-related proteins in the malaria parasite P. falciparum, using the protein-protein interaction networks in Escherichia coli as references. Eighteen out of these 24 proteins are associated with 418 other proteins that are related to DNA replication, transcriptional regulation, translation, signaling, metabolism, cell cycle regulation, as well as cytoadherence and entry to the host. CONCLUSIONS The subnetwork alignments and subsequent protein-protein association network mining predicted a group of malarial proteins that may be involved in parasite development and parasite-host interaction, opening a new systems-level view of parasite pathogenesis and virulence.
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Lapp SA, Mok S, Zhu L, Wu H, Preiser PR, Bozdech Z, Galinski MR. Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures. Malar J 2015; 14:110. [PMID: 25880967 PMCID: PMC4369371 DOI: 10.1186/s12936-015-0612-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/12/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plasmodium knowlesi is one of five Plasmodium species known to cause malaria in humans and can result in severe illness and death. While a zoonosis in humans, this simian malaria parasite species infects macaque monkeys and serves as an experimental model for in vivo, ex vivo and in vitro studies. It has underpinned malaria discoveries relating to host-pathogen interactions, the immune response and immune evasion strategies. This study investigated differences in P. knowlesi gene expression in samples from ex vivo and in vitro cultures. METHODS Gene expression profiles were generated using microarrays to compare the stage-specific transcripts detected for a clone of P. knowlesi propagated in the blood of a rhesus macaque host and then grown in an ex-vivo culture, and the same clone adapted to long-term in vitro culture. Parasite samples covering one blood-stage cycle were analysed at four-hour intervals. cDNA was generated and hybridized to an oligoarray representing the P. knowlesi genome. Two replicate experiments were developed from in vitro cultures. Expression values were filtered, normalized, and analysed using R and Perl language and applied to a sine wave model to determine changes in equilibrium and amplitude. Differentially expressed genes from ex vivo and in vitro time points were detected using limma R/Bioconductor and gene set enrichment analysis (GSEA). RESULTS Major differences were noted between the ex vivo and in vitro time courses in overall gene expression and the length of the cycle (25.5 hours ex vivo; 33.5 hours in vitro). GSEA of genes up-regulated ex vivo showed an enrichment of various genes including SICAvar, ribosomal- associated and histone acetylation pathway genes. In contrast, certain genes involved in metabolism and cell growth, such as porphobilinogen deaminase and tyrosine phosphatase, and one SICAvar gene, were significantly up-regulated in vitro. CONCLUSIONS This study demonstrates how gene expression in P. knowlesi blood-stage parasites can differ dramatically depending on whether the parasites are grown in vivo, with only one cycle of development ex vivo, or as an adapted isolate in long-term in vitro culture. These data bring emphasis to the importance of studying the parasite, its biology and disease manifestations in the context of the host.
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Affiliation(s)
- Stacey A Lapp
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Zybnek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, USA.
