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Inoue AH, Domingues PF, Serpeloni M, Hiraiwa PM, Vidal NM, Butterfield ER, del Pino RC, Ludwig A, Boehm C, Field MC, Ávila AR. Proteomics uncovers novel components of an interactive protein network supporting RNA export in trypanosomes. Mol Cell Proteomics 2022; 21:100208. [PMID: 35091090 PMCID: PMC8938319 DOI: 10.1016/j.mcpro.2022.100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/03/2022] Open
Abstract
In trypanosomatids, transcription is polycistronic and all mRNAs are processed by trans-splicing, with export mediated by noncanonical mechanisms. Although mRNA export is central to gene regulation and expression, few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes, necessitating direct identification of protein components. We previously described conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII (previously Hel45), a core component of the exon junction complex (EJC). Here, we searched for protein interactors of both proteins using cryomilling and mass spectrometry. Significant overlap between TcSub2 and TceIF4AIII-interacting protein cohorts suggests that both proteins associate with similar machinery. We identified several interactions with conserved core components of the EJC and multiple additional complexes, together with proteins specific to trypanosomatids. Additional immunoisolations of kinetoplastid-specific proteins both validated and extended the superinteractome, which is capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events. We also suggest that only proteomics is powerful enough to uncover the high connectivity between multiple aspects of mRNA metabolism and to uncover kinetoplastid-specific components that create a unique amalgam to support trypanosome mRNA maturation. Gene expression in trypanosomes is mediated by noncanonical mechanisms. Trypanosome mRNA nuclear export system comprises unique proteins to kinetoplastids. The present work highlights an amalgam of kinetoplastid-specific and conserved components. Our data support a highly coupled mRNA maturation pathway.
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Zuma AA, Dos Santos Barrias E, de Souza W. Basic Biology of Trypanosoma cruzi. Curr Pharm Des 2021; 27:1671-1732. [PMID: 33272165 DOI: 10.2174/1381612826999201203213527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
The present review addresses basic aspects of the biology of the pathogenic protozoa Trypanosoma cruzi and some comparative information of Trypanosoma brucei. Like eukaryotic cells, their cellular organization is similar to that of mammalian hosts. However, these parasites present structural particularities. That is why the following topics are emphasized in this paper: developmental stages of the life cycle in the vertebrate and invertebrate hosts; the cytoskeleton of the protozoa, especially the sub-pellicular microtubules; the flagellum and its attachment to the protozoan body through specialized junctions; the kinetoplast-mitochondrion complex, including its structural organization and DNA replication; glycosome and its role in the metabolism of the cell; acidocalcisome, describing its morphology, biochemistry, and functional role; cytostome and the endocytic pathway; the organization of the endoplasmic reticulum and Golgi complex; the nucleus, describing its structural organization during interphase and division; and the process of interaction of the parasite with host cells. The unique characteristics of these structures also make them interesting chemotherapeutic targets. Therefore, further understanding of cell biology aspects contributes to the development of drugs for chemotherapy.
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Affiliation(s)
- Aline A Zuma
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emile Dos Santos Barrias
- Laboratorio de Metrologia Aplicada a Ciencias da Vida, Diretoria de Metrologia Aplicada a Ciencias da Vida - Instituto Nacional de Metrologia, Qualidade e Tecnologia (Inmetro), Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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3
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Nocua PA, Requena JM, Puerta CJ. Identification of the interactomes associated with SCD6 and RBP42 proteins in Leishmania braziliensis. J Proteomics 2020; 233:104066. [PMID: 33296709 DOI: 10.1016/j.jprot.2020.104066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/29/2020] [Indexed: 02/04/2023]
Abstract
Leishmania are protozoan parasites responsible for leishmaniasis. These parasites present a precise gene regulation that allows them to survive different environmental conditions during their digenetic life cycle. This adaptation depends on the regulation of the expression of a wide variety of genes, which occurs, mainly at the post-transcriptional level. This differential gene expression is achieved by mechanisms based mainly in RNA binding proteins that regulate the translation and/or stability of mRNA targets by interaction with cis elements principally located in the untranslated regions (UTR). In recent studies, our group identified and characterized two proteins, SCD6 and RBP42, as RNA binding proteins in Leishmania braziliensis. To find clues about the cellular processes in which these proteins are involved, this work was aimed to determine the SCD6- and RBP42-interacting proteins (interactome) in L. braziliensis promastigotes. For this purpose, after an in vivo UV cross-linking, cellular extracts were used to immunoprecipitated, by specific antibodies, protein complexes in which SCD6 or RBP42 were present. Protein mass spectrometry analysis of the immunoprecipitated proteins identified 96 proteins presumably associated with SCD6 and 173 proteins associated with RBP42. Notably, a significant proportion of the identified proteins were shared in both interactomes, indicating a possible functional relationship between SCD6 and RBP42. Remarkably, many of the proteins identified in the SCD6 and RBP42 interactomes are related to RNA metabolism and translation processes, and many of them have been described as components of ribonucleoprotein (RNP) granules in Leishmania and related trypanosomatids. Thus, these results support a role of SCD6 and RBP42 in the assembly and/or function of mRNA-protein complexes, participating in the fate (decay/accumulation/translation) of L. braziliensis transcripts. SIGNIFICANCE: Parasites of the Leishmania genus present a particular regulation of gene expression, operating mainly at the post-transcriptional level, surely aimed to modulate quickly both mRNA and protein levels to survive the sudden environmental changes that occur during a parasite's life cycle as it moves from one host to another. This regulation of gene expression processes would be governed by the interaction of mRNA with RNA binding proteins. Nevertheless, the entirety of protein networks involved in these regulatory processes is far from being understood. In this regard, our work is contributing to stablish protein networks in which the L. braziliensis SCD6 and RBP42 proteins are involved; these proteins, in previous works, have been described as RNA binding proteins and found to participate in gene regulation in different cells and organisms. Additionally, our data point out a possible functional relationship between SCD6 and RBP42 proteins as constituents of mRNA granules, like processing bodies or stress granules, which are essential structures in the regulation of gene expression. This knowledge could provide a new approach for the development of therapeutic targets to control Leishmania infections.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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4
