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Nakanishi M, Takezaki R, Takeguchi M, Hino M, Nomoto H. Synthetic arrest of Man 5GlcNAc 2-PP-Dol increases procyclin mRNA level and induces cell death in the bloodstream form Trypanosoma brucei brucei. Parasitol Int 2024; 99:102831. [PMID: 38048903 DOI: 10.1016/j.parint.2023.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
The biosynthesis of N-linked glycan precursors in the endoplasmic reticulum is important for many eukaryotes. In particular, the synthesis of Man5GlcNAc2-PP-dolichol (M5-DLO) at the cytoplasmic face of the endoplasmic reticulum is essential for maintaining cellular functions. In Trypanosoma brucei, the unicellular organism that causes African trypanosomiasis, homologs of the mannosyltransferases ALG2 and ALG11, which are involved in the biosynthesis of M5-DLO, are found, but the effects of their deletion on cells remain unknown. In this study, we generated conditional gene knockout strains of TbALG2 and TbALG11 in the bloodstream form T. brucei. Decreased N-linked glycosylation and cell death were observed in both strains under non-permissive conditions, with TbALG2 having a greater effect than TbALG11. Transcriptomic analysis of cells losing expression of TbALG11 showed decrease in mRNAs for enzymes involved in glucose metabolism and increase in mRNAs for procyclins and variant surface glycoproteins. These results indicate that the M5-DLO biosynthetic pathway is essential for the proliferation of the bloodstream form T. brucei. They also suggest that the failure of this pathway induces the transcriptomic change.
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Affiliation(s)
- Masayuki Nakanishi
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.
| | - Reo Takezaki
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Masaki Takeguchi
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Mami Hino
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Hiroshi Nomoto
- Laboratory of Biochemistry, School of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
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2
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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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3
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Briggs EM, Marques CA, Oldrieve GR, Hu J, Otto TD, Matthews KR. Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomics. eLife 2023; 12:e86325. [PMID: 37166108 PMCID: PMC10212563 DOI: 10.7554/elife.86325] [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: 01/20/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023] Open
Abstract
African trypanosomes proliferate as bloodstream forms (BSFs) and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single-cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated (CCR) transcriptomes of both procyclic and slender BSF Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single-cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the CCR transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
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Affiliation(s)
- Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Catarina A Marques
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Guy R Oldrieve
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Jihua Hu
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Thomas D Otto
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
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Wen YZ, Tang HT, Cai XL, Wu N, Xu JZ, Su BX, Hide G, Lun ZR, Lai DH. PAG3 promotes the differentiation of bloodstream forms in Trypanosoma brucei and reveals the evolutionary relationship among the Trypanozoon trypanosomes. Front Cell Infect Microbiol 2022. [DOI: 10.3389/fcimb.2022.1021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
IntroductionTrypanosoma brucei, T. evansi and T. equiperdum are members of the subgenus Trypanozoon and are highly similar morphologically and genetically. The main differences between these three species are their differentiation patterns in the hosts and the role of vectors in their life cycles. However, the mechanisms causing these differences are still controversial.MethodsPAG3 gene was accessed by PCR amplification in 26 strains of Trypanozoon and sequences were then analyzed by BLAST accompanied with T. evansitype B group. RNA interference and CRISPR/Cas9 were used for revealing possible role of PAG3 in slender to stumpy transformation.ResultsThe procyclin associated gene 3 (PAG3) can be found in the pleomorphicspecies, T.brucei, which undergoes differentiation of slender forms to the stumpy form. This differentiation process is crucial for transmission to the tsetse fly vector. However, a homologue of PAG3 was not detected in either T. evansi or in the majority of T. equiperdum strains which are allmonomorphic. Furthere xperiments in T. brucei demonstrated that, when PAG3 was down-regulated or absent, there was a significant reduction in the differentiation from slender to stumpy forms.ConclusionTherefore, we conclude that PAG3 is a key nuclear gene involved in the slender to stumpy differentiation pathway of T.brucei in the mammalian host. Loss of this gene might also offer a simple evolutionary mechanism explaining why T. evansi and some T. equiperdum have lost the ability to differentiate and have been driven to adapt to transmission cycles that by pass the tsetse vector or mechanical contact.
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5
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Knüsel S, Jenni A, Benninger M, Bütikofer P, Roditi I. Persistence of Trypanosoma brucei as early procyclic forms and social motility are dependent on glycosylphosphatidylinositol transamidase. Mol Microbiol 2021; 117:802-817. [PMID: 34954848 PMCID: PMC9303471 DOI: 10.1111/mmi.14873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/10/2021] [Accepted: 12/21/2021] [Indexed: 12/04/2022]
Abstract
Glycosylphosphatidylinositol (GPI)‐linked molecules are surface‐exposed membrane components that influence the infectivity, virulence and transmission of many eukaryotic pathogens. Procyclic (insect midgut) forms of Trypanosoma brucei do not require GPI‐anchored proteins for growth in suspension culture. Deletion of TbGPI8, and inactivation of the GPI:protein transamidase complex, is tolerated by cultured procyclic forms. Using a conditional knockout, we show TbGPI8 is required for social motility (SoMo). This collective migration by cultured early procyclic forms has been linked to colonization of the tsetse fly digestive tract. The SoMo‐negative phenotype was observed after a lag phase with respect to loss of TbGPI8 and correlated with an unexpectedly slow loss of procyclins, the major GPI‐anchored proteins. Procyclins are not essential for SoMo, however, suggesting a requirement for at least one other GPI‐anchored protein. Loss of TbGPI8 initiates the transition from early to late procyclic forms; this effect was observed in a subpopulation in suspension culture, and was more pronounced when cells were cultured on SoMo plates. Our results indicate two, potentially interlinked, scenarios that may explain the previously reported failure of TbGPI8 deletion mutants to establish a midgut infection in the tsetse fly: interference with stage‐specific gene expression and absence of SoMo.