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Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays 2014; 37:182-94. [PMID: 25394267 DOI: 10.1002/bies.201400145] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plasmodium falciparum is the most deadly human malarial parasite, responsible for an estimated 207 million cases of disease and 627,000 deaths in 2012. Recent studies reveal that the parasite actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells and that epigenetics plays an important role in this precise gene regulation. Here, we discuss recent advances in our understanding of three aspects of epigenetic regulation in P. falciparum: changes in histone modifications, nucleosome occupancy and the three-dimensional genome structure. We compare these three aspects of the P. falciparum epigenome to those of other eukaryotes, and show that large-scale compartmentalization is particularly important in determining histone decomposition and gene regulation in P. falciparum. We conclude by presenting a gene regulation model for P. falciparum that combines the described epigenetic factors, and by discussing the implications of this model for the future of malaria research.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Rai R, Zhu L, Chen H, Gupta AP, Sze SK, Zheng J, Ruedl C, Bozdech Z, Featherstone M. Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle. BMC Genomics 2014; 15:959. [PMID: 25373614 PMCID: PMC4232647 DOI: 10.1186/1471-2164-15-959] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/23/2014] [Indexed: 01/06/2023] Open
Abstract
Background Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debate has focused on the relative importance of transcriptional versus post-transcriptional processes in the regulation of transcript levels. Enzymatically active forms of RNAPII in other organisms have been associated with phosphorylation on the serines at positions 2 and 5 of the heptad repeats within the C-terminal domain (CTD) of RNAPII. We reasoned that insight into the contribution of transcriptional mechanisms to gene expression in P. falciparum could be obtained by comparing the presence of enzymatically active forms of RNAPII at multiple genes with the abundance of their associated transcripts. Results We exploited the phosphorylation state of the CTD to detect enzymatically active forms of RNAPII at most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide occupancy of RNAPII. Our data reveal that the IDC is divided into early and late phases of RNAPII occupancy evident from simple bi-phasic RNAPII binding profiles. By comparison to mRNA abundance, we identified sub-sets of genes with high occupancy by enzymatically active forms of RNAPII and relatively low transcript levels and vice versa. We further show that the presence of active and repressive histone modifications correlates with RNAPII occupancy over the IDC. Conclusions The simple early/late occupancy by RNAPII cannot account for the complex dynamics of mRNA accumulation over the IDC, suggesting a major role for mechanisms acting downstream of RNAPII occupancy in the control of gene expression in this parasite. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-959) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Bogado SS, Dalmasso MC, Ganuza A, Kim K, Sullivan WJ, Angel SO, Vanagas L. Canonical histone H2Ba and H2A.X dimerize in an opposite genomic localization to H2A.Z/H2B.Z dimers in Toxoplasma gondii. Mol Biochem Parasitol 2014; 197:36-42. [PMID: 25286383 DOI: 10.1016/j.molbiopara.2014.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/22/2014] [Accepted: 09/25/2014] [Indexed: 02/01/2023]
Abstract
Histone H2Ba of Toxoplasma gondii was expressed as recombinant protein (rH2Ba) and used to generate antibody in mouse that is highly specific. Antibody recognizing rH2Ba detects a single band in tachyzoite lysate of the expected molecular weight (12kDa). By indirect immunofluorescence (IFA) in in vitro grown tachyzoites and bradyzoites, the signal was detected only in the parasite nucleus. The nucleosome composition of H2Ba was determined through co-immunoprecipitation assays. H2Ba was detected in the same immunocomplex as H2A.X, but not with H2A.Z. Through chromatin immunoprecipitation (ChIP) assays and qPCR, it was observed that H2Ba is preferentially located at promoters of inactive genes and silent regions, accompanying H2A.X and opposed to H2A.Z/H2B.Z dimers.
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Affiliation(s)
- Silvina S Bogado
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - María C Dalmasso
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina; Scientific Research Commission (CIC, Buenos Aires), Argentina
| | - Kami Kim
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - William J Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sergio O Angel
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, IIB-INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina.
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48
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Russell K, Cheng CH, Bizzaro JW, Ponts N, Emes RD, Le Roch K, Marx KA, Horrocks P. Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites. BMC Genomics 2014; 15:848. [PMID: 25281558 PMCID: PMC4194402 DOI: 10.1186/1471-2164-15-848] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/24/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Homopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions. RESULTS We describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences. CONCLUSIONS Previous comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion.
