1
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Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [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: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
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Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
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2
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Odell J, Lammerding J. Lamins as structural nuclear elements through evolution. Curr Opin Cell Biol 2023; 85:102267. [PMID: 37871500 PMCID: PMC10841731 DOI: 10.1016/j.ceb.2023.102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023]
Abstract
Lamins are nuclear intermediate filament proteins with important, well-established roles in humans and other vertebrates. Lamins interact with DNA and numerous proteins at the nuclear envelope to determine the mechanical properties of the nucleus, coordinate chromatin organization, and modulate gene expression. Many of these functions are conserved in the lamin homologs found in basal metazoan organisms, including Drosophila and Caenorhabditis elegans. Lamin homologs have also been recently identified in non-metazoans, like the amoeba Dictyostelium discoideum, yet how these proteins compare functionally to the metazoan isoforms is only beginning to emerge. A better understanding of these distantly related lamins is not only valuable for a more complete picture of eukaryotic evolution, but may also provide new insights into the function of vertebrate lamins.
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Affiliation(s)
- Jacob Odell
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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3
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Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
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4
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Touray AO, Rajesh R, Isebe T, Sternlieb T, Loock M, Kutova O, Cestari I. PI(3,4,5)P3 allosteric regulation of repressor activator protein 1 controls antigenic variation in trypanosomes. eLife 2023; 12:RP89331. [PMID: 38019264 PMCID: PMC10686619 DOI: 10.7554/elife.89331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
African trypanosomes evade host immune clearance by antigenic variation, causing persistent infections in humans and animals. These parasites express a homogeneous surface coat of variant surface glycoproteins (VSGs). They transcribe one out of hundreds of VSG genes at a time from telomeric expression sites (ESs) and periodically change the VSG expressed by transcriptional switching or recombination. The mechanisms underlying the control of VSG switching and its developmental silencing remain elusive. We report that telomeric ES activation and silencing entail an on/off genetic switch controlled by a nuclear phosphoinositide signaling system. This system includes a nuclear phosphatidylinositol 5-phosphatase (PIP5Pase), its substrate PI(3,4,5)P3, and the repressor-activator protein 1 (RAP1). RAP1 binds to ES sequences flanking VSG genes via its DNA binding domains and represses VSG transcription. In contrast, PI(3,4,5)P3 binds to the N-terminus of RAP1 and controls its DNA binding activity. Transient inactivation of PIP5Pase results in the accumulation of nuclear PI(3,4,5)P3, which binds RAP1 and displaces it from ESs, activating transcription of silent ESs and VSG switching. The system is also required for the developmental silencing of VSG genes. The data provides a mechanism controlling reversible telomere silencing essential for the periodic switching in VSG expression and its developmental regulation.
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Affiliation(s)
- Abdoulie O Touray
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
- Division of Experimental Medicine, Department of Medicine, McGill UniversityMontrealCanada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Tony Isebe
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Tamara Sternlieb
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Mira Loock
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Oksana Kutova
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
| | - Igor Cestari
- Institute of Parasitology, McGill University, Sainte-Anne-de-BellevueMontrealCanada
- Division of Experimental Medicine, Department of Medicine, McGill UniversityMontrealCanada
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5
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Girasol MJ, Krasilnikova M, Marques CA, Damasceno JD, Lapsley C, Lemgruber L, Burchmore R, Beraldi D, Carruthers R, Briggs EM, McCulloch R. RAD51-mediated R-loop formation acts to repair transcription-associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proc Natl Acad Sci U S A 2023; 120:e2309306120. [PMID: 37988471 PMCID: PMC10691351 DOI: 10.1073/pnas.2309306120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 11/23/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of all genomes that intersect with many processes, including transcription, telomere homeostasis, and centromere function. Increasing evidence suggests that RNA-DNA hybrids can provide two conflicting roles in the maintenance and transmission of genomes: They can be the triggers of DNA damage, leading to genome change, or can aid the DNA repair processes needed to respond to DNA lesions. Evasion of host immunity by African trypanosomes, such as Trypanosoma brucei, relies on targeted recombination of silent Variant Surface Glycoprotein (VSG) genes into a specialized telomeric locus that directs transcription of just one VSG from thousands. How such VSG recombination is targeted and initiated is unclear. Here, we show that a key enzyme of T. brucei homologous recombination, RAD51, interacts with RNA-DNA hybrids. In addition, we show that RNA-DNA hybrids display a genome-wide colocalization with DNA breaks and that this relationship is impaired by mutation of RAD51. Finally, we show that RAD51 acts to repair highly abundant, localised DNA breaks at the single transcribed VSG and that mutation of RAD51 alters RNA-DNA hybrid abundance at 70 bp repeats both around the transcribed VSG and across the silent VSG archive. This work reveals a widespread, generalised role for RNA-DNA hybrids in directing RAD51 activity during recombination and uncovers a specialised application of this interplay during targeted DNA break repair needed for the critical T. brucei immune evasion reaction of antigenic variation.
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Affiliation(s)
- Mark John Girasol
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Faculty of the MD-PhD in Molecular Medicine Program, College of Medicine, University of the Philippines Manila, Manila1000, Philippines
| | - Marija Krasilnikova
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Catarina A. Marques
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Jeziel D. Damasceno
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Craig Lapsley
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Richard Burchmore
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Dario Beraldi
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Ross Carruthers
- College of Medical, Veterinary and Life Sciences, School of Cancer Sciences, University of Glasgow, GlasgowG12 0YN, United Kingdom
| | - Emma M. Briggs
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Richard McCulloch
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
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6
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Padilla‐Mejia NE, Field MC. Evolutionary, structural and functional insights in nuclear organisation and nucleocytoplasmic transport in trypanosomes. FEBS Lett 2023; 597:2501-2518. [PMID: 37789516 PMCID: PMC10953052 DOI: 10.1002/1873-3468.14747] [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: 06/27/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope (NE), a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades, these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently, the critical roles of the lamina, NPC and other NE constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here, we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.
