1
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Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum. Biochem Biophys Res Commun 2018; 495:1285-1291. [DOI: 10.1016/j.bbrc.2017.11.131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/19/2017] [Indexed: 01/11/2023]
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2
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Duffy MF, Tang J, Sumardy F, Nguyen HHT, Selvarajah SA, Josling GA, Day KP, Petter M, Brown GV. Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences. FEBS J 2016; 284:237-257. [PMID: 27860263 DOI: 10.1111/febs.13967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/12/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Jingyi Tang
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Hanh H T Nguyen
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Shamista A Selvarajah
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Gabrielle A Josling
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA
| | - Karen P Day
- The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Michaela Petter
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,The School of BioSciences, Bio21, The University of Melbourne, Victoria, Australia
| | - Graham V Brown
- The Nossal Institute for Global Health, The University of Melbourne, Victoria, Australia
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3
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Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum. Microbiol Spectr 2016; 2. [PMID: 26104446 DOI: 10.1128/microbiolspec.mdna3-0022-2014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. These parasites invade and replicate within the circulating red blood cells of infected individuals leading to numerous disease manifestations, including severe anemia, altered circulation, and tissue inflammation. Malaria parasites are also known for their ability to maintain a chronic infection through antigenic variation, the ability to systematically alter the antigens displayed on the surface of infected cells and thereby avoid clearance by the host's antibody response. The genome of P. falciparum includes several large, multicopy gene families that encode highly variable forms of the surface proteins that are the targets of host immunity. Alterations in expression of genes within these families are responsible for antigenic variation. This process requires the continuous generation of new antigenic variants within these gene families, and studies have shown that new variants arise through extensive recombination and gene conversion events between family members. Malaria parasites possess an unusual complement of DNA repair pathways, thus the study of recombination between variant antigen encoding genes provides a unique view into the evolution of mobile DNA in an organism distantly related to the more closely studied model eukaryotes.
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4
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Abstract
Plasmodium falciparum is the protozoan parasite that causes most malaria-associated morbidity and mortality in humans with over 500,000 deaths annually. The disease symptoms are associated with repeated cycles of invasion and asexual multiplication inside red blood cells of the parasite. Partial, non-sterile immunity to P. falciparum malaria develops only after repeated infections and continuous exposure. The successful evasion of the human immune system relies on the large repertoire of antigenically diverse parasite proteins displayed on the red blood cell surface and on the merozoite membrane where they are exposed to the human immune system. Expression switching of these polymorphic proteins between asexual parasite generations provides an efficient mechanism to adapt to the changing environment in the host and to maintain chronic infection. This chapter discusses antigenic diversity and variation in the malaria parasite and our current understanding of the molecular mechanisms that direct the expression of these proteins.
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Affiliation(s)
- Michaela Petter
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
| | - Michael F Duffy
- Department of Medicine Royal Melbourne Hospital, Peter Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, VIC, 3010, Australia.
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5
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Hehl AB, Basso WU, Lippuner C, Ramakrishnan C, Okoniewski M, Walker RA, Grigg ME, Smith NC, Deplazes P. Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes. BMC Genomics 2015; 16:66. [PMID: 25757795 PMCID: PMC4340605 DOI: 10.1186/s12864-015-1225-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background The apicomplexan parasite Toxoplasma gondii is cosmopolitan in nature, largely as a result of its highly flexible life cycle. Felids are its only definitive hosts and a wide range of mammals and birds serve as intermediate hosts. The latent bradyzoite stage is orally infectious in all warm-blooded vertebrates and establishes chronic, transmissible infections. When bradyzoites are ingested by felids, they transform into merozoites in enterocytes and expand asexually as part of their coccidian life cycle. In all other intermediate hosts, however, bradyzoites differentiate exclusively to tachyzoites, and disseminate extraintestinally to many cell types. Both merozoites and tachyzoites undergo rapid asexual population expansion, yet possess different effector fates with respect to the cells and tissues they develop in and the subsequent stages they differentiate into. Results To determine whether merozoites utilize distinct suites of genes to attach, invade, and replicate within feline enterocytes, we performed comparative transcriptional profiling on purified tachyzoites and merozoites. We used high-throughput RNA-Seq to compare the merozoite and tachyzoite transcriptomes. 8323 genes were annotated with sequence reads across the two asexually replicating stages of the parasite life cycle. Metabolism was similar between the two replicating stages. However, significant stage-specific expression differences were measured, with 312 transcripts exclusive to merozoites versus 453 exclusive to tachyzoites. Genes coding for 177 predicted secreted proteins and 64 membrane- associated proteins were annotated as merozoite-specific. The vast majority of known dense-granule (GRA), microneme (MIC), and rhoptry (ROP) genes were not expressed in merozoites. In contrast, a large set of surface proteins (SRS) was expressed exclusively in merozoites. Conclusions The distinct expression profiles of merozoites and tachyzoites reveal significant additional complexity within the T. gondii life cycle, demonstrating that merozoites are distinct asexual dividing stages which are uniquely adapted to their niche and biological purpose. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1225-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrian B Hehl
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland.
| | - Walter U Basso
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland.
| | - Christoph Lippuner
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland. .,Current address: Department of Anaesthesiology and Pain Medicine, Inselspital, University of Bern, Freiburgstrasse, Bern, 3010, Switzerland.
| | - Chandra Ramakrishnan
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland.
| | - Michal Okoniewski
- Functional Genomics Center Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.
| | - Robert A Walker
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland. .,Queensland Tropical Health Alliance Research Laboratory, Faculty of Medicine, Health and Molecular Sciences, James Cook University, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland, USA.
| | - Nicholas C Smith
- Queensland Tropical Health Alliance Research Laboratory, Faculty of Medicine, Health and Molecular Sciences, James Cook University, Cairns Campus, McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Peter Deplazes
- Institute of Parasitology-University of Zurich, Winterthurerstrasse 266a, Zürich, 8057, Switzerland.
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6
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Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A, Rayner JC, Kwiatkowski D. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genet 2014; 10:e1004812. [PMID: 25521112 PMCID: PMC4270465 DOI: 10.1371/journal.pgen.1004812] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/08/2014] [Indexed: 11/25/2022] Open
Abstract
The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel var gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs) were scattered across the genome, structural variants (deletions, duplications, translocations) were focused in and around var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7–72.4%) yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby var gene sequence polymorphism is mainly generated during the asexual part of the life cycle. Malaria kills >600,000 people each year, with most deaths caused by Plasmodium falciparum. A family of proteins known as P. falciparum erythrocyte membrane protein 1, PfEMP1, is expressed on the surface of infected erythrocytes and plays an important role in pathogenesis. Each P. falciparum genome contains approximately 60 highly polymorphic var genes encoding the PfEMP1 proteins, and monoallelic expression with periodic switching results in immune evasion. Var gene polymorphism is thus critical to this survival strategy. We investigated how var gene diversity is generated by performing an in vitro evolution experiment, tracking var gene mutation in ‘real-time’ with whole genome sequencing. We found that genome structural variation is focused in and around var genes. These genetic rearrangements created new ‘chimeric’ var gene sequences during the mitotic part of the life cycle, and were consistent with processes of mitotic non-allelic homologous recombination. The recombinant var genes were always in frame and with conserved overall var gene architecture, and the recombination rate implies that many millions of rearranged var gene sequences are produced every 48-hour life cycle within infected individuals. In conclusion, we provide a detailed description of how new var gene sequences are continuously generated in the parasite genome, helping to explain long-term parasite survival within infected human hosts.