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Affiliation(s)
- Sebastian Knüsel
- Institute of Cell Biology, University of Bern, 3012, Bern, Switzerland
| | - Aurelio Jenni
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland.,Graduate School for Chemical and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Mattias Benninger
- Institute of Cell Biology, University of Bern, 3012, Bern, Switzerland
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, 3012, Bern, Switzerland
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6
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Borges AR, Link F, Engstler M, Jones NG. The Glycosylphosphatidylinositol Anchor: A Linchpin for Cell Surface Versatility of Trypanosomatids. Front Cell Dev Biol 2021; 9:720536. [PMID: 34790656 PMCID: PMC8591177 DOI: 10.3389/fcell.2021.720536] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
The use of glycosylphosphatidylinositol (GPI) to anchor proteins to the cell surface is widespread among eukaryotes. The GPI-anchor is covalently attached to the C-terminus of a protein and mediates the protein’s attachment to the outer leaflet of the lipid bilayer. GPI-anchored proteins have a wide range of functions, including acting as receptors, transporters, and adhesion molecules. In unicellular eukaryotic parasites, abundantly expressed GPI-anchored proteins are major virulence factors, which support infection and survival within distinct host environments. While, for example, the variant surface glycoprotein (VSG) is the major component of the cell surface of the bloodstream form of African trypanosomes, procyclin is the most abundant protein of the procyclic form which is found in the invertebrate host, the tsetse fly vector. Trypanosoma cruzi, on the other hand, expresses a variety of GPI-anchored molecules on their cell surface, such as mucins, that interact with their hosts. The latter is also true for Leishmania, which use GPI anchors to display, amongst others, lipophosphoglycans on their surface. Clearly, GPI-anchoring is a common feature in trypanosomatids and the fact that it has been maintained throughout eukaryote evolution indicates its adaptive value. Here, we explore and discuss GPI anchors as universal evolutionary building blocks that support the great variety of surface molecules of trypanosomatids.
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Affiliation(s)
- Alyssa R Borges
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Fabian Link
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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7
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Naguleswaran A, Fernandes P, Bevkal S, Rehmann R, Nicholson P, Roditi I. Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host. PLoS Negl Trop Dis 2021; 15:e0009504. [PMID: 34543277 PMCID: PMC8483307 DOI: 10.1371/journal.pntd.0009504] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/30/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Trypanosoma brucei ssp., unicellular parasites causing human and animal trypanosomiasis, are transmitted between mammals by tsetse flies. Periodic changes in variant surface glycoproteins (VSG), which form the parasite coat in the mammal, allow them to evade the host immune response. Different isolates of T. brucei show heterogeneity in their repertoires of VSG genes and have single nucleotide polymorphisms and indels that can impact on genome editing. T. brucei brucei EATRO1125 (AnTaR1 serodeme) is an isolate that is used increasingly often because it is pleomorphic in mammals and fly transmissible, two characteristics that have been lost by the most commonly used laboratory stocks. We present a genome assembly of EATRO1125, including contigs for the intermediate chromosomes and minichromosomes that serve as repositories of VSG genes. In addition, de novo transcriptome assemblies were performed using Illumina sequences from tsetse-derived trypanosomes. Reads of 150 bases enabled closely related members of multigene families to be discriminated. This revealed that the transcriptome of midgut-derived parasites is dynamic, starting with the expression of high affinity hexose transporters and glycolytic enzymes and then switching to proline uptake and catabolism. These changes resemble the transition from early to late procyclic forms in culture. Further metabolic reprogramming, including upregulation of tricarboxylic acid cycle enzymes, occurs in the proventriculus. Many transcripts upregulated in the salivary glands encode surface proteins, among them 7 metacyclic VSGs, multiple BARPs and GCS1/HAP2, a marker for gametes. A novel family of transmembrane proteins, containing polythreonine stretches that are predicted to be O-glycosylation sites, was also identified. Finally, RNA-Seq data were used to create an optimised annotation file with 5’ and 3’ untranslated regions accurately mapped for 9302 genes. We anticipate that this will be of use in identifying transcripts obtained by single cell sequencing technologies. Trypanosoma brucei ssp. are single-celled parasites that cause two tropical diseases: sleeping sickness in humans and nagana in domestic animals. Parasites survive in the host bloodstream because they periodically change their surface coats and also because they can switch from slender dividing forms to stumpy non-dividing forms. The latter can be transmitted to their second host, the tsetse fly. Although closely related, different geographical isolates differ in their repertoire of surface coats and have small, but important differences in their DNA sequences. In addition, laboratory strains that are transferred between mammals by needle passage lose the ability to produce stumpy forms and to infect flies. The isolate T. b. brucei EATRO1125 is often used for research as it produces stumpy forms and is fly transmissible. We provide an assembly of the genome of this isolate, including part of the repertoire of coat proteins, and a detailed analysis of the genes that the parasites express as they establish infection and progress through the fly. This has provided new insights into trypanosome biology. The combined genomic (DNA) and transcriptomic (RNA) data will be useful resources for the trypanosome research community.