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Ferreira TR, Dowle AA, Parry E, Alves-Ferreira EVC, Hogg K, Kolokousi F, Larson TR, Plevin MJ, Cruz AK, Walrad PB. PRMT7 regulates RNA-binding capacity and protein stability in Leishmania parasites. Nucleic Acids Res 2020; 48:5511-5526. [PMID: 32365184 PMCID: PMC7261171 DOI: 10.1093/nar/gkaa211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/17/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
RNA binding proteins (RBPs) are the primary gene regulators in kinetoplastids as transcriptional control is nearly absent, making Leishmania an exceptional model for investigating methylation of non-histone substrates. Arginine methylation is an evolutionarily conserved protein modification catalyzed by Protein aRginine Methyl Transferases (PRMTs). The chromatin modifier PRMT7 is the only Type III PRMT found in higher eukaryotes and a restricted number of unicellular eukaryotes. In Leishmania major, PRMT7 is a cytoplasmic protein implicit in pathogenesis with unknown substrates. Using comparative methyl-SILAC proteomics for the first time in protozoa, we identified 40 putative targets, including 17 RBPs hypomethylated upon PRMT7 knockout. PRMT7 can modify Alba3 and RBP16 trans-regulators (mammalian RPP25 and YBX2 homologs, respectively) as direct substrates in vitro. The absence of PRMT7 levels in vivo selectively reduces Alba3 mRNA-binding capacity to specific target transcripts and can impact the relative stability of RBP16 in the cytoplasm. RNA immunoprecipitation analyses demonstrate PRMT7-dependent methylation promotes Alba3 association with select target transcripts and thus indirectly stabilizes mRNA of a known virulence factor, δ-amastin surface antigen. These results highlight a novel role for PRMT7-mediated arginine methylation of RBP substrates, suggesting a regulatory pathway controlling gene expression and virulence in Leishmania. This work introduces Leishmania PRMTs as epigenetic regulators of mRNA metabolism with mechanistic insight into the functional manipulation of RBPs by methylation.
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Affiliation(s)
- Tiago R Ferreira
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Adam A Dowle
- Metabolomics and Proteomics Lab, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Ewan Parry
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Karen Hogg
- Imaging and Cytometry Lab, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Foteini Kolokousi
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Tony R Larson
- Metabolomics and Proteomics Lab, Bioscience Technology Facility, Department of Biology, University of York, UK
| | - Michael J Plevin
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Angela K Cruz
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Pegine B Walrad
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
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5
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Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F, Kramer S. Trypanosomes can initiate nuclear export co-transcriptionally. Nucleic Acids Res 2019; 47:266-282. [PMID: 30418648 PMCID: PMC6326799 DOI: 10.1093/nar/gky1136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/25/2018] [Indexed: 02/03/2023] Open
Abstract
The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.
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Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Ann M Wehman
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Elisabeth M-Natus
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Johannes Schmidt
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jack Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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6
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Poornima G, Mythili R, Nag P, Parbin S, Verma PK, Hussain T, Rajyaguru PI. RGG-motif self-association regulates eIF4G-binding translation repressor protein Scd6. RNA Biol 2019; 16:1215-1227. [PMID: 31157589 PMCID: PMC6693564 DOI: 10.1080/15476286.2019.1621623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Regulation of mRNA translation plays a key role in the control of gene expression. Scd6, a conserved RGG-motif containing protein represses translation by binding to translation initiation factor eIF4G1. Here we report that Scd6 binds itself in RGG-motif dependent manner and self-association regulates its repression activity. Scd6 self-interaction competes with eIF4G1 binding and methylation of Scd6 RGG-motif by Hmt1 negatively affects self-association. Results pertaining to Sbp1 indicate that self-association could be a general feature of RGG-motif containing translation repressor proteins. Taken together, our study reveals a mechanism of regulation of eIF4G-binding RGG-motif translation repressors.
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Affiliation(s)
| | - Ravishankar Mythili
- a Department of Biochemistry, Indian Institute of Science , Bangalore , India.,b Department of Biology, University of Western Ontario , London , Canada
| | - Priyabrata Nag
- c Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science , Bangalore , India
| | - Sabnam Parbin
- a Department of Biochemistry, Indian Institute of Science , Bangalore , India
| | - Praveen Kumar Verma
- a Department of Biochemistry, Indian Institute of Science , Bangalore , India
| | - Tanweer Hussain
- c Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science , Bangalore , India
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7
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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8
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Halliday C, Billington K, Wang Z, Madden R, Dean S, Sunter JD, Wheeler RJ. Cellular landmarks of Trypanosoma brucei and Leishmania mexicana. Mol Biochem Parasitol 2018; 230:24-36. [PMID: 30550896 PMCID: PMC6529878 DOI: 10.1016/j.molbiopara.2018.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 11/29/2022]
Abstract
Trypanosoma and Leishmania are single cell eukaryotic parasites. The cell organisation of these human pathogens is complex and highly structured. This describes an inventory of reliable reference markers for 32 cell structures. These light microscopy landmarks are a valuable resource for researchers.
