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Li B. Unwrap RAP1's Mystery at Kinetoplastid Telomeres. Biomolecules 2024; 14:67. [PMID: 38254667 PMCID: PMC10813129 DOI: 10.3390/biom14010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1's functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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2
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Barcons-Simon A, Carrington M, Siegel TN. Decoding the impact of nuclear organization on antigenic variation in parasites. Nat Microbiol 2023; 8:1408-1418. [PMID: 37524976 DOI: 10.1038/s41564-023-01424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Antigenic variation as a strategy to evade the host adaptive immune response has evolved in divergent pathogens. Antigenic variation involves restricted, and often mutually exclusive, expression of dominant antigens and a periodic switch in antigen expression during infection. In eukaryotes, nuclear compartmentalization, including three-dimensional folding of the genome and physical separation of proteins in compartments or condensates, regulates mutually exclusive gene expression and chromosomal translocations. In this Review, we discuss the impact of nuclear organization on antigenic variation in the protozoan pathogens Trypanosoma brucei and Plasmodium falciparum. In particular, we highlight the relevance of nuclear organization in both mutually exclusive antigen expression and genome stability, which underlie antigenic variation.
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Affiliation(s)
- Anna Barcons-Simon
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
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3
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Ashby EC, Havens JL, Rollosson LM, Hardin J, Schulz D. Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome. Microbiol Spectr 2023; 11:e0014723. [PMID: 37097159 PMCID: PMC10269879 DOI: 10.1128/spectrum.00147-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
The eukaryotic protozoan parasite Trypanosoma brucei is transmitted by the tsetse fly to both humans and animals, where it causes a fatal disease called African trypanosomiasis. While the parasite lacks canonical DNA sequence-specific transcription factors, it does possess histones, histone modifications, and proteins that write, erase, and read histone marks. Chemical inhibition of chromatin-interacting bromodomain proteins has previously been shown to perturb bloodstream specific trypanosome processes, including silencing of the variant surface glycoprotein (VSG) genes and immune evasion. Transcriptomic changes that occur in bromodomain-inhibited bloodstream parasites mirror many of the changes that occur as parasites developmentally progress from the bloodstream to the insect stage. We performed transcriptome sequencing (RNA-seq) time courses to determine the effects of chemical bromodomain inhibition in insect-stage parasites using the compound I-BET151. We found that treatment with I-BET151 causes large changes in the transcriptome of insect-stage parasites and also perturbs silencing of VSG genes. The transcriptomes of bromodomain-inhibited parasites share some features with early metacyclic-stage parasites in the fly salivary gland, implicating bromodomain proteins as important for regulating transcript levels for developmentally relevant genes. However, the downregulation of surface procyclin protein that typically accompanies developmental progression is absent in bromodomain-inhibited insect-stage parasites. We conclude that chemical modulation of bromodomain proteins causes widespread transcriptomic changes in multiple trypanosome life cycle stages. Understanding the gene-regulatory processes that facilitate transcriptome remodeling in this highly diverged eukaryote may shed light on how these mechanisms evolved. IMPORTANCE The disease African trypanosomiasis imposes a severe human and economic burden for communities in sub-Saharan Africa. The parasite that causes the disease is transmitted to the bloodstream of a human or ungulate via the tsetse fly. Because the environments of the fly and the bloodstream differ, the parasite modulates the expression of its genes to accommodate two different lifestyles in these disparate niches. Perturbation of bromodomain proteins that interact with histone proteins around which DNA is wrapped (chromatin) causes profound changes in gene expression in bloodstream-stage parasites. This paper reports that gene expression is also affected by chemical bromodomain inhibition in insect-stage parasites but that the genes affected differ depending on life cycle stage. Because trypanosomes diverged early from model eukaryotes, an understanding of how trypanosomes regulate gene expression may lend insight into how gene-regulatory mechanisms evolved. This could also be leveraged to generate new therapeutic strategies.
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Affiliation(s)
- Ethan C. Ashby
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | | | | | - Johanna Hardin
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Danae Schulz
- Department of Biology, Harvey Mudd College, Claremont, California, USA
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4
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Faria J, Briggs EM, Black JA, McCulloch R. Emergence and adaptation of the cellular machinery directing antigenic variation in the African trypanosome. Curr Opin Microbiol 2022; 70:102209. [PMID: 36215868 DOI: 10.1016/j.mib.2022.102209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 01/25/2023]
Abstract
Survival of the African trypanosome within its mammalian hosts, and hence transmission between hosts, relies upon antigenic variation, where stochastic changes in the composition of their protective variant-surface glycoprotein (VSG) coat thwart effective removal of the pathogen by adaptive immunity. Antigenic variation has evolved remarkable mechanistic complexity in Trypanosoma brucei, with switching of the VSG coat executed by either transcriptional or recombination reactions. In the former, a single T. brucei cell selectively transcribes one telomeric VSG transcription site, termed the expression site (ES), from a pool of around 15. Silencing of the active ES and activation of one previously silent ES can lead to a co-ordinated VSG coat switch. Outside the ESs, the T. brucei genome contains an enormous archive of silent VSG genes and pseudogenes, which can be recombined into the ES to execute a coat switch. Most such recombination involves gene conversion, including copying of a complete VSG and more complex reactions where novel 'mosaic' VSGs are formed as patchworks of sequences from several silent (pseudo)genes. Understanding of the cellular machinery that directs transcriptional and recombination VSG switching is growing rapidly and the emerging picture is of the use of proteins, complexes and pathways that are not limited to trypanosomes, but are shared across the wider grouping of kinetoplastids and beyond, suggesting co-option of widely used, core cellular reactions. We will review what is known about the machinery of antigenic variation and discuss if there remains the possibility of trypanosome adaptations, or even trypanosome-specific machineries, that might offer opportunities to impair this crucial parasite-survival process.
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Affiliation(s)
- Joana Faria
- York Biomedical Research Institute, Department of Biology, University of York, United Kingdom.
| | - Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom
| | - Jennifer A Black
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, United Kingdom.
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Maree JP, Tvardovskiy A, Ravnsborg T, Jensen ON, Rudenko G, Patterton HG. Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A. Nucleic Acids Res 2022; 50:9705-9723. [PMID: 36095123 PMCID: PMC9508842 DOI: 10.1093/nar/gkac759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/09/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.
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Affiliation(s)
- Johannes P Maree
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Tina Ravnsborg
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, and Center for Epigenetics, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hugh-G Patterton
- Center for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7600, South Africa
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6
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López-Escobar L, Hänisch B, Halliday C, Ishii M, Akiyoshi B, Dean S, Sunter JD, Wheeler RJ, Gull K. Stage-specific transcription activator ESB1 regulates monoallelic antigen expression in Trypanosoma brucei. Nat Microbiol 2022; 7:1280-1290. [PMID: 35879525 PMCID: PMC9352583 DOI: 10.1038/s41564-022-01175-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
Variant surface glycoprotein (VSG) coats bloodstream form Trypanosoma brucei parasites, and monoallelic VSG expression underpins the antigenic variation necessary for pathogenicity. One of thousands of VSG genes is transcribed by RNA polymerase I in a singular nuclear structure called the expression site body (ESB), but how monoallelic VSG transcription is achieved remains unclear. Using a localization screen of 153 proteins we found one, ESB-specific protein 1 (ESB1), that localized only to the ESB and is expressed only in VSG-expressing life cycle stages. ESB1 associates with DNA near the active VSG promoter and is necessary for VSG expression, with overexpression activating inactive VSG promoters. Mechanistically, ESB1 is necessary for recruitment of a subset of ESB components, including RNA polymerase I, revealing that the ESB has separately assembled subdomains. Because many trypanosomatid parasites have divergent ESB1 orthologues yet do not undergo antigenic variation, ESB1 probably represents an important class of transcription regulators.
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Affiliation(s)
| | - Benjamin Hänisch
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Clare Halliday
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Samuel Dean
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | | | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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7
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A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling. PLoS Pathog 2022; 18:e1010514. [PMID: 35675371 PMCID: PMC9236257 DOI: 10.1371/journal.ppat.1010514] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/27/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed. Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness) in humans and nagana in cattle. Its unusual genomic organisation featuring large polycistronic units requires a general mechanism of transcription initiation, because individual gene promoters are mostly absent. Despite the fact that the histone variant H2A.Z has previously been identified as a key player of transcription regulation, the complex responsible for correct H2A.Z incorporation at transcription start sites (TSS) remains elusive. In other eukaryotes, SWR1, a SNF2 ATPase-associated chromatin remodelling complex, is responsible for correct incorporation of this histone variant. This study identified a SWR1-like complex in T. brucei. Depletion of the SNF2 ATPase resulted in a reduction of H2A.Z incorporation at the TSS and decreased steady-state mRNA levels accompanied by chromatin condensation. In addition to the SWR1-like complex, we also identified a trypanosome-specific HAT2 complex that includes the histone acetyltransferases HAT2, a key player in the H2A.Z incorporation process. This complex has a trypanosome-specific composition that is different from the NuA4/TIP60 complex in Saccharomyces cerevisiae.
