1
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Ballmer D, Akiyoshi B. Dynamic localization of the chromosomal passenger complex in trypanosomes is controlled by the orphan kinesins KIN-A and KIN-B. eLife 2024; 13:RP93522. [PMID: 38564240 PMCID: PMC10987093 DOI: 10.7554/elife.93522] [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: 04/04/2024] Open
Abstract
The chromosomal passenger complex (CPC) is an important regulator of cell division, which shows dynamic subcellular localization throughout mitosis, including kinetochores and the spindle midzone. In traditional model eukaryotes such as yeasts and humans, the CPC consists of the catalytic subunit Aurora B kinase, its activator INCENP, and the localization module proteins Borealin and Survivin. Intriguingly, Aurora B and INCENP as well as their localization pattern are conserved in kinetoplastids, an evolutionarily divergent group of eukaryotes that possess unique kinetochore proteins and lack homologs of Borealin or Survivin. It is not understood how the kinetoplastid CPC assembles nor how it is targeted to its subcellular destinations during the cell cycle. Here, we identify two orphan kinesins, KIN-A and KIN-B, as bona fide CPC proteins in Trypanosoma brucei, the kinetoplastid parasite that causes African sleeping sickness. KIN-A and KIN-B form a scaffold for the assembly of the remaining CPC subunits. We show that the C-terminal unstructured tail of KIN-A interacts with the KKT8 complex at kinetochores, while its N-terminal motor domain promotes CPC translocation to spindle microtubules. Thus, the KIN-A:KIN-B complex constitutes a unique 'two-in-one' CPC localization module, which directs the CPC to kinetochores from S phase until metaphase and to the central spindle in anaphase. Our findings highlight the evolutionary diversity of CPC proteins and raise the possibility that kinesins may have served as the original transport vehicles for Aurora kinases in early eukaryotes.
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Affiliation(s)
- Daniel Ballmer
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological SciencesEdinburghUnited Kingdom
| | - Bungo Akiyoshi
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological SciencesEdinburghUnited Kingdom
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2
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Niemirowicz GT, Carlevaro G, Campetella O, Bouvier LA, Mucci J. A versatile 2A peptide-based strategy for ectopic expression and endogenous gene tagging in Trypanosoma cruzi. Heliyon 2024; 10:e24595. [PMID: 38304823 PMCID: PMC10830525 DOI: 10.1016/j.heliyon.2024.e24595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Nearly all expression vectors currently available for Trypanosoma cruzi were conceived to produce a single primary transcript containing the genes of interest along with those that confer antibiotic resistance. However, since each messenger RNA (mRNA) matures separately, drug selection will only guarantee the expression of those derived from the selectable marker. Therefore, commonly a considerable fraction of the cells recovered after selection with these expression vectors, although resistant do not express the protein of interest. Consequently, in order to counteract this disadvantage, we developed vectors with an alternative arrangement in which the gene of interest and antibiotic resistance are fused sharing the same mRNA. To test this configuration, we included the coding sequence for the green fluorescent protein (mEGFP) linked to the one conferring neomycin resistance (Neo). Additionally, to allow for the production of two independent proteins the sequence for a Thosea asigna virus self-cleaving 2A peptide (T2A) was inserted in-between. Cells obtained with these vectors displayed higher mEGFP expression levels with more homogeneous transgenic parasite populations than those transfected with more conventional independent mRNA-based alternatives. Moreover, as determined by Western blot, 2A mediated fusion protein dissociation occurred with high efficiency in all parasite stages. In addition, these vectors could easily be transformed into endogenous tagging constructs that allowed the insertion, by ends-in homologous recombination, of a hemagglutinin tag (HA) fused to the actin gene. The use of 2A self-cleaving peptides in the context of single mRNA vectors represents an interesting strategy capable of improving ectopic transgene expression in T. cruzi as well as providing a simple alternative to more sophisticated methods, such as the one based on CRISPR/Cas9, for the endogenous labeling of genes.
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Affiliation(s)
| | | | - Oscar Campetella
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
| | - León A. Bouvier
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
| | - Juan Mucci
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
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3
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Kevorkian ML, Vilchez Larrea SC, Fernández Villamil SH. Trypanosoma cruzi PARP is enriched in the nucleolus and is present in a thread connecting nuclei during mitosis. PLoS One 2022; 17:e0267329. [PMID: 36584038 PMCID: PMC9803098 DOI: 10.1371/journal.pone.0267329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) is responsible for the synthesis of ADP-ribose polymers, which are involved in a wide range of cellular processes such as preservation of genome integrity, DNA damage signaling and repair, molecular switches between distinct cell death pathways, and cell cycle progression. Previously, we demonstrated that the only PARP present in T. cruzi migrates to the nucleus upon genotoxic stimulus. In this work, we identify the N-terminal domain as being sufficient for TcPARP nuclear localization and describe for the first time that TcPARP is enriched in the parasite's nucleolus. We also describe that TcPARP is present in a thread-like structure that connects two dividing nuclei and co-localizes with nucleolar material and microtubules. Furthermore, ADP-ribose polymers could also be detected in this thread during mitosis. These findings represent a first approach to new potential TcPARP functions inside the nucleus and will help understand its role well beyond the largely described DNA damage response protein in trypanosomatids.
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Affiliation(s)
- María Laura Kevorkian
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Salomé C. Vilchez Larrea
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvia H. Fernández Villamil
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail: ,
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4
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Abstract
Targeted protein degradation is an invaluable tool in studying the function of proteins. Such a tool was not available in Trypanosoma brucei, an evolutionarily divergent eukaryote that causes human African trypanosomiasis. Here, we have adapted deGradFP (degrade green fluorescent protein [GFP]), a protein degradation system based on the SCF E3 ubiquitin ligase complex and anti-GFP nanobody, in T. brucei. As a proof of principle, we targeted a kinetoplastid kinetochore protein (KKT3) that constitutively localizes at kinetochores in the nucleus. Induction of deGradFP in a cell line that had both alleles of KKT3 tagged with yellow fluorescent protein (YFP) caused a more severe growth defect than RNAi in procyclic (insect form) cells. deGradFP also worked on a cytoplasmic protein (COPII subunit, SEC31). Given the ease in making GFP fusion cell lines in T. brucei, deGradFP can serve as a powerful tool to rapidly deplete proteins of interest, especially those with low turnover rates.
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Affiliation(s)
- Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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5
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Jeilani M, Billington K, Sunter JD, Dean S, Wheeler RJ. Nucleolar targeting in an early-branching eukaryote suggests a general mechanism for ribosome protein sorting. J Cell Sci 2022; 135:jcs259701. [PMID: 36052646 PMCID: PMC9659390 DOI: 10.1242/jcs.259701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The compartmentalised eukaryotic cell demands accurate targeting of proteins to the organelles in which they function, whether membrane-bound (like the nucleus) or non-membrane-bound (like the nucleolus). Nucleolar targeting relies on positively charged localisation signals and has received rejuvenated interest since the widespread recognition of liquid-liquid phase separation (LLPS) as a mechanism contributing to nucleolus formation. Here, we exploit a new genome-wide analysis of protein localisation in the early-branching eukaryote Trypanosoma brucei to analyse general nucleolar protein properties. T. brucei nucleolar proteins have similar properties to those in common model eukaryotes, specifically basic amino acids. Using protein truncations and addition of candidate targeting sequences to proteins, we show both homopolymer runs and distributed basic amino acids give nucleolar partition, further aided by a nuclear localisation signal (NLS). These findings are consistent with phase separation models of nucleolar formation and physical protein properties being a major contributing mechanism for eukaryotic nucleolar targeting, conserved from the last eukaryotic common ancestor. Importantly, cytoplasmic ribosome proteins, unlike mitochondrial ribosome proteins, have more basic residues - pointing to adaptation of physicochemical properties to assist segregation.
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Affiliation(s)
- Milad Jeilani
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Karen Billington
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Samuel Dean
- Warwick Medical School, Warwick University, Warwick CV4 7AL, UK
| | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
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6
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Ishii M, Akiyoshi B. Targeted protein degradation using deGradFP in Trypanosoma brucei. Wellcome Open Res 2022; 7:175. [PMID: 35865221 PMCID: PMC9277568 DOI: 10.12688/wellcomeopenres.17964.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 11/09/2023] Open
Abstract
Targeted protein degradation is an invaluable tool in studying the function of proteins. Such a tool was not available in Trypanosoma brucei, an evolutionarily divergent eukaryote that causes human African trypanosomiasis. Here, we have adapted deGradFP (degrade green fluorescent protein [GFP]), a protein degradation system based on the SCF E3 ubiquitin ligase complex and anti-GFP nanobody, in T. brucei. As a proof of principle, we targeted a kinetoplastid kinetochore protein (KKT3) that constitutively localizes at kinetochores in the nucleus. Induction of deGradFP in a cell line that had both alleles of KKT3 tagged with yellow fluorescent protein (YFP) caused a more severe growth defect than RNAi in procyclic (insect form) cells. deGradFP also worked on a cytoplasmic protein (COPII subunit, SEC31). Given the ease in making GFP fusion cell lines in T. brucei, deGradFP can serve as a powerful tool to rapidly deplete proteins of interest, especially those with low turnover rates.