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Affiliation(s)
| | - Paula Fernandes
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Shubha Bevkal
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ruth Rehmann
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Pamela Nicholson
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
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8
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Gilabert Carbajo C, Cornell LJ, Madbouly Y, Lai Z, Yates PA, Tinti M, Tiengwe C. Novel aspects of iron homeostasis in pathogenic bloodstream form Trypanosoma brucei. PLoS Pathog 2021; 17:e1009696. [PMID: 34161395 PMCID: PMC8259959 DOI: 10.1371/journal.ppat.1009696] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/06/2021] [Accepted: 06/04/2021] [Indexed: 01/09/2023] Open
Abstract
Iron is an essential regulatory signal for virulence factors in many pathogens. Mammals and bloodstream form (BSF) Trypanosoma brucei obtain iron by receptor-mediated endocytosis of transferrin bound to receptors (TfR) but the mechanisms by which T. brucei subsequently handles iron remains enigmatic. Here, we analyse the transcriptome of T. brucei cultured in iron-rich and iron-poor conditions. We show that adaptation to iron-deprivation induces upregulation of TfR, a cohort of parasite-specific genes (ESAG3, PAGS), genes involved in glucose uptake and glycolysis (THT1 and hexokinase), endocytosis (Phosphatidic Acid Phosphatase, PAP2), and most notably a divergent RNA binding protein RBP5, indicative of a non-canonical mechanism for regulating intracellular iron levels. We show that cells depleted of TfR by RNA silencing import free iron as a compensatory survival strategy. The TfR and RBP5 iron response are reversible by genetic complementation, the response kinetics are similar, but the regulatory mechanisms are distinct. Increased TfR protein is due to increased mRNA. Increased RBP5 expression, however, occurs by a post-transcriptional feedback mechanism whereby RBP5 interacts with its own, and with PAP2 mRNAs. Further observations suggest that increased RBP5 expression in iron-deprived cells has a maximum threshold as ectopic overexpression above this threshold disrupts normal cell cycle progression resulting in an accumulation of anucleate cells and cells in G2/M phase. This phenotype is not observed with overexpression of RPB5 containing a point mutation (F61A) in its single RNA Recognition Motif. Our experiments shed new light on how T. brucei BSFs reorganise their transcriptome to deal with iron stress revealing the first iron responsive RNA binding protein that is co-regulated with TfR, is important for cell viability and iron homeostasis; two essential processes for successful proliferation.
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Affiliation(s)
- Carla Gilabert Carbajo
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, United Kingdom
| | - Lucy J. Cornell
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, United Kingdom
| | - Youssef Madbouly
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, United Kingdom
| | - Zhihao Lai
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, United Kingdom
| | - Phillip A. Yates
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Michele Tinti
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Calvin Tiengwe
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, United Kingdom
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9
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Christiano R, Kolev NG, Shi H, Ullu E, Walther TC, Tschudi C. The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion. Mol Microbiol 2017; 106:74-92. [PMID: 28742275 DOI: 10.1111/mmi.13754] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2017] [Indexed: 01/22/2023]
Abstract
The infectious metacyclic forms of Trypanosoma brucei result from a complex development in the tsetse fly vector. When they infect mammals, they cause African sleeping sickness in humans. Due to scarcity of biological material and difficulties of the tsetse fly as an experimental system, very limited information is available concerning the gene expression profile of metacyclic forms. We used an in vitro system based on expressing the RNA binding protein 6 to obtain infectious metacyclics and determined their protein and mRNA repertoires by mass-spectrometry (MS) based proteomics and mRNA sequencing (RNA-Seq) in comparison to non-infectious procyclic trypanosomes. We showed that metacyclics are quiescent cells, and propose this influences the choice of a monocistronic variant surface glycoprotein expression site. Metacyclics have a largely bloodstream-form type transcriptome, and thus are programmed to translate a bloodstream-form type proteome upon entry into the mammalian host and resumption of cell division. Genes encoding cell surface components showed the largest changes between procyclics and metacyclics, observed at both the transcript and protein levels. Genes encoding metabolic enzymes exhibited expression in metacyclics with features of both procyclic and bloodstream forms, suggesting that this intermediate-type metabolism is dictated by the availability of nutrients in the tsetse fly vector.
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Affiliation(s)
- Romain Christiano
- Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nikolay G Kolev
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Huafang Shi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06520, USA
| | - Elisabetta Ullu
- Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT 06520, USA.,Department of Internal Medicine, School of Medicine, Yale University, 330 Cedar St, Boardman 110, New Haven, CT 06520, USA
| | - Tobias C Walther
- Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Harvard T.H. Chan School of Public Health Boston, MA 02115, USA
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06520, USA
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10
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Imhof S, Fragoso C, Hemphill A, von Schubert C, Li D, Legant W, Betzig E, Roditi I. Flagellar membrane fusion and protein exchange in trypanosomes; a new form of cell-cell communication? F1000Res 2016; 5:682. [PMID: 27239276 PMCID: PMC4870996 DOI: 10.12688/f1000research.8249.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
Diverse structures facilitate direct exchange of proteins between cells, including plasmadesmata in plants and tunnelling nanotubes in bacteria and higher eukaryotes. Here we describe a new mechanism of protein transfer, flagellar membrane fusion, in the unicellular parasite
Trypanosoma brucei. When fluorescently tagged trypanosomes were co-cultured, a small proportion of double-positive cells were observed. The formation of double-positive cells was dependent on the presence of extracellular calcium and was enhanced by placing cells in medium supplemented with fresh bovine serum. Time-lapse microscopy revealed that double-positive cells arose by bidirectional protein exchange in the absence of nuclear transfer. Furthermore, super-resolution microscopy showed that this process occurred in ≤1 minute, the limit of temporal resolution in these experiments. Both cytoplasmic and membrane proteins could be transferred provided they gained access to the flagellum. Intriguingly, a component of the RNAi machinery (Argonaute) was able to move between cells, raising the possibility that small interfering RNAs are transported as cargo. Transmission electron microscopy showed that shared flagella contained two axonemes and two paraflagellar rods bounded by a single membrane. In some cases flagellar fusion was partial and interactions between cells were transient. In other cases fusion occurred along the entire length of the flagellum, was stable for several hours and might be irreversible. Fusion did not appear to be deleterious for cell function: paired cells were motile and could give rise to progeny while fused. The motile flagella of unicellular organisms are related to the sensory cilia of higher eukaryotes, raising the possibility that protein transfer between cells via cilia or flagella occurs more widely in nature.