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Affiliation(s)
- Antoine Claessens
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | | | - Mihir Kekre
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Thomas D. Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Adnan Faizullabhoy
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Dominic Kwiatkowski
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
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7
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Brancucci NMB, Witmer K, Schmid C, Voss TS. A var gene upstream element controls protein synthesis at the level of translation initiation in Plasmodium falciparum. PLoS One 2014; 9:e100183. [PMID: 24937593 PMCID: PMC4061111 DOI: 10.1371/journal.pone.0100183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 05/23/2014] [Indexed: 01/14/2023] Open
Abstract
Clonally variant protein expression in the malaria parasite Plasmodium falciparum generates phenotypic variability and allows isogenic populations to adapt to environmental changes encountered during blood stage infection. The underlying regulatory mechanisms are best studied for the major virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 is encoded by the multicopy var gene family and only a single variant is expressed in individual parasites, a concept known as mutual exclusion or singular gene choice. var gene activation occurs in situ and is achieved through the escape of one locus from epigenetic silencing. Singular gene choice is controlled at the level of transcription initiation and var 5' upstream (ups) sequences harbour regulatory information essential for mutually exclusive transcription as well as for the trans-generational inheritance of the var activity profile. An additional level of control has recently been identified for the var2csa gene, where an mRNA element in the 5' untranslated region (5' UTR) is involved in the reversible inhibition of translation of var2csa transcripts. Here, we extend the knowledge on post-transcriptional var gene regulation to the common upsC type. We identified a 5' UTR sequence that inhibits translation of upsC-derived mRNAs. Importantly, this 5' UTR element efficiently inhibits translation even in the context of a heterologous upstream region. Further, we found var 5' UTRs to be significantly enriched in uAUGs which are known to impair the efficiency of protein translation in other eukaryotes. Our findings suggest that regulation at the post-transcriptional level is a common feature in the control of PfEMP1 expression in P. falciparum.
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Affiliation(s)
- Nicolas M. B. Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Kathrin Witmer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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8
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Voss TS, Bozdech Z, Bártfai R. Epigenetic memory takes center stage in the survival strategy of malaria parasites. Curr Opin Microbiol 2014; 20:88-95. [PMID: 24945736 DOI: 10.1016/j.mib.2014.05.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/13/2014] [Indexed: 11/19/2022]
Abstract
Malaria parasites run through a complex life cycle in the vertebrate host and mosquito vector. This not only requires tightly controlled mechanisms to govern stage-specific gene expression but also necessitates effective strategies for survival under changing environmental conditions. In recent years, the combination of different -omics approaches and targeted functional studies highlighted that Plasmodium falciparum blood stage parasites use heterochromatin-based gene silencing as a unifying strategy for clonally variant expression of hundreds of genes. In this article, we describe the epigenetic control mechanisms that mediate alternative expression states of genes involved in antigenic variation, nutrient uptake and sexual conversion and discuss the relevance of this strategy for the survival and transmission of malaria parasites.
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Affiliation(s)
- Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6525 GA, The Netherlands
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9
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Duffy MF, Selvarajah SA, Josling GA, Petter M. Epigenetic regulation of the Plasmodium falciparum genome. Brief Funct Genomics 2013; 13:203-16. [PMID: 24326119 DOI: 10.1093/bfgp/elt047] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent research has highlighted some unique aspects of chromatin biology in the malaria parasite Plasmodium falciparum. During its erythrocytic lifecycle P. falciparum maintains its genome primarily as unstructured euchromatin. Indeed there is no clear role for chromatin-mediated silencing of the majority of the developmentally expressed genes in P. falciparum. However discontinuous stretches of heterochromatin are critical for variegated expression of contingency genes that mediate key pathogenic processes in malaria. These range from invasion of erythrocytes and antigenic variation to solute transport and growth adaptation in response to environmental changes. Despite lack of structure within euchromatin the nucleus maintains functional compartments that regulate expression of many genes at the nuclear periphery, particularly genes with clonally variant expression. The typical components of the chromatin regulatory machinery are present in P. falciparum; however, some of these appear to have evolved novel species-specific functions, e.g. the dynamic regulation of histone variants at virulence gene promoters. The parasite also appears to have repeatedly acquired chromatin regulatory proteins through lateral transfer from endosymbionts and from the host. P. falciparum chromatin regulators have been successfully targeted with multiple drugs in laboratory studies; hopefully their functional divergence from human counterparts will allow the development of parasite-specific inhibitors.
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10
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Moraes CB, Dorval T, Contreras-Dominguez M, Dossin FDM, Hansen MAE, Genovesio A, Freitas-Junior LH. Transcription sites are developmentally regulated during the asexual cycle of Plasmodium falciparum. PLoS One 2013; 8:e55539. [PMID: 23408998 PMCID: PMC3567098 DOI: 10.1371/journal.pone.0055539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 12/29/2012] [Indexed: 11/18/2022] Open
Abstract
Increasing evidence shows that the spatial organization of transcription is an important epigenetic factor in eukaryotic gene regulation. The malaria parasite Plasmodium falciparum shows a remarkably complex pattern of gene expression during the erythrocytic cycle, paradoxically contrasting with the relatively low number of putative transcription factors encoded by its genome. The spatial organization of nuclear subcompartments has been correlated with the regulation of virulence genes. Here, we investigate the nuclear architecture of transcription during the asexual cycle of malaria parasites. As in mammals, transcription is organized into discrete nucleoplasmic sites in P. falciparum, but in a strikingly lower number of foci. An automated analysis of 3D images shows that the number and intensity of transcription sites vary significantly between rings and trophozoites, although the nuclear volume remains constant. Transcription sites are spatially reorganized during the asexual cycle, with a higher proportion of foci located in the outermost nuclear region in rings, whereas in trophozoites, foci are evenly distributed throughout the nucleoplasm. As in higher eukaryotes, transcription sites are predominantly found in areas of low chromatin density. Immunofluorescence analysis shows that transcription sites form an exclusive nuclear compartment, different from the compartments defined by the silenced or active chromatin markers. In conclusion, these data suggest that transcription is spatially contained in discrete foci that are developmentally regulated during the asexual cycle of malaria parasites and located in areas of low chromatin density.