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Affiliation(s)
- Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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7
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Dewar CE, Oeljeklaus S, Mani J, Mühlhäuser WWD, von Känel C, Zimmermann J, Ochsenreiter T, Warscheid B, Schneider A. Mistargeting of aggregation prone mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes. Nat Commun 2022; 13:3084. [PMID: 35654893 PMCID: PMC9163028 DOI: 10.1038/s41467-022-30748-z] [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: 08/10/2021] [Accepted: 05/02/2022] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial protein import in the parasitic protozoan Trypanosoma brucei is mediated by the atypical outer membrane translocase, ATOM. It consists of seven subunits including ATOM69, the import receptor for hydrophobic proteins. Ablation of ATOM69, but not of any other subunit, triggers a unique quality control pathway resulting in the proteasomal degradation of non-imported mitochondrial proteins. The process requires a protein of unknown function, an E3 ubiquitin ligase and the ubiquitin-like protein (TbUbL1), which all are recruited to the mitochondrion upon ATOM69 depletion. TbUbL1 is a nuclear protein, a fraction of which is released to the cytosol upon triggering of the pathway. Nuclear release is essential as cytosolic TbUbL1 can bind mislocalised mitochondrial proteins and likely transfers them to the proteasome. Mitochondrial quality control has previously been studied in yeast and metazoans. Finding such a pathway in the highly diverged trypanosomes suggests such pathways are an obligate feature of all eukaryotes. Mitochondria import most of their proteins posttranslationally. Here, Dewar et al. characterize the mitochondrial quality control mechanism of Trypanosoma brucei. Through proteomics and functional studies, they show that only ablation of ATOM69, one of the seven subunits of its mitochondrial protein translocase, triggers a unique quality control pathway resulting in TbUbL1 release from the nucleus and subsequent proteasomal degradation of non-imported mitochondrial proteins.
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Affiliation(s)
- Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, 97074, Würzburg, Germany.,Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Jan Mani
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Wignand W D Mühlhäuser
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - Johannes Zimmermann
- Faculty of Chemistry and Pharmacy, Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, 97074, Würzburg, Germany
| | - Torsten Ochsenreiter
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, CH-3012, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, 97074, Würzburg, Germany. .,Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.
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8
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Guo H, Cui Y, Huang L, Ge L, Xu X, Xue D, Tang M, Zheng J, Yi Y, Chen L. The RNA binding protein OsLa influences grain and anther development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1397-1414. [PMID: 35322500 DOI: 10.1111/tpj.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
La proteins are found widely in eukaryotes and play a variety of vital roles. AtLa1 has been identified as an La protein that is necessary for embryogenesis in Arabidopsis; however, the existence and biological functions of La proteins in rice (Oryza sativa L.) remain unclear. In this study, we identified and characterized two La proteins in rice that are homologous to AtLa1 and named them OsLa1 and OsLa2. Both the OsLa1 and OsLa2 genes encode RNA-binding proteins with an La domain and two RNA-binding domains. Mutant OsLa1 reduced grain length and pollen fertility, whereas OsLa1 overexpression caused the opposite phenotypes. Further experiments indicated that OsLa1 modulates grain size by influencing cell expansion. Interestingly, mutant OsLa2 resulted in thin grains with decreased weight and a low seed-setting rate. We also found that OsLa1 interacted with OsLa2 and that both OsLa1 and OsLa2 interacted with OseIF6.1, a eukaryotic translation initiation factor involved in ribosome biogenesis. In addition, OsLa1 was able to bind to OseIF6.1 mRNA to modulate its expression. Complete OseIF6.1 knockout caused lethality and OseIF6.1/oseif6.1 heterozygous plants displayed low fertility and low seed setting. Together, our results enrich our knowledge of the role of La proteins in rice growth and development, as well as the relationship between La and eIF6 in rice.
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Affiliation(s)
- Hongming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Linjuan Huang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Li Ge
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaorong Xu
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Danyang Xue
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Jingsheng Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
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9
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Pacheco-Lugo LA, Sáenz-García JL, Díaz-Olmos Y, Netto-Costa R, Brant RSC, DaRocha WD. CREditing: a tool for gene tuning in Trypanosoma cruzi. Int J Parasitol 2020; 50:1067-1077. [PMID: 32858036 DOI: 10.1016/j.ijpara.2020.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/30/2022]
Abstract
The genetic manipulation of Trypanosoma cruzi continues to be a challenge, mainly due to the lack of available and efficient molecular tools. The CRE-lox recombination system is a site-specific recombinase technology, widely used method of achieving conditional targeted deletions, inversions, insertions, gene activation, translocation, and other modifications in chromosomal or episomal DNA. In the present study, the CRE-lox system was adapted to expand the current genetic toolbox for this hard-to-manipulate parasite. For this, evaluations of whether direct protein delivery of CRE recombinase through electroporation could improve CRE-mediated recombination in T. cruzi were performed. CRE recombinase was fused to the C-terminus of T. cruzi histone H2B, which carries the nuclear localization signal and is expressed in the prokaryotic system. The fusion protein was affinity purified and directly introduced into epimastigotes and tissue culture-derived trypomastigotes. This enabled the control of gene expression as demonstrated by turning on a tandem dimer fluorescent protein reporter gene that had been previously transfected into parasites, achieving CRE-mediated recombination in up to 85% of parasites. This system was further tested for its ability to turn off gene expression, remove selectable markers integrated into the genome, and conditionally knock down the nitroreductase gene, which is involved in drug resistance. Additionally, CREditing also enabled the control of gene expression in tissue culture trypomastigotes, which are more difficult to transfect than epimastigotes. The considerable advances in genomic manipulation of T. cruzi shown in this study can be used by others to aid in the greater understanding of this parasite through gain- or loss-of-function approaches.
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Affiliation(s)
- Lisandro A Pacheco-Lugo
- Laboratório de Genômica Funcional de Parasitos (GFP), Universidade Federal de Paraná, Paraná, Brazil; Facultad de Ciencias Básicas Biomédicas, Universidad Simón Bolívar, Barranquilla, Colombia
| | - José L Sáenz-García
- Laboratório de Genômica Funcional de Parasitos (GFP), Universidade Federal de Paraná, Paraná, Brazil
| | - Yirys Díaz-Olmos
- Instituto Carlos Chagas, Fiocruz-Paraná, Paraná, Brazil; Facultad de Ciencias de la Salud, Universidad del Norte, Barranquilla, Colombia
| | | | - Rodrigo S C Brant
- Laboratório de Genômica Funcional de Parasitos (GFP), Universidade Federal de Paraná, Paraná, Brazil
| | - Wanderson D DaRocha
- Laboratório de Genômica Funcional de Parasitos (GFP), Universidade Federal de Paraná, Paraná, Brazil.
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10
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Hegedűsová E, Kulkarni S, Burgman B, Alfonzo JD, Paris Z. The general mRNA exporters Mex67 and Mtr2 play distinct roles in nuclear export of tRNAs in Trypanosoma brucei. Nucleic Acids Res 2019; 47:8620-8631. [PMID: 31392978 PMCID: PMC6794378 DOI: 10.1093/nar/gkz671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/18/2019] [Accepted: 07/29/2019] [Indexed: 01/09/2023] Open
Abstract
Transfer RNAs (tRNAs) are central players in protein synthesis, which in Eukarya need to be delivered from the nucleus to the cytoplasm by specific transport receptors, most of which belong to the evolutionarily conserved beta-importin family. Based on the available literature, we identified two candidates, Xpo-t and Xpo-5 for tRNA export in Trypanosoma brucei. However, down-regulation of expression of these genes did not disrupt the export of tRNAs to the cytoplasm. In search of alternative pathways, we tested the mRNA export complex Mex67-Mtr2, for a role in tRNA nuclear export, as described previously in yeast. Down-regulation of either exporter affected the subcellular distribution of tRNAs. However, contrary to yeast, TbMex67 and TbMtr2 accumulated different subsets of tRNAs in the nucleus. While TbMtr2 perturbed the export of all the tRNAs tested, silencing of TbMex67, led to the nuclear accumulation of tRNAs that are typically modified with queuosine. In turn, inhibition of tRNA nuclear export also affected the levels of queuosine modification in tRNAs. Taken together, the results presented demonstrate the dynamic nature of tRNA trafficking in T. brucei and its potential impact not only on the availability of tRNAs for protein synthesis but also on their modification status.
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Affiliation(s)
- Eva Hegedűsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Sneha Kulkarni
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Brandon Burgman
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,The University of Arizona, Tucson, AZ, USA
| | - Juan D Alfonzo
- Department of Microbiology, Ohio State Biochemistry Program and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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11
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Kolev NG, Rajan KS, Tycowski KT, Toh JY, Shi H, Lei Y, Michaeli S, Tschudi C. The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA. J Biol Chem 2019; 294:15559-15574. [PMID: 31439669 DOI: 10.1074/jbc.ra119.008580] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/07/2019] [Indexed: 11/06/2022] Open
Abstract
The vault ribonucleoprotein (RNP), comprising vault RNA (vtRNA) and telomerase-associated protein 1 (TEP1), is found in many eukaryotes. However, previous studies of vtRNAs, for example in mammalian cells, have failed to reach a definitive conclusion about their function. vtRNAs are related to Y RNAs, which are complexed with Ro protein and influence Ro's function in noncoding RNA (ncRNA) quality control and processing. In Trypanosoma brucei, the small noncoding TBsRNA-10 was first described in a survey of the ncRNA repertoire in this organism. Here, we report that TBsRNA-10 in T. brucei is a vtRNA, based on its association with TEP1 and sequence similarity to those of other known and predicted vtRNAs. We observed that like vtRNAs in other species, TBsRNA-10 is transcribed by RNA polymerase III, which in trypanosomes also generates the spliceosomal U-rich small nuclear RNAs. In T. brucei, spliced leader (SL)-mediated trans-splicing of pre-mRNAs is an obligatory step in gene expression, and we found here that T. brucei's vtRNA is highly enriched in a non-nucleolar locus in the cell nucleus implicated in SL RNP biogenesis. Using a newly developed permeabilized cell system for the bloodstream form of T. brucei, we show that down-regulated vtRNA levels impair trans-spliced mRNA production, consistent with a role of vtRNA in trypanosome mRNA metabolism. Our results suggest a common theme for the functions of vtRNAs and Y RNAs. We conclude that by complexing with their protein-binding partners TEP1 and Ro, respectively, these two RNA species modulate the metabolism of various RNA classes.