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8
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Florini F, Visone JE, Deitsch KW. Shared Mechanisms for Mutually Exclusive Expression and Antigenic Variation by Protozoan Parasites. Front Cell Dev Biol 2022; 10:852239. [PMID: 35350381 PMCID: PMC8957917 DOI: 10.3389/fcell.2022.852239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2022] [Indexed: 01/05/2023] Open
Abstract
Cellular decision-making at the level of gene expression is a key process in the development and evolution of every organism. Variations in gene expression can lead to phenotypic diversity and the development of subpopulations with adaptive advantages. A prime example is the mutually exclusive activation of a single gene from within a multicopy gene family. In mammals, this ranges from the activation of one of the two immunoglobulin (Ig) alleles to the choice in olfactory sensory neurons of a single odorant receptor (OR) gene from a family of more than 1,000. Similarly, in parasites like Trypanosoma brucei, Giardia lamblia or Plasmodium falciparum, the process of antigenic variation required to escape recognition by the host immune system involves the monoallelic expression of vsg, vsp or var genes, respectively. Despite the importance of this process, understanding how this choice is made remains an enigma. The development of powerful techniques such as single cell RNA-seq and Hi-C has provided new insights into the mechanisms these different systems employ to achieve monoallelic gene expression. Studies utilizing these techniques have shown how the complex interplay between nuclear architecture, physical interactions between chromosomes and different chromatin states lead to single allele expression. Additionally, in several instances it has been observed that high-level expression of a single gene is preceded by a transient state where multiple genes are expressed at a low level. In this review, we will describe and compare the different strategies that organisms have evolved to choose one gene from within a large family and how parasites employ this strategy to ensure survival within their hosts.
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Affiliation(s)
| | | | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
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9
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Faria JRC. A nuclear enterprise: zooming in on nuclear organization and gene expression control in the African trypanosome. Parasitology 2021; 148:1237-1253. [PMID: 33407981 PMCID: PMC8311968 DOI: 10.1017/s0031182020002437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022]
Abstract
African trypanosomes are early divergent protozoan parasites responsible for high mortality and morbidity as well as a great economic burden among the world's poorest populations. Trypanosomes undergo antigenic variation in their mammalian hosts, a highly sophisticated immune evasion mechanism. Their nuclear organization and mechanisms for gene expression control present several conventional features but also a number of striking differences to the mammalian counterparts. Some of these unorthodox characteristics, such as lack of controlled transcription initiation or enhancer sequences, render their monogenic antigen transcription, which is critical for successful antigenic variation, even more enigmatic. Recent technological developments have advanced our understanding of nuclear organization and gene expression control in trypanosomes, opening novel research avenues. This review is focused on Trypanosoma brucei nuclear organization and how it impacts gene expression, with an emphasis on antigen expression. It highlights several dedicated sub-nuclear bodies that compartmentalize specific functions, whilst outlining similarities and differences to more complex eukaryotes. Notably, understanding the mechanisms underpinning antigen as well as general gene expression control is of great importance, as it might help designing effective control strategies against these organisms.
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Affiliation(s)
- Joana R. C. Faria
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, DundeeDD1 5EH, UK
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10
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Li B, Zhao Y. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities. Pathogens 2021; 10:pathogens10080967. [PMID: 34451431 PMCID: PMC8402208 DOI: 10.3390/pathogens10080967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence: (B.L.); (Y.Z.)
| | - Yanxiang Zhao
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
- Correspondence: (B.L.); (Y.Z.)
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11
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Chandu AGS, Sengupta PP, Jacob SS, Borthakur SK, Patra G, Roy P. Mining the pervasiveness of surra in different animal species of Northeastern states of India: Assam, Mizoram and Tripura. J Parasit Dis 2021; 45:330-335. [PMID: 34295030 DOI: 10.1007/s12639-021-01392-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022] Open
Abstract
Trypanosoma evansi is a flagellated, extracellular haemoprotozoan parasite infecting a wide range of mammalian hosts including dromedaries, cattle, equines and dogs cause disease surra. Carrier animals with sub-clinical infection cause significant monetary losses to livestock holders and therefore detection of infection status using molecular diagnostic techniques becomes important in order to control the disease. In the current study cattle, buffalo, goat, pig and dog samples from three northeastern states of India-Assam, Mizoram and Tripura were screened to determine the prevalence of surra. A total of 1702 samples including 795 from Assam, 678 from Mizoram and 229 from Tripura were screened by CATT/T. evansi test out of which 16.8%, 27.1% and 22.3% samples in respective states were found to have antibodies against T. evansi. DNA detection of T. evansi by PCR amplification targeting VSG gene revealed the molecular prevalence of surra in Assam, Mizoram and Tripura as 8.5%, 7.5% and 4.4% respectively. The analysis of amplified partial VSG sequences showed 99% similarity within an animal species whereas 86-94% similarity was observed among different species of animals revealing the homogeneity. The study established the prevalence of surra in different species of animals in the three northeastern states of India-Assam, Mizoram and Tripura and this study is the first report of T. evansi infection in pig and goat from India. Supplementary Information The online version contains supplementary material available at 10.1007/s12639-021-01392-z.
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Affiliation(s)
- A G S Chandu
- ICAR- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Ramagondanahalli, Yelahanka, P.B. No. 6450, Bengaluru, Karnataka 560064 India.,Department of Biochemistry, School of Sciences, Jain University, Bengaluru, Karnataka India
| | - P P Sengupta
- ICAR- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Ramagondanahalli, Yelahanka, P.B. No. 6450, Bengaluru, Karnataka 560064 India
| | - S S Jacob
- ICAR- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Ramagondanahalli, Yelahanka, P.B. No. 6450, Bengaluru, Karnataka 560064 India
| | - S K Borthakur
- Department of Veterinary Parasitology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram India
| | - G Patra
- Department of Veterinary Parasitology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram India
| | - P Roy
- ICAR- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Ramagondanahalli, Yelahanka, P.B. No. 6450, Bengaluru, Karnataka 560064 India
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12
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Black JA, Crouch K, Lemgruber L, Lapsley C, Dickens N, Tosi LRO, Mottram JC, McCulloch R. Trypanosoma brucei ATR Links DNA Damage Signaling during Antigenic Variation with Regulation of RNA Polymerase I-Transcribed Surface Antigens. Cell Rep 2021; 30:836-851.e5. [PMID: 31968257 PMCID: PMC6988115 DOI: 10.1016/j.celrep.2019.12.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 08/19/2019] [Accepted: 12/13/2019] [Indexed: 11/29/2022] Open
Abstract
Trypanosoma brucei evades mammalian immunity by using recombination to switch its surface-expressed variant surface glycoprotein (VSG), while ensuring that only one of many subtelomeric multigene VSG expression sites are transcribed at a time. DNA repair activities have been implicated in the catalysis of VSG switching by recombination, not transcriptional control. How VSG switching is signaled to guide the appropriate reaction or to integrate switching into parasite growth is unknown. Here, we show that the loss of ATR, a DNA damage-signaling protein kinase, is lethal, causing nuclear genome instability and increased VSG switching through VSG-localized damage. Furthermore, ATR loss leads to the increased transcription of silent VSG expression sites and expression of mixed VSGs on the cell surface, effects that are associated with the altered localization of RNA polymerase I and VEX1. This work shows that ATR acts in antigenic variation both through DNA damage signaling and surface antigen expression control. Loss of the repair protein kinase ATR in Trypanosoma brucei is lethal Loss of T. brucei ATR alters VSG coat expression needed for immune evasion Monoallelic RNA polymerase I VSG expression is undermined by ATR loss ATR loss leads to expression of subtelomeric VSGs, indicative of recombination
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Affiliation(s)
- Jennifer Ann Black
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900 SP, Brazil
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Leandro Lemgruber
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Nicholas Dickens
- Marine Science Lab, FAU Harbor Branch Oceanographic Institute, 5600 US 1 North, Fort Pierce, FL 34946, USA
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900 SP, Brazil
| | - Jeremy C Mottram
- Centre for Immunology and Infection, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK.