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Affiliation(s)
- Carolina B. Moraes
- Center for Neglected Diseases Drug Discovery (CND3), Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Thierry Dorval
- Cell Differentiation and Toxicity Group, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | | | - Fernando de M. Dossin
- Center for Neglected Diseases Drug Discovery (CND3), Institut Pasteur Korea, Gyeonggi-do, South Korea
| | | | - Auguste Genovesio
- Image Mining Group, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Lucio H. Freitas-Junior
- Center for Neglected Diseases Drug Discovery (CND3), Institut Pasteur Korea, Gyeonggi-do, South Korea
- * E-mail:
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11
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Brancucci NMB, Witmer K, Schmid CD, Flueck C, Voss TS. Identification of a cis-acting DNA-protein interaction implicated in singular var gene choice in Plasmodium falciparum. Cell Microbiol 2012; 14:1836-48. [PMID: 22891919 PMCID: PMC3549481 DOI: 10.1111/cmi.12004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 01/23/2023]
Abstract
Plasmodium falciparum is responsible for the most severe form of malaria in humans. Antigenic variation of P. falciparum erythrocyte membrane protein 1 leads to immune evasion and occurs through switches in mutually exclusive var gene transcription. The recent progress in Plasmodium epigenetics notwithstanding, the mechanisms by which singularity of var activation is achieved are unknown. Here, we employed a functional approach to dissect the role of var gene upstream regions in mutually exclusive activation. Besides identifying sequence elements involved in activation and initiation of transcription, we mapped a region downstream of the transcriptional start site that is required to maintain singular var gene choice. Activation of promoters lacking this sequence occurs no longer in competition with endogenous var genes. Within this region we pinpointed a sequence-specific DNA–protein interaction involving a cis-acting sequence motif that is conserved in the majority of var loci. These results suggest an important role for this interaction in mutually exclusive locus recognition. Our findings are furthermore consistent with a novel mechanism for the control of singular gene choice in eukaryotes. In addition to their importance in P. falciparum antigenic variation, our results may also help to explain similar processes in other systems.
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Affiliation(s)
- Nicolas M B Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
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12
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Religa AA, Waters AP. Sirtuins of parasitic protozoa: in search of function(s). Mol Biochem Parasitol 2012; 185:71-88. [PMID: 22906508 PMCID: PMC3484402 DOI: 10.1016/j.molbiopara.2012.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 01/09/2023]
Abstract
The SIR2 family of NAD+-dependent protein deacetylases, collectively called sirtuins, has been of central interest due to their proposed roles in life-span regulation and ageing. Sirtuins are one group of environment sensors of a cell interpreting external information and orchestrating internal responses at the sub-cellular level, through participation in gene regulation mechanisms. Remarkably conserved across all kingdoms of life SIR2 proteins in several protozoan parasites appear to have both conserved and intriguing unique functions. This review summarises our current knowledge of the members of the sirtuin families in Apicomplexa, including Plasmodium, and other protozoan parasites such as Trypanosoma and Leishmania. The wide diversity of processes regulated by SIR2 proteins makes them targets worthy of exploitation in anti-parasitic therapies.
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Affiliation(s)
- Agnieszka A Religa
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.
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13
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Recker M, Buckee CO, Serazin A, Kyes S, Pinches R, Christodoulou Z, Springer AL, Gupta S, Newbold CI. Antigenic variation in Plasmodium falciparum malaria involves a highly structured switching pattern. PLoS Pathog 2011; 7:e1001306. [PMID: 21408201 PMCID: PMC3048365 DOI: 10.1371/journal.ppat.1001306] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 01/25/2011] [Indexed: 01/03/2023] Open
Abstract
Many pathogenic bacteria, fungi, and protozoa achieve chronic infection through
an immune evasion strategy known as antigenic variation. In the human malaria
parasite Plasmodium falciparum, this involves transcriptional
switching among members of the var gene family, causing
parasites with different antigenic and phenotypic characteristics to appear at
different times within a population. Here we use a genome-wide approach to
explore this process in vitro within a set of cloned parasite
populations. Our analyses reveal a non-random, highly structured switch pathway
where an initially dominant transcript switches via a set of
switch-intermediates either to a new dominant transcript, or back to the
original. We show that this specific pathway can arise through an evolutionary
conflict in which the pathogen has to optimise between safeguarding its limited
antigenic repertoire and remaining capable of establishing infections in
non-naïve individuals. Our results thus demonstrate a crucial role for
structured switching during the early phases of infections and provide a
unifying theory of antigenic variation in P. falciparum malaria
as a balanced process of parasite-intrinsic switching and immune-mediated
selection. The malaria parasite Plasmodium falciparum avoids recognition
and clearance by the immune system by sequentially switching between members of
the var multi-gene family which encode the immunodominant
surface proteins PfEMP1. However, some mechanism must exist to prevent rapid
exposure of the pathogen's entire antigenic repertoire as this would
quickly terminate the infection. It has previously been shown that the immune
system can play an important role in orchestrating the sequential display of
variants once an infection is established; however this does not explain how
repertoire exhaustion is avoided in the initial phases of infection before an
immune response has been established. Here we show that P.
falciparum has evolved a highly structured switching pattern to
prevent repertoire exhaustion in the early stages of infection without
compromising the ability to establish new infections among partially immune
individuals.
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Affiliation(s)
- Mario Recker
- Department of Zoology, University of Oxford,
Oxford, United Kingdom
- * E-mail:
| | - Caroline O. Buckee
- Department of Zoology, University of Oxford,
Oxford, United Kingdom
- Department of Epidemiology, Harvard School of
Public Health, Boston, Massachusetts, United States of America
| | - Andrew Serazin
- Weatherall Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford, United
Kingdom
| | - Sue Kyes
- Weatherall Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford, United
Kingdom
| | - Robert Pinches
- Weatherall Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford, United
Kingdom
| | - Zóe Christodoulou
- Weatherall Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford, United
Kingdom
| | - Amy L. Springer
- Department of Biology, Amherst College,
Amherst, Massachusetts, United States of America
| | - Sunetra Gupta
- Department of Zoology, University of Oxford,
Oxford, United Kingdom
| | - Chris I. Newbold
- Weatherall Institute of Molecular Medicine,
University of Oxford, John Radcliffe Hospital, Oxford, United
Kingdom
- * E-mail:
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14
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Expression of P. falciparum var genes involves exchange of the histone variant H2A.Z at the promoter. PLoS Pathog 2011; 7:e1001292. [PMID: 21379342 PMCID: PMC3040674 DOI: 10.1371/journal.ppat.1001292] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 01/12/2011] [Indexed: 12/31/2022] Open
Abstract
Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes. Plasmodium falciparum is a protist parasite that causes malaria and kills more than 800,000 people per year. The parasite escapes from the human immune response by antigenic variation through switching between expression of different var genes. These encode different variant antigens that are expressed on the surface of the infected erythrocyte and mediate pathogenic adhesion of the infected erythrocytes to host receptors. Understanding how this process is regulated may lead to the identification of factors that are essential for immune evasion and that could represent novel drug targets. Here, we have identified the parasite's histone variant PfH2A.Z as a novel contributor to the transcriptional regulation of antigenic variation. PfH2A.Z is enriched in the promoter of many genes, but enrichment correlates with gene expression only in var genes. Furthermore we show that PfH2A.Z enrichment in var promoters is antagonised by the var gene silencing factor PfSir2A. These findings further extend our knowledge of the complex mechanisms regulating gene expression in P. falciparum.