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Affiliation(s)
- Karen Russell
- />Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, ST5 5BG Staffordshire, UK
| | - Chia-Ho Cheng
- />Center for Intelligent Biomaterials, University of Massachusetts Lowell, Lowell, MA 01854 USA
- />Hebrew SeniorLife, Institute for Aging Research, Boston, MA 02131 USA
| | | | - Nadia Ponts
- />National Institute for Agricultural Research (INRA), UR1264-Mycology and Food Safety (MycSA), CS20032, 33882 Villenave d’Ornon Cedex, France
| | - Richard D Emes
- />School of Veterinary Medicine and Science, University of Nottingham, LE12 5RD Nottingham, Leicestershire, UK
- />Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK
| | - Karine Le Roch
- />Department Cell Biology and Neuroscience, University of California, Riverside, CA 92521 USA
| | - Kenneth A Marx
- />Center for Intelligent Biomaterials, University of Massachusetts Lowell, Lowell, MA 01854 USA
| | - Paul Horrocks
- />Institute for Science and Technology in Medicine, Keele University, Stoke-on-Trent, ST5 5BG Staffordshire, UK
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Subudhi AK, Boopathi PA, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Orekondy HB, Mugasimangalam RC, Sirohi P, Kochar SK, Kochar DK, Das A. Natural antisense transcripts in Plasmodium falciparum isolates from patients with complicated malaria. Exp Parasitol 2014; 141:39-54. [PMID: 24657575 DOI: 10.1016/j.exppara.2014.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 02/17/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how the parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which are best suited for better survival. With the discovery of natural antisense transcripts (NATs) in this parasite and considering the various proposed mechanisms by which NATs might regulate gene expression, it has been speculated that these might be playing a critical role in gene regulation. We report here the diversity of NATs in this parasite, using isolates taken directly from patients with differing clinical symptoms caused by malaria infection. Using a custom designed strand specific whole genome microarray, a total of 797 NATs targeted against annotated loci have been detected. Out of these, 545 NATs are unique to this study. The majority of NATs were positively correlated with the expression pattern of the sense transcript. However, 96 genes showed a change in sense/antisense ratio on comparison between uncomplicated and complicated disease conditions. The antisense transcripts map to a broad range of biochemical/metabolic pathways, especially pathways pertaining to the central carbon metabolism and stress related pathways. Our data strongly suggests that a large group of NATs detected here are unannotated transcription units antisense to annotated gene models. The results reveal a previously unknown set of NATs that prevails in this parasite, their differential regulation in disease conditions and mapping to functionally well annotated genes. The results detailed here call for studies to deduce the possible mechanism of action of NATs, which would further help in understanding the in vivo pathological adaptations of these parasites.
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Affiliation(s)
- Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - P A Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Sheetal Middha
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Jyoti Acharya
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Deepak Pakalapati
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | | | | | | | - Paramendra Sirohi
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Sanjay K Kochar
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Dhanpat K Kochar
- Rajasthan University of Health Sciences, Jaipur, Rajasthan, India.
| | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
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50
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Chen H, Lonardi S, Zheng J. Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput Biol Chem 2014; 50:3-10. [PMID: 24581698 DOI: 10.1016/j.compbiolchem.2014.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
Abstract
Histone modifications play a major role in the regulation of gene expression. Accumulated evidence has shown that histone modifications mediate biological processes such as transcription cooperatively. This has led to the hypothesis of 'histone code' which suggests that combinations of different histone modifications correspond to unique chromatin states and have distinct functions. In this paper, we propose a framework based on association rule mining to discover the potential regulatory relations between histone modifications and gene expression in Plasmodium falciparum. Our approach can output rules with statistical significance. Some of the discovered rules are supported by literature of experimental results. Moreover, we have also discovered de novo rules which can guide further research in epigenetic regulation of transcription. Based on our association rules we build a model to predict gene expression, which outperforms a published Bayesian network model for gene expression prediction by histone modifications. The results of our study reveal mechanisms for histone modifications to regulate transcription in large-scale. Among our findings, the cooperation among histone modifications provides new evidence for the hypothesis of histone code. Furthermore, the rules output by our method can be used to predict the change of gene expression.
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Affiliation(s)
- Haifen Chen
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore.
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| | - Jie Zheng
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Genome Institute of Singapore, A*STAR (Agency for Science, Technology, and Research), Biopolis, Singapore 138672, Singapore.
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