The kinetoplastids Trypanosoma brucei and Leishmania mexicana are eukaryotes with a highly structured cellular organisation that is reproduced with great fidelity in each generation. The pattern of signal from a fluorescently tagged protein can define the specific structure/organelle that this protein localises to, and can be extremely informative in phenotype analysis in experimental perturbations, life cycle tracking, post-genomic assays and functional analysis of organelles. Using the vast coverage of protein subcellular localisations provided by the TrypTag project, an ongoing project to determine the localisation of every protein encoded in the T. brucei genome, we have generated an inventory of reliable reference organelle markers for both parasites that combines epifluorescence images with a detailed description of the key features of each localisation. We believe this will be a useful comparative resource that will enable researchers to quickly and accurately pinpoint the localisation of their proteins of interest and will provide cellular markers for many types of cell biology studies. We see this as another important step in the post-genomic era analyses of these parasites, in which ever expanding datasets generate numerous candidates to analyse. Adoption of these reference proteins by the community is likely to enhance research studies and enable better comparison of data.
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Affiliation(s)
- Clare Halliday
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK; Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Karen Billington
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ziyin Wang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ross Madden
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Samuel Dean
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
| | - Richard John Wheeler
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK.
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9
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Vasquez JJ, Wedel C, Cosentino RO, Siegel TN. Exploiting CRISPR-Cas9 technology to investigate individual histone modifications. Nucleic Acids Res 2018; 46:e106. [PMID: 29912461 PMCID: PMC6182134 DOI: 10.1093/nar/gky517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/13/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination. By establishing an episome-based CRISPR-Cas9 system for T. brucei, we have edited wild type cells without inserting selectable markers, inserted a GFP tag between an ORF and its 3'UTR, deleted both alleles of a gene in a single transfection, and performed precise editing of genes that exist in multicopy arrays, replacing histone H4K4 with H4R4 in the absence of detectable off-target effects. The newly established genome editing toolbox allows for the generation of precise mutants without needing to change other regions of the genome, opening up opportunities to study the role of individual histone modifications, catalytic sites of enzymes or the regulatory potential of UTRs in their endogenous environments.
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Affiliation(s)
- Juan-José Vasquez
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Carolin Wedel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Raul O Cosentino
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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10
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Chakraborty C, Clayton C. Stress susceptibility in Trypanosoma brucei lacking the RNA-binding protein ZC3H30. PLoS Negl Trop Dis 2018; 12:e0006835. [PMID: 30273340 PMCID: PMC6181440 DOI: 10.1371/journal.pntd.0006835] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 10/11/2018] [Accepted: 09/11/2018] [Indexed: 01/17/2023] Open
Abstract
Trypanosomes rely on post-transcriptional mechanisms and mRNA-binding proteins for control of gene expression. Trypanosoma brucei ZC3H30 is an mRNA-binding protein that is expressed in both the bloodstream form (which grows in mammals) and the procyclic form (which grows in the tsetse fly midgut). Attachment of ZC3H30 to an mRNA causes degradation of that mRNA. Cells lacking ZC3H30 showed no growth defect under normal culture conditions; but they were more susceptible than wild-type cells to heat shock, starvation, and treatment with DTT, arsenite or ethanol. Transcriptomes of procyclic-form trypanosomes lacking ZC3H30 were indistinguishable from those of cells in which ZC3H30 had been re-expressed, but un-stressed bloodstream forms lacking ZC3H30 had about 2-fold more HSP70 mRNA. Results from pull-downs suggested that ZC3H30 mRNA binding may not be very specific. ZC3H30 was found in stress-induced granules and co-purified with another stress granule protein, Tb927.8.3820; but RNAi targeting Tb927.8.3820 did not affect either ZC3H30 granule association or stress resistance. The conservation of the ZC3H30 gene in both monogenetic and digenetic kinetoplastids, combined with the increased stress susceptibility of cells lacking it, suggests that ZC3H30 confers a selective advantage in the wild, where the parasites are subject to temperature fluctuations and immune attack in both the insect and mammalian hosts.
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Affiliation(s)
| | - Christine Clayton
- Zentrum für Molekular Biologie, Universität Heidelberg, Heidelberg, Germany
- * E-mail:
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11
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Romaniuk MA, Frasch AC, Cassola A. Translational repression by an RNA-binding protein promotes differentiation to infective forms in Trypanosoma cruzi. PLoS Pathog 2018; 14:e1007059. [PMID: 29864162 PMCID: PMC6002132 DOI: 10.1371/journal.ppat.1007059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 06/14/2018] [Accepted: 04/25/2018] [Indexed: 01/08/2023] Open
Abstract
Trypanosomes, protozoan parasites of medical importance, essentially rely on post-transcriptional mechanisms to regulate gene expression in insect vectors and vertebrate hosts. RNA binding proteins (RBPs) that associate to the 3'-UTR of mature mRNAs are thought to orchestrate master developmental programs for these processes to happen. Yet, the molecular mechanisms by which differentiation occurs remain largely unexplored in these human pathogens. Here, we show that ectopic inducible expression of the RBP TcUBP1 promotes the beginning of the differentiation process from non-infective epimastigotes to infective metacyclic trypomastigotes in Trypanosoma cruzi. In early-log epimastigotes TcUBP1 promoted a drop-like phenotype, which is characterized by the presence of metacyclogenesis hallmarks, namely repositioning of the kinetoplast, the expression of an infective-stage virulence factor such as trans-sialidase, increased resistance to lysis by human complement and growth arrest. Furthermore, TcUBP1-ectopic expression in non-infective late-log epimastigotes promoted full development into metacyclic trypomastigotes. TcUBP1-derived metacyclic trypomastigotes were infective in cultured cells, and developed normally into amastigotes in the cytoplasm. By artificial in vivo tethering of TcUBP1 to the 3' untranslated region of a reporter mRNA we were able to determine that translation of the reporter was reduced by 8-fold, while its mRNA abundance was not significantly compromised. Inducible ectopic expression of TcUBP1 confirmed its role as a translational repressor, revealing significant reduction in the translation rate of multiple proteins, a reduction of polysomes, and promoting the formation of mRNA granules. Expression of TcUBP1 truncated forms revealed the requirement of both N and C-terminal glutamine-rich low complexity sequences for the development of the drop-like phenotype in early-log epimastigotes. We propose that a rise in TcUBP1 levels, in synchrony with nutritional deficiency, can promote the differentiation of T. cruzi epimastigotes into infective metacyclic trypomastigotes.