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Affiliation(s)
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeUK
- Institute of Parasitology, Biology CentreCzech Academy of SciencesČeské BudějoviceCzechia
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7
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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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8
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Pozzi B, Naguleswaran A, Florini F, Rezaei Z, Roditi I. The RNA export factor TbMex67 connects transcription and RNA export in Trypanosoma brucei and sets boundaries for RNA polymerase I. Nucleic Acids Res 2023; 51:5177-5192. [PMID: 37070196 PMCID: PMC10250216 DOI: 10.1093/nar/gkad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
TbMex67 is the major mRNA export factor known to date in trypanosomes, forming part of the docking platform within the nuclear pore. To explore its role in co-transcriptional mRNA export, recently reported in Trypanosoma brucei, pulse labelling of nascent RNAs with 5-ethynyl uridine (5-EU) was performed with cells depleted of TbMex67 and complemented with a dominant-negative mutant (TbMex67-DN). RNA polymerase (Pol) II transcription was unaffected, but the procyclin loci, which encode mRNAs transcribed by Pol I from internal sites on chromosomes 6 and 10, showed increased levels of 5-EU incorporation. This was due to Pol I readthrough transcription, which proceeded beyond the procyclin and procyclin-associated genes up to the Pol II transcription start site on the opposite strand. Complementation by TbMex67-DN also increased Pol I-dependent formation of R-loops and γ-histone 2A foci. The DN mutant exhibited reduced nuclear localisation and binding to chromatin compared to wild-type TbMex67. Together with its interaction with chromatin remodelling factor TbRRM1 and Pol II, and transcription-dependent association of Pol II with nucleoporins, our findings support a role for TbMex67 in connecting transcription and export in T. brucei. In addition, TbMex67 stalls readthrough by Pol I in specific contexts, thereby limiting R-loop formation and replication stress.
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Affiliation(s)
- Berta Pozzi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | | | - Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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9
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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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10
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Sending the message: specialized RNA export mechanisms in trypanosomes. Trends Parasitol 2022; 38:854-867. [PMID: 36028415 PMCID: PMC9894534 DOI: 10.1016/j.pt.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.
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11
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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] [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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12
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Transcription Dependent Loss of an Ectopically Expressed Variant Surface Glycoprotein during Antigenic Variation in Trypanosoma brucei. mBio 2022; 13:e0384721. [PMID: 35229632 PMCID: PMC8941856 DOI: 10.1128/mbio.03847-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the mammalian host, Trypanosoma brucei is coated in a single-variant surface glycoprotein (VSG) species. Stochastic switching of the expressed VSG allows the parasite to escape detection by the host immune system. DNA double-strand breaks (DSB) trigger VSG switching, and repair via gene conversion results in an antigenically distinct VSG being expressed from the single active bloodstream-form expression site (BES). The single active BES is marked by VSG exclusion 2 (VEX2) protein. Here, we have disrupted monoallelic VSG expression by stably expressing a second telomeric VSG from a ribosomal locus. We found that cells expressing two VSGs contained one VEX2 focus that was significantly larger in size than the wild-type cells; this therefore suggests the ectopic VSG is expressed from the same nuclear position as the active BES. Unexpectedly, we report that in the double VSG-expressing cells, the DNA sequence of the ectopic copy is lost following a DSB in the active BES, despite it being spatially separated in the genome. The loss of the ectopic VSG is dependent on active transcription and does not disrupt the number or variety of templates used to repair a BES DSB and elicit a VSG switch. We propose that there are stringent mechanisms within the cell to reinforce monoallelic expression during antigenic variation. IMPORTANCE The single-cell parasite Trypanosoma brucei causes the fatal disease human African trypanosomiasis and is able to colonize the blood, fat, skin, and central nervous system. Trypanosomes survive in the mammalian host owing to a dense protective protein coat that consists of a single-variant surface glycoprotein species. Stochastic switching of one VSG for an immunologically distinct one enables the parasite to escape recognition by the host immune system. We have disrupted monoallelic antigen expression by expressing a second VSG and report that following DSB-triggered VSG switching, the DNA sequence of the ectopic VSG is lost in a transcription-dependent manner. We propose that there are strict requirements to ensure that only one variant antigen is expressed following a VSG switch, which has important implications for understanding how the parasite survives in the mammalian host.
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13
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Inoue AH, Domingues PF, Serpeloni M, Hiraiwa PM, Vidal NM, Butterfield ER, del Pino RC, Ludwig A, Boehm C, Field MC, Ávila AR. Proteomics uncovers novel components of an interactive protein network supporting RNA export in trypanosomes. Mol Cell Proteomics 2022; 21:100208. [PMID: 35091090 PMCID: PMC8938319 DOI: 10.1016/j.mcpro.2022.100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022] Open
Abstract
In trypanosomatids, transcription is polycistronic and all mRNAs are processed by trans-splicing, with export mediated by noncanonical mechanisms. Although mRNA export is central to gene regulation and expression, few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components. We previously described conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII (previously Hel45), a core component of the exon junction complex (EJC). Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry. Significant overlap between TcSub2 and TceIF4AIII-interacting protein cohorts suggests that both proteins associate with similar machinery. We identified several interactions with conserved core components of the EJC and multiple additional complexes, together with proteins specific to trypanosomatids. Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events. We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of mRNA metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome mRNA maturation. Gene expression in trypanosomes is mediated by noncanonical mechanisms. Trypanosome mRNA nuclear export system comprises unique proteins to kinetoplastids. The present work highlights an amalgam of kinetoplastid-specific and conserved components. Our data support a highly coupled mRNA maturation pathway.
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14
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Padilla-Mejia NE, Makarov AA, Barlow LD, Butterfield ER, Field MC. Evolution and diversification of the nuclear envelope. Nucleus 2021; 12:21-41. [PMID: 33435791 PMCID: PMC7889174 DOI: 10.1080/19491034.2021.1874135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.
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Affiliation(s)
- Norma E. Padilla-Mejia
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexandr A. Makarov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lael D. Barlow
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Erin R. Butterfield
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České, Czech Republic
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15
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Staneva DP, Carloni R, Auchynnikava T, Tong P, Rappsilber J, Jeyaprakash AA, Matthews KR, Allshire RC. A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination. Genome Res 2021; 31:2138-2154. [PMID: 34407985 PMCID: PMC8559703 DOI: 10.1101/gr.275368.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023]
Abstract
Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by "writer" and "eraser" enzymes, respectively. Nucleosomal PTMs are recognized by a variety of "reader" proteins that alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers, and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite's bloodstream form. ChIP-seq shows that 15 candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins show a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identify distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET- and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcription start regions. The systematic approach used provides details of the composition and organization of the chromatin regulatory machinery in T. brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.