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Affiliation(s)
- Nikolay G Kolev
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536
| | - Justin Y Toh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Huafang Shi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Yuling Lei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut 06536
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12
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Shan F, Mei S, Zhang J, Zhang X, Xu C, Liao S, Tu X. A telomerase subunit homolog La protein from
Trypanosoma brucei
plays an essential role in ribosomal biogenesis. FEBS J 2019; 286:3129-3147. [DOI: 10.1111/febs.14853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/23/2019] [Accepted: 04/13/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Fangzhen Shan
- Hefei National Laboratory for Physical Science at Microscale School of Life Science University of Science and Technology of China Hefei China
| | - Song Mei
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Kunming China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Science at Microscale School of Life Science University of Science and Technology of China Hefei China
| | | | - Chao Xu
- Hefei National Laboratory for Physical Science at Microscale School of Life Science University of Science and Technology of China Hefei China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Science at Microscale School of Life Science University of Science and Technology of China Hefei China
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Science at Microscale School of Life Science University of Science and Technology of China Hefei China
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13
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Fernandes CAH, Perez AM, Barros AC, Dreyer TR, da Silva MS, Morea EGO, Fontes MRM, Cano MIN. Dual cellular localization of the Leishmania amazonensis Rbp38 (LaRbp38) explains its affinity for telomeric and mitochondrial DNA. Biochimie 2019; 162:15-25. [PMID: 30930281 DOI: 10.1016/j.biochi.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Rbp38 is a protein exclusively found in trypanosomatid parasites, including Leishmania amazonensis, the etiologic agent of tegumentar leishmaniasis in the Americas. The protein was first described as a Leishmania tarentolae mitochondrial RNA binding protein. Later, it was shown that the trypanosomes Rbp38 orthologues were exclusively found in the mitochondria and involved in the stabilization and replication of kinetoplast DNA (kDNA). In contrast, L. amazonensis Rbp38 (LaRbp38), co-purifies with telomerase activity and interacts not only with kDNA but also with telomeric DNA, although shares with its counterparts high sequence identity and a putative N-terminal mitochondrial targeting signal (MTS). To understand how LaRbp38 interacts both with nuclear and kDNA, we have first investigated its subcellular localization. Using hydroxy-urea synchronized L. amazonensis promastigotes we could show that LaRbp38 shuttles from mitochondria to the nucleus at late S and G2 phases. Further, we identified a non-classical nuclear localization signal (NLS) at LaRbp38 C-terminal that binds with importin alpha, a protein involved in the nuclear transport of several proteins. Also, we obtained LaRbp38 truncated forms among which, some of them also showed an affinity for both telomeric DNA and kDNA. Analysis of these truncated forms showed that LaRbp38 DNA-binding region is located between amino acid residues 95-235. Together, our findings strongly suggest that LaRbp38 is multifunctional with dual subcellular localization.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil; Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Arina M Perez
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Andrea C Barros
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcelo S da Silva
- Laboratório Especial de Ciclo Cellular, (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
| | - Edna Gicela O Morea
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Department of Genetics, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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14
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Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 2019; 8:e43630. [PMID: 30855230 PMCID: PMC6453568 DOI: 10.7554/elife.43630] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/09/2019] [Indexed: 01/29/2023] Open
Abstract
We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggests that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.
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Affiliation(s)
- Abhilash Padavannil
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Prithwijit Sarkar
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Seung Joong Kim
- Department of PhysicsKorea Advanced Institute of Science and Technology (KAIST)DaejeonKorea
| | - Tolga Cagatay
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Jenny Jiou
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Chad A Brautigam
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Diana R Tomchick
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited states
| | - Sheena D'Arcy
- Department of Chemistry and BiochemistryUniversity of Texas at DallasRichardsonUnited States
| | - Yuh Min Chook
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
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15
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Canela-Pérez I, López-Villaseñor I, Mendoza L, Cevallos AM, Hernández R. Nuclear localization signals in trypanosomal proteins. Mol Biochem Parasitol 2019; 229:15-23. [PMID: 30772422 DOI: 10.1016/j.molbiopara.2019.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/14/2019] [Accepted: 02/09/2019] [Indexed: 01/04/2023]
Abstract
The nuclear import of proteins in eukaryotic cells is a fundamental biological process. While it has been analysed to different extents in model eukaryotic organisms, this event has rarely been studied in the early divergent protozoa of the order Kinetoplastida. The work presented here represents an overview of nuclear import in these important species of human pathogens. Initially, an in silico study of classical nuclear localization signals within the published nuclear proteomes of Trypanosoma brucei and Trypanosoma cruzi was carried out. The basic amino acids that comprise the monopartite and bipartite classical nuclear localization signals (cNLS) in trypanosomal proteins are similar to the consensus sequences observed for the nuclear proteins of yeasts, animals and plants. In addition, a summarized description of published studies that experimentally address the NLS of nuclear proteins in trypanosomatids is presented, and the clear occurrence of non-classical NLS (NLS that lack the consensus motifs of basic amino acids) in the analysed reports indicate a complex scenario for the types of receptors in these species. In general, the information presented here agrees with the hypothetical appearance of mechanisms for the recognition of nuclear proteins in early eukaryotic evolution.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México.
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16
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Rico E, Jeacock L, Kovářová J, Horn D. Inducible high-efficiency CRISPR-Cas9-targeted gene editing and precision base editing in African trypanosomes. Sci Rep 2018; 8:7960. [PMID: 29785042 PMCID: PMC5962531 DOI: 10.1038/s41598-018-26303-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022] Open
Abstract
The Cas9 endonuclease can be programmed by guide RNA to introduce sequence-specific breaks in genomic DNA. Thus, Cas9-based approaches present a range of novel options for genome manipulation and precision editing. African trypanosomes are parasites that cause lethal human and animal diseases. They also serve as models for studies on eukaryotic biology, including 'divergent' biology. Genome modification, exploiting the native homologous recombination machinery, has been important for studies on trypanosomes but often requires multiple rounds of transfection using selectable markers that integrate at low efficiency. We report a system for delivering tetracycline inducible Cas9 and guide RNA to Trypanosoma brucei. In these cells, targeted DNA cleavage and gene disruption can be achieved at close to 100% efficiency without further selection. Disruption of aquaglyceroporin (AQP2) or amino acid transporter genes confers resistance to the clinical drugs pentamidine or eflornithine, respectively, providing simple and robust assays for editing efficiency. We also use the new system for homology-directed, precision base editing; a single-stranded oligodeoxyribonucleotide repair template was delivered to introduce a single AQP2 - T791G/L264R mutation in this case. The technology we describe now enables a range of novel programmed genome-editing approaches in T. brucei that would benefit from temporal control, high-efficiency and precision.
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Affiliation(s)
- Eva Rico
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Laura Jeacock
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Julie Kovářová
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - David Horn
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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17
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Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
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18
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Canela-Pérez I, López-Villaseñor I, Cevallos AM, Hernández R. Nuclear distribution of the Trypanosoma cruzi RNA Pol I subunit RPA31 during growth and metacyclogenesis, and characterization of its nuclear localization signal. Parasitol Res 2018; 117:911-918. [PMID: 29322297 DOI: 10.1007/s00436-018-5747-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/03/2018] [Indexed: 11/28/2022]
Abstract
Trypanosoma cruzi is the aetiologic agent of Chagas disease. Our research group studies ribosomal RNA (rRNA) gene transcription and nucleolus dynamics in this species of trypanosomes. RPA31 is an essential subunit of RNA polymerase I (Pol I) whose presence is apparently restricted to trypanosomes. Using fluorescent-tagged versions of this protein (TcRPA31-EGFP), we describe its nuclear distribution during growth and metacyclogenesis. Our findings indicate that TcRPA31-EGFP alters its nuclear presence from concentrated nucleolar localization in exponentially growing epimastigotes to a dispersed granular distribution in the nucleoplasm of stationary epimastigotes and metacyclic trypomastigotes. These changes likely reflect a structural redistribution of the Pol I transcription machinery in quiescent cellular stages where downregulation of rRNA synthesis is known to occur. In addition, and related to the nuclear internalization of this protein, the presence of a classical bipartite-type nuclear localization signal was identified towards its C-terminal end. The functionality of this motif was demonstrated by its partial or total deletion in recombinant versions of the tagged fluorescent protein. Moreover, ivermectin inhibited the nuclear localization of the labelled chimaera, suggesting the involvement of the importin α/β transport system.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, CDMX, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, CDMX, Mexico
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, CDMX, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, CDMX, Mexico.