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Affiliation(s)
- Maria Albertina Romaniuk
- Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Alberto Carlos Frasch
- Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
- * E-mail:
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12
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Roy D, Rajyaguru PI. Suppressor of clathrin deficiency (Scd6)-An emerging RGG-motif translation repressor. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1479. [DOI: 10.1002/wrna.1479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Debadrita Roy
- Department of Biochemistry; Indian Institute of Science; Bangalore India
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13
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Nocua PA, Ramirez CA, Requena JM, Puerta CJ. Leishmania braziliensis SCD6 and RBP42 proteins, two factors with RNA binding capacity. Parasit Vectors 2017; 10:610. [PMID: 29258569 PMCID: PMC5735676 DOI: 10.1186/s13071-017-2557-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/26/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The study of RNA binding proteins (RBPs) is of great relevance for understanding processes like post-transcriptional control of gene expression. The post-transcriptional mechanisms are particularly important in Leishmania parasites and related trypanosomatids since transcriptional regulation is almost absent in them. Thus, RBPs should be essential during the development of these parasites and for survival strategies against the adverse conditions that they face during their life-cycle. This work was aimed to do a structural and biochemical characterization of two Leishmania braziliensis proteins, which were previously found in pull-down assays using an HSP70 RNA as bait. At that time, these proteins were annotated as hypothetical proteins (LbrM.25.2210 and LbrM.30.3080) in the GeneDB database. RESULTS Structural analysis indicated that these two proteins belong to evolutionarily conserved families; thus, they have been renamed accordingly as LbSCD6 (LbrM.25.2210) and LbRBP42 (LbrM.30.3080). We have demonstrated experimentally that these proteins are RBPs, in agreement with their structural features. Both proteins were able to bind to the complete 3' UTR-II region of HSP70-type II mRNA, and to an A + U rich element (ARE) present in that UTR. Cellular localization assays suggested that both proteins are mainly distributed in the cytoplasm of promastigotes growing at 26 °C, but they accumulate in foci around the nucleus when the parasites are under heat-shock conditions. Also, our study showed that steady-state levels of LbSCD6 and LbRBP42 transcripts decreased significantly during incubation of L. braziliensis promastigotes at heat-shock temperatures. However, in these conditions, the cellular content of both proteins remained unaltered. CONCLUSIONS Our data suggest that LbSCD6 and LbRBP42, as occurs for their orthologues in other organisms, are involved in mRNA regulation, and probably they have a relevant role facing the stress conditions that L. braziliensis encounters during insect-to-mammalian transmission.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Cesar A Ramirez
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006560. [PMID: 28800584 PMCID: PMC5568443 DOI: 10.1371/journal.ppat.1006560] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 07/29/2017] [Indexed: 01/06/2023] Open
Abstract
In nearly all eukaryotes, cellular differentiation is governed by changes in transcription, and stabilized by chromatin and DNA modification. Gene expression control in the pathogen Trypanosoma brucei, in contrast, relies almost exclusively on post-transcriptional mechanisms, so RNA binding proteins must assume the burden that is usually borne by transcription factors. T. brucei multiply in the blood of mammals as bloodstream forms, and in the midgut of Tsetse flies as procyclic forms. We show here that a single RNA-binding protein, RBP10, promotes the bloodstream-form trypanosome differentiation state. Depletion of RBP10 from bloodstream-form trypanosomes gives cells that can grow only as procyclic forms; conversely, expression of RBP10 in procyclic forms converts them to bloodstream forms. RBP10 binds to procyclic-specific mRNAs containing an UAUUUUUU motif, targeting them for translation repression and destruction. Products of RBP10 target mRNAs include not only the major procyclic surface protein and enzymes of energy metabolism, but also protein kinases and stage-specific RNA-binding proteins: this suggests that alterations in RBP10 trigger a regulatory cascade.