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Affiliation(s)
- Simon Imhof
- Institute of Cell Biology, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Cristina Fragoso
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Conrad von Schubert
- Division of Molecular Pathobiology, DCR-VPH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Dong Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Wesley Legant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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11
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Reynolds D, Hofmeister BT, Cliffe L, Alabady M, Siegel TN, Schmitz RJ, Sabatini R. Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei. PLoS Genet 2016; 12:e1005758. [PMID: 26796527 PMCID: PMC4721609 DOI: 10.1371/journal.pgen.1005758] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/01/2015] [Indexed: 01/22/2023] Open
Abstract
Base J, β-D-glucosyl-hydroxymethyluracil, is a chromatin modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. In Trypanosoma brucei, J is enriched, along with histone H3 variant (H3.V), at sites involved in RNA Polymerase (RNAP) II termination and telomeric sites involved in regulating variant surface glycoprotein gene (VSG) transcription by RNAP I. Reduction of J in T. brucei indicated a role of J in the regulation of RNAP II termination, where the loss of J at specific sites within polycistronic gene clusters led to read-through transcription and increased expression of downstream genes. We now demonstrate that the loss of H3.V leads to similar defects in RNAP II termination within gene clusters and increased expression of downstream genes. Gene derepression is intensified upon the subsequent loss of J in the H3.V knockout. mRNA-seq indicates gene derepression includes VSG genes within the silent RNAP I transcribed telomeric gene clusters, suggesting an important role for H3.V in telomeric gene repression and antigenic variation. Furthermore, the loss of H3.V at regions of overlapping transcription at the end of convergent gene clusters leads to increased nascent RNA and siRNA production. Our results suggest base J and H3.V can act independently as well as synergistically to regulate transcription termination and expression of coding and non-coding RNAs in T. brucei, depending on chromatin context (and transcribing polymerase). As such these studies provide the first direct evidence for histone H3.V negatively influencing transcription elongation to promote termination.
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Affiliation(s)
- David Reynolds
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Brigitte T. Hofmeister
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Laura Cliffe
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - T. Nicolai Siegel
- Research Center for Infectious Diseases, University of Wuerzburg, Wuerzburg, Germany
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
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12
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Bühlmann M, Walrad P, Rico E, Ivens A, Capewell P, Naguleswaran A, Roditi I, Matthews KR. NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway. Nucleic Acids Res 2015; 43:4491-504. [PMID: 25873624 PMCID: PMC4482084 DOI: 10.1093/nar/gkv330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 02/03/2023] Open
Abstract
Trypanosomes mostly regulate gene expression through post-transcriptional mechanisms, particularly mRNA stability. However, much mRNA degradation is cytoplasmic such that mRNA nuclear export must represent an important level of regulation. Ribosomal RNAs must also be exported from the nucleus and the trypanosome orthologue of NMD3 has been confirmed to be involved in rRNA processing and export, matching its function in other organisms. Surprisingly, we found that TbNMD3 depletion also generates mRNA accumulation of procyclin-associated genes (PAGs), these being co-transcribed by RNA polymerase I with the procyclin surface antigen genes expressed on trypanosome insect forms. By whole transcriptome RNA-seq analysis of TbNMD3-depleted cells we confirm the regulation of the PAG transcripts by TbNMD3 and using reporter constructs reveal that PAG1 regulation is mediated by its 5'UTR. Dissection of the mechanism of regulation demonstrates that it is not dependent upon translational inhibition mediated by TbNMD3 depletion nor enhanced transcription. However, depletion of the nuclear export factors XPO1 or MEX67 recapitulates the effects of TbNMD3 depletion on PAG mRNAs and mRNAs accumulated in the nucleus of TbNMD3-depleted cells. These results invoke a novel RNA regulatory mechanism involving the NMD3-dependent nuclear export of mRNA cargos, suggesting a shared platform for mRNA and rRNA export.
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Affiliation(s)
- Melanie Bühlmann
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Pegine Walrad
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK Centre for Immunology and Infection, Department of Biology, University of York, YO10 5DD, UK
| | - Eva Rico
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Paul Capewell
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | | | - Isabel Roditi
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
| | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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13
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Abstract
TbRRM1 of Trypanosoma brucei is a nucleoprotein that was previously identified in a search for splicing factors in T. brucei. We show that TbRRM1 associates with mRNAs and with the auxiliary splicing factor polypyrimidine tract-binding protein 2, but not with components of the core spliceosome. TbRRM1 also interacts with several retrotransposon hot spot (RHS) proteins and histones. RNA immunoprecipitation of a tagged form of TbRRM1 from procyclic (insect) form trypanosomes identified ca. 1,500 transcripts that were enriched and 3,000 transcripts that were underrepresented compared to cellular mRNA. Enriched transcripts encoded RNA-binding proteins, including TbRRM1 itself, several RHS transcripts, mRNAs with long coding regions, and a high proportion of stage-regulated mRNAs that are more highly expressed in bloodstream forms. Transcripts encoding ribosomal proteins, other factors involved in translation, and procyclic-specific transcripts were underrepresented. Knockdown of TbRRM1 by RNA interference caused widespread changes in mRNA abundance, but these changes did not correlate with the binding of the protein to transcripts, and most splice sites were unchanged, negating a general role for TbRRM1 in splice site selection. When changes in mRNA abundance were mapped across the genome, regions with many downregulated mRNAs were identified. Two regions were analyzed by chromatin immunoprecipitation, both of which exhibited increases in nucleosome occupancy upon TbRRM1 depletion. In addition, subjecting cells to heat shock resulted in translocation of TbRRM1 to the cytoplasm and compaction of chromatin, consistent with a second role for TbRRM1 in modulating chromatin structure. Trypanosoma brucei, the parasite that causes human sleeping sickness, is transmitted by tsetse flies. The parasite progresses through different life cycle stages in its two hosts, altering its pattern of gene expression in the process. In trypanosomes, protein-coding genes are organized as polycistronic units that are processed into monocistronic mRNAs. Since genes in the same unit can be regulated independently of each other, it is believed that gene regulation is essentially posttranscriptional. In this study, we investigated the role of a nuclear RNA-binding protein, TbRRM1, in the insect stage of the parasite. We found that TbRRM1 binds nuclear mRNAs and also affects chromatin status. Reduction of nuclear TbRRM1 by RNA interference or heat shock resulted in chromatin compaction. We propose that TbRRM1 regulates RNA polymerase II-driven gene expression both cotranscriptionally, by facilitating transcription and efficient splicing, and posttranscriptionally, via its interaction with nuclear mRNAs.