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Affiliation(s)
- Desislava P Staneva
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Roberta Carloni
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Tatsiana Auchynnikava
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | | | - Juri Rappsilber
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Biotechnology, Technische Universität, 13355 Berlin, Germany
| | - A Arockia Jeyaprakash
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Keith R Matthews
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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16
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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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17
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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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18
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Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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19
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Padilla-Mejia NE, Koreny L, Holden J, Vancová M, Lukeš J, Zoltner M, Field MC. A hub-and-spoke nuclear lamina architecture in trypanosomes. J Cell Sci 2021; 134:jcs251264. [PMID: 34151975 PMCID: PMC8255026 DOI: 10.1242/jcs.251264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 05/10/2021] [Indexed: 01/11/2023] Open
Abstract
The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration.
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Affiliation(s)
| | - Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Holden
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Marie Vancová
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV 252 50, Vestec, Czech Republic
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
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20
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Davies C, Ooi CP, Sioutas G, Hall BS, Sidhu H, Butter F, Alsford S, Wickstead B, Rudenko G. TbSAP is a novel chromatin protein repressing metacyclic variant surface glycoprotein expression sites in bloodstream form Trypanosoma brucei. Nucleic Acids Res 2021; 49:3242-3262. [PMID: 33660774 PMCID: PMC8034637 DOI: 10.1093/nar/gkab109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
The African trypanosome Trypanosoma brucei is a unicellular eukaryote, which relies on a protective variant surface glycoprotein (VSG) coat for survival in the mammalian host. A single trypanosome has >2000 VSG genes and pseudogenes of which only one is expressed from one of ∼15 telomeric bloodstream form expression sites (BESs). Infectious metacyclic trypanosomes present within the tsetse fly vector also express VSG from a separate set of telomeric metacyclic ESs (MESs). All MESs are silenced in bloodstream form T. brucei. As very little is known about how this is mediated, we performed a whole genome RNAi library screen to identify MES repressors. This allowed us to identify a novel SAP domain containing DNA binding protein which we called TbSAP. TbSAP is enriched at the nuclear periphery and binds both MESs and BESs. Knockdown of TbSAP in bloodstream form trypanosomes did not result in cells becoming more ‘metacyclic-like'. Instead, there was extensive global upregulation of transcripts including MES VSGs, VSGs within the silent VSG arrays as well as genes immediately downstream of BES promoters. TbSAP therefore appears to be a novel chromatin protein playing an important role in silencing the extensive VSG repertoire of bloodstream form T. brucei.
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Affiliation(s)
- Carys Davies
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Cher-Pheng Ooi
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Georgios Sioutas
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Belinda S Hall
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Haneesh Sidhu
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Falk Butter
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Sam Alsford
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Bill Wickstead
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Gloria Rudenko
- Sir Alexander Fleming Building, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
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21
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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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22
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Sureka R, Mishra R. Identification of Evolutionarily Conserved Nuclear Matrix Proteins and Their Prokaryotic Origins. J Proteome Res 2020; 20:518-530. [PMID: 33289389 DOI: 10.1021/acs.jproteome.0c00550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Compared to prokaryotic cells, a typical eukaryotic cell is much more complex along with its endomembrane system and membrane-bound organelles. Although the endosymbiosis theories convincingly explain the evolution of membrane-bound organelles such as mitochondria and chloroplasts, very little is understood about the evolutionary origins of the nucleus, the defining feature of eukaryotes. Most studies on nuclear evolution have not been able to take into consideration the underlying structural framework of the nucleus, attributed to the nuclear matrix (NuMat), a ribonucleoproteinaceous structure. This can largely be attributed to the lack of annotation of its core components. Since NuMat has been shown to provide a structural platform for facilitating a variety of nuclear functions such as replication, transcription, and splicing, it is important to identify its protein components to better understand these processes. In this study, we address this issue using the developing embryos of Drosophila melanogaster and Danio rerio and identify 362 core NuMat proteins that are conserved between the two organisms. We further compare our results with publicly available Mus musculus NuMat dataset and Homo sapiens cellular localization dataset to define the core homologous NuMat proteins consisting of 252 proteins. We find that of them, 86 protein groups have originated from pre-existing proteins in prokaryotes. While 36 were conserved across all eukaryotic supergroups, 14 new proteins evolved before the evolution of the last eukaryotic common ancestor and together, these 50 proteins out of the 252 core conserved NuMat proteins are conserved across all eukaryotes, indicating their indispensable nature for nuclear function for over 1.5 billion years of eukaryotic history. Our analysis paves the way to understand the evolution of the complex internal nuclear architecture and its functions.
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Affiliation(s)
- Rahul Sureka
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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23
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Leal AZ, Schwebs M, Briggs E, Weisert N, Reis H, Lemgruber L, Luko K, Wilkes J, Butter F, McCulloch R, Janzen CJ. Genome maintenance functions of a putative Trypanosoma brucei translesion DNA polymerase include telomere association and a role in antigenic variation. Nucleic Acids Res 2020; 48:9660-9680. [PMID: 32890403 PMCID: PMC7515707 DOI: 10.1093/nar/gkaa686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/03/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Maintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to offspring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to host-parasite interactions. Here, we describe a dual function of one putative translesion Pol in African trypanosomes, which we now name TbPolIE. Previously, we demonstrated that TbPolIE is associated with telomeric sequences and here we show that RNAi-mediated depletion of TbPolIE transcripts results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. We also show that TbPolIE displays pronounced localization at the nuclear periphery, and that its depletion leads to chromosome segregation defects and increased levels of endogenous DNA damage. Finally, we demonstrate that TbPolIE depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this putative translesion DNA polymerase to host immune evasion by antigenic variation.