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Díaz-Olmos Y, Batista M, Ludwig A, Marchini FK. Characterising ISWI chromatin remodeler in Trypanosoma cruzi. Mem Inst Oswaldo Cruz 2020; 115:e190457. [PMID: 32428081 PMCID: PMC7233268 DOI: 10.1590/0074-02760190457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/23/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Imitation SWItch (ISWI) ATPase is the catalytic subunit in diverse chromatin remodeling complexes. These complexes modify histone-DNA interactions and therefore play a pivotal role in different DNA-dependent processes. In Trypanosoma cruzi, a protozoan that controls gene expression principally post-transcriptionally, the transcriptional regulation mechanisms mediated by chromatin remodeling are poorly understood. OBJECTIVE To characterise the ISWI remodeler in T. cruzi (TcISWI). METHODS A new version of pTcGW vectors was constructed to express green fluorescent protein (GFP)-tagged TcISWI. CRISPR-Cas9 system was used to obtain parasites with inactivated TcISWI gene and we determined TcISWI partners by cryomilling-affinity purification-mass spectrometry (MS) assay as an approximation to start to unravel the function of this protein. FINDINGS Our approach identified known ISWI partners [nucleoplasmin-like protein (NLP), regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP)], previously characterised in T. brucei, and new components in TcISWI complex [DRBD2, DHH1 and proteins containing a domain characteristic of structural maintenance of chromosomes (SMC) proteins]. Data are available via ProteomeXchange with identifier PXD017869. MAIN CONCLUSIONS In addition to its participation in transcriptional silencing, as it was reported in T. brucei, the data generated here provide a framework that suggests a role for TcISWI chromatin remodeler in different nuclear processes in T. cruzi, including mRNA nuclear export control and chromatin compaction. Further work is necessary to clarify the TcISWI functional diversity that arises from this protein interaction study.
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Affiliation(s)
- Yirys Díaz-Olmos
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Michel Batista
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Fabricio K Marchini
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
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14
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Saha A, Nanavaty VP, Li B. Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes. J Mol Biol 2019; 432:4167-4185. [PMID: 31682833 DOI: 10.1016/j.jmb.2019.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022]
Abstract
Trypanosoma brucei is a kinetoplastid parasite that causes African trypanosomiasis, which is fatal if left untreated. T. brucei regularly switches its major surface antigen, VSG, to evade the host immune responses. VSGs are exclusively expressed from subtelomeric expression sites (ESs) where VSG genes are flanked by upstream 70 bp repeats and downstream telomeric repeats. The telomere downstream of the active VSG is transcribed into a long-noncoding RNA (TERRA), which forms RNA:DNA hybrids (R-loops) with the telomeric DNA. At an elevated level, telomere R-loops cause more telomeric and subtelomeric double-strand breaks (DSBs) and increase VSG switching rate. In addition, stabilized R-loops are observed at the 70 bp repeats and immediately downstream of ES-linked VSGs in RNase H defective cells, which also have an increased amount of subtelomeric DSBs and more frequent VSG switching. Although subtelomere plasticity is expected to be beneficial to antigenic variation, severe defects in subtelomere integrity and stability increase cell lethality. Therefore, regulation of the telomere and 70 bp repeat R-loop levels is important for the balance between antigenic variation and cell fitness in T. brucei. In addition, the high level of the active ES transcription favors accumulation of R-loops at the telomere and 70 bp repeats, providing an intrinsic mechanism for local DSB formation, which is a strong inducer of VSG switching.
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Affiliation(s)
- Arpita Saha
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Vishal P Nanavaty
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Science and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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15
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Nuclear Phosphatidylinositol 5-Phosphatase Is Essential for Allelic Exclusion of Variant Surface Glycoprotein Genes in Trypanosomes. Mol Cell Biol 2019; 39:MCB.00395-18. [PMID: 30420356 DOI: 10.1128/mcb.00395-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/23/2018] [Indexed: 11/20/2022] Open
Abstract
Allelic exclusion of variant surface glycoprotein (VSG) genes is essential for African trypanosomes to evade the host antibody response by antigenic variation. The mechanisms by which this parasite expresses only one of its ∼2,000 VSG genes at a time are unknown. We show that nuclear phosphatidylinositol 5-phosphatase (PIP5Pase) interacts with repressor activator protein 1 (RAP1) in a multiprotein complex and functions in the control of VSG allelic exclusion. RAP1 binds PIP5Pase substrate phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3], and catalytic mutation of PIP5Pase that inhibits PI(3,4,5)P3 dephosphorylation results in simultaneous transcription of VSGs from all telomeric expression sites (ESs) and from silent subtelomeric VSG arrays. PIP5Pase and RAP1 bind to telomeric ESs, especially at 70-bp repeats and telomeres, and their binding is altered by PIP5Pase inactivation or knockdown, implying changes in ES chromatin organization. Our data suggest a model whereby PIP5Pase controls PI(3,4,5)P3 binding by RAP1 and, thus, RAP1 silencing of telomeric and subtelomeric VSG genes. Hence, allelic exclusion of VSG genes may entail control of nuclear phosphoinositides.
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16
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Martínez-Calvillo S, Romero-Meza G, Vizuet-de-Rueda JC, Florencio-Martínez LE, Manning-Cela R, Nepomuceno-Mejía T. Epigenetic Regulation of Transcription in Trypanosomatid Protozoa. Curr Genomics 2018; 19:140-149. [PMID: 29491742 PMCID: PMC5814962 DOI: 10.2174/1389202918666170911163517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/13/2017] [Accepted: 04/18/2017] [Indexed: 12/15/2022] Open
Abstract
The Trypanosomatid family includes flagellated parasites that cause fatal human diseases. Remarkably, protein-coding genes in these organisms are positioned in long tandem arrays that are transcribed polycistronically. However, the knowledge about regulation of transcription initiation and termination in trypanosomatids is scarce. The importance of epigenetic regulation in these processes has become evident in the last years, as distinctive histone modifications and histone variants have been found in transcription initiation and termination regions. Moreover, multiple chromatin-related proteins have been identified and characterized in trypanosomatids, including histone-modifying enzymes, effector complexes, chromatin-remodelling enzymes and histone chaperones. Notably, base J, a modified thymine residue present in the nuclear DNA of trypanosomatids, has been implicated in transcriptional regulation. Here we review the current knowledge on epigenetic control of transcription by all three RNA polymerases in this group of early-diverged eukaryotes.
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Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Gabriela Romero-Meza
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Juan C. Vizuet-de-Rueda
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Luis E. Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Rebeca Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, México, D.F., CP 07360, México
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México. Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
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Cestari I, Stuart K. Transcriptional Regulation of Telomeric Expression Sites and Antigenic Variation in Trypanosomes. Curr Genomics 2018; 19:119-132. [PMID: 29491740 PMCID: PMC5814960 DOI: 10.2174/1389202918666170911161831] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/03/2017] [Accepted: 05/04/2017] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Trypanosoma brucei uses antigenic variation to evade the host antibody clearance by periodically changing its Variant Surface Glycoprotein (VSGs) coat. T. brucei encode over 2,500 VSG genes and pseudogenes, however they transcribe only one VSG gene at time from one of the 20 telomeric Expression Sites (ESs). VSGs are transcribed in a monoallelic fashion by RNA polymerase I from an extranucleolar site named ES body. VSG antigenic switching occurs by transcriptional switching between telomeric ESs or by recombination of the VSG gene expressed. VSG expression is developmentally regulated and its transcription is controlled by epigenetic mechanisms and influenced by a telomere position effect. CONCLUSION Here, we discuss 1) the molecular basis underlying transcription of telomeric ESs and VSG antigenic switching; 2) the current knowledge of VSG monoallelic expression; 3) the role of inositol phosphate pathway in the regulation of VSG expression and switching; and 4) the developmental regulation of Pol I transcription of procyclin and VSG genes.
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Affiliation(s)
- Igor Cestari
- Center for Infectious Disease Research, Seattle, WA98109, USA
| | - Ken Stuart
- Center for Infectious Disease Research, Seattle, WA98109, USA
- Department of Global Health, University of Washington, Seattle, WA98195, USA
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18
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How to create coats for all seasons: elucidating antigenic variation in African trypanosomes. Emerg Top Life Sci 2017; 1:593-600. [PMID: 33525853 PMCID: PMC7289013 DOI: 10.1042/etls20170105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 11/17/2022]
Abstract
Extracellular parasites of the mammalian bloodstream face considerable challenges including incessant assault by the immune system. African trypanosomes are consummate survivors in this inclement environment and are renowned for their supremely sophisticated strategy of antigenic variation of their protective surface coat during the course of chronic infections. Recent developments are making us realize how complex this antigenic machinery is and are allowing us to tackle previously intractable problems. However, many of the simplest (and arguably the most important) questions still remain unanswered!