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14
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Carnes J, Anupama A, Balmer O, Jackson A, Lewis M, Brown R, Cestari I, Desquesnes M, Gendrin C, Hertz-Fowler C, Imamura H, Ivens A, Kořený L, Lai DH, MacLeod A, McDermott SM, Merritt C, Monnerat S, Moon W, Myler P, Phan I, Ramasamy G, Sivam D, Lun ZR, Lukeš J, Stuart K, Schnaufer A. Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty. PLoS Negl Trop Dis 2015; 9:e3404. [PMID: 25568942 PMCID: PMC4288722 DOI: 10.1371/journal.pntd.0003404] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/09/2014] [Indexed: 11/18/2022] Open
Abstract
Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Atashi Anupama
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Oliver Balmer
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Andrew Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Michael Lewis
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rob Brown
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Igor Cestari
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Marc Desquesnes
- CIRAD, UMR-InterTryp, Montpellier, France
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Claire Gendrin
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Christiane Hertz-Fowler
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Hideo Imamura
- Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alasdair Ivens
- Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Luděk Kořený
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
| | - De-Hua Lai
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People′s Republic of China
| | - Annette MacLeod
- Wellcome Trust Centre for Molecular Parasitology, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Chris Merritt
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Severine Monnerat
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Wonjong Moon
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Peter Myler
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Isabelle Phan
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Gowthaman Ramasamy
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Dhileep Sivam
- Seattle Biomedical Research Institute, Seattle, United States of America
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People′s Republic of China
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, Centre, České Budějovice (Budweis), Czech Republic
- Canadian Institute for Advanced Research, Toronto, Canada
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Ken Stuart
- Seattle Biomedical Research Institute, Seattle, United States of America
- Department of Global Health, University of Washington, Seattle, United States of America
- * E-mail: (ZRL); (JL); (KS); (AS)
| | - Achim Schnaufer
- Centre of Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (ZRL); (JL); (KS); (AS)
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15
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Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Pinto-Neves D, Aresta-Branco F, Rijo-Ferreira F, Guegan F, Pedro Coelho L, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. Mol Microbiol 2014; 93:645-63. [PMID: 24946224 PMCID: PMC4285223 DOI: 10.1111/mmi.12677] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2014] [Indexed: 11/30/2022]
Abstract
Trypanosoma brucei is a unicellular parasite that causes sleeping sickness in humans. Most of its transcription is constitutive and driven by RNA polymerase II. RNA polymerase I (Pol I) transcribes not only ribosomal RNA genes, but also protein-encoding genes, including variant surface glycoproteins (VSGs) and procyclins. In T. brucei, histone H1 (H1) is required for VSG silencing and chromatin condensation. However, whether H1 has a genome-wide role in transcription is unknown. Here, using RNA sequencing we show that H1 depletion changes the expression of a specific cohort of genes. Interestingly, the predominant effect is partial loss of silencing of Pol I loci, such as VSG and procyclin genes. Labelling of nascent transcripts with 4-thiouridine showed that H1 depletion does not alter the level of labelled Pol II transcripts. In contrast, the levels of 4sU-labelled Pol I transcripts were increased by two- to sixfold, suggesting that H1 preferentially blocks transcription at Pol I loci. Finally, we observed that parasites depleted of H1 grow almost normally in culture but they have a reduced fitness in mice, suggesting that H1 is important for host-pathogen interactions.
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Affiliation(s)
- Ana C Pena
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisboa, Portugal
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16
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Abstract
The storage of translationally inactive mRNAs in cytosolic granules enables cells to react flexibly to environmental changes. In eukaryotes, Scd6 (suppressor of clathrin deficiency 6)/Rap55 (RNA-associated protein 55), a member of the LSm14 (like-Sm14) family, is an important factor in the formation and activity of P-bodies, where mRNA decay factors accumulate, in stress granules that store mRNAs under adverse conditions and in granules that store developmentally regulated mRNAs. SCD6 from Trypanosoma brucei (TbSCD6) shares the same domain architecture as orthologous proteins in other organisms and is also present in cytosolic granules (equivalent to P-bodies). We show that TbSCD6 is a general repressor of translation and that its depletion by RNAi results in a global increase in protein synthesis. With few exceptions, the steady-state levels of proteins are unchanged. TbSCD6 is not required for the formation of starvation-induced granules in trypanosomes, and unlike Scd6 from yeast, Plasmodium and all multicellular organisms analysed to date, it does not form a complex with the helicase Dhh1 (DExD/H-box helicase 1). In common with Xenopus laevis RAP55, TbSCD6 co-purifies with two arginine methyltransferases; moreover, TbSCD6 itself is methylated on three arginine residues. Finally, a detailed analysis identified roles for the Lsm and N-rich domains in both protein localization and translational repression.