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Affiliation(s)
- Andrea Zurita Leal
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Marie Schwebs
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emma Briggs
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Nadine Weisert
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Helena Reis
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Leandro Lemgruber
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Katarina Luko
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jonathan Wilkes
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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24
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Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. The chromatin bound proteome of the human malaria parasite. Microb Genom 2020; 6:e000327. [PMID: 32017676 PMCID: PMC7067212 DOI: 10.1099/mgen.0.000327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins interacting with DNA are fundamental for mediating processes such as gene expression, DNA replication and maintenance of genome integrity. Accumulating evidence suggests that the chromatin of apicomplexan parasites, such as Plasmodium falciparum, is highly organized, and this structure provides an epigenetic mechanism for transcriptional regulation. To investigate how parasite chromatin structure is being regulated, we undertook comparative genomics analysis using 12 distinct eukaryotic genomes. We identified conserved and parasite-specific chromatin-associated domains (CADs) and proteins (CAPs). We then used the chromatin enrichment for proteomics (ChEP) approach to experimentally capture CAPs in P. falciparum. A topological scoring analysis of the proteomics dataset revealed stage-specific enrichments of CADs and CAPs. Finally, we characterized, two candidate CAPs: a conserved homologue of the structural maintenance of chromosome 3 protein and a homologue of the crowded-like nuclei protein, a plant-like protein functionally analogous to animal nuclear lamina proteins. Collectively, our results provide a comprehensive overview of CAPs in apicomplexans, and contribute to our understanding of the complex molecular components regulating chromatin structure and genome architecture in these deadly parasites.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M. Lu
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Michael P. Washburn
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
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25
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Sima N, McLaughlin EJ, Hutchinson S, Glover L. Escaping the immune system by DNA repair and recombination in African trypanosomes. Open Biol 2019; 9:190182. [PMID: 31718509 PMCID: PMC6893398 DOI: 10.1098/rsob.190182] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
African trypanosomes escape the mammalian immune response by antigenic variation-the periodic exchange of one surface coat protein, in Trypanosoma brucei the variant surface glycoprotein (VSG), for an immunologically distinct one. VSG transcription is monoallelic, with only one VSG being expressed at a time from a specialized locus, known as an expression site. VSG switching is a predominantly recombination-driven process that allows VSG sequences to be recombined into the active expression site either replacing the currently active VSG or generating a 'new' VSG by segmental gene conversion. In this review, we describe what is known about the factors that influence this process, focusing specifically on DNA repair and recombination.
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Affiliation(s)
- Núria Sima
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Emilia Jane McLaughlin
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Sebastian Hutchinson
- Trypanosome Cell Biology and INSERM U1201, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Lucy Glover
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
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Saura A, Iribarren PA, Rojas-Barros D, Bart JM, López-Farfán D, Andrés-León E, Vidal-Cobo I, Boehm C, Alvarez VE, Field MC, Navarro M. SUMOylated SNF2PH promotes variant surface glycoprotein expression in bloodstream trypanosomes. EMBO Rep 2019; 20:e48029. [PMID: 31693280 PMCID: PMC6893287 DOI: 10.15252/embr.201948029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
SUMOylation is a post‐translational modification that positively regulates monoallelic expression of the trypanosome variant surface glycoprotein (VSG). The presence of a highly SUMOylated focus associated with the nuclear body, where the VSG gene is transcribed, further suggests an important role of SUMOylation in regulating VSG expression. Here, we show that SNF2PH, a SUMOylated plant homeodomain (PH)‐transcription factor, is upregulated in the bloodstream form of the parasite and enriched at the active VSG telomere. SUMOylation promotes the recruitment of SNF2PH to the VSG promoter, where it is required to maintain RNA polymerase I and thus to regulate VSG transcript levels. Further, ectopic overexpression of SNF2PH in insect forms, but not of a mutant lacking the PH domain, induces the expression of bloodstream stage‐specific surface proteins. These data suggest that SNF2PH SUMOylation positively regulates VSG monoallelic transcription, while the PH domain is required for the expression of bloodstream‐specific surface proteins. Thus, SNF2PH functions as a positive activator, linking expression of infective form surface proteins and VSG regulation, thereby acting as a major regulator of pathogenicity.
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Affiliation(s)
- Andreu Saura
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | | | - Domingo Rojas-Barros
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | - Jean M Bart
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | - Diana López-Farfán
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | - Isabel Vidal-Cobo
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
| | - Cordula Boehm
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada, Spain
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27
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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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28
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African trypanosomes expressing multiple VSGs are rapidly eliminated by the host immune system. Proc Natl Acad Sci U S A 2019; 116:20725-20735. [PMID: 31554700 PMCID: PMC6789922 DOI: 10.1073/pnas.1905120116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many parasites escape the host immune system by undergoing antigenic variation, a process in which surface antigens are regularly shed and replaced by new ones. Trypanosoma brucei employs multiple sophisticated molecular mechanisms to ensure the expression of a homogeneous VSG coat. We generated a mutant parasite that expresses multiple distinct VSGs and studied the consequences of having a multi-VSG coat during an infection. We showed that expression of multiple VSGs makes the parasites more vulnerable to the immune response, which can now control the trypanosomes from the onset of the infection, allowing most mice to survive. In the future, trypanosome infections may be treated using drugs that generate parasites with multi-VSG coats. Trypanosoma brucei parasites successfully evade the host immune system by periodically switching the dense coat of variant surface glycoprotein (VSG) at the cell surface. Each parasite expresses VSGs in a monoallelic fashion that is tightly regulated. The consequences of exposing multiple VSGs during an infection, in terms of antibody response and disease severity, remain unknown. In this study, we overexpressed a high-mobility group box protein, TDP1, which was sufficient to open the chromatin of silent VSG expression sites, to disrupt VSG monoallelic expression, and to generate viable and healthy parasites with a mixed VSG coat. Mice infected with these parasites mounted a multi-VSG antibody response, which rapidly reduced parasitemia. Consequently, we observed prolonged survival in which nearly 90% of the mice survived a 30-d period of infection with undetectable parasitemia. Immunodeficient RAG2 knock-out mice were unable to control infection with TDP1-overexpressing parasites, showing that the adaptive immune response is critical to reducing disease severity. This study shows that simultaneous exposure of multiple VSGs is highly detrimental to the parasite, even at the very early stages of infection, suggesting that drugs that disrupt VSG monoallelic expression could be used to treat trypanosomiasis.
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29
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Klebanov-Akopyan O, Mishra A, Glousker G, Tzfati Y, Shlomai J. Trypanosoma brucei UMSBP2 is a single-stranded telomeric DNA binding protein essential for chromosome end protection. Nucleic Acids Res 2019; 46:7757-7771. [PMID: 30007364 PMCID: PMC6125633 DOI: 10.1093/nar/gky597] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/06/2018] [Indexed: 01/22/2023] Open
Abstract
Universal minicircle sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind a single-stranded G-rich sequence, UMS, conserved at the replication origins of the mitochondrial (kinetoplast) DNA of trypanosomatids. Here, we report that Trypanosoma brucei TbUMSBP2, which has been previously proposed to function in the replication and segregation of the mitochondrial DNA, colocalizes with telomeres at the nucleus and is essential for their structure, protection and function. Knockdown of TbUMSBP2 resulted in telomere clustering in one or few foci, phosphorylation of histone H2A at the vicinity of the telomeres, impaired nuclear division, endoreduplication and cell growth arrest. Furthermore, TbUMSBP2 depletion caused rapid reduction in the G-rich telomeric overhang, and an increase in C-rich single-stranded telomeric DNA and in extrachromosomal telomeric circles. These results indicate that TbUMSBP2 is essential for the integrity and function of telomeres. The sequence similarity between the mitochondrial UMS and the telomeric overhang and the finding that UMSBPs bind both sequences suggest a common origin and/or function of these interactions in the replication and maintenance of the genomes in the two organelles. This feature could have converged or preserved during the evolution of the nuclear and mitochondrial genomes from their ancestral (likely circular) genome in early diverged protists.