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19
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Maree JP, Povelones ML, Clark DJ, Rudenko G, Patterton HG. Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei. Epigenetics Chromatin 2017; 10:14. [PMID: 28344657 PMCID: PMC5359979 DOI: 10.1186/s13072-017-0121-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization of chromatin in early genomes. Results We have mapped nucleosome positions in T. brucei and identified important differences compared to other eukaryotes: The RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion, and show little evidence for defined −1 and +1 nucleosomes. In contrast, a well-positioned nucleosome is present directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were depleted of nucleosomes, with a single well-positioned nucleosome present immediately downstream of the predicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays of well-positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared with replication origins in other chromosomal core regions. Conclusions Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0121-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Megan Lindsay Povelones
- Department of Biology, Pennsylvania State University (Brandywine Campus), Media, PA 19063 USA
| | - David Johannes Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ UK
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20
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Rout MP, Obado SO, Schenkman S, Field MC. Specialising the parasite nucleus: Pores, lamins, chromatin, and diversity. PLoS Pathog 2017; 13:e1006170. [PMID: 28253370 PMCID: PMC5333908 DOI: 10.1371/journal.ppat.1006170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael P. Rout
- The Rockefeller University, New York, New York, United States of America
| | - Samson O. Obado
- The Rockefeller University, New York, New York, United States of America
| | | | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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21
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The nuclear envelope and gene organization in parasitic protozoa: Specializations associated with disease. Mol Biochem Parasitol 2016; 209:104-113. [PMID: 27475118 DOI: 10.1016/j.molbiopara.2016.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/12/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The parasitic protozoa Trypanosoma brucei and Plasmodium falciparum are lethal human parasites that have developed elegant strategies of immune evasion by antigenic variation. Despite the vast evolutionary distance between the two taxa, both parasites employ strict monoallelic expression of their membrane proteins, variant surface glycoproteins in Trypanosomes and the var, rif and stevor genes in Plasmodium, in order to evade their host's immune system. Additionally, both telomeric location and epigenetic controls are prominent features of these membrane proteins. As such, telomeres, chromatin structure and nuclear organization all contribute to control of gene expression and immune evasion. Here, we discuss the importance of epigenetics and sub-nuclear context for the survival of these disease-causing parasites.
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22
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Reynolds DL, Hofmeister BT, Cliffe L, Siegel TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R. Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination. Mol Microbiol 2016; 101:559-74. [PMID: 27125778 DOI: 10.1111/mmi.13408] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 12/27/2022]
Abstract
The genomes of kinetoplastids are organized into polycistronic gene clusters that are flanked by the modified DNA base J. Previous work has established a role of base J in promoting RNA polymerase II termination in Leishmania spp. where the loss of J leads to termination defects and transcription into adjacent gene clusters. It remains unclear whether these termination defects affect gene expression and whether read through transcription is detrimental to cell growth, thus explaining the essential nature of J. We now demonstrate that reduction of base J at specific sites within polycistronic gene clusters in L. major leads to read through transcription and increased expression of downstream genes in the cluster. Interestingly, subsequent transcription into the opposing polycistronic gene cluster does not lead to downregulation of sense mRNAs. These findings indicate a conserved role for J regulating transcription termination and expression of genes within polycistronic gene clusters in trypanosomatids. In contrast to the expectations often attributed to opposing transcription, the essential nature of J in Leishmania spp. is related to its role in gene repression rather than preventing transcriptional interference resulting from read through and dual strand transcription.
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Affiliation(s)
- David L Reynolds
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | | | - Laura Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany
| | - Britta A Anderson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
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Schulz D, Mugnier MR, Paulsen EM, Kim HS, Chung CWW, Tough DF, Rioja I, Prinjha RK, Papavasiliou FN, Debler EW. Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome. PLoS Biol 2015; 13:e1002316. [PMID: 26646171 PMCID: PMC4672894 DOI: 10.1371/journal.pbio.1002316] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/30/2015] [Indexed: 01/01/2023] Open
Abstract
Trypanosoma brucei, the causative agent of African sleeping sickness, is transmitted to its mammalian host by the tsetse. In the fly, the parasite's surface is covered with invariant procyclin, while in the mammal it resides extracellularly in its bloodstream form (BF) and is densely covered with highly immunogenic Variant Surface Glycoprotein (VSG). In the BF, the parasite varies this highly immunogenic surface VSG using a repertoire of ~2500 distinct VSG genes. Recent reports in mammalian systems point to a role for histone acetyl-lysine recognizing bromodomain proteins in the maintenance of stem cell fate, leading us to hypothesize that bromodomain proteins may maintain the BF cell fate in trypanosomes. Using small-molecule inhibitors and genetic mutants for individual bromodomain proteins, we performed RNA-seq experiments that revealed changes in the transcriptome similar to those seen in cells differentiating from the BF to the insect stage. This was recapitulated at the protein level by the appearance of insect-stage proteins on the cell surface. Furthermore, bromodomain inhibition disrupts two major BF-specific immune evasion mechanisms that trypanosomes harness to evade mammalian host antibody responses. First, monoallelic expression of the antigenically varied VSG is disrupted. Second, rapid internalization of antibodies bound to VSG on the surface of the trypanosome is blocked. Thus, our studies reveal a role for trypanosome bromodomain proteins in maintaining bloodstream stage identity and immune evasion. Importantly, bromodomain inhibition leads to a decrease in virulence in a mouse model of infection, establishing these proteins as potential therapeutic drug targets for trypanosomiasis. Our 1.25Å resolution crystal structure of a trypanosome bromodomain in complex with I-BET151 reveals a novel binding mode of the inhibitor, which serves as a promising starting point for rational drug design.
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Affiliation(s)
- Danae Schulz
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, United States of America
| | - Monica R. Mugnier
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, United States of America
| | - Eda-Margaret Paulsen
- Laboratory of Cell Biology, The Rockefeller University, New York, New York, United States of America
| | - Hee-Sook Kim
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, United States of America
| | - Chun-wa W. Chung
- Computational and Structural Chemistry, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage, United Kingdom
| | - David F. Tough
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Inmaculada Rioja
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Rab K. Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - F. Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Erik W. Debler
- Laboratory of Cell Biology, The Rockefeller University, New York, New York, United States of America
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Stanne T, Narayanan MS, Ridewood S, Ling A, Witmer K, Kushwaha M, Wiesler S, Wickstead B, Wood J, Rudenko G. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei. J Biol Chem 2015; 290:26954-26967. [PMID: 26378228 PMCID: PMC4646403 DOI: 10.1074/jbc.m115.679019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/25/2022] Open
Abstract
ISWI chromatin remodelers are highly conserved in eukaryotes and are important for the assembly and spacing of nucleosomes, thereby controlling transcription initiation and elongation. ISWI is typically associated with different subunits, forming specialized complexes with discrete functions. In the unicellular parasite Trypanosoma brucei, which causes African sleeping sickness, TbISWI down-regulates RNA polymerase I (Pol I)-transcribed variant surface glycoprotein (VSG) gene expression sites (ESs), which are monoallelically expressed. Here, we use tandem affinity purification to determine the interacting partners of TbISWI. We identify three proteins that do not show significant homology with known ISWI-associated partners. Surprisingly, one of these is nucleoplasmin-like protein (NLP), which we had previously shown to play a role in ES control. In addition, we identify two novel ISWI partners, regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP), both containing protein motifs typically found on chromatin proteins. Knockdown of RCCP or FYRP in bloodstream form T. brucei results in derepression of silent variant surface glycoprotein ESs, as had previously been shown for TbISWI and NLP. All four proteins are expressed and interact with each other in both major life cycle stages and show similar distributions at Pol I-transcribed loci. They are also found at Pol II strand switch regions as determined with ChIP. ISWI, NLP, RCCP, and FYRP therefore appear to form a single major ISWI complex in T. brucei (TbIC). This reduced complexity of ISWI regulation and the presence of novel ISWI partners highlights the early divergence of trypanosomes in evolution.
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Affiliation(s)
- Tara Stanne
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Sophie Ridewood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Alexandra Ling
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Kathrin Witmer
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Manish Kushwaha
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Simone Wiesler
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Bill Wickstead
- the School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jennifer Wood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and.
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25
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Inositol phosphate pathway controls transcription of telomeric expression sites in trypanosomes. Proc Natl Acad Sci U S A 2015; 112:E2803-12. [PMID: 25964327 DOI: 10.1073/pnas.1501206112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
African trypanosomes evade clearance by host antibodies by periodically changing their variant surface glycoprotein (VSG) coat. They transcribe only one VSG gene at a time from 1 of about 20 telomeric expression sites (ESs). They undergo antigenic variation by switching transcription between telomeric ESs or by recombination of the VSG gene expressed. We show that the inositol phosphate (IP) pathway controls transcription of telomeric ESs and VSG antigenic switching in Trypanosoma brucei. Conditional knockdown of phosphatidylinositol 5-kinase (TbPIP5K) or phosphatidylinositol 5-phosphatase (TbPIP5Pase) or overexpression of phospholipase C (TbPLC) derepresses numerous silent ESs in T. brucei bloodstream forms. The derepression is specific to telomeric ESs, and it coincides with an increase in the number of colocalizing telomeric and RNA polymerase I foci in the nucleus. Monoallelic VSG transcription resumes after reexpression of TbPIP5K; however, most of the resultant cells switched the VSG gene expressed. TbPIP5K, TbPLC, their substrates, and products localize to the plasma membrane, whereas TbPIP5Pase localizes to the nucleus proximal to telomeres. TbPIP5Pase associates with repressor/activator protein 1 (TbRAP1), and their telomeric silencing function is altered by TbPIP5K knockdown. These results show that specific steps in the IP pathway control ES transcription and antigenic switching in T. brucei by epigenetic regulation of telomere silencing.