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17
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Schumann Burkard G, Käser S, de Araújo PR, Schimanski B, Naguleswaran A, Knüsel S, Heller M, Roditi I. Nucleolar proteins regulate stage-specific gene expression and ribosomal RNA maturation in Trypanosoma brucei. Mol Microbiol 2013; 88:827-40. [PMID: 23617823 DOI: 10.1111/mmi.12227] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 12/20/2022]
Abstract
Different life-cycle stages of Trypanosoma brucei are characterized by stage-specific glycoprotein coats. GPEET procyclin, the major surface protein of early procyclic (insect midgut) forms, is transcribed in the nucleolus by RNA polymerase I as part of a polycistronic precursor that is processed to monocistronic mRNAs. In culture, when differentiation to late procyclic forms is triggered by removal of glycerol, the precursor is still transcribed, but accumulation of GPEET mRNA is prevented by a glycerol-responsive element in the 3' UTR. A genome-wide RNAi screen for persistent expression of GPEET in glycerol-free medium identified a novel protein, NRG1 (Nucleolar Regulator of GPEET 1), as a negative regulator. NRG1 associates with GPEET mRNA and with several nucleolar proteins. These include two PUF proteins, TbPUF7 and TbPUF10, and BOP1, a protein required for rRNA processing in other organisms. RNAi against each of these components prolonged or even increased GPEET expression in the absence of glycerol as well as causing a significant reduction in 5.8S rRNA and its immediate precursor. These results indicate that components of a complex used for rRNA maturation can have an additional role in regulating mRNAs that originate in the nucleolus.
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18
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Dostalova A, Käser S, Cristodero M, Schimanski B. The nuclear mRNA export receptor Mex67-Mtr2 ofTrypanosoma bruceicontains a unique and essential zinc finger motif. Mol Microbiol 2013; 88:728-39. [DOI: 10.1111/mmi.12217] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2013] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Bernd Schimanski
- Institute of Cell Biology; University of Bern; Bern; Switzerland
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19
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Brenndörfer M, Boshart M. Selection of reference genes for mRNA quantification in Trypanosoma brucei. Mol Biochem Parasitol 2010; 172:52-5. [PMID: 20302889 DOI: 10.1016/j.molbiopara.2010.03.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/08/2010] [Accepted: 03/10/2010] [Indexed: 12/16/2022]
Abstract
Internal normalization is an established procedure that is necessary for accurate and reliable quantification of differentially regulated mRNAs. The profound changes of gene expression in parasitic life cycles pose a particular challenge on selection of appropriate reference genes for normalization, most importantly when using quantitative real time PCR (qPCR). Here we use the ranking algorithm implemented in the geNorm application to identify suitable Trypanosoma brucei reference genes for comparisons between the bloodstream and procyclic developmental stages and for analysis of mRNA induction by environmental conditions. For these conditions, the TERT gene is a good choice for valid normalization of qPCR and is clearly superior to some other reference genes reported in the literature. For comparison of other conditions, the ranking algorithm is recommended to verify a reliable and valid normalization that is instrumental to quantitative analysis of gene expression.
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Affiliation(s)
- Martin Brenndörfer
- Biozentrum, Department Biologie I, Genetik, Ludwig-Maximilians-Universität München, D-82152 Martinsried, Germany
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20
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Veitch NJ, Johnson PCD, Trivedi U, Terry S, Wildridge D, MacLeod A. Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. BMC Genomics 2010; 11:124. [PMID: 20175885 PMCID: PMC2837033 DOI: 10.1186/1471-2164-11-124] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 02/22/2010] [Indexed: 12/29/2022] Open
Abstract
Background The evolutionarily ancient parasite, Trypanosoma brucei, is unusual in that the majority of its genes are regulated post-transcriptionally, leading to the suggestion that transcript abundance of most genes does not vary significantly between different life cycle stages despite the fact that the parasite undergoes substantial cellular remodelling and metabolic changes throughout its complex life cycle. To investigate this in the clinically relevant sub-species, Trypanosoma brucei gambiense, which is the causative agent of the fatal human disease African sleeping sickness, we have compared the transcriptome of two different life cycle stages, the potentially human-infective bloodstream forms with the non-human-infective procyclic stage using digital gene expression (DGE) analysis. Results Over eleven million unique tags were generated, producing expression data for 7360 genes, covering 81% of the genes in the genome. Compared to microarray analysis of the related T. b. brucei parasite, approximately 10 times more genes with a 2.5-fold change in expression levels were detected. The transcriptome analysis revealed the existence of several differentially expressed gene clusters within the genome, indicating that contiguous genes, presumably from the same polycistronic unit, are co-regulated either at the level of transcription or transcript stability. Conclusions DGE analysis is extremely sensitive for detecting gene expression differences, revealing firstly that a far greater number of genes are stage-regulated than had previously been identified and secondly and more importantly, this analysis has revealed the existence of several differentially expressed clusters of genes present on what appears to be the same polycistronic units, a phenomenon which had not previously been observed in microarray studies. These differentially regulated clusters of genes are in addition to the previously identified RNA polymerase I polycistronic units of variant surface glycoproteins and procyclin expression sites, which encode the major surface proteins of the parasite. This raises a number of questions regarding the function and regulation of the gene clusters that clearly warrant further study.
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Affiliation(s)
- Nicola J Veitch
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, G12 8TA, UK
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21
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Abstract
The eukaryotic flagellum is a highly conserved organelle serving motility, sensory, and transport functions. Although genetic, genomic, and proteomic studies have led to the identification of hundreds of flagellar and putative flagellar proteins, precisely how these proteins function individually and collectively to drive flagellum motility and other functions remains to be determined. In this chapter we provide an overview of tools and approaches available for studying flagellum protein function in the protozoan parasite Trypanosoma brucei. We begin by outlining techniques for in vitro cultivation of both T. brucei life cycle stages, as well as transfection protocols for the delivery of DNA constructs. We then describe specific assays used to assess flagellum function including flagellum preparation and quantitative motility assays. We conclude the chapter with a description of molecular genetic approaches for manipulating gene function. In summary, the availability of potent molecular tools, as well as the health and economic relevance of T. brucei as a pathogen, combine to make the parasite an attractive and integral experimental system for the functional analysis of flagellar proteins.