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19
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Maraia RJ, Mattijssen S, Cruz-Gallardo I, Conte MR. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1430. [PMID: 28782243 PMCID: PMC5647580 DOI: 10.1002/wrna.1430] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/02/2023]
Abstract
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding. Related to this, we review evidence that suggests that La and its link to RNAP III were significant in the great expansions of the tRNAomes that occurred in eukaryotes. Four families of La-related proteins (LARPs) emerged during eukaryotic evolution with specialized functions. We provide an overview of the high-resolution structural biology of La and LARPs. LARP7 family members most closely resemble La but function with a single RNAP III nuclear transcript, 7SK, or telomerase RNA. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA. New structures of LARP domains, some complexed with RNA, provide novel insights into the functional versatility of these proteins. We also consider LARPs in relation to ancestral La protein and potential retention of links to specific RNA-related pathways. One such link may be tRNA surveillance and codon usage by LARP-associated mRNAs. WIREs RNA 2017, 8:e1430. doi: 10.1002/wrna.1430 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD USA
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Isabel Cruz-Gallardo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
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20
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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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21
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Chiurillo MA, Moraes Barros RR, Souza RT, Marini MM, Antonio CR, Cortez DR, Curto MÁ, Lorenzi HA, Schijman AG, Ramirez JL, da Silveira JF. Subtelomeric I-SceI-Mediated Double-Strand Breaks Are Repaired by Homologous Recombination in Trypanosoma cruzi. Front Microbiol 2016; 7:2041. [PMID: 28066363 PMCID: PMC5177640 DOI: 10.3389/fmicb.2016.02041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/05/2016] [Indexed: 11/21/2022] Open
Abstract
Trypanosoma cruzi chromosome ends are enriched in surface protein genes and pseudogenes (e.g., trans-sialidases) surrounded by repetitive sequences. It has been proposed that the extensive sequence variability among members of these protein families could play a role in parasite infectivity and evasion of host immune response. In previous reports we showed evidence suggesting that sequences located in these regions are subjected to recombination. To support this hypothesis we introduced a double-strand break (DSB) at a specific target site in a T. cruzi subtelomeric region cloned into an artificial chromosome (pTAC). This construct was used to transfect T. cruzi epimastigotes expressing the I-SceI meganuclease. Examination of the repaired sequences showed that DNA repair occurred only through homologous recombination (HR) with endogenous subtelomeric sequences. Our findings suggest that DSBs in subtelomeric repetitive sequences followed by HR between them may contribute to increased variability in T. cruzi multigene families.
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Affiliation(s)
- Miguel A Chiurillo
- Laboratorio de Genética Molecular "Dr. Yunis-Turbay," Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado Barquisimeto, Venezuela
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville MD, USA
| | - Renata T Souza
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Marjorie M Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Cristiane R Antonio
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Danielle R Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - María Á Curto
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular - Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
| | - Hernán A Lorenzi
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville MD, USA
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular - Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
| | - José L Ramirez
- Centro de Biotecnología, Fundación Instituto de Estudios Avanzados Caracas, Venezuela
| | - José F da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
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22
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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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Sunter JD. A vanillic acid inducible expression system for Trypanosoma brucei. Mol Biochem Parasitol 2016; 207:45-8. [PMID: 27063979 PMCID: PMC4920640 DOI: 10.1016/j.molbiopara.2016.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 01/30/2023]
Abstract
Inducible gene expression system for Trypanosoma brucei. Addition of vanillic acid results in gene expression. Tetracycline and vanillic acid inducible systems are independent of each other. Tetracycline and vanillic acid inducible systems can be used simultaneously.
Reverse genetics in Trypanosoma brucei is dependent on the tetracycline inducible system for the precise control over the expression of both genes and dsRNA. Another independent inducible system for trypanosomes would enable the control of the activities of two different genes in the same cell, providing greater experimental sophistication. Here, I describe the development of the vanillic acid based inducible expression system for T. brucei, which operates independently of, and can be used in parallel with the tetracycline inducible system.
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Affiliation(s)
- Jack D Sunter
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK.
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24
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Nerusheva OO, Akiyoshi B. Divergent polo box domains underpin the unique kinetoplastid kinetochore. Open Biol 2016; 6:150206. [PMID: 26984294 PMCID: PMC4821238 DOI: 10.1098/rsob.150206] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/21/2016] [Indexed: 11/12/2022] Open
Abstract
Kinetochores are macromolecular machines that drive eukaryotic chromosome segregation by interacting with centromeric DNA and spindle microtubules. While most eukaryotes possess conventional kinetochore proteins, evolutionarily distant kinetoplastid species have unconventional kinetochore proteins, composed of at least 19 proteins (KKT1-19). Polo-like kinase (PLK) is not a structural kinetochore component in either system. Here, we report the identification of an additional kinetochore protein, KKT20, in Trypanosoma brucei. KKT20 has sequence similarity with KKT2 and KKT3 in the Cys-rich region, and all three proteins have weak but significant similarity to the polo box domain (PBD) of PLK. These divergent PBDs of KKT2 and KKT20 are sufficient for kinetochore localization in vivo. We propose that the ancestral PLK acquired a Cys-rich region and then underwent gene duplication events to give rise to three structural kinetochore proteins in kinetoplastids.
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Affiliation(s)
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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25
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BRF1, a subunit of RNA polymerase III transcription factor TFIIIB, is essential for cell growth of Trypanosoma brucei. Parasitology 2015; 142:1563-73. [PMID: 26337955 DOI: 10.1017/s0031182015001122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA polymerase III (Pol III) synthesizes small RNA molecules that are essential for cell viability. Accurate initiation of transcription by Pol III requires general transcription factor TFIIIB, which is composed of three subunits: TFIIB-related factor BRF1, TATA-binding protein and BDP1. Here we report the molecular characterization of BRF1 in Trypanosoma brucei (TbBRF1), a parasitic protozoa that shows distinctive transcription characteristics. In silico analysis allowed the detection in TbBRF1 of the three conserved domains located in the N-terminal region of all BRF1 orthologues, namely a zinc ribbon motif and two cyclin repeats. Homology modelling suggested that, similarly to other BRF1 and TFIIB proteins, the TbBRF1 cyclin repeats show the characteristic structure of five α-helices per repeat, connected by a short random-coiled linker. As expected for a transcription factor, TbBRF1 was localized in the nucleus. Knock-down of TbBRF1 by RNA interference (RNAi) showed that this protein is essential for the viability of procyclic forms of T. brucei, since ablation of TbBRF1 led to growth arrest of the parasites. Nuclear run-on and quantitative real-time PCR analyses demonstrated that transcription of all the Pol III-dependent genes analysed was reduced, at different levels, after RNAi induction.
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26
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Isnard A, Christian JG, Kodiha M, Stochaj U, McMaster WR, Olivier M. Impact of Leishmania infection on host macrophage nuclear physiology and nucleopore complex integrity. PLoS Pathog 2015; 11:e1004776. [PMID: 25826301 PMCID: PMC4380401 DOI: 10.1371/journal.ppat.1004776] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 03/03/2015] [Indexed: 12/23/2022] Open
Abstract
The protease GP63 is an important virulence factor of Leishmania parasites. We previously showed that GP63 reaches the perinuclear area of host macrophages and that it directly modifies nuclear translocation of the transcription factors NF-κB and AP-1. Here we describe for the first time, using molecular biology and in-depth proteomic analyses, that GP63 alters the host macrophage nuclear envelope, and impacts on nuclear processes. Our results suggest that GP63 does not appear to use a classical nuclear localization signal common between Leishmania species for import, but degrades nucleoporins, and is responsible for nuclear transport alterations. In the nucleoplasm, GP63 activity accounts for the degradation and mislocalization of proteins involved amongst others in gene expression and in translation. Collectively, our data indicates that Leishmania infection strongly affects nuclear physiology, suggesting that targeting of nuclear physiology may be a strategy beneficial for virulent Leishmania parasites. Unicellular parasites of the genus Leishmania are the causative agent of leishmaniasis, a disease affecting 12 million people worldwide, mainly in tropical and subtropical regions of the developing world. They have evolved strategies to circumvent cellular defense mechanisms favouring their survival. This includes the cleavage and activation of proteins and the subsequent block of signals within the host cells. In this study we discovered that a Leishmania virulence factor, GP63, is able to reach host cell nuclei and affect protein transport from and into the nucleus. Through the analysis of the protein content of nuclei after parasite infection we revealed that Leishmania, predominantly through the protein cleaving enzyme GP63, can alter several processes within the nucleus, amongst others mechanisms associated with gene expression and nucleic acid metabolism. Thus, we here introduce a novel strategy of how Leishmania parasites may overcome host cell defense and ensure their own survival.
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Affiliation(s)
- Amandine Isnard
- Departments of Medicine and Microbiology & Immunology, The Research Institute of the McGill University Health Centre, McGill University, Montréal, Quebec, Canada
| | - Jan G. Christian
- Departments of Medicine and Microbiology & Immunology, The Research Institute of the McGill University Health Centre, McGill University, Montréal, Quebec, Canada
| | - Mohamed Kodiha
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montréal, Quebec, Canada
| | - W. Robert McMaster
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Olivier
- Departments of Medicine and Microbiology & Immunology, The Research Institute of the McGill University Health Centre, McGill University, Montréal, Quebec, Canada
- * E-mail:
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27
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Brasseur A, Bayat S, Chua XL, Zhang Y, Zhou Q, Low BC, He CY. The bi-lobe-associated LRRP1 regulates Ran activity in Trypanosoma brucei. J Cell Sci 2014; 127:4846-56. [PMID: 25217630 DOI: 10.1242/jcs.148015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cilia and flagella are conserved eukaryotic organelles important for motility and sensory. The RanGTPase, best known for nucleocytoplasmic transport functions, may also play a role in protein trafficking into the specialized flagellar/ciliary compartments, although the regulatory mechanisms controlling Ran activity at the flagellum remain unclear. The unicellular parasite Trypanosoma brucei contains a single flagellum necessary for cell movement, division and morphogenesis. Correct flagellum functions require flagellar attachment to the cell body, which is mediated by a specialized flagellum attachment zone (FAZ) complex that is assembled together with the flagellum during the cell cycle. We have previously identified the leucine-rich-repeat protein 1 LRRP1 on a bi-lobe structure at the proximal base of flagellum and FAZ. LRRP1 is essential for bi-lobe and FAZ biogenesis, consequently affecting flagellum-driven cell motility and division. Here, we show that LRRP1 forms a complex with Ran and a Ran-binding protein, and regulates Ran-GTP hydrolysis in T. brucei. In addition to mitotic inhibition, depletion of Ran inhibits FAZ assembly in T. brucei, supporting the presence of a conserved mechanism that involves Ran in the regulation of flagellum functions in an early divergent eukaryote.