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Mony BM, Matthews KR. Assembling the components of the quorum sensing pathway in African trypanosomes. Mol Microbiol 2015; 96:220-32. [PMID: 25630552 PMCID: PMC4403954 DOI: 10.1111/mmi.12949] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2015] [Indexed: 12/14/2022]
Abstract
African trypanosomes, parasites that cause human sleeping sickness, undergo a density-dependent differentiation in the bloodstream of their mammalian hosts. This process is driven by a released parasite-derived factor that causes parasites to accumulate in G1 and become quiescent. This is accompanied by morphological transformation to 'stumpy' forms that are adapted to survival and further development when taken up in the blood meal of tsetse flies, the vector for trypanosomiasis. Although the soluble signal driving differentiation to stumpy forms is unidentified, a recent genome-wide RNAi screen identified many of the intracellular signalling and effector molecules required for the response to this signal. These resemble components of nutritional starvation and quiescence pathways in other eukaryotes, suggesting that parasite development shares similarities with the adaptive quiescence of organisms such as yeasts and Dictyostelium in response to nutritional starvation and stress. Here, the trypanosome signalling pathway is discussed in the context of these conserved pathways and the possible contributions of opposing 'slender retainer' and 'stumpy inducer' arms described. As evolutionarily highly divergent eukaryotes, the organisation and conservation of this developmental pathway can provide insight into the developmental cycle of other protozoan parasites, as well as the adaptive and programmed developmental responses of all eukaryotic cells.
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Affiliation(s)
- Binny M Mony
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghCharlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghCharlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- *For correspondence. E-mail ; Tel. (+44) 131 651 3639; Fax (+44) 131 651 3670
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Matthews KR. 25 years of African trypanosome research: From description to molecular dissection and new drug discovery. Mol Biochem Parasitol 2015; 200:30-40. [PMID: 25736427 PMCID: PMC4509711 DOI: 10.1016/j.molbiopara.2015.01.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 01/27/2023]
Abstract
The Molecular Parasitology conference was first held at the Marine Biological laboratory, Woods Hole, USA 25 years ago. Since that first meeting, the conference has evolved and expanded but has remained the showcase for the latest research developments in molecular parasitology. In this perspective, I reflect on the scientific discoveries focussed on African trypanosomes (Trypanosoma brucei spp.) that have occurred since the inaugural MPM meeting and discuss the current and future status of research on these parasites.
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Affiliation(s)
- Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.
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DNA double-strand breaks and telomeres play important roles in trypanosoma brucei antigenic variation. EUKARYOTIC CELL 2015; 14:196-205. [PMID: 25576484 DOI: 10.1128/ec.00207-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human-infecting microbial pathogens all face a serious problem of elimination by the host immune response. Antigenic variation is an effective immune evasion mechanism where the pathogen regularly switches its major surface antigen. In many cases, the major surface antigen is encoded by genes from the same gene family, and its expression is strictly monoallelic. Among pathogens that undergo antigenic variation, Trypanosoma brucei (a kinetoplastid), which causes human African trypanosomiasis, Plasmodium falciparum (an apicomplexan), which causes malaria, Pneumocystis jirovecii (a fungus), which causes pneumonia, and Borrelia burgdorferi (a bacterium), which causes Lyme disease, also express their major surface antigens from loci next to the telomere. Except for Plasmodium, DNA recombination-mediated gene conversion is a major pathway for surface antigen switching in these pathogens. In the last decade, more sophisticated molecular and genetic tools have been developed in T. brucei, and our knowledge of functions of DNA recombination in antigenic variation has been greatly advanced. VSG is the major surface antigen in T. brucei. In subtelomeric VSG expression sites (ESs), VSG genes invariably are flanked by a long stretch of upstream 70-bp repeats. Recent studies have shown that DNA double-strand breaks (DSBs), particularly those in 70-bp repeats in the active ES, are a natural potent trigger for antigenic variation in T. brucei. In addition, telomere proteins can influence VSG switching by reducing the DSB amount at subtelomeric regions. These findings will be summarized and their implications will be discussed in this review.
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29
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Abstract
African trypanosomes have been around for more than 100 million years, and have adapted to survival in a very wide host range. While various indigenous African mammalian host species display a tolerant phenotype towards this parasitic infection, and hence serve as perpetual reservoirs, many commercially important livestock species are highly disease susceptible. When considering humans, they too display a highly sensitive disease progression phenotype for infections with Trypanosoma brucei rhodesiense or Trypanosoma brucei gambiense, while being intrinsically resistant to infections with other trypanosome species. As extracellular trypanosomes proliferate and live freely in the bloodstream and lymphatics, they are constantly exposed to the immune system. Due to co-evolution, this environment however no longer poses a hostile threat, but has become the niche environment where trypanosomes thrive and obligatory await transmission through the bites of tsetse flies or other haematophagic vectors, ideally without causing severe side infection-associated pathology to their host. Hence, African trypanosomes have acquired various mechanisms to manipulate and control the host immune response, evading effective elimination. Despite the extensive research into trypanosomosis over the past 40 years, many aspects of the anti-parasite immune response remain to be solved and no vaccine is currently available. Here we review the recent work on the different escape mechanisms employed by African Trypanosomes to ensure infection chronicity and transmission potential.
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31
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Denninger V, Rudenko G. FACT plays a major role in histone dynamics affecting VSG expression site control in Trypanosoma brucei. Mol Microbiol 2014; 94:945-62. [PMID: 25266856 PMCID: PMC4625058 DOI: 10.1111/mmi.12812] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2014] [Indexed: 12/21/2022]
Abstract
Chromatin remodelling is involved in the transcriptional regulation of the RNA polymerase I transcribed variant surface glycoprotein (VSG) expression sites (ESs) of Trypanosoma brucei. We show that the T. brucei FACT complex contains the Pob3 and Spt16 subunits, and plays a key role in ES silencing. We see an inverse correlation between transcription and condensed chromatin, whereby FACT knockdown results in ES derepression and more open chromatin around silent ES promoters. Derepressed ESs show increased sensitivity to micrococcal nuclease (MNase) digestion, and a decrease in histones at silent ES promoters but not telomeres. In contrast, FACT knockdown results in more histones at the active ES, correlated with transcription shut-down. ES promoters are derepressed in cells stalled at the G2/M cell cycle stage after knockdown of FACT, but not in G2/M cells stalled after knockdown of cyclin 6. This argues that the observed ES derepression is a direct consequence of histone chaperone activity by FACT at the G2/M cell cycle stage which could affect transcription elongation, rather than an indirect consequence of a cell cycle checkpoint. These experiments highlight the role of the FACT complex in cell cycle-specific chromatin remodelling within VSG ESs.
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Affiliation(s)
- Viola Denninger
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, South Kensington, London, SW7 2AZ, UK
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32
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Mono-allelic VSG expression by RNA polymerase I in Trypanosoma brucei: expression site control from both ends? Gene 2014; 556:68-73. [PMID: 25261847 DOI: 10.1016/j.gene.2014.09.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 02/01/2023]
Abstract
Trypanosoma brucei is a vector borne, lethal protistan parasite of humans and livestock in sub-Saharan Africa. Antigenic variation of its cell surface coat enables the parasite to evade adaptive immune responses and to live freely in the blood of its mammalian hosts. The coat consists of ten million copies of variant surface glycoprotein (VSG) that is expressed from a single VSG gene, drawn from a large repertoire and located near the telomere at one of fifteen so-called bloodstream expression sites (BESs). Thus, antigenic variation is achieved by switching to the expression of a different VSG gene. A BES is a tandem array of expression site-associated genes and a terminal VSG gene. It is polycistronically transcribed by a multifunctional RNA polymerase I (RNAPI) from a short promoter that is located 45-60 kb upstream of the VSG gene. The mechanism(s) restricting VSG expression to a single BES are not well understood. There is convincing evidence that epigenetic silencing and transcription attenuation play important roles. Furthermore, recent data indicated that there is regulation at the level of transcription initiation and that, surprisingly, the VSG mRNA appears to have a role in restricting VSG expression to a single gene. Here, we review BES expression regulation and propose a model in which telomere-directed, epigenetic BES silencing is opposed by BES promoter-directed, activated RNAPI transcription.