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22
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Fragoso CM, Schumann Burkard G, Oberle M, Renggli CK, Hilzinger K, Roditi I. PSSA-2, a membrane-spanning phosphoprotein of Trypanosoma brucei, is required for efficient maturation of infection. PLoS One 2009; 4:e7074. [PMID: 19759911 PMCID: PMC2739429 DOI: 10.1371/journal.pone.0007074] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 08/20/2009] [Indexed: 12/04/2022] Open
Abstract
The coat of Trypanosoma brucei consists mainly of glycosylphosphatidylinositol-anchored proteins that are present in several million copies and are characteristic of defined stages of the life cycle. While these major components of the coats of bloodstream forms and procyclic (insect midgut) forms are well characterised, very little is known about less abundant stage-regulated surface proteins and their roles in infection and transmission. By creating epitope-tagged versions of procyclic-specific surface antigen 2 (PSSA-2) we demonstrated that it is a membrane-spanning protein that is expressed by several different life cycle stages in tsetse flies, but not by parasites in the mammalian bloodstream. In common with other membrane-spanning proteins in T. brucei, PSSA-2 requires its cytoplasmic domain in order to exit the endoplasmic reticulum. Correct localisation of PSSA-2 requires phosphorylation of a cytoplasmic threonine residue (T305), a modification that depends on the presence of TbMAPK4. Mutation of T305 to alanine (T305A) has no effect on the localisation of the protein in cells that express wild type PSSA-2. In contrast, this protein is largely intracellular when expressed in a null mutant background. A variant with a T305D mutation gives strong surface expression in both the wild type and null mutant, but slows growth of the cells, suggesting that it may function as a dominant negative mutant. The PSSA-2 null mutant exhibits no perceptible phenotype in culture and is fully competent at establishing midgut infections in tsetse, but is defective in colonising the salivary glands and the production of infectious metacyclic forms. Given the protein's structure and the effects of mutation of T305 on proliferation and localisation, we postulate that PSSA-2 might sense and transmit signals that contribute to the parasite's decision to divide, differentiate or migrate.
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23
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Haenni S, Studer E, Burkard GS, Roditi I. Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma brucei. Nucleic Acids Res 2009; 37:5007-18. [PMID: 19531741 PMCID: PMC2731899 DOI: 10.1093/nar/gkp513] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The procyclin genes in Trypanosoma brucei are transcribed by RNA polymerase I as part of 5–10 kb long polycistronic transcription units on chromosomes VI and X. Each procyclin locus begins with two procyclin genes followed by at least one procyclin-associated gene (PAG). In procyclic (insect midgut) form trypanosomes, PAG mRNA levels are about 100-fold lower than those of procyclins. We show that deletion of PAG1, PAG2 or PAG3 results in increased mRNA levels from downstream genes in the same transcription unit. Nascent RNA analysis revealed that most of the effects are due to increased transcription elongation in the knockouts. Furthermore, transient and stable transfections showed that sequence elements on both strands of PAG1 can inhibit Pol I transcription. Finally, by database mining we identified 30 additional PAG-related sequences that are located almost exclusively at strand switch regions and/or at sites where a change of RNA polymerase type is likely to occur.
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Affiliation(s)
- Simon Haenni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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24
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Vassella E, Oberle M, Urwyler S, Renggli CK, Studer E, Hemphill A, Fragoso C, Bütikofer P, Brun R, Roditi I. Major surface glycoproteins of insect forms of Trypanosoma brucei are not essential for cyclical transmission by tsetse. PLoS One 2009; 4:e4493. [PMID: 19223969 PMCID: PMC2637416 DOI: 10.1371/journal.pone.0004493] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 12/30/2008] [Indexed: 11/19/2022] Open
Abstract
Procyclic forms of Trypanosoma brucei reside in the midgut of tsetse flies where they are covered by several million copies of glycosylphosphatidylinositol-anchored proteins known as procyclins. It has been proposed that procyclins protect parasites against proteases and/or participate in tropism, directing them from the midgut to the salivary glands. There are four different procyclin genes, each subject to elaborate levels of regulation. To determine if procyclins are essential for survival and transmission of T. brucei, all four genes were deleted and parasite fitness was compared in vitro and in vivo. When co-cultured in vitro, the null mutant and wild type trypanosomes (tagged with cyan fluorescent protein) maintained a near-constant equilibrium. In contrast, when flies were infected with the same mixture, the null mutant was rapidly overgrown in the midgut, reflecting a reduction in fitness in vivo. Although the null mutant is patently defective in competition with procyclin-positive parasites, on its own it can complete the life cycle and generate infectious metacyclic forms. The procyclic form of T. brucei thus differs strikingly from the bloodstream form, which does not tolerate any perturbation of its variant surface glycoprotein coat, and from other parasites such as Plasmodium berghei, which requires the circumsporozoite protein for successful transmission to a new host.