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Affiliation(s)
- Anaïs Brasseur
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Shima Bayat
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Xiu Ling Chua
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | - Yu Zhang
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
| | | | - Boon Chuan Low
- Singapore Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, S1A #06-04, Singapore 117543, Singapore
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28
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Demmel L, Schmidt K, Lucast L, Havlicek K, Zankel A, Koestler T, Reithofer V, de Camilli P, Warren G. The endocytic activity of the flagellar pocket in Trypanosoma brucei is regulated by an adjacent phosphatidylinositol phosphate kinase. J Cell Sci 2014; 127:2351-64. [PMID: 24639465 DOI: 10.1242/jcs.146894] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Phosphoinositides are spatially restricted membrane signaling molecules. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]--a phosphoinositide that is highly enriched in, and present throughout, the plasma membrane--has been implicated in endocytosis. Trypanosoma brucei has one of the highest known rates of endocytosis, a process it uses to evade the immune system. To determine whether phosphoinositides play a role in endocytosis in this organism, we have identified and characterized one of the enzymes that is responsible for generating PI(4,5)P2. Surprisingly, this phosphoinositide was found to be highly concentrated in the flagellar pocket, the only site of endocytosis and exocytosis in this organism. The enzyme (designated TbPIPKA, annotated as Tb927.10.1620) was present at the neck of the pocket, towards the anterior-end of the parasite. Depletion of TbPIPKA led to depletion of PI(4,5)P2 and enlargement of the pocket, the result of impaired endocytosis. Taken together, these data suggest that TbPIPKA and its product PI(4,5)P2 are important for endocytosis and, consequently, for homeostasis of the flagellar pocket.
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Affiliation(s)
- Lars Demmel
- Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Katy Schmidt
- Department of Cell Biology and Ultrastructure Research, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Louise Lucast
- Department of Cell Biology, Howard Hughes Medical Institute, and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Katharina Havlicek
- Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Armin Zankel
- Institute for Electron Microscopy, Graz University of Technology and Center for Electron Microscopy Graz, 8010 Graz, Austria
| | - Tina Koestler
- Center for Integrative Bioinformatics, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Viktoria Reithofer
- University of Applied Sciences Wiener Neustadt, Department of Biomedical Analytics, 2700 Wiener Neustadt, Austria
| | - Pietro de Camilli
- Department of Cell Biology, Howard Hughes Medical Institute, and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Graham Warren
- Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
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29
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Kovárová J, Horáková E, Changmai P, Vancová M, Lukeš J. Mitochondrial and nucleolar localization of cysteine desulfurase Nfs and the scaffold protein Isu in Trypanosoma brucei. EUKARYOTIC CELL 2014; 13:353-62. [PMID: 24243795 PMCID: PMC3957590 DOI: 10.1128/ec.00235-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023]
Abstract
Trypanosoma brucei has a complex life cycle during which its single mitochondrion is subjected to major metabolic and morphological changes. While the procyclic stage (PS) of the insect vector contains a large and reticulated mitochondrion, its counterpart in the bloodstream stage (BS) parasitizing mammals is highly reduced and seems to be devoid of most functions. We show here that key Fe-S cluster assembly proteins are still present and active in this organelle and that produced clusters are incorporated into overexpressed enzymes. Importantly, the cysteine desulfurase Nfs, equipped with the nuclear localization signal, was detected in the nucleolus of both T. brucei life stages. The scaffold protein Isu, an interacting partner of Nfs, was also found to have a dual localization in the mitochondrion and the nucleolus, while frataxin and both ferredoxins are confined to the mitochondrion. Moreover, upon depletion of Isu, cytosolic tRNA thiolation dropped in the PS but not BS parasites.
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Affiliation(s)
- Julie Kovárová
- Biology Center, Institute of Parasitology, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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30
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Poon SK, Peacock L, Gibson W, Gull K, Kelly S. A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor. Open Biol 2013; 2:110037. [PMID: 22645659 PMCID: PMC3352093 DOI: 10.1098/rsob.110037] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 01/24/2012] [Indexed: 11/24/2022] Open
Abstract
Here, we present a simple modular extendable vector system for introducing the T7
RNA polymerase and tetracycline repressor genes into Trypanosoma
brucei. This novel system exploits developments in our
understanding of gene expression and genome organization to produce a
streamlined plasmid optimized for high levels of expression of the introduced
transgenes. We demonstrate the utility of this novel system in bloodstream and
procyclic forms of Trypanosoma brucei, including the genome
strain TREU927/4. We validate these cell lines using a variety of inducible
experiments that recapture previously published lethal and non-lethal
phenotypes. We further demonstrate the utility of the single marker (SmOx)
TREU927/4 cell line for in vivo experiments in the tsetse fly
and provide a set of plasmids that enable both whole-fly and salivary
gland-specific inducible expression of transgenes.
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Affiliation(s)
- S K Poon
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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31
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Krüger T, Hofweber M, Kramer S. SCD6 induces ribonucleoprotein granule formation in trypanosomes in a translation-independent manner, regulated by its Lsm and RGG domains. Mol Biol Cell 2013; 24:2098-111. [PMID: 23676662 PMCID: PMC3694794 DOI: 10.1091/mbc.e13-01-0068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Trypanosomes lack many core components of ribonucleoprotein (RNP) granules identified in yeast and humans (e.g., DCP1/2). This study provides evidence for SCD6 being the core RNP granule component in trypanosomes: overexpression induces granules independent of translation, and even when SCD6 is targeted to the nucleus. Granule type and granule number are dependent on the RGG domain. Ribonucleoprotein (RNP) granules are cytoplasmic, microscopically visible structures composed of RNA and protein with proposed functions in mRNA decay and storage. Trypanosomes have several types of RNP granules, but lack most of the granule core components identified in yeast and humans. The exception is SCD6/Rap55, which is essential for processing body (P-body) formation. In this study, we analyzed the role of trypanosome SCD6 in RNP granule formation. Upon overexpression, the majority of SCD6 aggregates to multiple granules enriched at the nuclear periphery that recruit both P-body and stress granule proteins, as well as mRNAs. Granule protein composition depends on granule distance to the nucleus. In contrast to findings in yeast and humans, granule formation does not correlate with translational repression and can also take place in the nucleus after nuclear targeting of SCD6. While the SCD6 Lsm domain alone is both necessary and sufficient for granule induction, the RGG motif determines granule type and number: the absence of an intact RGG motif results in the formation of fewer granules that resemble P-bodies. The differences in granule number remain after nuclear targeting, indicating translation-independent functions of the RGG domain. We propose that, in trypanosomes, a local increase in SCD6 concentration may be sufficient to induce granules by recruiting mRNA. Proteins that bind selectively to the RGG and/or Lsm domain of SCD6 could be responsible for regulating granule type and number.
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Affiliation(s)
- Timothy Krüger
- Lehrstuhl für Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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32
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Cámara MDLM, Bouvier LA, Canepa GE, Miranda MR, Pereira CA. Molecular and functional characterization of a Trypanosoma cruzi nuclear adenylate kinase isoform. PLoS Negl Trop Dis 2013; 7:e2044. [PMID: 23409202 PMCID: PMC3567042 DOI: 10.1371/journal.pntd.0002044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/17/2012] [Indexed: 01/30/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas' disease, is an early divergent eukaryote in which control of gene expression relies mainly in post-transcriptional mechanisms. Transcription levels are globally up and down regulated during the transition between proliferating and non-proliferating life-cycle stages. In this work we characterized a nuclear adenylate kinase isoform (TcADKn) that is involved in ribosome biogenesis. Nuclear adenylate kinases have been recently described in a few organisms, being all related to RNA metabolism. Depending on active transcription and translation, TcADKn localizes in the nucleolus or the cytoplasm. A non-canonical nuclear localization signal was mapped towards the N-terminal of the protein, being the phosphate-binding loop essential for its localization. In addition, TcADKn nuclear exportation depends on the nuclear exportation adapter CRM1. TcADKn nuclear shuttling is governed by nutrient availability, oxidative stress and by the equivalent in T. cruzi of the mammalian TOR (Target of Rapamycin) pathway. One of the biological functions of TcADKn is ribosomal 18S RNA processing by direct interaction with ribosomal protein TcRps14. Finally, TcADKn expression is regulated by its 3′ UTR mRNA. Depending on extracellular conditions, cells modulate protein translation rates regulating ribosome biogenesis and nuclear adenylate kinases are probably key components in these processes. Infection with Trypanosoma cruzi produces a condition known as Chagas disease which affects at least 17 million people. Adenylate kinases, so called myokinases, are involved in a wide variety of processes, mainly related to their role in nucleotide interconversion and energy management. Recently, nuclear isoforms have been described in several organisms. This “atypical” isoform in terms of primary structure was associated to ribosomes biogenesis in yeast and to Cajal body organization in humans. Moreover nuclear adenylate kinases are essential for maintaining cellular homeostasis. In this manuscript we characterized T. cruzi nuclear adenylate kinase (TcADKn). TcADKn localizes in the nucleolus or cell cytoplasm. Nuclear shuttling mechanisms were also studied for the first time, being dependent on nutrient availability, oxidative stress and by the equivalent of the mammalian TOR pathway in T. cruzi. Furthermore we characterized the signals involved in nuclear importation and exportation processes. In addition, TcADKn expression levels are regulated at an mRNA level, being its 3′UTR involved in this process. These findings are the first steps in the understanding of ribosome processing in trypanosomatids.