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33
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Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Pinto-Neves D, Aresta-Branco F, Rijo-Ferreira F, Guegan F, Pedro Coelho L, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. Mol Microbiol 2014; 93:645-63. [PMID: 24946224 PMCID: PMC4285223 DOI: 10.1111/mmi.12677] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2014] [Indexed: 11/30/2022]
Abstract
Trypanosoma brucei is a unicellular parasite that causes sleeping sickness in humans. Most of its transcription is constitutive and driven by RNA polymerase II. RNA polymerase I (Pol I) transcribes not only ribosomal RNA genes, but also protein-encoding genes, including variant surface glycoproteins (VSGs) and procyclins. In T. brucei, histone H1 (H1) is required for VSG silencing and chromatin condensation. However, whether H1 has a genome-wide role in transcription is unknown. Here, using RNA sequencing we show that H1 depletion changes the expression of a specific cohort of genes. Interestingly, the predominant effect is partial loss of silencing of Pol I loci, such as VSG and procyclin genes. Labelling of nascent transcripts with 4-thiouridine showed that H1 depletion does not alter the level of labelled Pol II transcripts. In contrast, the levels of 4sU-labelled Pol I transcripts were increased by two- to sixfold, suggesting that H1 preferentially blocks transcription at Pol I loci. Finally, we observed that parasites depleted of H1 grow almost normally in culture but they have a reduced fitness in mice, suggesting that H1 is important for host-pathogen interactions.
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Affiliation(s)
- Ana C Pena
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisboa, Portugal
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34
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Transcription is initiated on silent variant surface glycoprotein expression sites despite monoallelic expression in Trypanosoma brucei. Proc Natl Acad Sci U S A 2014; 111:8943-8. [PMID: 24889641 DOI: 10.1073/pnas.1404873111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
African trypanosomes survive the immune defense of their hosts by regularly changing their antigenic coat made of variant surface glycoprotein (VSG). The Trypanosoma brucei genome contains more than 1,000 VSG genes. To be expressed, a given VSG gene must be located in one of 15 telomeric regions termed "VSG expression sites" (ESs), each of which contains a polycistronic transcription unit that includes ES-associated genes. Only one ES is fully active at a time, so only one VSG gene is transcribed per cell. Although this monoallelic expression is controlled at the transcriptional level, the precise molecular mechanism for this control is not understood. Here we report that in single cells transcription is initiated on several ESs simultaneously, indicating that the monoallelic control is not determined only at transcription initiation, but also at further control steps such as transcription elongation or RNA processing.
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35
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Nguyen TN, Müller LSM, Park SH, Siegel TN, Günzl A. Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression sites in Trypanosoma brucei. Nucleic Acids Res 2013; 42:3164-76. [PMID: 24353315 PMCID: PMC3950698 DOI: 10.1093/nar/gkt1301] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Monoallelic expression within a gene family is found in pathogens exhibiting antigenic variation and in mammalian olfactory neurons. Trypanosoma brucei, a lethal parasite living in the human bloodstream, expresses variant surface glycoprotein (VSG) from 1 of 15 bloodstream expression sites (BESs) by virtue of a multifunctional RNA polymerase I. The active BES is transcribed in an extranucleolar compartment termed the expression site body (ESB), whereas silent BESs, located elsewhere within the nucleus, are repressed epigenetically. The regulatory mechanisms, however, are poorly understood. Here we show that two essential subunits of the basal class I transcription factor A (CITFA) predominantly occupied the promoter of the active BES relative to that of a silent BES, a phenotype that was maintained after switching BESs in situ. In these experiments, high promoter occupancy of CITFA was coupled to high levels of both promoter-proximal RNA abundance and RNA polymerase I occupancy. Accordingly, fluorescently tagged CITFA-7 was concentrated in the nucleolus and the ESB. Because a ChIP-seq analysis found that along the entire BES, CITFA-7 is specifically enriched only at the promoter, our data strongly indicate that monoallelic BES transcription is activated by a mechanism that functions at the level of transcription initiation.
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Affiliation(s)
- Tu N Nguyen
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA and Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
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36
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Wyse BA, Oshidari R, Jeffery DC, Yankulov KY. Parasite epigenetics and immune evasion: lessons from budding yeast. Epigenetics Chromatin 2013; 6:40. [PMID: 24252437 PMCID: PMC3843538 DOI: 10.1186/1756-8935-6-40] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022] Open
Abstract
The remarkable ability of many parasites to evade host immunity is the key to their success and pervasiveness. The immune evasion is directly linked to the silencing of the members of extended families of genes that encode for major parasite antigens. At any time only one of these genes is active. Infrequent switches to other members of the gene family help the parasites elude the immune system and cause prolonged maladies. For most pathogens, the detailed mechanisms of gene silencing and switching are poorly understood. On the other hand, studies in the budding yeast Saccharomyces cerevisiae have revealed similar mechanisms of gene repression and switching and have provided significant insights into the molecular basis of these phenomena. This information is becoming increasingly relevant to the genetics of the parasites. Here we summarize recent advances in parasite epigenetics and emphasize the similarities between S. cerevisiae and pathogens such as Plasmodium, Trypanosoma, Candida, and Pneumocystis. We also outline current challenges in the control and the treatment of the diseases caused by these parasites and link them to epigenetics and the wealth of knowledge acquired from budding yeast.
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Affiliation(s)
| | | | | | - Krassimir Y Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2 W1, Canada.
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37
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Pandya UM, Sandhu R, Li B. Silencing subtelomeric VSGs by Trypanosoma brucei RAP1 at the insect stage involves chromatin structure changes. Nucleic Acids Res 2013; 41:7673-82. [PMID: 23804762 PMCID: PMC3763547 DOI: 10.1093/nar/gkt562] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen variant surface glycoprotein (VSG) to evade mammalian host immune responses at the bloodstream form (BF) stage. Monoallelic expression of BF Expression Site (BES)-linked VSGs and silencing of metacyclic VSGs (mVSGs) in BF cells are essential for antigenic variation, whereas silencing of both BES-linked and mVSGs in the procyclic form (PF) cells is important for cell survival in the midgut of its insect vector. We have previously shown that silencing BES-linked VSGs in BF cells depends on TbRAP1. We now show that TbRAP1 silences both BES-linked and mVSGs at both BF and PF stages. The strength of TbRAP1-mediated BES-linked VSG silencing is stronger in the PF cells than that in BF cells. In addition, Formaldehyde-Assisted Isolation of Regulatory Elements analysis and MNase digestion demonstrated that depletion of TbRAP1 in PF cells led to a chromatin structure change, which is significantly stronger at the subtelomeric VSG loci than at chromosome internal loci. On the contrary, no significant chromatin structure changes were detected on depletion of TbRAP1 in BF cells. Our observations indicate that TbRAP1 helps to determine the chromatin structure at the insect stage, which likely contributes to its strong silencing effect on VSGs.
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Affiliation(s)
- Unnati M Pandya
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA
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38
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Kim HS, Park SH, Günzl A, Cross GAM. MCM-BP is required for repression of life-cycle specific genes transcribed by RNA polymerase I in the mammalian infectious form of Trypanosoma brucei. PLoS One 2013; 8:e57001. [PMID: 23451133 PMCID: PMC3581582 DOI: 10.1371/journal.pone.0057001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/16/2013] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma brucei variant surface glycoprotein (VSG) expression is a classic example of allelic exclusion. While the genome of T. brucei contains >2,000 VSG genes and VSG pseudogenes, only one allele is expressed at the surface of each infectious trypanosome and the others are repressed. Along with recombinatorial VSG switching, allelic exclusion provides a major host evasion mechanism for trypanosomes, a phenomenon known as antigenic variation. To extend our understanding of how trypanosomes escape host immunity by differential expression of VSGs, we attempted to identify genes that contribute to VSG silencing, by performing a loss-of-silencing screen in T. brucei using a transposon-mediated random insertional mutagenesis. One identified gene, which we initially named LOS1, encodes a T. brucei MCM-Binding Protein (TbMCM-BP). Here we show that TbMCM-BP is essential for viability of infectious bloodstream-form (BF) trypanosome and is required for proper cell-cycle progression. Tandem affinity purification of TbMCM-BP followed by mass spectrometry identified four subunits (MCM4-MCM7) of the T. brucei MCM complex, a replicative helicase, and MCM8, a subunit that is uniquely co-purified with TbMCM-BP. TbMCM-BP is required not only for repression of subtelomeric VSGs but also for silencing of life-cycle specific, insect-stage genes, procyclin and procyclin-associated genes (PAGs), that are normally repressed in BF trypanosomes and are transcribed by RNA polymerase I. Our study uncovers a functional link between chromosome maintenance and RNA pol I-mediated gene silencing in T. brucei.
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Affiliation(s)
- Hee-Sook Kim
- Laboratory of Molecular Parasitology, The Rockefeller University, New York, New York, United States of America.