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15
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Abstract
5’-3’ decay is the major mRNA decay pathway in many eukaryotes, including trypanosomes. After deadenylation, mRNAs are decapped by the nudix hydrolase DCP2 of the decapping complex and finally degraded by the 5’-3’ exoribonuclease. Uniquely, trypanosomes lack homologues to all subunits of the decapping complex, while deadenylation and 5’-3’ degradation are conserved. Here, I show that the parasites use an ApaH-like phosphatase (ALPH1) as their major mRNA decapping enzyme. The protein was recently identified as a novel trypanosome stress granule protein and as involved in mRNA binding. A fraction of ALPH1 co-localises exclusively with the trypanosome 5’-3’ exoribonuclease XRNA to a special granule at the posterior pole of the cell, indicating a connection between the two enzymes. RNAi depletion of ALPH1 is lethal and causes a massive increase in total mRNAs that are deadenylated, but have not yet started 5’-3’ decay. These data suggest that ALPH1 acts downstream of deadenylation and upstream of mRNA degradation, consistent with a function in mRNA decapping. In vitro experiments show that recombinant, N-terminally truncated ALHP1 protein, but not a catalytically inactive mutant, sensitises the capped trypanosome spliced leader RNA to yeast Xrn1, but only if an RNA 5’ polyphosphatase is included. This indicates that the decapping mechanism of ALPH1 differs from the decapping mechanism of Dcp2 by leaving more than one phosphate group at the mRNA’s 5’ end. This is the first reported function of a eukaryotic ApaH-like phosphatase, a bacterial-derived class of enzymes present in all phylogenetic super-groups of the eukaryotic kingdom. The substrates of eukaryotic ApaH-like phosphatases are unknown. However, the substrate of the related bacterial enzyme ApaH, diadenosine tetraphosphate, is highly reminiscent of a eukaryotic mRNA cap. Eukaryotic mRNAs are stabilised by a 5’ cap and one important step in mRNA decay is the removal of this cap by the nudix domain protein Dcp2 of the decapping complex. The decapping complex is highly conserved throughout eukaryotes, with the exception of trypanosomes that lack the entire complex. Here, I show that trypanosomes have evolved to use an ApaH-like phosphatase instead of a nudix domain protein as their major decapping enzyme. This work closes an important gap in the knowledge of trypanosome mRNA metabolism. Moreover, this is the first reported function of an ApaH-like phosphatase, a bacterial derived class of enzymes that are widespread throughout eukaryotes.
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Affiliation(s)
- Susanne Kramer
- Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail:
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16
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Exosome secretion affects social motility in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006245. [PMID: 28257521 PMCID: PMC5352147 DOI: 10.1371/journal.ppat.1006245] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/15/2017] [Accepted: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EV) secreted by pathogens function in a variety of biological processes. Here, we demonstrate that in the protozoan parasite Trypanosoma brucei, exosome secretion is induced by stress that affects trans-splicing. Following perturbations in biogenesis of spliced leader RNA, which donates its spliced leader (SL) exon to all mRNAs, or after heat-shock, the SL RNA is exported to the cytoplasm and forms distinct granules, which are then secreted by exosomes. The exosomes are formed in multivesicular bodies (MVB) utilizing the endosomal sorting complexes required for transport (ESCRT), through a mechanism similar to microRNA secretion in mammalian cells. Silencing of the ESCRT factor, Vps36, compromised exosome secretion but not the secretion of vesicles derived from nanotubes. The exosomes enter recipient trypanosome cells. Time-lapse microscopy demonstrated that cells secreting exosomes or purified intact exosomes affect social motility (SoMo). This study demonstrates that exosomes are delivered to trypanosome cells and can change their migration. Exosomes are used to transmit stress signals for communication between parasites. Trypanosomes are the causative agent of major parasitic diseases such as African sleeping sickness, leishmaniosis and Chagas' disease that affect millions of people. These parasites cycle between an insect and a mammalian host. Communication between the parasites and the host must be essential for executing a productive infection and for cycling of the parasite between its hosts. Exosomes are 40-100nm vesicles of endocytic origin, and were shown to affect a variety of biological processes and human diseases. Exosomes were also shown to help pathogens evade the immune system. In this study, we demonstrate that exosomes are secreted from Trypanosoma brucei parasites when trans-splicing is inhibited. These exosomes contain, among many other constituents, a type of RNA known as spliced leader RNA (SL RNA), which is essential in these parasites for formation of all mature mRNA. These exosomes are able to enter neighboring trypanosomes, and only intact exosomes affect the social motility of these parasites. We propose that exosomes can potentially control parasite migration in the insect host by acting as a repellent that drives the fit parasites away from either damaged cells or an unfavorable environment. This mechanism could secure a productive infection.
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Minia I, Merce C, Terrao M, Clayton C. Translation Regulation and RNA Granule Formation after Heat Shock of Procyclic Form Trypanosoma brucei: Many Heat-Induced mRNAs Are also Increased during Differentiation to Mammalian-Infective Forms. PLoS Negl Trop Dis 2016; 10:e0004982. [PMID: 27606618 PMCID: PMC5015846 DOI: 10.1371/journal.pntd.0004982] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/16/2016] [Indexed: 11/18/2022] Open
Abstract
African trypanosome procyclic forms multiply in the midgut of tsetse flies, and are routinely cultured at 27°C. Heat shocks of 37°C and above result in general inhibition of translation, and severe heat shock (41°C) results in sequestration of mRNA in granules. The mRNAs that are bound by the zinc-finger protein ZC3H11, including those encoding refolding chaperones, escape heat-induced translation inhibition. At 27°C, ZC3H11 mRNA is predominantly present as an untranslated cytosolic messenger ribonucleoprotein particle, but after heat shocks of 37°C—41°C, the ZC3H11 mRNA moves into the polysomal fraction. To investigate the scope and specificities of heat-shock translational regulation and granule formation, we analysed the distributions of mRNAs on polysomes at 27°C and after 1 hour at 39°C, and the mRNA content of 41°C heat shock granules. We found that mRNAs that bind to ZC3H11 remained in polysomes at 39°C and were protected from sequestration in granules at 41°C. As previously seen for starvation stress granules, the mRNAs that encode ribosomal proteins were excluded from heat-shock granules. 70 mRNAs moved towards the polysomal fraction after the 39°C heat shock, and 260 increased in relative abundance. Surprisingly, many of these mRNAs are also increased when trypanosomes migrate to the tsetse salivary glands. It therefore seems possible that in the wild, temperature changes due to diurnal variations and periodic intake of warm blood might influence the efficiency with which procyclic forms develop into mammalian-infective forms. When trypanosomes are inside tsetse flies, they have to cope with temperature variations from below 20°C up to 37°C, due to diurnal variations and periodic intake of warm blood. In the laboratory, procyclic forms (the form that multiplies in the midgut), are routinely cultured at 27°C. When procyclic forms are heated to temperatures of 37°C and above, they decrease protein production, and at 41°C, mRNAs aggregate into granules. We show here that quite a large number of mRNAs are not included in granules and continue to be used for making proteins. Some of the proteins that continue to be made are needed in order to defend the cells against the effects of heat shock. Interestingly, however, a moderate heat shock stimulates expression of genes needed for the parasites to develop further into forms that can colonise the salivary glands. It thus seems possible that in the field, temperature variations might influence the efficiency with which of trypanosomes in tsetse flies become infective for mammals.