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Affiliation(s)
- Olga Klebanov-Akopyan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada and Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Amartya Mishra
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada and Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Galina Glousker
- Department of Genetics, The Silberman Institute of Life Sciences, Edmond Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, Edmond Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Shlomai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada and Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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30
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Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC. Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell 2019; 29:1100-1110. [PMID: 29496964 PMCID: PMC5921576 DOI: 10.1091/mbc.e17-06-0430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The nuclear pore complex is an ancient component of the eukaryotic cell. We show here that an FG nucleoporin, TbNup53b, in trypanosomes has an association with the splicing machinery and roles in gene expression, indicating that moonlighting roles for nucleoporins are highly ancient and present in the earliest eukaryotes. Components of the nuclear periphery coordinate a multitude of activities, including macromolecular transport, cell-cycle progression, and chromatin organization. Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport, mRNA processing, and transcriptional regulation, and NPC components can define regions of high transcriptional activity in some organisms at the nuclear periphery and nucleoplasm. Lineage-specific features underpin several core nuclear functions and in trypanosomatids, which branched very early from other eukaryotes, unique protein components constitute the lamina, kinetochores, and parts of the NPCs. Here we describe a phenylalanine-glycine (FG)-repeat nucleoporin, TbNup53b, that has dual localizations within the nucleoplasm and NPC. In addition to association with nucleoporins, TbNup53b interacts with a known trans-splicing component, TSR1, and has a role in controlling expression of surface proteins including the nucleolar periphery-located, procyclin genes. Significantly, while several nucleoporins are implicated in intranuclear transcriptional regulation in metazoa, TbNup53b appears orthologous to components of the yeast/human Nup49/Nup58 complex, for which no transcriptional functions are known. These data suggest that FG-Nups are frequently co-opted to transcriptional functions during evolution and extend the presence of FG-repeat nucleoporin control of gene expression to trypanosomes, suggesting that this is a widespread and ancient eukaryotic feature, as well as underscoring once more flexibility within nucleoporin function.
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Affiliation(s)
| | - Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Alexander V Ratushny
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | - Wei-Ming Chen
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | - Jean-Mathieu Bart
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, 18016 Armilla (Granada), Spain
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas, 18016 Armilla (Granada), Spain
| | | | - John D Aitchison
- Center for Infectious Disease Research (formerly Seattle Biomed) and Institute for Systems Biology, Seattle, WA 98109-5234
| | | | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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31
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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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32
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Halliday C, Billington K, Wang Z, Madden R, Dean S, Sunter JD, Wheeler RJ. Cellular landmarks of Trypanosoma brucei and Leishmania mexicana. Mol Biochem Parasitol 2018; 230:24-36. [PMID: 30550896 PMCID: PMC6529878 DOI: 10.1016/j.molbiopara.2018.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 11/29/2022]
Abstract
Trypanosoma and Leishmania are single cell eukaryotic parasites. The cell organisation of these human pathogens is complex and highly structured. This describes an inventory of reliable reference markers for 32 cell structures. These light microscopy landmarks are a valuable resource for researchers.
The kinetoplastids Trypanosoma brucei and Leishmania mexicana are eukaryotes with a highly structured cellular organisation that is reproduced with great fidelity in each generation. The pattern of signal from a fluorescently tagged protein can define the specific structure/organelle that this protein localises to, and can be extremely informative in phenotype analysis in experimental perturbations, life cycle tracking, post-genomic assays and functional analysis of organelles. Using the vast coverage of protein subcellular localisations provided by the TrypTag project, an ongoing project to determine the localisation of every protein encoded in the T. brucei genome, we have generated an inventory of reliable reference organelle markers for both parasites that combines epifluorescence images with a detailed description of the key features of each localisation. We believe this will be a useful comparative resource that will enable researchers to quickly and accurately pinpoint the localisation of their proteins of interest and will provide cellular markers for many types of cell biology studies. We see this as another important step in the post-genomic era analyses of these parasites, in which ever expanding datasets generate numerous candidates to analyse. Adoption of these reference proteins by the community is likely to enhance research studies and enable better comparison of data.
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Affiliation(s)
- Clare Halliday
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK; Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Karen Billington
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ziyin Wang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ross Madden
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Samuel Dean
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
| | - Richard John Wheeler
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK.
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Garapati HS, Mishra K. Comparative genomics of nuclear envelope proteins. BMC Genomics 2018; 19:823. [PMID: 30445911 PMCID: PMC6240307 DOI: 10.1186/s12864-018-5218-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as a hub for a number of important nuclear events including transcription, repair, and regulated gene expression. The proteins associated with the nuclear envelope mediate the NE functions and maintain its structural integrity, which is crucial for survival. In spite of the importance of this structure, knowledge of the protein composition of the nuclear envelope and their function, are limited to very few organisms belonging to Opisthokonta and Archaeplastida supergroups. The NE composition is largely unknown in organisms outside these two supergroups. RESULTS In this study, we have taken a comparative sequence analysis approach to identify the NE proteome that is present across all five eukaryotic supergroups. We identified 22 proteins involved in various nuclear functions to be part of the core NE proteome. The presence of these proteins across eukaryotes, suggests that they are traceable to the Last Eukaryotic Common Ancestor (LECA). Additionally, we also identified the NE proteins that have evolved in a lineage specific manner and those that have been preserved only in a subset of organisms. CONCLUSIONS Our study identifies the conserved features of the nuclear envelope across eukaryotes and provides insights into the potential composition and the functionalities that were constituents of the LECA NE.