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39
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Narayanan MS, Rudenko G. TDP1 is an HMG chromatin protein facilitating RNA polymerase I transcription in African trypanosomes. Nucleic Acids Res 2013; 41:2981-92. [PMID: 23361461 PMCID: PMC3597664 DOI: 10.1093/nar/gks1469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unusually for a eukaryote, Trypanosoma brucei transcribes its variant surface glycoprotein (VSG) gene expression sites (ESs) in a monoallelic fashion using RNA polymerase I (Pol I). It is still unclear how ES transcription is controlled in T. brucei. Here, we show that the TDP1 architectural chromatin protein is an essential high mobility group box (HMGB) protein facilitating Pol I transcription in T. brucei. TDP1 is specifically enriched at the active compared with silent VSG ES and immediately downstream of ribosomal DNA promoters and is abundant in the nucleolus and the expression site body subnuclear compartments. Distribution of TDP1 at Pol I-transcribed loci is inversely correlated with histones. Depletion of TDP1 results in up to 40–90% reduction in VSG and rRNA transcripts and a concomitant increase in histones H3, H2A and H1 at these Pol I transcription units. TDP1 shares features with the Saccharomyces cerevisiae HMGB protein Hmo1, but it is the first architectural chromatin protein facilitating Pol I-mediated transcription of both protein coding genes as well as rRNA. These results show that TDP1 has a mutually exclusive relationship with histones on actively transcribed Pol I transcription units, providing insight into how Pol I transcription is controlled.
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Affiliation(s)
- Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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40
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Benmerzouga I, Concepción-Acevedo J, Kim HS, Vandoros AV, Cross GAM, Klingbeil MM, Li B. Trypanosoma brucei Orc1 is essential for nuclear DNA replication and affects both VSG silencing and VSG switching. Mol Microbiol 2012; 87:196-210. [PMID: 23216794 DOI: 10.1111/mmi.12093] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 11/29/2022]
Abstract
Binding of the Origin Recognition Complex (ORC) to replication origins is essential for initiation of DNA replication, but ORC has non-essential functions outside of DNA replication, including in heterochromatic gene silencing and telomere maintenance. Trypanosoma brucei, a protozoan parasite that causes human African trypanosomiasis, uses antigenic variation as a major virulence mechanism to evade the host's immune attack by expressing its major surface antigen, the Variant Surface Glycoprotein (VSG), in a monoallelic manner. An Orc1/Cdc6 homologue has been identified in T. brucei, but its role in DNA replication has not been directly confirmed and its potential involvement in VSG repression or switching has not been thoroughly investigated. In this study, we show that TbOrc1 is essential for nuclear DNA replication in mammalian-infectious bloodstream and tsetse procyclic forms (BF and PF). Depletion of TbOrc1 resulted in derepression of telomere-linked silent VSGs in both BF and PF, and increased VSG switching particularly through the in situ transcriptional switching mechanism. TbOrc1 associates with telomere repeats but appears to do so independently of two known T. brucei telomere proteins, TbRAP1 and TbTRF. We conclude that TbOrc1 has conserved functions in DNA replication and is also required to control telomere-linked VSG expression and VSG switching.
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Affiliation(s)
- Imaan Benmerzouga
- Center for Gene Regulation in Health & Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
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41
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Povelones ML, Gluenz E, Dembek M, Gull K, Rudenko G. Histone H1 plays a role in heterochromatin formation and VSG expression site silencing in Trypanosoma brucei. PLoS Pathog 2012; 8:e1003010. [PMID: 23133390 PMCID: PMC3486875 DOI: 10.1371/journal.ppat.1003010] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 09/20/2012] [Indexed: 11/30/2022] Open
Abstract
The African sleeping sickness parasite Trypanosoma brucei evades the host immune system through antigenic variation of its variant surface glycoprotein (VSG) coat. Although the T. brucei genome contains ∼1500 VSGs, only one VSG is expressed at a time from one of about 15 subtelomeric VSG expression sites (ESs). For antigenic variation to work, not only must the vast VSG repertoire be kept silent in a genome that is mainly constitutively transcribed, but the frequency of VSG switching must be strictly controlled. Recently it has become clear that chromatin plays a key role in silencing inactive ESs, thereby ensuring monoallelic expression of VSG. We investigated the role of the linker histone H1 in chromatin organization and ES regulation in T. brucei. T. brucei histone H1 proteins have a different domain structure to H1 proteins in higher eukaryotes. However, we show that they play a key role in the maintenance of higher order chromatin structure in bloodstream form T. brucei as visualised by electron microscopy. In addition, depletion of histone H1 results in chromatin becoming generally more accessible to endonucleases in bloodstream but not in insect form T. brucei. The effect on chromatin following H1 knock-down in bloodstream form T. brucei is particularly evident at transcriptionally silent ES promoters, leading to 6–8 fold derepression of these promoters. T. brucei histone H1 therefore appears to be important for the maintenance of repressed chromatin in bloodstream form T. brucei. In particular H1 plays a role in downregulating silent ESs, arguing that H1-mediated chromatin functions in antigenic variation in T. brucei. Trypanosoma brucei causes African sleeping sickness, endemic to sub-Saharan Africa. Bloodstream form T. brucei is covered with a dense coat of variant surface glycoprotein (VSG). Only one VSG is expressed at a time out of a vast repertoire of ∼1500 VSGs. The active VSG is transcribed in a telomeric VSG expression site (ES), and VSG switching allows immune evasion. Exactly how monoallelic exclusion of VSG ESs operates, and how switching between ESs is mediated remains mysterious, although epigenetics and chromatin structure clearly play a major role. The linker histone H1 is thought to orchestrate higher order chromatin structure in eukaryotes, but its exact function is unclear. We investigated the role of histone H1 in the regulation of antigenic variation in T. brucei. We show that histone H1 is associated with chromatin and is required for higher order chromatin structure. Depletion of histone H1 results in derepression of silent VSG ES promoters, indicating that H1-mediated chromatin functions in antigenic variation in T. brucei.
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Affiliation(s)
- Megan L. Povelones
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Eva Gluenz
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marcin Dembek
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Keith Gull
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London, United Kingdom
- * E-mail:
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42
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Li B. Telomere components as potential therapeutic targets for treating microbial pathogen infections. Front Oncol 2012; 2:156. [PMID: 23125966 PMCID: PMC3485576 DOI: 10.3389/fonc.2012.00156] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/16/2012] [Indexed: 01/12/2023] Open
Abstract
In a number of microbial pathogens that undergoes antigenic variation to evade the host's immune attack, genes encoding surface antigens are located at subtelomeric loci, and recent studies have revealed that telomere components play important roles in regulation of surface antigen expression in several of these pathogens, indicating that telomeres play critical roles in microbial pathogen virulence regulation. Importantly, although telomere protein components and their functions are largely conserved from protozoa to mammals, telomere protein homologs in microbial pathogens and humans have low sequence homology. Therefore, pathogen telomere components are potential drug targets for therapeutic approaches because first, most telomere proteins are essential for pathogens' survival, and second, disruption of pathogens' antigenic variation mechanism would facilitate host's immune system to clear the infection.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University Cleveland, OH, USA
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43
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Abstract
The African trypanosome Trypanosoma brucei is a flagellated unicellular parasite transmitted by tsetse flies that causes African sleeping sickness in sub-Saharan Africa. Trypanosomes are highly adapted for life in the hostile environment of the mammalian bloodstream, and have various adaptations to their cell biology that facilitate immune evasion. These include a specialized morphology, with most nutrient uptake occurring in the privileged location of the flagellar pocket. In addition, trypanosomes show extremely high rates of recycling of a protective VSG (variant surface glycoprotein) coat, whereby host antibodies are stripped off of the VSG before it is re-used. VSG recycling therefore functions as a mechanism for cleaning the VSG coat, allowing trypanosomes to survive in low titres of anti-VSG antibodies. Lastly, T. brucei has developed an extremely sophisticated strategy of antigenic variation of its VSG coat allowing it to evade host antibodies. A single trypanosome has more than 1500 VSG genes, most of which are located in extensive silent arrays. Strikingly, most of these silent VSGs are pseudogenes, and we are still in the process of trying to understand how non-intact VSGs are recombined to produce genes encoding functional coats. Only one VSG is expressed at a time from one of approximately 15 telomeric VSG ES (expression site) transcription units. It is becoming increasingly clear that chromatin remodelling must play a critical role in ES control. Hopefully, a better understanding of these unique trypanosome adaptations will eventually allow us to disrupt their ability to multiply in the mammalian bloodstream.
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Epigenetic mechanisms, nuclear architecture and the control of gene expression in trypanosomes. Expert Rev Mol Med 2012; 14:e13. [PMID: 22640744 DOI: 10.1017/erm.2012.7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The control of gene expression, and more significantly gene cohorts, requires tight transcriptional coordination and is an essential feature of probably all cells. In higher eukaryotes, the mechanisms used involve controlled modifications to both local and global DNA environments, principally through changes in chromatin structure as well as cis-element-driven mechanisms. Although the mechanisms regulating chromatin in terms of transcriptional permissiveness and the relation to developmental programmes and responses to the environment are becoming better understood for animal and fungal cells, it is only just beginning to become clear how these processes operate in other taxa, including the trypanosomatids. Recent advances are now illuminating how African trypanosomes regulate higher-order chromatin structure, and, further, how these mechanisms impact on the expression of major surface antigens that are of fundamental importance to life-cycle progression. It is now apparent that several mechanisms are rather more similar between animal and fungal cells and trypanosomes than it originally appeared, but some aspects do involve gene products unique to trypanosomes. Therefore, both evolutionarily common and novel mechanisms cohabit in trypanosomes, offering both important biological insights and possible therapeutic opportunity.