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Affiliation(s)
- Igor Minia
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Clementine Merce
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Monica Terrao
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
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Romaniuk MA, Cervini G, Cassola A. Regulation of RNA binding proteins in trypanosomatid protozoan parasites. World J Biol Chem 2016; 7:146-157. [PMID: 26981203 PMCID: PMC4768119 DOI: 10.4331/wjbc.v7.i1.146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/04/2015] [Accepted: 01/29/2016] [Indexed: 02/05/2023] Open
Abstract
Posttranscriptional mechanisms have a critical role in the overall outcome of gene expression. These mechanisms are especially relevant in protozoa from the genus Trypanosoma, which is composed by death threatening parasites affecting people in Sub-saharan Africa or in the Americas. In these parasites the classic view of regulation of transcription initiation to modulate the products of a given gene cannot be applied. This is due to the presence of transcription start sites that give rise to long polycistronic units that need to be processed costranscriptionally by trans-splicing and polyadenylation to give mature monocistronic mRNAs. Posttranscriptional mechanisms such as mRNA degradation and translational repression are responsible for the final synthesis of the required protein products. In this context, RNA-binding proteins (RBPs) in trypanosomes have a relevant role as modulators of mRNA abundance and translational repression by associating to the 3’ untranslated regions in mRNA. Many different RBPs have been proposed to modulate cohorts of mRNAs in trypanosomes. However, the current understanding of their functions lacks a dynamic view on the different steps at which these RBPs are regulated. Here, we discuss different evidences to propose regulatory events for different RBPs in these parasites. These events vary from regulated developmental expression, to biogenesis of cytoplasmic ribonucleoprotein complexes in the nucleus, and condensation of RBPs and mRNA into large cytoplasmic granules. Finally, we discuss how newly identified posttranslational modifications of RBPs and mRNA metabolism-related proteins could have an enormous impact on the modulation of mRNA abundance. To understand these modifications is especially relevant in these parasites due to the fact that the enzymes involved could be interesting targets for drug therapy.
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Thandapani P, Song J, Gandin V, Cai Y, Rouleau SG, Garant JM, Boisvert FM, Yu Z, Perreault JP, Topisirovic I, Richard S. Aven recognition of RNA G-quadruplexes regulates translation of the mixed lineage leukemia protooncogenes. eLife 2015; 4. [PMID: 26267306 PMCID: PMC4561382 DOI: 10.7554/elife.06234] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 08/11/2015] [Indexed: 12/17/2022] Open
Abstract
G-quadruplexes (G4) are extremely stable secondary structures forming stacks of guanine tetrads. DNA G4 structures have been extensively studied, however, less is known about G4 motifs in mRNAs, especially in their coding sequences. Herein, we show that Aven stimulates the mRNA translation of the mixed lineage leukemia (MLL) proto-oncogene in an arginine methylation-dependent manner. The Aven RGG/RG motif bound G4 structures within the coding regions of the MLL1 and MLL4 mRNAs increasing their polysomal association and translation, resulting in the induction of transcription of leukemic genes. The DHX36 RNA helicase associated with the Aven complex and was required for optimal translation of G4 mRNAs. Depletion of Aven led to a decrease in synthesis of MLL1 and MLL4 proteins resulting in reduced proliferation of leukemic cells. These findings identify an Aven-centered complex that stimulates the translation of G4 harboring mRNAs, thereby promoting survival of leukemic cells. DOI:http://dx.doi.org/10.7554/eLife.06234.001 To make a protein, the DNA sequence that encodes it is first copied to make a molecule of messenger RNA (or mRNA for short). The mRNA is then used as a set of instructions to assemble a protein in a process called translation. Both DNA and RNA molecules can fold into particular shapes. One such structure is known as a G-quartet and involves the DNA or RNA folding back on itself to form a highly stable planar structure. Stacks of G-quartets can form structures known as G-quadruplexes, but little is known about the G-quadruplexes that form in mRNA molecules. Leukemia affects cells in the bone marrow and causes blood cells to develop abnormally. A protein called Aven is often found in increased amounts in certain types of leukemic cells, but it was not clear how Aven affects how leukemia develops. Thandapani, Song et al. have now found that in leukemic cells, Aven binds to G-quadruplexes found in two mRNA molecules that encode proteins that are linked to leukemia. This binding increases the translation of these mRNAs, with translation occurring most efficiently when a particular enzyme called a helicase—which remodels RNA—also bound to Aven. Reducing the amount of Aven in cells caused fewer of the leukemic proteins to be produced, which also reduced the growth and multiplcation of leukemic cells. These findings raise the possibility that drugs that disrupt how Aven works could form part of treatments for leukemia. The next challenge will be to identify the signaling pathways that communicate with Aven and to define all the G-quadruplex mRNAs that are regulated by Aven. DOI:http://dx.doi.org/10.7554/eLife.06234.002
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Affiliation(s)
- Palaniraja Thandapani
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | - Jingwen Song
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | - Valentina Gandin
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | - Yutian Cai
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | - Samuel G Rouleau
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Francois-Michel Boisvert
- Département d'Anatomie et de Biologie Cellulaire, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Canada
| | - Zhenbao Yu
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | | | - Ivan Topisirovic
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group, Segal Cancer Center, Jewish General Hospital, Montréal, Canada