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Affiliation(s)
- Hita Sony Garapati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Söderholm N, Javadi A, Flores IS, Flärdh K, Sandblad L. Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins. Sci Rep 2018; 8:16524. [PMID: 30410115 PMCID: PMC6224456 DOI: 10.1038/s41598-018-34886-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/25/2018] [Indexed: 01/14/2023] Open
Abstract
Coiled-coil domains of intermediate filaments (IF) and prokaryotic IF-like proteins enable oligomerisation and filamentation, and no additional function is ascribed to these coiled-coil domains. However, an IF-like protein from Streptomyces reticuli was reported to display cellulose affinity. We demonstrate that cellulose affinity is an intrinsic property of the IF-like proteins FilP and Scy and the coiled-coil protein DivIVA from the genus Streptomyces. Furthermore, IF-like proteins and DivIVA from other prokaryotic species and metazoan IF display cellulose affinity despite having little sequence homology. Cellulose affinity-based purification is utilised to isolate native FilP protein from the whole cell lysate of S. coelicolor. Moreover, cellulose affinity allowed for the isolation of IF and IF-like protein from the whole cell lysate of C. crescentus and a mouse macrophage cell line. The binding to cellulose is mediated by certain combinations of coiled-coil domains, as demornstrated for FilP and lamin. Fusions of target proteins to cellulose-binding coiled-coil domains allowed for cellulose-based protein purification. The data presented show that cellulose affinity is a novel function of certain coiled-coil domains of IF and IF-like proteins from evolutionary diverse species.
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Affiliation(s)
- Niklas Söderholm
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Ala Javadi
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | | | - Klas Flärdh
- Department of Biology, Lund University, 22362, Lund, Sweden
| | - Linda Sandblad
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden.
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35
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Iribarren PA, Di Marzio LA, Berazategui MA, De Gaudenzi JG, Alvarez VE. SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PLoS One 2018; 13:e0193528. [PMID: 29474435 PMCID: PMC5825156 DOI: 10.1371/journal.pone.0193528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 01/10/2023] Open
Abstract
SUMOylation is a post-translational modification conserved in eukaryotic organisms that involves the covalent attachment of the small ubiquitin-like protein SUMO to internal lysine residues in target proteins. This tag usually alters the interaction surface of the modified protein and can be translated into changes in its biological activity, stability or subcellular localization, among other possible outputs. SUMO can be attached as a single moiety or as SUMO polymers in case there are internal acceptor sites in SUMO itself. These chains have been shown to be important for proteasomal degradation as well as for the formation of subnuclear structures such as the synaptonemal complex in Saccharomyces cerevisiae or promyelocytic leukemia nuclear bodies in mammals. In this work, we have examined SUMO chain formation in the protozoan parasite Trypanosoma brucei. Using a recently developed bacterial strain engineered to produce SUMOylated proteins we confirmed the ability of TbSUMO to form polymers and determined the type of linkage using site-directed mutational analysis. By generating transgenic procyclic parasites unable to form chains we demonstrated that although not essential for normal growth, SUMO polymerization determines the localization of the modified proteins in the nucleus. In addition, FISH analysis of telomeres showed a differential positioning depending on the polySUMOylation abilities of the cells. Thus, our observations suggest that TbSUMO chains might play a role in establishing interaction platforms contributing to chromatin organization.
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Affiliation(s)
- Paula Ana Iribarren
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Lucía Ayelén Di Marzio
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - María Agustina Berazategui
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Javier Gerardo De Gaudenzi
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
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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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Ávila AR, Cabezas-Cruz A, Gissot M. mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway. Parasit Vectors 2018; 11:62. [PMID: 29370868 PMCID: PMC5785795 DOI: 10.1186/s13071-018-2648-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/15/2018] [Indexed: 01/08/2023] Open
Abstract
Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.
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Affiliation(s)
- Andréa Rodrigues Ávila
- Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR, 81350-010, Brazil. .,UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.
| | - Alexjandro Cabezas-Cruz
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, ENVA, Maisons Alfort, Cedex, France.,Institute of Parasitology, Biology Center, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mathieu Gissot
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
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38
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Abstract
Many pathogens evade host immunity by periodically changing the proteins they express on their surface - a phenomenon termed antigenic variation. An extreme form of antigenic variation, based around switching the composition of a Variant Surface Glycoprotein (VSG) coat, is exhibited by the African trypanosome Trypanosoma brucei, which causes human disease. The molecular details of VSG switching in T. brucei have been extensively studied over the last three decades, revealing in increasing detail the machinery and mechanisms by which VSG expression is controlled and altered. However, several key components of the models of T. brucei antigenic variation that have emerged have been challenged through recent discoveries. These discoveries include new appreciation of the importance of gene mosaics in generating huge levels of new VSG variants, the contributions of parasite development and body compartmentation in the host to the infection dynamics and, finally, potential differences in the strategies of antigenic variation and host infection used by the crucial livestock trypanosomes T. congolense and T. vivax. This review will discuss all these observations, which raise questions regarding how secure the existing models of trypanosome antigenic variation are. In addition, we will discuss the importance of continued mathematical modelling to understand the purpose of this widespread immune survival process.
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Abstract
Protozoan parasites colonize numerous metazoan hosts and insect vectors through their life cycles, with the need to respond quickly and reversibly while encountering diverse and often hostile ecological niches. To succeed, parasites must also persist within individuals until transmission between hosts is achieved. Several parasitic protozoa cause a huge burden of disease in humans and livestock, and here we focus on the parasites that cause malaria and African trypanosomiasis. Efforts to understand how these pathogens adapt to survive in varied host environments, cause disease, and transmit between hosts have revealed a wealth of epigenetic phenomena. Epigenetic switching mechanisms appear to be ideally suited for the regulation of clonal antigenic variation underlying successful parasitism. We review the molecular players and complex mechanistic layers that mediate the epigenetic regulation of virulence gene expression. Understanding epigenetic processes will aid the development of antiparasitic therapeutics.
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Affiliation(s)
- Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA.
| | - David Horn
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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40
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Goos C, Dejung M, Janzen CJ, Butter F, Kramer S. The nuclear proteome of Trypanosoma brucei. PLoS One 2017; 12:e0181884. [PMID: 28727848 PMCID: PMC5519215 DOI: 10.1371/journal.pone.0181884] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022] Open
Abstract
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes.
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Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
- * E-mail: (SK); (FB)
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail: (SK); (FB)
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41
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Obado SO, Field MC, Rout MP. Comparative interactomics provides evidence for functional specialization of the nuclear pore complex. Nucleus 2017; 8:340-352. [PMID: 28463551 DOI: 10.1080/19491034.2017.1313936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineage-specific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.