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15
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Chromatin-mediated epigenetic regulation in the malaria parasite Plasmodium falciparum. EUKARYOTIC CELL 2010; 9:1138-49. [PMID: 20453074 DOI: 10.1128/ec.00036-10] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Malaria is a major public health problem in many developing countries, with the malignant tertian parasite Plasmodium falciparum causing the most malaria-associated mortality. Extensive research, especially with the advancement of genomics and transfection tools, has highlighted the fundamental importance of chromatin-mediated gene regulation in the developmental program of this early-branching eukaryote. The Plasmodium parasite genomes reveal the existence of both canonical and variant histones that make up the nucleosomes, as well as a full collection of conserved enzymes for chromatin remodeling and histone posttranslational modifications (PTMs). Recent studies have identified a wide array of both conserved and novel histone PTMs in P. falciparum, indicating the presence of a complex and divergent "histone code." Genome-wide analysis has begun to decipher the nucleosome landscape and histone modifications associated with the dynamic organization of chromatin structures during the parasite's life cycle. Focused studies on malaria-specific phenomena such as antigenic variation and red cell invasion pathways shed further light on the involvement of epigenetic mechanisms in these processes. Here we review our current understanding of chromatin-mediated gene regulation in malaria parasites, with specific reference to exemplar studies on antigenic variation and host cell invasion.
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16
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Contreras-Dominguez M, Moraes CB, Dorval T, Genovesio A, Dossin FDM, Freitas-Junior LH. A modified fluorescence in situ hybridization protocol for Plasmodium falciparum greatly improves nuclear architecture conservation. Mol Biochem Parasitol 2010; 173:48-52. [PMID: 20433875 DOI: 10.1016/j.molbiopara.2010.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 04/14/2010] [Accepted: 04/19/2010] [Indexed: 12/17/2022]
Abstract
Fluorescence in situ hybridization (FISH) has been used extensively in the study of nuclear organization and gene positioning in Plasmodium falciparum. While performing FISH with published protocols, we observed large variations in parasite nuclear morphology. We hypothesized that these inconsistencies might be due to the type of parasite preparation prior to FISH, which commonly involves air-drying, prompting us to develop a new fixation protocol. Here we show both qualitatively and quantitatively that compared to air-dried and briefly fixed parasites, longer fixation in suspension leads to improved conservation of nuclear structure and lower intra-population variation of nuclear shape as well as area after FISH development. While the fixation protocol per se does not cause detectable disruptions in nuclear morphology, it greatly influences the conservation of nuclear shape and size during the most stringent steps of FISH. The type of fixation used also influences the detection of telomeric clusters, and we show that the new fixation protocol permits improved conservation of the chromosome end cluster perinuclear distribution and higher colocalization indexes for two adjacent chromosome end probes, Rep20 and telomere. Overall, the results indicate that our alternative protocol dramatically improves conservation of the nuclear architecture compared to previously reported Plasmodium DNA-FISH protocols and highlights the necessity of carefully choosing the fixation protocol for FISH.
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Affiliation(s)
- Monica Contreras-Dominguez
- Center for Neglected Diseases Drug Discovery, Institut Pasteur Korea, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea
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17
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Flueck C, Bartfai R, Niederwieser I, Witmer K, Alako BTF, Moes S, Bozdech Z, Jenoe P, Stunnenberg HG, Voss TS. A major role for the Plasmodium falciparum ApiAP2 protein PfSIP2 in chromosome end biology. PLoS Pathog 2010; 6:e1000784. [PMID: 20195509 PMCID: PMC2829057 DOI: 10.1371/journal.ppat.1000784] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 01/20/2010] [Indexed: 12/30/2022] Open
Abstract
The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum. While recent studies assigned important roles for reversible histone modifications, silent information regulator 2 and heterochromatin protein 1 (PfHP1) in epigenetic control of variegated expression, factors involved in the recruitment and organization of subtelomeric heterochromatin remain unknown. Here, we describe the purification and characterization of PfSIP2, a member of the ApiAP2 family of putative transcription factors, as the unknown nuclear factor interacting specifically with cis-acting SPE2 motif arrays in subtelomeric domains. Interestingly, SPE2 is not bound by the full-length protein but rather by a 60kDa N-terminal domain, PfSIP2-N, which is released during schizogony. Our experimental re-definition of the SPE2/PfSIP2-N interaction highlights the strict requirement of both adjacent AP2 domains and a conserved bipartite SPE2 consensus motif for high-affinity binding. Genome-wide in silico mapping identified 777 putative binding sites, 94% of which cluster in heterochromatic domains upstream of subtelomeric var genes and in telomere-associated repeat elements. Immunofluorescence and chromatin immunoprecipitation (ChIP) assays revealed co-localization of PfSIP2-N with PfHP1 at chromosome ends. Genome-wide ChIP demonstrated the exclusive binding of PfSIP2-N to subtelomeric SPE2 landmarks in vivo but not to single chromosome-internal sites. Consistent with this specialized distribution pattern, PfSIP2-N over-expression has no effect on global gene transcription. Hence, contrary to the previously proposed role for this factor in gene activation, our results provide strong evidence for the first time for the involvement of an ApiAP2 factor in heterochromatin formation and genome integrity. These findings are highly relevant for our understanding of chromosome end biology and variegated expression in P. falciparum and other eukaryotes, and for the future analysis of the role of ApiAP2-DNA interactions in parasite biology.
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Affiliation(s)
- Christian Flueck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Richard Bartfai
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Kathrin Witmer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Blaise T. F. Alako
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Suzette Moes
- Biozentrum, University of Basel, Basel, Switzerland
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Paul Jenoe
- Biozentrum, University of Basel, Basel, Switzerland
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
- * E-mail:
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18
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Mackinnon MJ, Li J, Mok S, Kortok MM, Marsh K, Preiser PR, Bozdech Z. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 2009; 5:e1000644. [PMID: 19898609 PMCID: PMC2764095 DOI: 10.1371/journal.ppat.1000644] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted field isolates of Plasmodium falciparum, the species responsible for most malarial disease. It was found that genes coding for parasite protein export into the red cell cytosol and onto its surface, and genes coding for sexual stage proteins involved in parasite transmission are up-regulated in field isolates compared with long-term laboratory isolates. Much of this variability was associated with the loss of small or large chromosomal segments, or other forms of gene copy number variation that are prevalent in the P. falciparum genome (copy number variants, CNVs). Expression levels of genes inside these segments were correlated to that of genes outside and adjacent to the segment boundaries, and this association declined with distance from the CNV boundary. This observation could not be explained by copy number variation in these adjacent genes. This suggests a local-acting regulatory role for CNVs in transcription of neighboring genes and helps explain the chromosomal clustering that we observed here. Transcriptional co-regulation of physical clusters of adaptive genes may provide a way for the parasite to readily adapt to its highly heterogeneous and strongly selective environment.