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Kroschwald S, Maharana S, Mateju D, Malinovska L, Nüske E, Poser I, Richter D, Alberti S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife 2015; 4:e06807. [PMID: 26238190 PMCID: PMC4522596 DOI: 10.7554/elife.06807] [Citation(s) in RCA: 379] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/25/2015] [Indexed: 12/27/2022] Open
Abstract
RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine. DOI:http://dx.doi.org/10.7554/eLife.06807.001 Genes consist of long stretches of DNA that code for proteins. The DNA is first ‘transcribed’ to produce an RNA molecule, which is then translated into a protein. In most cells, RNA molecules are present within a structure called ribonucleoprotein (RNP for short) granules. These contain the protein machinery needed to transport, store, and break down RNAs. P bodies and stress granules are two types of RNP granules found in all cells, from yeast to human. P bodies are present at all times, whereas stress granules assemble when a cell experiences stressful conditions, such as a lack of nutrients or high temperatures. Once the stress has been overcome, the stress granules are disassembled. The precise details of how RNP granules assemble in cells remain poorly understood. One theory suggests that RNP granules form through a physical process called ‘phase separation’ in which RNA molecules and proteins above a certain critical concentration condense to form a liquid droplet. Other research has suggested that RNP granules arise when so-called prion-like proteins spontaneously clump together and start aggregating to form fibers. These granules would behave more like solids than liquids. Kroschwald et al. have now analyzed how P bodies and stress granules form in yeast and human cells using a chemical compound that can distinguish between liquid-like and solid-like structures. The results revealed that P bodies and stress granules behave very differently in yeast cells. While P bodies are indeed liquid droplets, stress granules are more solid in nature and act like protein aggregates. So why is there a difference between the two? It is known from previous work that when cells are stressed, many proteins misfold and start aggregating. Kroschwald et al. found that the formation of stress granules coincides with the formation of aggregates, suggesting that stress granules themselves are a type of aggregate. Furthermore, stress granule formation does not seem to involve prion-like fibers, but rather prion-like proteins can easily interact with other proteins in a promiscuous way, thus promoting the seeding of stress granules and their growth. Kroschwald et al. next studied human cells and observed that in these cells, both P bodies and stress granules were liquid droplets. These results together suggest that the physical properties and method of assembling P bodies and stress granules can vary from one organism to another. Future work will investigate whether the ability to form solid rather than liquid stress granules provides extra protection to yeast cells when they are stressed. It also remains to be tested whether and how stress granules convert into the pathological RNP aggregates that are often seen in neurodegenerative diseases. DOI:http://dx.doi.org/10.7554/eLife.06807.002
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Affiliation(s)
- Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Kroschwald S, Maharana S, Mateju D, Malinovska L, Nüske E, Poser I, Richter D, Alberti S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife 2015; 4:e06807. [PMID: 26238190 DOI: 10.7554/elife.06807.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/25/2015] [Indexed: 05/23/2023] Open
Abstract
RNA-protein (RNP) granules have been proposed to assemble by forming solid RNA/protein aggregates or through phase separation into a liquid RNA/protein phase. Which model describes RNP granules in living cells is still unclear. In this study, we analyze P bodies in budding yeast and find that they have liquid-like properties. Surprisingly, yeast stress granules adopt a different material state, which is reminiscent of solid protein aggregates and controlled by protein disaggregases. By using an assay to ectopically nucleate RNP granules, we further establish that RNP granule formation does not depend on amyloid-like aggregation but rather involves many promiscuous interactions. Finally, we show that stress granules have different properties in mammalian cells, where they show liquid-like behavior. Thus, we propose that the material state of RNP granules is flexible and that the solid state of yeast stress granules is an adaptation to extreme environments, made possible by the presence of a powerful disaggregation machine.
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Affiliation(s)
- Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Moutaoufik MT, El Fatimy R, Nassour H, Gareau C, Lang J, Tanguay RM, Mazroui R, Khandjian EW. UVC-induced stress granules in mammalian cells. PLoS One 2014; 9:e112742. [PMID: 25409157 PMCID: PMC4237350 DOI: 10.1371/journal.pone.0112742] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/14/2014] [Indexed: 01/26/2023] Open
Abstract
Stress granules (SGs) are well characterized cytoplasmic RNA bodies that form under various stress conditions. We have observed that exposure of mammalian cells in culture to low doses of UVC induces the formation of discrete cytoplasmic RNA granules that were detected by immunofluorescence staining using antibodies to RNA-binding proteins. UVC-induced cytoplasmic granules are not Processing Bodies (P-bodies) and are bone fide SGs as they contain TIA-1, TIA-1/R, Caprin1, FMRP, G3BP1, PABP1, well known markers, and mRNA. Concomitant with the accumulation of the granules in the cytoplasm, cells enter a quiescent state, as they are arrested in G1 phase of the cell cycle in order to repair DNA damages induced by UVC irradiation. This blockage persists as long as the granules are present. A tight correlation between their decay and re-entry into S-phase was observed. However the kinetics of their formation, their low number per cell, their absence of fusion into larger granules, their persistence over 48 hours and their slow decay, all differ from classical SGs induced by arsenite or heat treatment. The induction of these SGs does not correlate with major translation inhibition nor with phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). We propose that a restricted subset of mRNAs coding for proteins implicated in cell cycling are removed from the translational apparatus and are sequestered in a repressed form in SGs.