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Affiliation(s)
- Erik Vassella
- Institut für Zellbiologie, Universität Bern, Bern, Switzerland
| | | | - Simon Urwyler
- Institut für Zellbiologie, Universität Bern, Bern, Switzerland
| | | | - Erwin Studer
- Institut für Zellbiologie, Universität Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institut für Parasitologie, Universität Bern, Bern, Switzerland
| | | | - Peter Bütikofer
- Institut für Biochemie und Molekulare Medizin, Universität Bern, Bern, Switzerland
| | - Reto Brun
- Swiss Tropical Institute, Basel, Switzerland
| | - Isabel Roditi
- Institut für Zellbiologie, Universität Bern, Bern, Switzerland
- * E-mail:
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Roditi I, Lehane MJ. Interactions between trypanosomes and tsetse flies. Curr Opin Microbiol 2008; 11:345-51. [DOI: 10.1016/j.mib.2008.06.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 06/18/2008] [Indexed: 11/27/2022]
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Estévez AM. The RNA-binding protein TbDRBD3 regulates the stability of a specific subset of mRNAs in trypanosomes. Nucleic Acids Res 2008; 36:4573-86. [PMID: 18611951 PMCID: PMC2504296 DOI: 10.1093/nar/gkn406] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In trypanosomes, the apparent lack of regulation of RNA polymerase II-dependent transcription initiation poses a challenge to understand how these eukaryotes adjust gene expression to adapt to the contrasting environments they find during their life cycles. Evidence so far indicates that mRNA turnover and translation are the major control points in which regulation is exerted in trypanosomes. However, very little is known about which proteins are involved, and how do they regulate the abundance and translation of different mRNAs in different life stages. In this work, an RNA-binding protein, TbDRBD3, has been identified by affinity chromatography, and its function addressed using RNA interference, microarray analysis and immunoprecipitation of mRNA-protein complexes. The results obtained indicate that TbDRBD3 binds to a subset of developmentally regulated mRNAs encoding membrane proteins, and that this association promotes the stabilization of the target transcripts. These observations raise the possibility that TbDRBD3-mRNA complexes act as a post-transcriptional operon, and provide a framework to interpret how trypanosomes regulate gene expression in the absence of transcriptional control.
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Affiliation(s)
- Antonio M Estévez
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC Avda. del Conocimiento s/n, Armilla, 18100-Granada, Spain.
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Peacock L, Ferris V, Bailey M, Gibson W. Dynamics of infection and competition between two strains of Trypanosoma brucei brucei in the tsetse fly observed using fluorescent markers. KINETOPLASTID BIOLOGY AND DISEASE 2007; 6:4. [PMID: 17553128 PMCID: PMC1899512 DOI: 10.1186/1475-9292-6-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 06/06/2007] [Indexed: 11/23/2022]
Abstract
Background Genetic exchange occurs between Trypanosoma brucei strains during the complex developmental cycle in the tsetse vector, probably within the salivary glands. Successful mating will depend on the dynamics of co-infection with multiple strains, particularly if intraspecific competition occurs. We have previously used T. brucei expressing green fluorescent protein to study parasite development in the vector, enabling even one trypanosome to be visualized. Here we have used two different trypanosome strains transfected with either green or red fluorescent proteins to study the dynamics of co-infection directly in the tsetse fly. Results The majority of infected flies had both trypanosome strains present in the midgut, but the relative proportion of red and green trypanosome strains varied considerably between flies and between different sections of the midgut in individual flies. Colonization of the paired salivary glands revealed greater variability than for midguts, as each gland could be infected with red and/or green trypanosome strains in variable proportions. Salivary glands with a mixed infection appeared to have a higher density of trypanosomes than glands containing a single strain. Comparison of the numbers of red and green trypanosomes in the proventriculus, salivary exudate and glands from individual flies showed no correlation between the composition of the trypanosome population of the proventriculus and foregut and that of the salivary glands. For each compartment examined (midgut, foregut, salivary glands), there was a significantly higher proportion of mixed infections than expected, assuming the null hypothesis that the development of each trypanosome strain is independent. Conclusion Both the trypanosome strains used were fully capable of infecting tsetse, but the probabilities of infection with each strain were not independent, there being a significantly higher proportion of mixed infections than expected in each of three compartments examined: midgut, proventriculus and salivary glands. Hence there was no evidence of competition between trypanosome strains, but instead co-infection was frequent. Infection rates in co-infected flies were no different to those found routinely in flies infected with a single strain, ruling out the possibility that one strain enhanced infection with the other. We infer that each fly is either permissive or non-permissive of trypanosome infection with at least 3 sequential checkpoints imposed by the midgut, proventriculus and salivary glands. Salivary glands containing both trypanosome strains appeared to contain more trypanosomes than singly-infected glands, suggesting that lack of competition enhances the likelihood of genetic exchange.
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Affiliation(s)
- Lori Peacock
- School of Biological Sciences University of Bristol, Bristol BS8 1UG, UK
- Department of Clinical Veterinary Science, University of Bristol, Langford, Bristol BS40 7DU, UK
| | - Vanessa Ferris
- School of Biological Sciences University of Bristol, Bristol BS8 1UG, UK
- Department of Clinical Veterinary Science, University of Bristol, Langford, Bristol BS40 7DU, UK
| | - Mick Bailey
- Department of Clinical Veterinary Science, University of Bristol, Langford, Bristol BS40 7DU, UK
| | - Wendy Gibson
- School of Biological Sciences University of Bristol, Bristol BS8 1UG, UK
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Abstract
Trypanosomes are members of the kinetoplastida, a group of divergent protozoan parasites responsible for considerable morbidity and mortality worldwide. These organisms have highly complex life cycles requiring modification of their cell surface together with engagement of immune evasion systems to effect survival; both processes intimately involve the membrane trafficking system. The completion of three trypanosomatid and several additional protist genomes in the last few years is providing an exciting opportunity to evaluate, at the molecular level, the evolution and diversity of membrane trafficking across deep evolutionary time as well as to analyse in unprecedented detail the membrane trafficking systems of trypanosomes.
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Affiliation(s)
- Mark C Field
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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Kramer S, Klöckner T, Selmayr M, Boshart M. Interstrain sequence comparison, transcript map and clonal genomic rearrangement of a 28 kb locus on chromosome 9 of Trypanosoma brucei. Mol Biochem Parasitol 2006; 151:129-32. [PMID: 17112605 DOI: 10.1016/j.molbiopara.2006.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 09/27/2006] [Accepted: 10/10/2006] [Indexed: 11/23/2022]
Affiliation(s)
- Susanne Kramer
- Ludwig-Maximilians-Universität München, Department of Biology, Section Genetics, Maria-Ward-Str. 1a, D-80638 München, Germany
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