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Affiliation(s)
| | | | | | | | - Claudio A. Pereira
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
- * E-mail:
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33
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Kramer S, Bannerman-Chukualim B, Ellis L, Boulden EA, Kelly S, Field MC, Carrington M. Differential localization of the two T. brucei poly(A) binding proteins to the nucleus and RNP granules suggests binding to distinct mRNA pools. PLoS One 2013; 8:e54004. [PMID: 23382864 PMCID: PMC3559699 DOI: 10.1371/journal.pone.0054004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 12/06/2012] [Indexed: 12/30/2022] Open
Abstract
The number of paralogs of proteins involved in translation initiation is larger in trypanosomes than in yeasts or many metazoan and includes two poly(A) binding proteins, PABP1 and PABP2, and four eIF4E variants. In many cases, the paralogs are individually essential and are thus unlikely to have redundant functions although, as yet, distinct functions of different isoforms have not been determined. Here, trypanosome PABP1 and PABP2 have been further characterised. PABP1 and PABP2 diverged subsequent to the differentiation of the Kinetoplastae lineage, supporting the existence of specific aspects of translation initiation regulation. PABP1 and PABP2 exhibit major differences in intracellular localization and distribution on polysome fractionation under various conditions that interfere with mRNA metabolism. Most striking are differences in localization to the four known types of inducible RNP granules. Moreover, only PABP2 but not PABP1 can accumulate in the nucleus. Taken together, these observations indicate that PABP1 and PABP2 likely associate with distinct populations of mRNAs. The differences in localization to inducible RNP granules also apply to paralogs of components of the eIF4F complex: eIF4E1 showed similar localization pattern to PABP2, whereas the localisation of eIF4E4 and eIF4G3 resembled that of PABP1. The grouping of translation initiation as either colocalizing with PABP1 or with PABP2 can be used to complement interaction studies to further define the translation initiation complexes in kinetoplastids.
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Affiliation(s)
- Susanne Kramer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Louise Ellis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Steve Kelly
- Department of Plant Sciences, University of Oxford, and Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark C. Field
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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34
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Field MC, Adung'a V, Obado S, Chait BT, Rout MP. Proteomics on the rims: insights into the biology of the nuclear envelope and flagellar pocket of trypanosomes. Parasitology 2012; 139:1158-67. [PMID: 22309600 PMCID: PMC4241632 DOI: 10.1017/s0031182011002125] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Trypanosomatids represent the causative agents of major diseases in humans, livestock and plants, with inevitable suffering and economic hardship as a result. They are also evolutionarily highly divergent organisms, and the many unique aspects of trypanosome biology provide opportunities in terms of identification of drug targets, the challenge of exploiting these putative targets and, at the same time, significant scope for exploration of novel and divergent cell biology. We can estimate from genome sequences that the degree of divergence of trypanosomes from animals and fungi is extreme, with perhaps one third to one half of predicted trypanosome proteins having no known function based on homology or recognizable protein domains/architecture. Two highly important aspects of trypanosome biology are the flagellar pocket and the nuclear envelope, where in silico analysis clearly suggests great potential divergence in the proteome. The flagellar pocket is the sole site of endo- and exocytosis in trypanosomes and plays important roles in immune evasion via variant surface glycoprotein (VSG) trafficking and providing a location for sequestration of various invariant receptors. The trypanosome nuclear envelope has been largely unexplored but, by analogy with higher eukaryotes, roles in the regulation of chromatin and most significantly, in controlling VSG gene expression are expected. Here we discuss recent successful proteomics-based approaches towards characterization of the nuclear envelope and the endocytic apparatus, the identification of conserved and novel trypanosomatid-specific features, and the implications of these findings.
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Affiliation(s)
- Mark C Field
- Department of Pathology, University of Cambridge, Cambridge, UK.
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Kumar D, Kumar D, Saha S. A highly basic sequence at the N-terminal region is essential for targeting the DNA replication protein ORC1 to the nucleus in Leishmania donovani. MICROBIOLOGY-SGM 2012; 158:1775-1782. [PMID: 22575896 DOI: 10.1099/mic.0.055640-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conserved eukaryotic DNA replication protein ORC1 is one of the constituents of pre-replication complexes that assemble at or very near origins prior to replication initiation. ORC1 has been shown to be constitutively nuclear in Leishmania major. This study investigates the sequences involved in nuclear localization of ORC1 in Leishmania donovani, the causative agent of visceral leishmaniasis. Nuclear localization signals (NLSs) have been reported in only a few Leishmania proteins. Functional analyses have delineated NLSs to regions of ~60 amino acids in length in the tyrosyl DNA phosphodiesterase I and type II DNA topoisomerase of L. donovani, and in the L. major kinesin KIN13-1. Using a panel of site-directed mutations we have identified a sequence essential for nuclear import of LdORC1. This sequence at the N terminus of the protein comprises residues 2-5 (KRSR), with K2, R3 and R5 being crucial. Independent mutation of the K2 residue causes exclusion of the protein from the nucleus, while mutating the R5 residue leads to diffusion of the protein throughout the cell. This sequence, however, is insufficient for targeting a heterologous protein (β-galactosidase) to the nucleus. Analysis of additional ORC1 mutations and reporter constructs reveals that while the highly basic tetra-amino acid sequence at the N terminus is essential for nuclear localization, the ORC1 NLS in its entirety is more complex, and of a distributive character. Our results suggest that nuclear localization signalling sequences in Leishmania nuclear proteins are more complex than what is typically seen in higher eukaryotes.
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Affiliation(s)
- Devanand Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Diwakar Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Daniels JP, Gull K, Wickstead B. The trypanosomatid-specific N terminus of RPA2 is required for RNA polymerase I assembly, localization, and function. EUKARYOTIC CELL 2012; 11:662-72. [PMID: 22389385 PMCID: PMC3346432 DOI: 10.1128/ec.00036-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 02/23/2012] [Indexed: 11/20/2022]
Abstract
African trypanosomes are the only organisms known to use RNA polymerase I (pol I) to transcribe protein-coding genes. These genes include VSG, which is essential for immune evasion and is transcribed from an extranucleolar expression site body (ESB). Several trypanosome pol I subunits vary compared to their homologues elsewhere, and the question arises as to how these variations relate to pol I function. A clear example is the N-terminal extension found on the second-largest subunit of pol I, RPA2. Here, we identify an essential role for this region. RPA2 truncation leads to nuclear exclusion and a growth defect which phenocopies single-allele knockout. The N terminus is not a general nuclear localization signal (NLS), however, and it fails to accumulate unrelated proteins in the nucleus. An ectopic NLS is sufficient to reinstate nuclear localization of truncated RPA2, but it does not restore function. Moreover, NLS-tagged, truncated RPA2 has a different subnuclear distribution to full-length protein and is unable to build stable pol I complexes. We conclude that the RPA2 N-terminal extension does not have a role exclusive to the expression of protein-coding genes, but it is essential for all pol I functions in trypanosomes because it directs trypanosomatid-specific interactions with RPA1.
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Affiliation(s)
- Jan-Peter Daniels
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Centre for Genetics and Genomics, University of Nottingham, Nottingham, United Kingdom
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A highly organized structure mediating nuclear localization of a Myb2 transcription factor in the protozoan parasite Trichomonas vaginalis. EUKARYOTIC CELL 2011; 10:1607-17. [PMID: 22021237 DOI: 10.1128/ec.05177-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nuclear proteins usually contain specific peptide sequences, referred to as nuclear localization signals (NLSs), for nuclear import. These signals remain unexplored in the protozoan pathogen, Trichomonas vaginalis. The nuclear import of a Myb2 transcription factor was studied here using immunodetection of a hemagglutinin-tagged Myb2 overexpressed in the parasite. The tagged Myb2 was localized to the nucleus as punctate signals. With mutations of its polybasic sequences, 48KKQK51 and 61KR62, Myb2 was localized to the nucleus, but the signal was diffusive. When fused to a C-terminal non-nuclear protein, the Myb2 sequence spanning amino acid (aa) residues 48 to 143, which is embedded within the R2R3 DNA-binding domain (aa 40 to 156), was essential and sufficient for efficient nuclear import of a bacterial tetracycline repressor (TetR), and yet the transport efficiency was reduced with an additional fusion of a firefly luciferase to TetR, while classical NLSs from the simian virus 40 T-antigen had no function in this assay system. Myb2 nuclear import and DNA-binding activity were substantially perturbed with mutation of a conserved isoleucine (I74) in helix 2 to proline that altered secondary structure and ternary folding of the R2R3 domain. Disruption of DNA-binding activity alone by point mutation of a lysine residue, K51, preceding the structural domain had little effect on Myb2 nuclear localization, suggesting that nuclear translocation of Myb2, which requires an ordered structural domain, is independent of its DNA binding activity. These findings provide useful information for testing whether myriad Mybs in the parasite use a common module to regulate nuclear import.