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Affiliation(s)
- Mohamed Taha Moutaoufik
- Centre de recherche, Institut universitaire en santé mentale de Québec, Département de psychiatrie et de neurosciences, Université Laval, Québec, PQ, Canada
| | - Rachid El Fatimy
- Centre de recherche, Institut universitaire en santé mentale de Québec, Département de psychiatrie et de neurosciences, Université Laval, Québec, PQ, Canada
| | - Hassan Nassour
- Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Cristina Gareau
- Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Jérôme Lang
- Centre de recherche, Institut universitaire en santé mentale de Québec, Département de psychiatrie et de neurosciences, Université Laval, Québec, PQ, Canada
| | - Robert M. Tanguay
- Laboratoire de génétique cellulaire et du développement, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche du CHU de Québec. Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Edouard W. Khandjian
- Centre de recherche, Institut universitaire en santé mentale de Québec, Département de psychiatrie et de neurosciences, Université Laval, Québec, PQ, Canada
- * E-mail:
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Clayton CE. Networks of gene expression regulation in Trypanosoma brucei. Mol Biochem Parasitol 2014; 195:96-106. [PMID: 24995711 DOI: 10.1016/j.molbiopara.2014.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
Regulation of gene expression in Kinetoplastids relies mainly on post-transcriptional mechanisms. Recent high-throughput analyses, combined with mathematical modelling, have demonstrated possibilities for transcript-specific regulation at every stage: trans splicing, polyadenylation, translation, and degradation of both the precursor and the mature mRNA. Different mRNA degradation pathways result in different types of degradation kinetics. The original idea that the fate of an mRNA - or even just its degradation kinetics - can be defined by a single "regulatory element" is an over-simplification. It is now clear that every mRNA can bind many different proteins, some of which may compete with each other. Superimposed upon this complexity are the interactions of those proteins with effectors of gene expression. The amount of protein that is made from a gene is therefore determined by a complex network of interactions.
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Affiliation(s)
- C E Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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Abstract
The storage of translationally inactive mRNAs in cytosolic granules enables cells to react flexibly to environmental changes. In eukaryotes, Scd6 (suppressor of clathrin deficiency 6)/Rap55 (RNA-associated protein 55), a member of the LSm14 (like-Sm14) family, is an important factor in the formation and activity of P-bodies, where mRNA decay factors accumulate, in stress granules that store mRNAs under adverse conditions and in granules that store developmentally regulated mRNAs. SCD6 from Trypanosoma brucei (TbSCD6) shares the same domain architecture as orthologous proteins in other organisms and is also present in cytosolic granules (equivalent to P-bodies). We show that TbSCD6 is a general repressor of translation and that its depletion by RNAi results in a global increase in protein synthesis. With few exceptions, the steady-state levels of proteins are unchanged. TbSCD6 is not required for the formation of starvation-induced granules in trypanosomes, and unlike Scd6 from yeast, Plasmodium and all multicellular organisms analysed to date, it does not form a complex with the helicase Dhh1 (DExD/H-box helicase 1). In common with Xenopus laevis RAP55, TbSCD6 co-purifies with two arginine methyltransferases; moreover, TbSCD6 itself is methylated on three arginine residues. Finally, a detailed analysis identified roles for the Lsm and N-rich domains in both protein localization and translational repression.
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Kramer S. RNA in development: how ribonucleoprotein granules regulate the life cycles of pathogenic protozoa. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:263-84. [PMID: 24339376 DOI: 10.1002/wrna.1207] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 12/11/2022]
Abstract
Ribonucleoprotein (RNP) granules are important posttranscriptional regulators of messenger RNA (mRNA) fate. Several types of RNP granules specifically regulate gene expression during development of multicellular organisms and are commonly referred to as germ granules. The function of germ granules is not entirely understood and probably diverse, but it is generally agreed that one main function is posttranscriptional regulation of gene expression during early development, when transcription is silent. One example is the translational repression of maternally derived mRNAs in oocytes. Here, I hope to show that the need for regulation of gene expression by RNP granules is not restricted to animal development, but plays an equally important role during the development of pathogenic protozoa. Apicomplexa and Trypanosomatidae have complex life cycles with frequent host changes. The need to quickly adapt gene expression to a new environment as well as the ability to suppress translation to survive latencies is critical for successful completion of life cycles. Posttranscriptional gene regulation is not necessarily simpler in protozoa. Apicomplexa surprise with the presence of micro RNA (miRNAs) and upstream open reading frames (µORFs). Trypanosomes have an unusually large repertoire of different RNP granule types. A better understanding of RNP granules in protozoa may help to gain insight into the evolutionary origin of RNP granules: Trypanosomes for example have two types of granules with interesting similarities to animal germ granules.
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Affiliation(s)
- Susanne Kramer
- Lehrstuhl für Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
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