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19
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Brolin KJM, Ribacke U, Nilsson S, Ankarklev J, Moll K, Wahlgren M, Chen Q. Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites. Genome Biol 2009; 10:R117. [PMID: 19849836 PMCID: PMC2784332 DOI: 10.1186/gb-2009-10-10-r117] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 08/22/2009] [Accepted: 10/22/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms are common in duplicated genes, causing functional preservation, alteration or silencing. The Plasmodium falciparum genes var2csa and Pf332 are duplicated in the haploid genome of the HB3 parasite line. Whereas the molecular function of Pf332 remains to be elucidated, VAR2CSA is known to be the main adhesin in placental parasite sequestration. Sequence variations introduced upon duplication of these genes provide discriminative possibilities to analyze allele-specific transcription with a bearing towards understanding gene dosage impact on parasite biology. RESULTS We demonstrate an approach combining real-time PCR allelic discrimination and discriminative RNA-FISH to distinguish between highly similar gene copies in P. falciparum parasites. The duplicated var2csa variants are simultaneously transcribed, both on a population level and intriguingly also in individual cells, with nuclear co-localization of the active genes and corresponding transcripts. This indicates transcriptional functionality of duplicated genes, challenges the dogma of mutually exclusive var gene transcription and suggests mechanisms behind antigenic variation, at least in respect to the duplicated and highly similar var2csa genes. CONCLUSIONS Allelic discrimination assays have traditionally been applied to study zygosity in diploid genomes. The assays presented here are instead successfully applied to the identification and evaluation of transcriptional activity of duplicated genes in the haploid genome of the P. falciparum parasite. Allelic discrimination and gene or transcript localization by FISH not only provide insights into transcriptional regulation of genes such as the virulence associated var genes, but also suggest that this sensitive and precise approach could be used for further investigation of genome dynamics and gene regulation.
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Affiliation(s)
- Kim JM Brolin
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
| | - Sandra Nilsson
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
| | - Johan Ankarklev
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-751 21 Uppsala, Sweden
| | - Kirsten Moll
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
| | - Qijun Chen
- Department of Microbiology, Tumor and Cell Biology, Nobels Väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Swedish Institute for Infectious Disease Control, Nobels Väg 18, SE-171 82, Stockholm, Sweden
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, China
- Laboratory of Parasitology, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Dong Dan San Tiao 9, Beijing 100730, China
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20
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Flueck C, Bartfai R, Volz J, Niederwieser I, Salcedo-Amaya AM, Alako BTF, Ehlgen F, Ralph SA, Cowman AF, Bozdech Z, Stunnenberg HG, Voss TS. Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS Pathog 2009; 5:e1000569. [PMID: 19730695 PMCID: PMC2731224 DOI: 10.1371/journal.ppat.1000569] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 08/07/2009] [Indexed: 02/01/2023] Open
Abstract
Epigenetic processes are the main conductors of phenotypic variation in eukaryotes. The malaria parasite Plasmodium falciparum employs antigenic variation of the major surface antigen PfEMP1, encoded by 60 var genes, to evade acquired immune responses. Antigenic variation of PfEMP1 occurs through in situ switches in mono-allelic var gene transcription, which is PfSIR2-dependent and associated with the presence of repressive H3K9me3 marks at silenced loci. Here, we show that P. falciparum heterochromatin protein 1 (PfHP1) binds specifically to H3K9me3 but not to other repressive histone methyl marks. Based on nuclear fractionation and detailed immuno-localization assays, PfHP1 constitutes a major component of heterochromatin in perinuclear chromosome end clusters. High-resolution genome-wide chromatin immuno-precipitation demonstrates the striking association of PfHP1 with virulence gene arrays in subtelomeric and chromosome-internal islands and a high correlation with previously mapped H3K9me3 marks. These include not only var genes, but also the majority of P. falciparum lineage-specific gene families coding for exported proteins involved in host-parasite interactions. In addition, we identified a number of PfHP1-bound genes that were not enriched in H3K9me3, many of which code for proteins expressed during invasion or at different life cycle stages. Interestingly, PfHP1 is absent from centromeric regions, implying important differences in centromere biology between P. falciparum and its human host. Over-expression of PfHP1 results in an enhancement of variegated expression and highlights the presence of well-defined heterochromatic boundaries. In summary, we identify PfHP1 as a major effector of virulence gene silencing and phenotypic variation. Our results are instrumental for our understanding of this widely used survival strategy in unicellular pathogens.
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Affiliation(s)
- Christian Flueck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
| | - Richard Bartfai
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jennifer Volz
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
| | - Adriana M. Salcedo-Amaya
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Blaise T. F. Alako
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Florian Ehlgen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Stuart A. Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Alan F. Cowman
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
- * E-mail:
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21
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Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, da Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol 2009; 7:e84. [PMID: 19402747 PMCID: PMC2672602 DOI: 10.1371/journal.pbio.1000084] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/02/2009] [Indexed: 11/19/2022] Open
Abstract
Cytoadherance of Plasmodium falciparum-infected erythrocytes in the brain, organs and peripheral microvasculature is linked to morbidity and mortality associated with severe malaria. Parasite-derived P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) molecules displayed on the erythrocyte surface are responsible for cytoadherance and undergo antigenic variation in the course of an infection. Antigenic variation of PfEMP1 is achieved by in situ switching and mutually exclusive transcription of the var gene family, a process that is controlled by epigenetic mechanisms. Here we report characterisation of the P. falciparum silent information regulator's A and B (PfSir2A and PfSir2B) and their involvement in mutual exclusion and silencing of the var gene repertoire. Analysis of P. falciparum parasites lacking either PfSir2A or PfSir2B shows that these NAD+-dependent histone deacetylases are required for silencing of different var gene subsets classified by their conserved promoter type. We also demonstrate that in the absence of either of these molecules mutually exclusive expression of var genes breaks down. We show that var gene silencing originates within the promoter and PfSir2 paralogues are involved in cis spreading of silenced chromatin into adjacent regions. Furthermore, parasites lacking PfSir2A but not PfSir2B have considerably longer telomeric repeats, demonstrating a role for this molecule in telomeric end protection. This work highlights the pivotal but distinct role for both PfSir2 paralogues in epigenetic silencing of P. falciparum virulence genes and the control of pathogenicity of malaria infection. The unicellular parasite Plasmodium falciparum is the cause of the most severe form of malaria and is responsible for 300 million infections and ∼2 million deaths a year. Infected erythrocytes clump and block capillaries in the peripheral circulation, the brain, and placenta and are a major contributor to the pathology of malaria. A parasite-derived protein displayed on the surface of the infected erythrocyte is responsible for erythrocyte clumping in capillaries. Although 60 subtelomeric var genes can encode different versions of this “sticky” capillary-binding protein, only one protein is expressed at a time, and switches in expression between these genes causes variation of this pathogenic molecule enabling the parasite to evade the immune system. Here we identify two chromatin-modifying proteins that cooperate to mediate silencing and mutual exclusive expression of var genes. These proteins are thus important virulence factors of the malaria-causing parasite. Investigation into two Sir2 histone deacetylases in the malaria-causing parasite revealstrans-acting epigenetic factors control mutually exclusive expression of a major subtelomeric virulence gene family.