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Názer E, Verdún RE, Sánchez DO. Nucleolar localization of RNA binding proteins induced by actinomycin D and heat shock in Trypanosoma cruzi. PLoS One 2011; 6:e19920. [PMID: 21629693 PMCID: PMC3101214 DOI: 10.1371/journal.pone.0019920] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/14/2011] [Indexed: 11/18/2022] Open
Abstract
In this work we show that under Actinomycin D (ActD) treatment, several RNA Binding Proteins (RBPs) involved in mRNA metabolism are relocalized into the nucleolus in Trypanosoma cruzi as a specific stress response. ATP depletion as well as kinase inhibition markedly reduced the nucleolar localization response, suggesting that an energy-dependent transport modulated by the phosphorylation status of the parasite might be required. Deletion analyses in one of such proteins, TcSR62, showed that a domain bearing basic amino acids located in the COOH terminal region was sufficient to promote its nucleolar relocalization. Interestingly, we showed that in addition to RBPs, poly(A)+ RNA is also accumulated into the nucleolus in response to ActD treatment. Finally, we found out that nucleolar relocalization of RBPs is also triggered by severe heat shock in a reversible way. Together, these results suggest that the nucleolus of an early divergent eukaryote is either able to sequester key factors related to mRNA metabolism in response to transcriptional stress or behaves as a RBP processing center, arguing in favour to the hypothesis that the non-traditional features of the nucleolus could be acquired early during evolution.
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Affiliation(s)
- Ezequiel Názer
- Instituto de Investigaciones Biotecnólogicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Ramiro E. Verdún
- Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnólogicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
- * E-mail:
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Ersfeld K. Nuclear architecture, genome and chromatin organisation in Trypanosoma brucei. Res Microbiol 2011; 162:626-36. [PMID: 21392575 DOI: 10.1016/j.resmic.2011.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/29/2011] [Indexed: 11/29/2022]
Abstract
The nucleus of the human pathogen Trypanosoma brucei not only has unusual chromosomal composition, characterised by the presence of megabase, intermediate and minichromosomes, but also chromosome and gene organisation that is unique amongst eukaryotes. Here I provide an overview of current knowledge of nuclear structure, chromatin organisation and chromosome dynamics during interphase and mitosis. New technologies such as chromatin immunoprecipitation, in combination with new generation sequencing and proteomic analysis of subnuclear fractions, have led to novel insights into the organisation of the nucleus and chromatin. In particular, we are beginning to understand how universal mechanisms of chromatin modifications and nuclear position effects are deployed for parasite-specific functions and are centrally involved in genomic organisation and transcriptional regulation. These advances also have a major impact on progress in understanding the molecular basis of antigenic variation.
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Affiliation(s)
- Klaus Ersfeld
- Department of Biological Sciences and Hull York Medical School, University of Hull, Hull HU6 7RX, UK.
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40
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Chaves SR, Rosenblum JS. Efficient nuclear transport of structurally disturbed cargo: mutations in a cargo protein switch its cognate karyopherin. PLoS One 2011; 6:e16846. [PMID: 21347375 PMCID: PMC3036716 DOI: 10.1371/journal.pone.0016846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 01/16/2011] [Indexed: 11/18/2022] Open
Abstract
The Karyopherin (Kap) family of nuclear transport receptors enables trafficking of proteins to and from the nucleus in a precise, regulated manner. Individual members function in overlapping pathways, while simultaneously being very specific for their main cargoes. The details of this apparent contradiction and rules governing pathway preference remain to be further elucidated. S. cerevisiae Lhp1 is an abundant protein that functions as an RNA chaperone in a variety of biologically important processes. It localizes almost exclusively to the nucleus and is imported by Kap108. We show that mutation of 3 of the 275 residues in Lhp1 alters its import pathway to a Kap121-dependent process. This mutant does not retain wild-type function and is bound by several chaperones. We propose that Kap121 also acts as a chaperone, one that can act as a genetic buffer by transporting mutated proteins to the nucleus.
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Affiliation(s)
- Susana R Chaves
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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Dodson HC, Lyda TA, Chambers JW, Morris MT, Christensen KA, Morris JC. Quercetin, a fluorescent bioflavanoid, inhibits Trypanosoma brucei hexokinase 1. Exp Parasitol 2010; 127:423-8. [PMID: 20971104 DOI: 10.1016/j.exppara.2010.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 09/22/2010] [Accepted: 10/14/2010] [Indexed: 12/01/2022]
Abstract
Hexokinases from the African trypanosome, Trypanosoma brucei, are attractive targets for the development of anti-parasitic drugs, in part because the parasite utilizes glycolysis exclusively for ATP production during the mammalian infection. Here, we have demonstrated that the bioflavanoid quercetin (QCN), a known trypanocide, is a mixed inhibitor of Trypanosoma brucei hexokinase 1 (TbHK1) (IC(50) = 4.1 ± 0.8μM). Spectroscopic analysis of QCN binding to TbHK1, taking advantage of the intrinsically fluorescent single tryptophan (Trp177) in TbHK1, revealed that QCN quenches emission of Trp177, which is located near the hinge region of the enzyme. ATP similarly quenched Trp177 emission, while glucose had no impact on fluorescence. Supporting the possibility that QCN toxicity is a consequence of inhibition of the essential hexokinase, in live parasites QCN fluorescence localizes to glycosomes, the subcellular home of TbHK1. Additionally, RNAi-mediated silencing of TbHK1 expression expedited QCN induced death, while over-expressing TbHK1 protected trypanosomes from the compound. In summary, these observations support the suggestion that QCN toxicity is in part attributable to inhibition of the essential TbHK1.
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Affiliation(s)
- Heidi C Dodson
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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da Costa Lima TD, Moura DMN, Reis CRS, Vasconcelos JRC, Ellis L, Carrington M, Figueiredo RCBQ, de Melo Neto OP. Functional characterization of three leishmania poly(a) binding protein homologues with distinct binding properties to RNA and protein partners. EUKARYOTIC CELL 2010; 9:1484-94. [PMID: 20675580 PMCID: PMC2950419 DOI: 10.1128/ec.00148-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022]
Abstract
Trypanosomatid protozoans are reliant on posttranscriptional processes to control gene expression. Regulation occurs at the levels of mRNA processing, stability, and translation, events that may require the participation of the poly(A) binding protein (PABP). Here, we have undertaken a functional study of the three distinct Leishmania major PABP (LmPABP) homologues: the previously described LmPABP1; LmPABP2, orthologous to the PABP described from Trypanosoma species; and LmPABP3, unique to Leishmania. Sequence identity between the three PABPs is no greater than 40%. In assays measuring binding to A-rich sequences, LmPABP1 binding was poly(A) sensitive but heparin insensitive; LmPABP2 binding was heparin sensitive and less sensitive to poly(A), compatible with unique substitutions observed in residues implicated in poly(A) binding; and LmPABP3 displayed intermediate properties. All three homologues are simultaneously expressed as abundant cytoplasmic proteins in L. major promastigotes, but only LmPABP1 is present as multiple isoforms. Upon transcription inhibition, LmPABP2 and -3 migrated to the nucleus, while LmPABP1 remained predominantly cytoplasmic. Immunoprecipitation assays showed an association between LmPABP2 and -3. Although the three proteins bound to a Leishmania homologue of the translation initiation factor eukaryotic initiation factor 4G (eIF4G) (LmEIF4G3) in vitro, LmPABP1 was the only one to copurify with native LmEIF4G3 from cytoplasmic extracts. Functionality was tested using RNA interference (RNAi) in Trypanosoma brucei, where both orthologues to LmPABP1 and -2 are required for cellular viability. Our results indicate that these homologues have evolved divergent functions, some of which may be unique to the trypanosomatids, and reinforces a role for LmPABP1 in translation through its interaction with the eIF4G homologue.
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Affiliation(s)
- Tamara D. da Costa Lima
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Danielle M. N. Moura
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Christian R. S. Reis
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - J. Ronnie C. Vasconcelos
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Louise Ellis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Regina C. B. Q. Figueiredo
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
| | - Osvaldo P. de Melo Neto
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães/Fiocruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
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Droll D, Archer S, Fenn K, Delhi P, Matthews K, Clayton C. The trypanosome Pumilio-domain protein PUF7 associates with a nuclear cyclophilin and is involved in ribosomal RNA maturation. FEBS Lett 2010; 584:1156-62. [PMID: 20153321 PMCID: PMC2855960 DOI: 10.1016/j.febslet.2010.02.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 12/17/2009] [Accepted: 02/05/2010] [Indexed: 01/27/2023]
Abstract
Proteins with Pumilio RNA binding domains (Puf proteins) are ubiquitous in eukaryotes. Some Puf proteins bind to the 3′-untranslated regions of mRNAs, acting to repress translation and promote degradation; others are involved in ribosomal RNA maturation. The genome of Trypanosoma brucei encodes eleven Puf proteins whose function cannot be predicted by sequence analysis. We show here that epitope-tagged TbPUF7 is located in the nucleolus, and associated with a nuclear cyclophilin-like protein, TbNCP1. RNAi targeting PUF7 reduced trypanosome growth and inhibited two steps in ribosomal RNA processing.