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Abstract
Parasitic diseases cause significant global morbidity and mortality, particularly in underdeveloped regions of the world. Malaria alone causes ~800000 deaths each year, with children and pregnant women being at highest risk. There is no licensed vaccine available for any human parasitic disease and drug resistance is compromising the efficacy of many available anti-parasitic drugs. This is driving drug discovery research on new agents with novel modes of action. Histone deacetylase (HDAC) inhibitors are being investigated as drugs for a range of diseases, including cancers and infectious diseases such as HIV/AIDS, and several parasitic diseases. This review focuses on the current state of knowledge of HDAC inhibitors targeted to the major human parasitic diseases malaria, schistosomiasis, trypanosomiasis, toxoplasmosis and leishmaniasis. Insights are provided into the unique challenges that will need to be considered if HDAC inhibitors are to be progressed towards clinical development as potential new anti-parasitic drugs.
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Affiliation(s)
- Katherine T Andrews
- Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Queensland, Australia.
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46
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Manful T, Fadda A, Clayton C. The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA (NEW YORK, N.Y.) 2011; 17:2039-2047. [PMID: 21947264 PMCID: PMC3198596 DOI: 10.1261/rna.2837311] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/16/2011] [Indexed: 05/31/2023]
Abstract
The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation and mRNA abundance on a transcriptome-wide scale. The model organism used was the bloodstream form of Trypanosoma brucei, a protist that lacks regulation of RNA polymerase II initiation. The mRNA half-lives varied over two orders of magnitude, with a median half-life of 13 min for total (rRNA-depleted) mRNA. Data for poly(A)+ RNA yielded shorter half-lives than for total RNA, indicating that removal of the poly(A) tail was usually the first step in degradation. Depletion of the major 5'-3' exoribonuclease, XRNA, resulted in the stabilization of most mRNAs with half-lives under 30 min. Thus, on a transcriptome-wide scale, degradation of most mRNAs is initiated by deadenylation. Trypanosome mRNA levels are strongly influenced by gene copy number and mRNA half-life: Very abundant mRNAs that are required throughout the life-cycle may be encoded by multicopy genes and have intermediate-to-long half-lives; those encoding ribosomal proteins, with one to two gene copies, are exceptionally stable. Developmentally regulated transcripts with a lower abundance in the bloodstream forms than the procyclic forms had half-lives around the median, whereas those with a higher abundance in the bloodstream forms than the procyclic forms, such as those encoding glycolytic enzymes, had longer half-lives.
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Affiliation(s)
- Theresa Manful
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
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47
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Epigenetic regulation of polymerase II transcription initiation in Trypanosoma cruzi: modulation of nucleosome abundance, histone modification, and polymerase occupancy by O-linked thymine DNA glucosylation. EUKARYOTIC CELL 2011; 10:1465-72. [PMID: 21926332 DOI: 10.1128/ec.05185-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Very little is understood regarding how transcription is initiated/regulated in the early-diverging eukaryote Trypanosoma cruzi. Unusually for a eukaryote, genes transcribed by RNA polymerase (Pol) II in T. cruzi are arranged in polycistronic transcription units (PTUs). On the basis of this gene organization, it was previously thought that trypanosomes rely solely on posttranscriptional processes to regulate gene expression. We recently localized a novel glucosylated thymine DNA base, called base J, to potential promoter regions of PTUs throughout the trypanosome genome. Loss of base J, following the deletion of JBP1, a thymidine hydroxylase involved with synthesis, led to a global increase in the Pol II transcription rate and gene expression. In order to determine the mechanism by which base J regulates transcription, we have characterized changes in chromatin structure and Pol II recruitment to promoter regions following the loss of base J. The loss of base J coincides with a decrease in nucleosome abundance, increased histone H3/H4 acetylation, and increased Pol II occupancy at promoter regions, including the well-characterized spliced leader RNA gene promoter. These studies present the first direct evidence for epigenetic regulation of Pol II transcription initiation via DNA modification and chromatin structure in kinetoplastids as well as provide a mechanism for regulation of trypanosome gene expression via the novel hypermodified base J.
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TbISWI regulates multiple polymerase I (Pol I)-transcribed loci and is present at Pol II transcription boundaries in Trypanosoma brucei. EUKARYOTIC CELL 2011; 10:964-76. [PMID: 21571922 DOI: 10.1128/ec.05048-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The unicellular eukaryote Trypanosoma brucei is unusual in having very little transcriptional control. The bulk of the T. brucei genome is constitutively transcribed by RNA polymerase II (Pol II) as extensive polycistronic transcription units. Exceptions to this rule include several RNA Pol I transcription units such as the VSG expression sites (ESs), which are mono-allelically expressed. TbISWI, a member of the SWI2/SNF2 related chromatin remodeling ATPases, plays a role in repression of Pol I-transcribed ESs in both bloodstream- and procyclic-form T. brucei. We show that TbISWI binds both active and silent ESs but is depleted from the ES promoters themselves. TbISWI knockdown results in an increase in VSG transcripts from the silent VSG ESs. In addition to its role in the repression of the silent ESs, TbISWI also contributes to the downregulation of the Pol I-transcribed procyclin loci, as well as nontranscribed VSG basic copy arrays and minichromosomes. We also show that TbISWI is enriched at a number of strand switch regions which form the boundaries between Pol II transcription units. These strand switch regions are the presumed sites of Pol II transcription initiation and termination and are enriched in modified histones and histone variants. Our results indicate that TbISWI is a versatile chromatin remodeler that regulates transcription at multiple Pol I loci and is particularly abundant at many Pol II transcription boundaries in T. brucei.
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Ersfeld K. Nuclear architecture, genome and chromatin organisation in Trypanosoma brucei. Res Microbiol 2011; 162:626-36. [PMID: 21392575 DOI: 10.1016/j.resmic.2011.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/29/2011] [Indexed: 11/29/2022]
Abstract
The nucleus of the human pathogen Trypanosoma brucei not only has unusual chromosomal composition, characterised by the presence of megabase, intermediate and minichromosomes, but also chromosome and gene organisation that is unique amongst eukaryotes. Here I provide an overview of current knowledge of nuclear structure, chromatin organisation and chromosome dynamics during interphase and mitosis. New technologies such as chromatin immunoprecipitation, in combination with new generation sequencing and proteomic analysis of subnuclear fractions, have led to novel insights into the organisation of the nucleus and chromatin. In particular, we are beginning to understand how universal mechanisms of chromatin modifications and nuclear position effects are deployed for parasite-specific functions and are centrally involved in genomic organisation and transcriptional regulation. These advances also have a major impact on progress in understanding the molecular basis of antigenic variation.
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Affiliation(s)
- Klaus Ersfeld
- Department of Biological Sciences and Hull York Medical School, University of Hull, Hull HU6 7RX, UK.
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50
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Narayanan MS, Kushwaha M, Ersfeld K, Fullbrook A, Stanne TM, Rudenko G. NLP is a novel transcription regulator involved in VSG expression site control in Trypanosoma brucei. Nucleic Acids Res 2010; 39:2018-31. [PMID: 21076155 PMCID: PMC3064810 DOI: 10.1093/nar/gkq950] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trypanosoma brucei mono-allelically expresses one of approximately 1500 variant surface glycoprotein (VSG) genes while multiplying in the mammalian bloodstream. The active VSG is transcribed by RNA polymerase I in one of approximately 15 telomeric VSG expression sites (ESs). T. brucei is unusual in controlling gene expression predominantly post-transcriptionally, and how ESs are mono-allelically controlled remains a mystery. Here we identify a novel transcription regulator, which resembles a nucleoplasmin-like protein (NLP) with an AT-hook motif. NLP is key for ES control in bloodstream form T. brucei, as NLP knockdown results in 45- to 65-fold derepression of the silent VSG221 ES. NLP is also involved in repression of transcription in the inactive VSG Basic Copy arrays, minichromosomes and procyclin loci. NLP is shown to be enriched on the 177- and 50-bp simple sequence repeats, the non-transcribed regions around rDNA and procyclin, and both active and silent ESs. Blocking NLP synthesis leads to downregulation of the active ES, indicating that NLP plays a role in regulating appropriate levels of transcription of ESs in both their active and silent state. Discovery of the unusual transcription regulator NLP provides new insight into the factors that are critical for ES control.
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Affiliation(s)
- Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, UK
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