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Affiliation(s)
| | - Céline K Carret
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Manoj T Duraisingh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Till S Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Stuart A Ralph
- Department of Biochemistry, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Mirja Hommel
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Michael F Duffy
- Department of Medicine RMH/WH, The University of Melbourne, Melbourne, Australia
| | | | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur and CNRS, Paris, France
| | - Alasdair Ivens
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Terence P Speed
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - James G Beeson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- * To whom correspondence should be addressed. E-mail:
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22
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Florent I, Porcel BM, Guillaume E, Da Silva C, Artiguenave F, Maréchal E, Bréhélin L, Gascuel O, Charneau S, Wincker P, Grellier P. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. BMC Genomics 2009; 10:235. [PMID: 19454033 PMCID: PMC2695484 DOI: 10.1186/1471-2164-10-235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 05/19/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting P. falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. RESULTS A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9). CONCLUSION This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of P. falciparum ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the P. falciparum gene structure, polymorphism and expression.
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Affiliation(s)
- Isabelle Florent
- FRE3206 CNRS/MNHN, USM504, Biologie Fonctionnelle des Protozoaires, RDDM, Muséum National d'Histoire Naturelle, Paris, France.
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23
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Duffy MF, Byrne TJ, Carret C, Ivens A, Brown GV. Ectopic recombination of a malaria var gene during mitosis associated with an altered var switch rate. J Mol Biol 2009; 389:453-69. [PMID: 19389407 PMCID: PMC3898907 DOI: 10.1016/j.jmb.2009.04.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 04/14/2009] [Accepted: 04/16/2009] [Indexed: 01/27/2023]
Abstract
The Plasmodium falciparum var multigene family encodes P. falciparum erythrocyte membrane protein 1, which is responsible for the pathogenic traits of antigenic variation and adhesion of infected erythrocytes to host receptors during malaria infection. Clonal antigenic variation of P. falciparum erythrocyte membrane protein 1 is controlled by the switching between exclusively transcribed var genes. The tremendous diversity of the var gene repertoire both within and between parasite strains is critical for the parasite's strategy of immune evasion. We show that ectopic recombination between var genes occurs during mitosis, providing P. falciparum with opportunities to diversify its var repertoire, even during the course of a single infection. We show that the regulation of the recombined var gene has been disrupted, resulting in its persistent activation although the regulation of most other var genes is unaffected. The var promoter and intron of the recombined var gene are not responsible for its atypically persistent activity, and we conclude that altered subtelomeric cis sequence is the most likely cause of the persistent activity of the recombined var gene.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine at RMH, University of Melbourne, Parkville 3050, Australia.
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24
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Lopez-Rubio JJ, Mancio-Silva L, Scherf A. Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites. Cell Host Microbe 2009; 5:179-90. [PMID: 19218088 DOI: 10.1016/j.chom.2008.12.012] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 12/05/2008] [Accepted: 12/31/2008] [Indexed: 10/21/2022]
Abstract
Clonally variant gene families underlie phenotypic plasticity in Plasmodium falciparum, a process indispensable for survival of the pathogen in its human host. Differential transcription of one of these gene families in clonal parasite lineages has been associated with chromatin modifications. Here, we determine the genome-wide distribution in P. falciparum of a histone mark of heterochromatin, trimethylation of histone H3 lysine 9 (H3K9me3), using high-resolution ChIP-chip analysis. We show that H3K9me3 is specifically associated with clonally variant gene families, which are clustered on subtelomeric and some chromosome internal regions. High levels of H3K9me3 correlate with genes localized to the nuclear periphery, implying chromosome loop formation. Disruption of the histone deacetylase PfSir2 causes changes in H3K9me3 that are discontinuous along chromosomes and associated with disrupted monoallelic transcription. Our data point to the existence of perinuclear repressive centers associated with control of expression of malaria parasite genes involved in phenotypic variation and pathogenesis.
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Affiliation(s)
- Jose-Juan Lopez-Rubio
- Unité de Biologie des Interactions Hôte-Parasite, CNRS URA2581, Institut Pasteur, Paris, France
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Mancio-Silva L, Rojas-Meza AP, Vargas M, Scherf A, Hernandez-Rivas R. Differential association of Orc1 and Sir2 proteins to telomeric domains in Plasmodium falciparum. J Cell Sci 2009; 121:2046-53. [PMID: 18525026 DOI: 10.1242/jcs.026427] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Telomeres have the capacity to recruit proteins that facilitate the spreading of heterochromatin into subtelomeric DNA regions. In the human protozoan pathogen Plasmodium falciparum, the telomere-associated protein Sir2 has been shown to control the silencing of members of virulence genes at some, but not all, chromosome-end loci, indicating that additional proteins are involved in telomere position effect. Here, we identified, in P. falciparum, a novel telomere-associated protein that displays homology with the origin-of-recognition-complex 1 protein Orc1. Antibodies raised against this P. falciparum protein localized to telomeric clusters in the nuclear periphery and the nucleolus. It was found that, prior to DNA replication, P. falciparum Orc1 and Sir2 undergo drastic subcellular reorganization, such as dissociation from the telomere cluster and spreading into the nucleus and parasite cytoplasm. Relocation of Orc1 and Sir2 was also linked to the partial dissociation of telomere clusters. Super gel-shift and chromatin-immunoprecipitation experiments showed the physical association of Orc1 with telomere repeats but revealed a differential association with adjacent non-coding repeat DNA elements. Our data suggest that Plasmodium telomeres might fold back and that Orc1 cooperates with Sir2 in telomeric silencing.
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Affiliation(s)
- Liliana Mancio-Silva
- Unité de Biologie des Interactions Hôte-Parasite, CNRS URA 2581, Institut Pasteur, Paris, France
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Abstract
The persistence of the human malaria parasite Plasmodium falciparum during blood stage proliferation in its host depends on the successive expression of variant molecules at the surface of infected erythrocytes. This variation is mediated by the differential control of a family of surface molecules termed PfEMP1 encoded by approximately 60 var genes. Each individual parasite expresses a single var gene at a time, maintaining all other members of the family in a transcriptionally silent state. PfEMP1/var enables parasitized erythrocytes to adhere within the microvasculature, resulting in severe disease. This review highlights key regulatory mechanisms thought to be critical for monoallelic expression of var genes. Antigenic variation is orchestrated by epigenetic factors including monoallelic var transcription at separate spatial domains at the nuclear periphery, differential histone marks on otherwise identical var genes, and var silencing mediated by telomeric heterochromatin. In addition, controversies surrounding var genetic elements in antigenic variation are discussed.
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Affiliation(s)
- Artur Scherf
- Biology of Host-Parasite Interactions Unit, CNRS URA2581, Institut Pasteur 75724 Paris, France.
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Chookajorn T, Ponsuwanna P, Cui L. Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation. Trends Parasitol 2008; 24:455-61. [PMID: 18771955 DOI: 10.1016/j.pt.2008.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 02/05/2023]
Abstract
As a major factor in Plasmodium falciparum malaria pathogenesis, the var gene family has been the focus of extensive research, which has contributed to our current understanding of Plasmodium antigenic variation. In recent years, sophisticated molecular tools have enabled the generation of interesting data regarding the regulation of mutually exclusive var expression. Although their results are still inconclusive, these studies have demonstrated the existence of multiple layers of control over gene activation, silencing, memory and 'counting'. This review attempts to summarize recent findings and dissect the different layers of var regulation.