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Affiliation(s)
- Dorothea Droll
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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Cassola A, Frasch AC. An RNA recognition motif mediates the nucleocytoplasmic transport of a trypanosome RNA-binding protein. J Biol Chem 2009; 284:35015-28. [PMID: 19801539 DOI: 10.1074/jbc.m109.031633] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) and RNA metabolism are considered to be important for modulating gene expression in trypanosomes, because these protozoan parasites mainly rely on post-transcriptional mechanisms to regulate protein levels. Previously, we have identified TcUBP1, a single RNA recognition motif (RRM)-type RBP from Trypanosoma cruzi. TcUBP1 is a cytoplasmic protein with roles in stabilization/degradation of mRNAs and in the protection of transcripts through their recruitment into cytoplasmic granules. We now show that TcUBP1, and the closely related protein TcUBP2, can be found in small amounts in the nucleus under normal conditions, and are able to accumulate in the nucleus under arsenite stress. The kinetics of nuclear accumulation, and export to the cytoplasm, are consistent with the shuttling of TcUBP1 between the nucleus and the cytoplasm. The sequence required for TcUBP1 nuclear accumulation was narrowed to the RRM, and point mutations affecting RNA binding abolished nuclear import. This RRM was also shown to be efficiently exported from the nucleus in unstressed parasites, a property that relied on the binding to RNA. TcUBP1 nuclear accumulation was dependent on active transcription, and colocalized with transcripts in the nucleus, suggesting nuclear binding of the mRNA. We propose that TcUBP1 could be linking the mRNA metabolism at both sides of the nuclear pore complex, using the RRM as a nuclear localization signal, and being exported as a cargo on mRNA.
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Affiliation(s)
- Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, (1650) San Martín, Provincia de Buenos Aires, Argentina
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Spliceosomal proteomics in Trypanosoma brucei reveal new RNA splicing factors. EUKARYOTIC CELL 2009; 8:990-1000. [PMID: 19429779 DOI: 10.1128/ec.00075-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In trypanosomatid parasites, spliced leader (SL) trans splicing is an essential nuclear mRNA maturation step which caps mRNAs posttranscriptionally and, in conjunction with polyadenylation, resolves individual mRNAs from polycistronic precursors. While all trypanosomatid mRNAs are trans spliced, intron removal by cis splicing is extremely rare and predicted to occur in only four pre-mRNAs. trans- and cis-splicing reactions are carried out by the spliceosome, which consists of U-rich small nuclear ribonucleoprotein particles (U snRNPs) and of non-snRNP factors. Mammalian and yeast spliceosome complexes are well characterized and found to be associated with up to 170 proteins. Despite the central importance of trans splicing in trypanosomatid gene expression, only the core RNP proteins and a few snRNP-specific proteins are known. To characterize the trypanosome spliceosomal protein repertoire, we conducted a proteomic analysis by tagging and tandem affinity-purifying the canonical core RNP protein SmD1 in Trypanosoma brucei and by identifying copurified proteins by mass spectrometry. The set of 47 identified proteins harbored nearly all spliceosomal snRNP factors characterized in trypanosomes thus far and 21 proteins lacking a specific annotation. A bioinformatic analysis combined with protein pull-down assays and immunofluorescence microscopy identified 10 divergent orthologues of known splicing factors, including the missing U1-specific protein U1A. In addition, a novel U5-specific, and, as we show, an essential splicing factor was identified that shares a short, highly conserved N-terminal domain with the yeast protein Cwc21p and was thus tentatively named U5-Cwc21. Together, these data strongly indicate that most of the identified proteins are components of the spliceosome.
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Kramer S, Queiroz R, Ellis L, Webb H, Hoheisel JD, Clayton C, Carrington M. Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. J Cell Sci 2008; 121:3002-14. [PMID: 18713834 DOI: 10.1242/jcs.031823] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In trypanosomes there is an almost total reliance on post-transcriptional mechanisms to alter gene expression; here, heat shock was used to investigate the response to an environmental signal. Heat shock rapidly and reversibly induced a decrease in polysome abundance, and the consequent changes in mRNA metabolism were studied. Both heat shock and polysome dissociation were necessary for (1) a reduction in mRNA levels that was more rapid than normal turnover, (2) an increased number of P-body-like granules that contained DHH1, SCD6 and XRNA, (3) the formation of stress granules that remained largely separate from the P-body-like granules and localise to the periphery of the cell and, (4) an increase in the size of a novel focus located at the posterior pole of the cell that contain XRNA, but neither DHH1 nor SCD6. The response differed from mammalian cells in that neither the decrease in polysomes nor stress-granule formation required phosphorylation of eIF2alpha at the position homologous to that of serine 51 in mammalian eIF2alpha and in the occurrence of a novel XRNA-focus.
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Affiliation(s)
- Susanne Kramer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Nykamp K, Lee MH, Kimble J. C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis. RNA (NEW YORK, N.Y.) 2008; 14:1378-89. [PMID: 18515547 PMCID: PMC2441978 DOI: 10.1261/rna.1066008] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Accepted: 04/16/2008] [Indexed: 05/09/2023]
Abstract
RNA regulators are critical for animal development, especially in the germ line where gene expression is often modulated by changes in mRNA stability, translation, and localization. In this paper, we focus on Caenorhabditis elegans LARP-1, a representative of one La-related protein (Larp) family found broadly among eukaryotes. LARP-1 possesses a signature La motif, which is an ancient RNA-binding domain, plus a second conserved motif, typical of LARP-1 homologs and therefore dubbed the LARP1 domain. LARP-1 appears to bind RNA in vitro via both the La motif and the LARP1 domain. larp-1 null mutants have an oogenesis defect reminiscent of hyperactive Ras-MAPK signaling; this defect is suppressed or enhanced by down- or up-regulating the Ras-MAPK pathway, respectively. Consistent with a role in down-regulating the Ras-MAPK pathway, larp-1 null mutants have higher than normal levels of selected pathway mRNAs and proteins. LARP-1 protein colocalizes with P bodies, which function in RNA degradation. We suggest that LARP-1 functions in P bodies to attenuate the abundance of conserved Ras-MAPK mRNAs. We also propose that the cluster of LARP-1 homologs may function generally to control the expression of key developmental regulators.
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Affiliation(s)
- Keith Nykamp
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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48
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Ramirez IBR, de Graffenried CL, Ebersberger I, Yelinek J, He CY, Price A, Warren G. TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei. J Cell Sci 2008; 121:1538-46. [PMID: 18411253 DOI: 10.1242/jcs.014324] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Golgins are coiled-coil proteins that have been implicated in the structure and function of the Golgi complex. Here, we identify and characterize a trypanosomal golgin, TbG63, showing that it has a C-terminal membrane anchor and an N-terminus that projects into the cytoplasm. TbG63 in procyclic parasites is localized to the Golgi and interacts with the active, GTP-form of TbRab1A. Overexpression of TbG63 has dramatic effects on Golgi architecture -- effects that require the N-terminus -- whereas depletion has little, if any, effect on the growth rate. By contrast, in the bloodstream form of the parasite, depletion of TbG63 slows growth, although it has no obvious effect on the transport of a variant surface glycoprotein (VSG) or on Golgi structure. TbG63 might be a useful tool to study the structure and functioning of the Golgi complex.
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Cassola A, De Gaudenzi JG, Frasch AC. Recruitment of mRNAs to cytoplasmic ribonucleoprotein granules in trypanosomes. Mol Microbiol 2007; 65:655-70. [PMID: 17635187 DOI: 10.1111/j.1365-2958.2007.05833.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Trypanosomes are outstanding examples of the importance of mRNA metabolism in the regulation of gene expression, as these unicellular eukaryotes mostly control protein synthesis by post-transcriptional mechanisms. Here, we show that mRNA metabolism in these organisms involves recruitment of mRNAs and proteins to microscopically visible ribonucleoprotein granules in the cytoplasm. These structures engage transcripts that are being translated and protect mRNAs from degradation. Analysis of the protein composition of trypanosomal mRNA granules indicated that they contain orthologous proteins to those present in P bodies and stress granules from metazoan organisms. Formation of mRNA granules was observed after carbon-source deprivation of parasites in axenic culture. More important, mRNA granules are formed naturally in trypanosomes present in the intestinal tract of the insect vector. We suggest that trypanosomes make use of mRNA granules for transient transcript protection as a strategy to cope with periods of starvation that they have to face during their complex life cycles.
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Affiliation(s)
- Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, 1650 San Martín, Provincia de Buenos Aires, Argentina
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Ruan JP, Ullu E, Tschudi C. Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol 2007; 155:66-9. [PMID: 17610965 PMCID: PMC2075351 DOI: 10.1016/j.molbiopara.2007.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/04/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Many U-snRNAs contain a hypermodified 2,2,7-trimethylguanosine (TMG) cap structure, which is formed by post-transcriptional methylation of an m(7)G cap. At present, little is known about the maturation of U-snRNAs in trypanosomes. The current evidence is consistent with the primary transcript containing an m(7)G moiety, but it is not clear whether the conversion of m(7)G to TMG takes place in the cytoplasm or in the nucleus. To address this issue, we characterized the Trypanosoma brucei homologue of the trimethylguanosine synthase (TbTgs1), a 28kDa protein, which is mainly composed of the conserved catalytic domain and lacks a large N-terminal domain present in higher eukaryotes. A GFP fusion with TbTgs1 revealed that this protein localizes throughout the nucleoplasm, as well as in one or two dots outside the nucleolus and RNAi-mediated downregulation of TbTgs1 suggests that this protein is responsible for hypermethylation of the m(7)G cap of both snRNAs and snoRNAs.
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Affiliation(s)
- Jia-peng Ruan
- Department of Epidemiology and Public Health, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA
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