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Affiliation(s)
| | - Mark C Field
- b Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences , University of Dundee , Dundee , UK
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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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Manna PT, Obado SO, Boehm C, Gadelha C, Sali A, Chait BT, Rout MP, Field MC. Lineage-specific proteins essential for endocytosis in trypanosomes. J Cell Sci 2017; 130:1379-1392. [PMID: 28232524 PMCID: PMC5399782 DOI: 10.1242/jcs.191478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is the most evolutionarily ancient endocytic mechanism known, and in many lineages the sole mechanism for internalisation. Significantly, in mammalian cells CME is responsible for the vast bulk of endocytic flux and has likely undergone multiple adaptations to accommodate specific requirements by individual species. In African trypanosomes, we previously demonstrated that CME is independent of the AP-2 adaptor protein complex, that orthologues to many of the animal and fungal CME protein cohort are absent, and that a novel, trypanosome-restricted protein cohort interacts with clathrin and drives CME. Here, we used a novel cryomilling affinity isolation strategy to preserve transient low-affinity interactions, giving the most comprehensive trypanosome clathrin interactome to date. We identified the trypanosome AP-1 complex, Trypanosoma brucei (Tb)EpsinR, several endosomal SNAREs plus orthologues of SMAP and the AP-2 associated kinase AAK1 as interacting with clathrin. Novel lineage-specific proteins were identified, which we designate TbCAP80 and TbCAP141. Their depletion produced extensive defects in endocytosis and endomembrane system organisation, revealing a novel molecular pathway subtending an early-branching and highly divergent form of CME, which is conserved and likely functionally important across the kinetoplastid parasites. Summary: Endocytosis is a vital process in most cells, and here we identify important proteins required for this process in trypanosomes. Significantly, these are unique and not present in animals, fungi or plants.
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Affiliation(s)
- Paul T Manna
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| | - Samson O Obado
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Cordula Boehm
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham NG2 7UH, UK
| | - Andrej Sali
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Brian T Chait
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Michael P Rout
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
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44
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Poulet A, Probst AV, Graumann K, Tatout C, Evans D. Exploring the evolution of the proteins of the plant nuclear envelope. Nucleus 2017; 8:46-59. [PMID: 27644504 PMCID: PMC5287204 DOI: 10.1080/19491034.2016.1236166] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/22/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022] Open
Abstract
In this study, we explore the plasticity during evolution of proteins of the higher plant nuclear envelope (NE) from the most ancestral plant species to advanced angiosperms. The higher plant NE contains a functional Linker of Nucleoskeleton and Cytoskeleton (LINC) complex based on conserved Sad1-Unc84 (SUN) domain proteins and plant specific Klarsicht/Anc1/Syne homology (KASH) domain proteins. Recent evidence suggests the presence of a plant lamina underneath the inner membrane and various coiled-coil proteins have been hypothesized to be associated with it including Crowded Nuclei (CRWN; also termed LINC and NMCP), Nuclear Envelope Associated Protein (NEAP) protein families as well as the CRWN binding protein KAKU4. SUN domain proteins appear throughout with a key role for mid-SUN proteins suggested. Evolution of KASH domain proteins has resulted in increasing complexity, with some appearing in all species considered, while other KASH proteins are progressively gained during evolution. Failure to identify CRWN homologs in unicellular organisms included in the study and their presence in plants leads us to speculate that convergent evolution may have occurred in the formation of the lamina with each kingdom having new proteins such as the Lamin B receptor (LBR) and Lamin-Emerin-Man1 (LEM) domain proteins (animals) or NEAPs and KAKU4 (plants). Our data support a model in which increasing complexity at the nuclear envelope occurred through the plant lineage and suggest a key role for mid-SUN proteins as an early and essential component of the nuclear envelope.
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Affiliation(s)
- Axel Poulet
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - Aline V. Probst
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - Katja Graumann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Christophe Tatout
- UMR CNRS 6293 INSERM U1103 Clermont Université, GReD, Aubière, France
| | - David Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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45
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Abstract
For years intermediate filaments (IF), belonging to the third class of filamentous cytoskeletal proteins alongside microtubules and actin filaments, were thought to be exclusive to metazoan cells. Structurally these eukaryote IFs are very well defined, consisting of globular head and tail domains, which flank the central rod-domain. This central domain is dominated by an α-helical secondary structure predisposed to form the characteristic coiled-coil, parallel homo-dimer. These elementary dimers can further associate, both laterally and longitudinally, generating a variety of filament-networks built from filaments in the range of 10 nm in diameter. The general role of these filaments with their characteristic mechano-elastic properties both in the cytoplasm and in the nucleus of eukaryote cells is to provide mechanical strength and a scaffold supporting diverse shapes and cellular functions.Since 2003, after the first bacterial IF-like protein, crescentin was identified, it has been evident that bacteria also employ filamentous networks, other than those built from bacterial tubulin or actin homologues, in order to support their cell shape, growth and, in some cases, division. Intriguingly, compared to their eukaryote counterparts, the group of bacterial IF-like proteins shows much wider structural diversity. The sizes of both the head and tail domains are markedly reduced and there is great variation in the length of the central rod-domain. Furthermore, bacterial rod-domains often lack the sub-domain organisation of eukaryote IFs that is the defining feature of the IF-family. However, the fascinating display of filamentous assemblies, including rope, striated cables and hexagonal laces together with the conditions required for their formation both in vitro and in vivo strongly resemble that of eukaryote IFs suggesting that these bacterial proteins are deservedly classified as part of the IF-family and that the current definition should be relaxed slightly to allow their inclusion. The lack of extensive head and tail domains may well make the bacterial proteins more amenable for structural characterisation, which will be essential for establishing the mechanism for their association into filaments. What is more, the well-developed tools for bacterial manipulations provide an excellent opportunity of studying the bacterial systems with the prospect of making significant progress in our understanding of the general underlying principles of intermediate filament assemblies.
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Affiliation(s)
- Gabriella H Kelemen
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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46
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Fernández-Álvarez A, Cooper JP. Chromosomes Orchestrate Their Own Liberation: Nuclear Envelope Disassembly. Trends Cell Biol 2016; 27:255-265. [PMID: 28024902 DOI: 10.1016/j.tcb.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
The mammalian nuclear division cycle is coordinated with nuclear envelope breakdown (NEBD), in which the entire nuclear envelope (NE) is dissolved to allow chromosomes to access their segregation vehicle, the spindle. In other eukaryotes, complete NEBD is replaced by localized disassembly or remodeling of the NE. Although the molecular mechanisms controlling NE disassembly are incompletely understood, coordinated cycles of modification of specific NE components drive breakdown. Here, we review the current state of knowledge regarding NE disassembly and argue for a role of chromosome-NE contacts in triggering initiation of NE disassembly and thereby, cell division.