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Affiliation(s)
- Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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Dossin FDM, Dufour A, Dusch E, Siqueira-Neto JL, Moraes CB, Yang GS, Cano MI, Genovesio A, Freitas-Junior LH. Automated nuclear analysis of Leishmania major telomeric clusters reveals changes in their organization during the parasite's life cycle. PLoS One 2008; 3:e2313. [PMID: 18545650 PMCID: PMC2396463 DOI: 10.1371/journal.pone.0002313] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Accepted: 04/20/2008] [Indexed: 12/16/2022] Open
Abstract
Parasite virulence genes are usually associated with telomeres. The clustering of the telomeres, together with their particular spatial distribution in the nucleus of human parasites such as Plasmodium falciparum and Trypanosoma brucei, has been suggested to play a role in facilitating ectopic recombination and in the emergence of new antigenic variants. Leishmania parasites, as well as other trypanosomes, have unusual gene expression characteristics, such as polycistronic and constitutive transcription of protein-coding genes. Leishmania subtelomeric regions are even more unique because unlike these regions in other trypanosomes they are devoid of virulence genes. Given these peculiarities of Leishmania, we sought to investigate how telomeres are organized in the nucleus of Leishmania major parasites at both the human and insect stages of their life cycle. We developed a new automated and precise method for identifying telomere position in the three-dimensional space of the nucleus, and we found that the telomeres are organized in clusters present in similar numbers in both the human and insect stages. While the number of clusters remained the same, their distribution differed between the two stages. The telomeric clusters were found more concentrated near the center of the nucleus in the human stage than in the insect stage suggesting reorganization during the parasite's differentiation process between the two hosts. These data provide the first 3D analysis of Leishmania telomere organization. The possible biological implications of these findings are discussed.
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Affiliation(s)
| | | | - Elodie Dusch
- Image Mining Group, Institut Pasteur Korea, Seoul, South Korea
| | | | - Carolina B. Moraes
- Systems Biology of Pathogens Group, Institut Pasteur Korea, Seoul, South Korea
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gyong Seon Yang
- Systems Biology of Pathogens Group, Institut Pasteur Korea, Seoul, South Korea
| | - Maria Isabel Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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29
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Paeschke K, Juranek S, Rhodes D, Lipps HJ. Cell cycle-dependent regulation of telomere tethering in the nucleus. Chromosome Res 2008; 16:721-8. [DOI: 10.1007/s10577-008-1222-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 03/24/2008] [Accepted: 03/24/2008] [Indexed: 10/22/2022]
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Frank M, Kirkman L, Costantini D, Sanyal S, Lavazec C, Templeton TJ, Deitsch KW. Frequent recombination events generate diversity within the multi-copy variant antigen gene families of Plasmodium falciparum. Int J Parasitol 2008; 38:1099-109. [PMID: 18395207 DOI: 10.1016/j.ijpara.2008.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Revised: 01/17/2008] [Accepted: 01/24/2008] [Indexed: 11/25/2022]
Abstract
The human malaria parasite Plasmodium falciparum utilises a mechanism of antigenic variation to avoid the antibody response of its human host and thereby generates a long-term, persistent infection. This process predominantly results from systematic changes in expression of the primary erythrocyte surface antigen, a parasite-produced protein called PfEMP1 that is encoded by a repertoire of over 60 var genes in the P. falciparum genome. var genes exhibit extensive sequence diversity, both within a single parasite's genome as well as between different parasite isolates, and thus provide a large repertoire of antigenic determinants to be alternately displayed over the course of an infection. Whilst significant work has recently been published documenting the extreme level of diversity displayed by var genes found in natural parasite populations, little work has been done regarding the mechanisms that lead to sequence diversification and heterogeneity within var genes. In the course of producing transgenic lines from the original NF54 parasite isolate, we cloned and characterised a parasite line, termed E5, which is closely related to but distinct from 3D7, the parasite used for the P. falciparum genome nucleotide sequencing project. Analysis of the E5 var gene repertoire, as well as that of the surrounding rif and stevor multi-copy gene families, identified examples of frequent recombination events within these gene families, including an example of a duplicative transposition which indicates that recombination events play a significant role in the generation of diversity within the antigen encoding genes of P. falciparum.
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Affiliation(s)
- Matthias Frank
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, Box 62, New York, NY 10021, USA
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31
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Li F, Sonbuchner L, Kyes SA, Epp C, Deitsch KW. Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin. J Biol Chem 2007; 283:5692-8. [PMID: 18165241 DOI: 10.1074/jbc.m707344200] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play an important role in a variety of nuclear processes, including genetic imprinting, RNA interference-mediated transcriptional repression, and dosage compensation. These transcripts are thought to influence chromosome organization and, in some cases, gene expression by directing the assembly of specific chromatin modifications to targeted regions of the genome. In the malaria parasite Plasmodium falciparum, little is known about the regulation of nuclear organization or gene expression, although a notable scarcity of identifiable transcription factors encoded in its genome has led to speculation that this organism may be unusually reliant on chromatin modifications as a mechanism for regulating gene expression. To study the mechanisms that regulate chromatin structure in malaria parasites, we examined the role of ncRNAs in the assembly of chromatin at the centromeres of P. falciparum. We show that centromeric regions within the Plasmodium genome contain bidirectional promoter activity driving the expression of short ncRNAs that are localized within the nucleus and appear to associate with the centromeres themselves, strongly suggesting that they are central characters in the maintenance and function of centromeric chromatin. These observations support the hypothesis that ncRNAs play an important role in the proper organizational assembly of chromatin in P. falciparum, perhaps compensating for a lack of both regulatory transcription factors and RNA interference machinery.
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Affiliation(s)
- Felomena Li
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10021, USA
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32
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Abstract
Epigenetic phenomena have been shown to play a role in the regulated expression of virulence genes in several pathogenic organisms, including the var gene family in Plasmodium falciparum. A better understanding of how P. falciparum can both maintain a single active var gene locus through many erythrocytic cycles and also achieve successive switching to different loci in order to evade the host immune system is greatly needed. Disruption of this tightly co-ordinated expression system presents an opportunity for increased clearance of the parasites by the immune system and, in turn, reduced mortality and morbidity. In the current issue of Molecular Microbiology, Lopez-Rubio and colleagues investigate the correlation of specific post-translational histone modifications with different transcriptional states of a single var gene, var2csa. Quantitative chromatin immunoprecipitation is used to demonstrate that different histone methylation marks are enriched at the 5' flanking and coding regions of active, poised or silenced var genes. They identify an increase of H3K4me2 and H3K4me3 in the 5' flanking region of an active var locus and expand on an earlier finding that H3K9me3 is enriched in the coding regions of silenced var genes. The authors also present evidence that H3K4me2 bookmarks the active var gene locus during later developmental stages for expression in the subsequent asexual cycle, hinting at a potential mechanism for transcriptional 'memory'. The stage is now set for work generating a complete catalogue of all histone modifications associated with var gene regulation as well as functional studies striving to uncover the precise mechanisms underlying these observations.
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Affiliation(s)
- Christy A Comeaux
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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Voss TS, Tonkin CJ, Marty AJ, Thompson JK, Healer J, Crabb BS, Cowman AF. Alterations in local chromatin environment are involved in silencing and activation of subtelomeric var genes in Plasmodium falciparum. Mol Microbiol 2007; 66:139-50. [PMID: 17725559 PMCID: PMC2169929 DOI: 10.1111/j.1365-2958.2007.05899.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the var gene family, undergoes antigenic variation and plays an important role in chronic infection and severe malaria. Only a single var gene is transcribed per parasite, and epigenetic control mechanisms are fundamental in this strategy of mutually exclusive transcription. We show that subtelomeric upsB var gene promoters carried on episomes are silenced by default, and that promoter activation is sufficient to silence all other family members. However, they are active by default when placed downstream of a second active var promoter, underscoring the significance of local chromatin environment and nuclear compartmentalization in var promoter regulation. Native chromatin covering the SPE2-repeat array in upsB promoters is resistant to nuclease digestion, and insertion of these regulatory elements into a heterologous promoter causes local alterations in nucleosomal organization and promoter repression. Our findings suggest a common logic underlying the transcriptional control of all var genes, and have important implications for our understanding of the epigenetic processes involved in the regulation of this major virulence gene family.
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Affiliation(s)
- Till S Voss
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
| | - Christopher J Tonkin
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
| | - Allison J Marty
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
- Department of Microbiology, Monash UniversityClayton 3800, Australia
| | - Jennifer K Thompson
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
| | - Julie Healer
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
| | - Brendan S Crabb
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
| | - Alan F Cowman
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical ResearchParkville 3050, Australia
- E-mail ; Tel. (+61) 3 9345 2555; Fax (+61) 3 9347 0852
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Kyes SA, Kraemer SM, Smith JD. Antigenic variation in Plasmodium falciparum: gene organization and regulation of the var multigene family. EUKARYOTIC CELL 2007; 6:1511-20. [PMID: 17644655 PMCID: PMC2043368 DOI: 10.1128/ec.00173-07] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Sue A Kyes
- Molecular Parasitology Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
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35
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Duffy MF, Tham WH. Transcription and coregulation of multigene families in Plasmodium falciparum. Trends Parasitol 2007; 23:183-6; discussion 186-7. [PMID: 17350338 DOI: 10.1016/j.pt.2007.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 02/05/2007] [Accepted: 02/26/2007] [Indexed: 11/16/2022]
Abstract
Subtelomeric regions in the Plasmodium genome are enriched with members of three major multigene families: var, rif and stevor. In this article, we discuss a recent study by Sharp and colleagues that focused on the transcribed repertoire of var and stevor genes in asexual and sexual Plasmodium parasites. Transcription of these two multigene families seems to be unlinked in asexual parasites. Parasites in the gametocyte stages transcribe members of the upsC subset of var genes, which indicates the intriguing possibility of their involvement in gametocyte adhesion.
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Affiliation(s)
- Michael F Duffy
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia.
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36
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Abstract
In recent years, the sequencing and annotation of complete genomes, together with the development of genetic and proteomic techniques to study previously intractable eukaryotic microbes, has revealed interesting new themes in the control of virulence gene expression. Families of variantly expressed genes are found adjacent to telomeres in the genomes of both pathogenic and non-pathogenic organisms. This subtelomeric DNA is normally heterochromatic and higher-order chromatin structure has now come to be recognized as an important factor controlling both the evolution and expression dynamics of these multigene families. In eukaryotic cells, higher-order chromatin structure plays a central role in many DNA processes including the control of chromosome integrity and recombination, DNA partitioning during cell division, and transcriptional control. DNA can be packaged in two distinct forms: euchromatin is relatively accessible to DNA binding proteins and generally contains active genes, while heterochromatin is densely packaged, relatively inaccessible and usually transcriptionally silent. These features of chromatin are epigenetically inherited from cell cycle to cell cycle. This review will focus on the epigenetic mechanisms used to control expression of virulence genes in medically important microbial pathogens. Examples of such control have now been reported in several evolutionarily distant species, revealing what may be a common strategy used to regulate many very different families of genes.
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Affiliation(s)
- Catherine J Merrick
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Ave, Building I, Rm 706, Boston, MA 02115, USA
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37
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Kyes S, Christodoulou Z, Pinches R, Kriek N, Horrocks P, Newbold C. Plasmodium falciparum var
gene expression is developmentally controlled at the level of RNA polymerase II‐mediated transcription initiation. Mol Microbiol 2007; 63:1237-47. [PMID: 17257309 DOI: 10.1111/j.1365-2958.2007.05587.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Plasmodium falciparum var gene family codes for a major virulence factor in this most lethal of human malaria parasites. A single var protein variant type is expressed on each infected red blood cell, with antigenic variation allowing progeny parasites to escape host immune detection. The control of mutually exclusive var gene expression in the parasite relies on in situ epigenetic changes. Whether control of expression occurs at transcription initiation or post transcription, however, remains to be established. Recent evidence supports existence of a unique var transcription site at the nuclear periphery containing the dominantly expressed var gene, although silent var genes can colocalize to the same region. We demonstrate here that exclusive var gene expression is controlled at the level of transcription initiation during ring stages and that var genes are transcribed by RNA polymerase II. This represents another example where P. falciparum differs from the paradigm for antigenic variation, Trypanosoma brucei.
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Affiliation(s)
- Sue Kyes
- Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headington, Oxford, UK.
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38
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Tham WH, Payne PD, Brown GV, Rogerson SJ. Identification of basic transcriptional elements required for rif gene transcription. Int J Parasitol 2006; 37:605-15. [PMID: 17196595 DOI: 10.1016/j.ijpara.2006.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 11/16/2006] [Accepted: 11/19/2006] [Indexed: 10/23/2022]
Abstract
The rif gene family is the largest multi-gene family in the malaria parasite Plasmodium falciparum. The gene products of rif genes, rifins, are clonally variant and transported to the surface of the infected erythrocyte where they are targets of the human immune response. Maximal rif transcription occurs during the late ring to early trophozoite stages of the intra-erythrocytic cycle. The factors involved in the transcriptional activation and repression of rif genes are not known. In this paper, we characterize several DNA elements involved in the regulation of rif transcription. We identify the upstream region that contains a functional promoter and the transcriptional start site of a rif gene. In addition, we identify two distinct regions within the rif upstream region involved in the transcriptional repression of these genes. These repressor sites are bound by nuclear protein factors expressed in different stages of the Plasmodium life cycle. We propose that the differential timing of binding provides a mechanism for the temporal repression of rif genes. In addition, we find that transcription profiles of upsA var genes and their neighbouring rif genes are unlinked.
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Affiliation(s)
- Wai-Hong Tham
- Department of Medicine, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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