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Affiliation(s)
- Alfonso Fernández-Álvarez
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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47
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Leandro de Jesus TC, Calderano SG, Vitorino FNDL, Llanos RP, Lopes MDC, de Araújo CB, Thiemann OH, Reis MDS, Elias MC, Chagas da Cunha JP. Quantitative Proteomic Analysis of Replicative and Nonreplicative Forms Reveals Important Insights into Chromatin Biology of Trypanosoma cruzi. Mol Cell Proteomics 2016; 16:23-38. [PMID: 27852749 DOI: 10.1074/mcp.m116.061200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/02/2016] [Indexed: 01/02/2023] Open
Abstract
Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and nonreplicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and nonreplicative (trypomastigote) forms by high-resolution mass spectrometry. More than 2000 proteins were identified and quantified both in chromatin and nonchromatin extracts. Besides histones and other known nuclear proteins, trypanosomes chromatin also contains metabolic (mainly from carbohydrate pathway), cytoskeleton and many other proteins with unknown functions. Strikingly, the two parasite forms differ greatly regarding their chromatin-associated factors composition and amount. Although the nucleosome content is the same for both life forms (as seen by MNase digestion), the remaining proteins were much less detected in nonreplicative forms, suggesting that they have a naked chromatin. Proteins associated to DNA proliferation, such as PCNA, RPA, and DNA topoisomerases were exclusively found in the chromatin of replicative stages. On the other hand, the nonreplicative stages have an enrichment of a histone H2B variant. Furthermore, almost 20% of replicative stages chromatin-associated proteins are expressed in nonreplicative forms, but located at nonchromatin space. We identified different classes of proteins including phosphatases and a Ran-binding protein, that may shuttle between chromatin and nonchromatin space during differentiation. Seven proteins, including those with unknown functions, were selected for further validation. We confirmed their location in chromatin and their differential expression, using Western blotting assays and chromatin immunoprecipitation (ChIP). Our results indicate that the replicative state in trypanosomes involves an increase of chromatin associated proteins content. We discuss in details, the qualitative and quantitative implication of this chromatin set in trypanosome chromatin biology. Because trypanosomes are early-branching organisms, this data can boost our understanding of chromatin-associated processes in other cell types.
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Affiliation(s)
- Teresa Cristina Leandro de Jesus
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,§Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo - USP, São Carlos, SP, 13563-120, Brazil
| | - Simone Guedes Calderano
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,¶Laboratório de Parasitologia, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Francisca Nathalia de Luna Vitorino
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Ricardo Pariona Llanos
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Mariana de Camargo Lopes
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Christiane Bezerra de Araújo
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Otavio Henrique Thiemann
- §Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo - USP, São Carlos, SP, 13563-120, Brazil
| | - Marcelo da Silva Reis
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Maria Carolina Elias
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Julia Pinheiro Chagas da Cunha
- From the ‡Laboratório Especial de Ciclo Celular - Center of Toxins, Immune-Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, SP, 05503-900, Brazil;
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48
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Abstract
The last decade has seen rapid advances in our understanding of the proteins of the nuclear envelope, which have multiple roles including positioning the nucleus, maintaining its structural organization, and in events ranging from mitosis and meiosis to chromatin positioning and gene expression. Diverse new and stimulating results relating to nuclear organization and genome function from across kingdoms were presented in a session stream entitled “Dynamic Organization of the Nucleus” at this year's Society of Experimental Biology (SEB) meeting in Brighton, UK (July 2016). This was the first session stream run by the Nuclear Dynamics Special Interest Group, which was organized by David Evans, Katja Graumann (both Oxford Brookes University, UK) and Iris Meier (Ohio State University, USA). The session featured presentations on areas relating to nuclear organization across kingdoms including the nuclear envelope, chromatin organization, and genome function.
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Affiliation(s)
- Stephen D Thorpe
- a Institute of Bioengineering, School of Engineering and Materials Science , Queen Mary University of London , London , UK
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49
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Abstract
The emergence of the nucleus was a major event of eukaryogenesis. How the nuclear envelope (NE) arose and acquired functions governing chromatin organization and epigenetic control has direct bearing on origins of developmental/stage-specific expression programs. The configuration of the NE and the associated lamina in the last eukaryotic common ancestor (LECA) is of major significance and can provide insight into activities within the LECA nucleus. Subsequent lamina evolution, alterations, and adaptations inform on the variation and selection of distinct mechanisms that subtend gene expression in distinct taxa. Understanding lamina evolution has been difficult due to the diversity and limited taxonomic distributions of the three currently known highly distinct nuclear lamina. We rigorously searched available sequence data for an expanded view of the distribution of known lamina and lamina-associated proteins. While the lamina proteins of plants and trypanosomes are indeed taxonomically restricted, homologs of metazoan lamins and key lamin-binding proteins have significantly broader distributions, and a lamin gene tree supports vertical evolution from the LECA. Two protist lamins from highly divergent taxa target the nucleus in mammalian cells and polymerize into filamentous structures, suggesting functional conservation of distant lamin homologs. Significantly, a high level of divergence of lamin homologs within certain eukaryotic groups and the apparent absence of lamins and/or the presence of seemingly different lamina proteins in many eukaryotes suggests great evolutionary plasticity in structures at the NE, and hence mechanisms of chromatin tethering and epigenetic gene control.
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Affiliation(s)
- Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK
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Maishman L, Obado SO, Alsford S, Bart JM, Chen WM, Ratushny AV, Navarro M, Horn D, Aitchison JD, Chait BT, Rout MP, Field MC. Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression. Nucleic Acids Res 2016; 44:10554-10570. [PMID: 27625397 PMCID: PMC5159534 DOI: 10.1093/nar/gkw751] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/02/2016] [Accepted: 08/20/2016] [Indexed: 12/17/2022] Open
Abstract
The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component.
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Affiliation(s)
- Luke Maishman
- School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - Samson O Obado
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sam Alsford
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jean-Mathieu Bart
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Cientificas, 18100 Grenada, Spain
| | - Wei-Ming Chen
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA
| | - Alexander V Ratushny
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA.,Institute for Systems Biology, Seattle, WA 98109, USA
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Cientificas, 18100 Grenada, Spain
| | - David Horn
- School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - John D Aitchison
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA.,Institute for Systems Biology, Seattle, WA 98109, USA
| | - Brian T Chait
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael P Rout
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK
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